From f2fef41a37fdee0889eb7940fe4a8bdba85d822b Mon Sep 17 00:00:00 2001 From: pozsa_k Date: Tue, 7 Feb 2023 16:26:13 +0100 Subject: [PATCH 001/158] Add aws cli Close: #258 --- Tools/awscli/build | 25 +++++++++++++++++++++++++ Tools/awscli/files/variants | 1 + Tools/awscli/modulefile | 12 ++++++++++++ 3 files changed, 38 insertions(+) create mode 100755 Tools/awscli/build create mode 100644 Tools/awscli/files/variants create mode 100644 Tools/awscli/modulefile diff --git a/Tools/awscli/build b/Tools/awscli/build new file mode 100755 index 0000000..ca3ba54 --- /dev/null +++ b/Tools/awscli/build @@ -0,0 +1,25 @@ +#!/usr/bin/env modbuild + +# download url actually not used, but the build script fails without it +pbuild::set_download_url "https://github.com/aws/aws-cli/archive/refs/tags/$V.tar.gz" +# pbuild::set_sha256sum 'gnuplot-5.2.4.tar.gz:1515f000bd373aaa53b16183f274189d4f5e0ae47d22f434857933d16a4770cb' +# pbuild::install_docfiles 'Copyright' 'NEWS' 'README' + +pbuild::add_to_group 'Tools' + +pbuild::configure() { + : +} +pbuild::compile() { + : +} +pbuild::install() { + curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-$V.zip" -o "awscliv2.zip" + unzip awscliv2.zip + ./aws/install -i $PREFIX -b ${PREFIX}/bin --update +} +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Tools/awscli/files/variants b/Tools/awscli/files/variants new file mode 100644 index 0000000..a749239 --- /dev/null +++ b/Tools/awscli/files/variants @@ -0,0 +1 @@ +awscli/2.9.21 unstable diff --git a/Tools/awscli/modulefile b/Tools/awscli/modulefile new file mode 100644 index 0000000..aa96a06 --- /dev/null +++ b/Tools/awscli/modulefile @@ -0,0 +1,12 @@ +#%Pmodule + +module-whatis "Universal Command Line Interface for Amazon Web Services" +module-url "https://github.com/aws/aws-cli/tree/v2" +module-license "https://github.com/aws/aws-cli/blob/v2/LICENSE.txt" +module-maintainer "Krisztian Pozsa " + +module-help " +The AWS Command Line Interface (AWS CLI) is a unified tool to manage your +AWS services. With just one tool to download and configure, you can control +multiple AWS services from the command line and automate them through scripts. +" From cef27d8920ec98addcaa32538da56d2b022b4f1d Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Wed, 16 Aug 2023 11:19:04 +0200 Subject: [PATCH 002/158] Built dynamo/1.1.538 --- EM/dynamo/1.1.538/config | 3 +++ EM/dynamo/README.md | 18 +++++++++++++++--- EM/dynamo/build | 2 ++ EM/dynamo/dynamo_activate_MCR.sh | 18 ++++++++++++++++++ EM/dynamo/files/variants | 1 + 5 files changed, 39 insertions(+), 3 deletions(-) create mode 100644 EM/dynamo/1.1.538/config create mode 100644 EM/dynamo/dynamo_activate_MCR.sh diff --git a/EM/dynamo/1.1.538/config b/EM/dynamo/1.1.538/config new file mode 100644 index 0000000..ba8d2f5 --- /dev/null +++ b/EM/dynamo/1.1.538/config @@ -0,0 +1,3 @@ +# Google drive file hash, from https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Downloads +DYNAMO_ID=11_HqORqfwX21odS4zTuQKLbzHDSYgeog + diff --git a/EM/dynamo/README.md b/EM/dynamo/README.md index cef3056..a8fb8c3 100644 --- a/EM/dynamo/README.md +++ b/EM/dynamo/README.md @@ -10,9 +10,21 @@ Installation should be done on merlin with an -adm account 2. Add google drive download link to `$V/config`. 3. Run `build ` 4. module load dynamo/$V -5. Compile stand-alone: `dynamo_setup_linux.sh` -6. Compile MPI: `source dynamo_setup_cluster.sh mpic++ dynamo_activate_linux_shipped_MCR.sh` -7. Compile Cuda: +5. `cd $DYNAMO_HOME/bin`. Further steps are taken from `README_dynamo_installation.txt` +6. [Compile stand-alone](https://www.dynamo-em.org/w/index.php?title=Installation) + + dynamo_setup_linux.sh + +7. [Compile MPI](https://www.dynamo-em.org/w/index.php?title=MPI_Cluster): + - With the shipped MCRLinux directory: + + source dynamo_setup_cluster.sh mpic++ dynamo_activate_linux_shipped_MCR.sh + + - With MCR from pmodules: + + source dynamo_setup_cluster.sh mpic++ dynamo_activate_MCR.sh + +8. Compile Cuda: cd $DYNAMO_ROOT/cuda make clean diff --git a/EM/dynamo/build b/EM/dynamo/build index f4e547a..cf1303c 100755 --- a/EM/dynamo/build +++ b/EM/dynamo/build @@ -51,6 +51,8 @@ pbuild::prep() { download_dynamo "$DYNAMO_ID" "$TAR_FILE" mkdir -p "$PREFIX" unpack "$TAR_FILE" "$PREFIX/bin" + + cp -n "$BUILDBLOCK_DIR/dynamo_activate_MCR.sh" "$PREFIX/bin/" } pbuild::configure() { diff --git a/EM/dynamo/dynamo_activate_MCR.sh b/EM/dynamo/dynamo_activate_MCR.sh new file mode 100644 index 0000000..2a45d91 --- /dev/null +++ b/EM/dynamo/dynamo_activate_MCR.sh @@ -0,0 +1,18 @@ +# Activates MCR from pmodules + +DYNAMO_FOLDER=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) +MCR_ROOT=${MATLAB_DIR:?No matlab module loaded} + + +# Checks availability of the MCR folder +if ! [ -d $MCR_ROOT ]; then + echo "ATTENTION: the Matlab module is not loaded." + return +fi + +echo "MCR for linux has been found in location:" $MCR_ROOT +export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MCR_ROOT/runtime/glnxa64:$MCR_ROOT/bin/glnxa64:$MCR_ROOT/sys/os/glnxa64:$MCR_ROOT/sys/opengl/lib/glnxa64 + +echo Activating Dynamo as standalone + +source $DYNAMO_FOLDER/dynamo_activate_linux.sh diff --git a/EM/dynamo/files/variants b/EM/dynamo/files/variants index d7b2939..21537f4 100644 --- a/EM/dynamo/files/variants +++ b/EM/dynamo/files/variants @@ -1 +1,2 @@ dynamo/1.1.514 unstable b:psi-python36/5.0.1 gcc/9.3.0 openmpi/4.0.4_slurm cuda/11.1.0 matlab/2019a +dynamo/1.1.538 unstable b:psi-python36/5.0.1 gcc/11.2.0 cuda/11.5.1 openmpi/4.1.4_slurm matlab/2023a From b8f8d2545fc407ccaac4d4106fda3c8a76da979c Mon Sep 17 00:00:00 2001 From: germann_e Date: Thu, 21 Sep 2023 11:31:02 +0200 Subject: [PATCH 003/158] ADD: newest ANSYS version and prepending of ANSYS lumerical bin path --- Tools/ANSYS/files/variants.overlay_merlin | 1 + Tools/ANSYS/modulefile | 2 ++ 2 files changed, 3 insertions(+) diff --git a/Tools/ANSYS/files/variants.overlay_merlin b/Tools/ANSYS/files/variants.overlay_merlin index 7590380..c7ad54d 100644 --- a/Tools/ANSYS/files/variants.overlay_merlin +++ b/Tools/ANSYS/files/variants.overlay_merlin @@ -4,3 +4,4 @@ ANSYS/2021R1 stable ANSYS/2021R2 stable ANSYS/2022R1 stable ANSYS/2022R2 unstable +ANSYS/2023R2 unstable diff --git a/Tools/ANSYS/modulefile b/Tools/ANSYS/modulefile index 1f33b35..a54cd94 100644 --- a/Tools/ANSYS/modulefile +++ b/Tools/ANSYS/modulefile @@ -32,6 +32,8 @@ prepend-path PATH $PREFIX/$version/polyflow/bin prepend-path PATH $PREFIX/$version/RSM/bin prepend-path PATH $PREFIX/$version/SystemCoupling/bin prepend-path PATH $PREFIX/$version/TurboGrid/bin +# 20.09.2023 add lumerical bin +prepend-path PATH $PREFIX/$version/lumerical/$version/bin # 07.04.2020 prepend-path PATH $PREFIX/$version/Electronics/Linux64 prepend-path PATH $PREFIX/$version/Framework/bin/Linux64 From 9f70872eea4b2158f5012eb4638d003d8f8e2e06 Mon Sep 17 00:00:00 2001 From: caubet_m Date: Mon, 9 Oct 2023 16:19:00 +0200 Subject: [PATCH 004/158] Fix Lumerical LD_LIBRARY_PATH --- Tools/ANSYS/modulefile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Tools/ANSYS/modulefile b/Tools/ANSYS/modulefile index a54cd94..8705cca 100644 --- a/Tools/ANSYS/modulefile +++ b/Tools/ANSYS/modulefile @@ -52,5 +52,8 @@ prepend-path LD_LIBRARY_PATH $PREFIX/$version/CFX/tools/qwt-6.1.2/linx64/lib prepend-path LD_LIBRARY_PATH $PREFIX/$version/CFX/tools/qwtpolar-1.1.1/linx64/lib prepend-path LD_LIBRARY_PATH $PREFIX/$version/CFX/tools/xerces-3.2.2/linx64/lib +# Lumerical +prepend-path LD_LIBRARY_PATH $PREFIX/$version/lumerical/$version/lib/ + # RSM prepend-path PATH $PREFIX/$version/RSM/Config/tools/linux From a5d40df1fe6b0716e9c70c101b2d4805198ee6d2 Mon Sep 17 00:00:00 2001 From: caubet_m Date: Thu, 26 Oct 2023 15:27:14 +0200 Subject: [PATCH 005/158] UCX 1.15.0 --- Libraries/ucx/files/variants.merlin6 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Libraries/ucx/files/variants.merlin6 b/Libraries/ucx/files/variants.merlin6 index 467f758..c3574d0 100644 --- a/Libraries/ucx/files/variants.merlin6 +++ b/Libraries/ucx/files/variants.merlin6 @@ -12,11 +12,11 @@ ucx/1.11.2-3_slurm stable cuda/11.1.0 b:doxygen/1.9.2 b:knem/1.1.4 b ucx/1.12.1_slurm stable cuda/11.5.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 ucx/1.13.1_slurm stable b:cuda/11.5.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 -ucx/1.13.1-3_slurm unstable b:cuda/11.1.0 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 +ucx/1.13.1-3_slurm stable b:cuda/11.1.0 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 -ucx/1.14.0-5_slurm unstable b:cuda/11.5.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 -ucx/1.14.0_slurm removed b:cuda/12.1.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.3.0 -ucx/1.14.1_slurm unstable b:cuda/12.1.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.3.0 +ucx/1.14.0-5_slurm stable b:cuda/11.5.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 +ucx/1.14.1_slurm stable b:cuda/12.1.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.3.0 +ucx/1.15.0_slurm unstable b:cuda/12.1.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.3.0 ucx/1.9.0_dgx deprecated cuda/11.1.0 b:doxygen/1.8.14 b:knem/1.1.4 ucx/1.10.0-1_dgx deprecated cuda/11.2.2 b:doxygen/1.8.14 b:knem/1.1.4 b:GDRCopy/2.2.0 From 892dbbdc45855b3f1d1c665d2e67ea2bb87fa79e Mon Sep 17 00:00:00 2001 From: Assmann Greta Marie Date: Mon, 30 Oct 2023 17:01:11 +0100 Subject: [PATCH 006/158] add finddqe build folder --- EM/finddqe/README | 2 ++ EM/finddqe/build | 28 +++++++++++++++++++++ EM/finddqe/files/Makefile | 51 +++++++++++++++++++++++++++++++++++++++ EM/finddqe/files/variants | 1 + EM/finddqe/modulefile | 9 +++++++ 5 files changed, 91 insertions(+) create mode 100644 EM/finddqe/README create mode 100755 EM/finddqe/build create mode 100644 EM/finddqe/files/Makefile create mode 100644 EM/finddqe/files/variants create mode 100644 EM/finddqe/modulefile diff --git a/EM/finddqe/README b/EM/finddqe/README new file mode 100644 index 0000000..c21a410 --- /dev/null +++ b/EM/finddqe/README @@ -0,0 +1,2 @@ +Installation information: +The Makefile_linux_amd64_gnu that is given with the tar file is not sufficient for installation. Requires two small changes, adding of two flags to the Makefile. This is done with the pbuild::configure step , where the corrected Makefile is copied into the src folder. diff --git a/EM/finddqe/build b/EM/finddqe/build new file mode 100755 index 0000000..abc6d96 --- /dev/null +++ b/EM/finddqe/build @@ -0,0 +1,28 @@ +#!/usr/bin/env modbuild + +# Binary distribution with manual installation. See README.md + +pbuild::add_to_group 'EM' + +pbuild::set_download_url "https://grigoriefflab.umassmed.edu/system/tdf?path=FindDQE_150706.tar.gz&file=1&type=node&id=4220" "$P-$V_PKG.tar.gz" + +pbuild::configure() { + cp "$BUILDBLOCK_DIR/files/Makefile" "$SRC_DIR/src" +} + +pbuild::compile() { + cd "$SRC_DIR/src" + make +} + +pbuild::install() { + mkdir -p "$PREFIX/bin" + cp "$SRC_DIR/bin/finddqe.exe" "$PREFIX/bin/finddqe" +} + + + + + + + diff --git a/EM/finddqe/files/Makefile b/EM/finddqe/files/Makefile new file mode 100644 index 0000000..589e95f --- /dev/null +++ b/EM/finddqe/files/Makefile @@ -0,0 +1,51 @@ +# +# ------ MAKEFILE FILE FOR Linux FREALIGN ----------- +# +# Using: gnu compiler +# +# Thanks to: Shixin Yang & Dr Edward Egelman at University of Virginia +# for providing this file +# +# Notes: To create executable: make -f Makefile_linux_amd64_gnu +# + +SHELL = /bin/sh + +FFLAGS = -m64 -O3 -s -fomit-frame-pointer -Wall -falign-functions=4 \ + -funroll-loops -fexpensive-optimizations -fschedule-insns2 \ + -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE \ + -cpp -w -c + +CFLAGS = -m64 -O3 -DPROTOTYPE -D_FILE_OFFSET_BITS=64 \ + -D_LARGEFILE_SOURCE -cpp -w -c + +COMP = gfortran + +CC = gcc + +ifeq ($(MKLROOT),"") + LF = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE +else + LF = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_sequential.a -Wl,--end-group -ldl -lpthread +endif + +PGM = finddqe + +LIB = $(PGM).a + +.PRECIOUS : $(PGM) $(LIB) + +include Makefile.inc + +ioc.o : ioc.c + $(CC) $(CFLAGS) -o ioc.o ioc.c + $(AR) r $(LIB) ioc.o + @\rm ioc.o + +$(LIB) : ioc.o $(ELEMENTS) + @echo all object files placed in library + +.f.a: + $(COMP) $(FFLAGS) $< + $(AR) r $(LIB) $*.o + @\rm $*.o diff --git a/EM/finddqe/files/variants b/EM/finddqe/files/variants new file mode 100644 index 0000000..880f337 --- /dev/null +++ b/EM/finddqe/files/variants @@ -0,0 +1 @@ +finddqe/1.6 unstable b:intel/22.2 diff --git a/EM/finddqe/modulefile b/EM/finddqe/modulefile new file mode 100644 index 0000000..724a0e5 --- /dev/null +++ b/EM/finddqe/modulefile @@ -0,0 +1,9 @@ +#%Module1.0 + +module-whatis "FindDQE determines the detective quantum efficiency (DQE) of a detector." +module-url "https://grigoriefflab.umassmed.edu/finddqe" +module-license "The Janelia Research Campus Software License 1.2 http://license.janelia.org/license/janelia_license_1_2.html" +module-maintainer "Greta Assmann " + +module-help "Ruskin RS Yu Z Grigorieff N 2013 Quantitative characterization of electron detectors for transmission electron microscopy J Struct Biol 184 385-393 " + From edb6f50ad2b45df771efd2930dfa8249a2f17be9 Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Tue, 31 Oct 2023 13:59:04 +0100 Subject: [PATCH 007/158] add line to README --- EM/finddqe/README | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/EM/finddqe/README b/EM/finddqe/README index c21a410..ad99060 100644 --- a/EM/finddqe/README +++ b/EM/finddqe/README @@ -1,2 +1,3 @@ Installation information: -The Makefile_linux_amd64_gnu that is given with the tar file is not sufficient for installation. Requires two small changes, adding of two flags to the Makefile. This is done with the pbuild::configure step , where the corrected Makefile is copied into the src folder. +The Makefile_linux_amd64_gnu that is given with the tar file is not sufficient for installation. Requires two small changes, adding of two flags to the Makefile. This is done with the pbuild::configure step , where the corrected Makefile is copied into the src folder. +Also, installation was done from/on the Merlin-Login Node. From 4ecf88ce69f88bc46d8abc68ba598ba7fbeb2d58 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Fri, 3 Nov 2023 17:23:39 +0100 Subject: [PATCH 008/158] Add jinja2 to the hpce-tools environment --- .../anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml b/Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml index ebab9ed..c7b4f79 100644 --- a/Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml +++ b/Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml @@ -18,3 +18,6 @@ dependencies: - tox-conda - pytest - bpython + - jinja2 # for relion templates + - pip: + - j2cli[yaml] From c8e9a2b0943465f967c671e7ccca12177b853513 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 14:45:41 +0100 Subject: [PATCH 009/158] version 3.23.2 added, YAML build files added --- Compiler/OpenBLAS/build-yaml | 9 ++ Compiler/OpenBLAS/files/config.yaml | 100 ++++++++++++++++++ Compiler/OpenBLAS/files/variants.rhel6 | 4 +- .../files/{variants.yaml => config.yaml} | 0 .../files/{variants.yaml => config.yaml} | 0 5 files changed, 112 insertions(+), 1 deletion(-) create mode 100755 Compiler/OpenBLAS/build-yaml create mode 100644 Compiler/OpenBLAS/files/config.yaml rename Compiler/hdf5_serial/files/{variants.yaml => config.yaml} (100%) rename Programming/cmake/files/{variants.yaml => config.yaml} (100%) diff --git a/Compiler/OpenBLAS/build-yaml b/Compiler/OpenBLAS/build-yaml new file mode 100755 index 0000000..87289c3 --- /dev/null +++ b/Compiler/OpenBLAS/build-yaml @@ -0,0 +1,9 @@ +#!/usr/bin/env modbuild + +pbuild::install_docfiles 'LICENSE' 'README.md' + +pbuild::pre_configure() { + pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=Release" + pbuild::add_configure_args "-DDYNAMIC_ARCH=ON" +} + diff --git a/Compiler/OpenBLAS/files/config.yaml b/Compiler/OpenBLAS/files/config.yaml new file mode 100644 index 0000000..8cdf3f0 --- /dev/null +++ b/Compiler/OpenBLAS/files/config.yaml @@ -0,0 +1,100 @@ +--- +# yamllint disable rule:line-length +format: 1 +OpenBLAS: + defaults: + group: Compiler + overlay: base + relstage: stable + systems: [rhel6, rhel7, rhel8] + urls: + - url: http://github.com/xianyi/$P/archive/v${V_PKG}.tar.gz + name: OpenBLAS-${V_PKG}.tar.gz + + shasums: + OpenBLAS-0.2.9.tar.gz: e899c70b8771896655765f5c64c00c990f8dd0fe569e96788d8c971a23ecb22a + OpenBLAS-0.2.19.tar.gz: 9c40b5e4970f27c5f6911cb0a28aa26b6c83f17418b69f8e5a116bb983ca8557 + OpenBLAS-0.2.20.tar.gz: 5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394 + OpenBLAS-0.3.7.tar.gz: bde136122cef3dd6efe2de1c6f65c10955bbb0cc01a520c2342f5287c28f9379 + OpenBLAS-0.3.9.tar.gz: 17d4677264dfbc4433e97076220adc79b050e4f8a083ea3f853a53af253bc380 + OpenBLAS-0.3.10.tar.gz: 0484d275f87e9b8641ff2eecaa9df2830cbe276ac79ad80494822721de6e1693 + OpenBLAS-0.3.13.tar.gz: 79197543b17cc314b7e43f7a33148c308b0807cd6381ee77f77e15acf3e6459e + OpenBLAS-0.3.15.tar.gz: 30a99dec977594b387a17f49904523e6bc8dd88bd247266e83485803759e4bbe + OpenBLAS-0.3.20.tar.gz: 8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c + OpenBLAS-0.3.21.tar.gz: f36ba3d7a60e7c8bcc54cd9aaa9b1223dd42eaf02c811791c37e8ca707c241ca + OpenBLAS-0.3.23.tar.gz: 5d9491d07168a5d00116cdc068a40022c3455bf9293c7cb86a65b1054d7e5114 + OpenBLAS-0.3.24.tar.gz: ceadc5065da97bd92404cac7254da66cc6eb192679cf1002098688978d4d5132 + + versions: + 0.3.24: + config: + group_deps: + compiler: + gcc: [12.3.0, 13.1.0] + build_requires: [cmake/3.23.2] + relstage: unstable + overlay: devel + 0.3.23: + variants: + - group_deps: + compiler: + gcc: [7.5.0, 8.5.0, 9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0] + build_requires: [cmake/3.23.2] + 0.3.21: + variants: + - group_deps: + compiler: + gcc: [7.5.0, 8.5.0, 9.5.0, 10.4.0, 11.3.0, 12.1.0] + build_requires: [cmake/3.23.2] + 0.3.20: + variants: + - group_deps: + compiler: + gcc: [7.5.0, 8.5.0, 9.5.0, 10.3.0, 11.3.0, 12.1.0] + 0.3.15: + variants: + - group_deps: + compiler: + gcc: [7.5.0, 8.4.0, 9.3.0, 10.3.0] + 0.3.13: + variants: + - group_deps: + compiler: + gcc: [7.5.0, 8.4.0, 9.3.0, 10.2.0, 10.3.0] + 0.3.10;0.3.9: + variants: + - group_deps: + compiler: + gcc: [7.5.0, 8.4.0, 9.3.0, 10.1.0] + 0.3.9: + variants: + - group_deps: + compiler: + gcc: [7.5.0, 8.4.0, 9.3.0, 10.1.0] + 0.3.7: + variants: + - group_deps: + compiler: + gcc: [7.4.0, 8.3.0, 9.2.0] + 0.2.20: + variants: + - group_deps: + compiler: + gcc: [5.5.0, 6.4.0, 7.3.0] + - group_deps: + compiler: + intel: [17.4] + relstage: deprecated + 0.2.19: + variants: + - group_deps: + gcc: [4.8.5, 4.9.4, 5.3.0, 5.4.0, 6.2.0, 6.3.0] + 0.2.9: + variants: + - group_deps: + compiler: + gcc: [4.7.4, 4.8.2, 4.8.3, 4.8.4, 4.8.5, 4.9.2, 6.1.0, 6.2.0] + - group_deps: + compiler: + intel: [15.3] + relstage: deprecated diff --git a/Compiler/OpenBLAS/files/variants.rhel6 b/Compiler/OpenBLAS/files/variants.rhel6 index 3070e47..7a8f953 100644 --- a/Compiler/OpenBLAS/files/variants.rhel6 +++ b/Compiler/OpenBLAS/files/variants.rhel6 @@ -20,4 +20,6 @@ OpenBLAS/0.3.15 stable gcc/{7.5.0,8.4.0,9.3.0,10.3.0} OpenBLAS/0.3.20 stable gcc/{7.5.0,8.5.0,9.5.0,10.3.0,11.3.0,12.1.0} -OpenBLAS/0.3.21 stable gcc/{7.5.0,8.5.0,9.5.0,10.4.0,11.3.0,12.1.0} b:cmake/3.23.2 +OpenBLAS/0.3.21 stable gcc/{7.5.0,8.5.0,9.5.0,10.4.0,11.3.0,12.1.0} b:cmake/3.23.2 + +OpenBLAS/0.3.23 stable gcc/{7.5.0,8.5.0,9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} b:cmake/3.23.2 diff --git a/Compiler/hdf5_serial/files/variants.yaml b/Compiler/hdf5_serial/files/config.yaml similarity index 100% rename from Compiler/hdf5_serial/files/variants.yaml rename to Compiler/hdf5_serial/files/config.yaml diff --git a/Programming/cmake/files/variants.yaml b/Programming/cmake/files/config.yaml similarity index 100% rename from Programming/cmake/files/variants.yaml rename to Programming/cmake/files/config.yaml From e556089f277b8494f207616141d8253be7160c73 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 14:47:30 +0100 Subject: [PATCH 010/158] gsl/2.7: compile with gcc/{11.4.0,12.1.0} added --- Compiler/gsl/files/variants.rhel6 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Compiler/gsl/files/variants.rhel6 b/Compiler/gsl/files/variants.rhel6 index 415e68f..d3d44c3 100644 --- a/Compiler/gsl/files/variants.rhel6 +++ b/Compiler/gsl/files/variants.rhel6 @@ -16,4 +16,4 @@ gsl/2.5 deprecated intel/19.4 gsl/2.6 stable gcc/{7.4.0,7.5.0,8.3.0,8.4.0,8.5.0,9.1.0,9.2.0,9.3.0,9.5.0,10.1.0,10.2.0,10.3.0,11.2.0,12.1.0} -gsl/2.7 stable gcc/{7.5.0,8.4.0,8.5.0,9.3.0,9.5.0,10.3.0,10.4.0,11.3.0,12.1.0} +gsl/2.7 stable gcc/{7.5.0,8.4.0,8.5.0,9.3.0,9.5.0,10.3.0,10.4.0,11.3.0,11.4.0,12.1.0,12.3.0,13.1.0} From ce9266c735ab6a5d5ee9983e3b1dcfe9003418c6 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 14:50:42 +0100 Subject: [PATCH 011/158] hdf5_serial: YAML config file and build script added --- Compiler/hdf5_serial/files/config.yaml | 301 ++++++++++++++++--------- 1 file changed, 198 insertions(+), 103 deletions(-) diff --git a/Compiler/hdf5_serial/files/config.yaml b/Compiler/hdf5_serial/files/config.yaml index 1a52a81..00cbb15 100644 --- a/Compiler/hdf5_serial/files/config.yaml +++ b/Compiler/hdf5_serial/files/config.yaml @@ -1,109 +1,204 @@ -overlay: base -relstage: stable - -hdf5_serial/1.8.12: - - with: gcc/{4.7.4,4.8.3,4.8.4,4.9.2} - relstage: deprecated - - with: intel/15.2 - relstage: deprecated - -hdf5_serial/1.8.13: - - with: gcc/4.7.4 - relstage: deprecated - -hdf5_serial/1.8.14: - - with: gcc/{4.7.4,4.8.5,4.9.3} - relstage: deprecated - - with: intel/15.2 - relstage: deprecated - -hdf5_serial/1.8.15-patch1: - - with: gcc/5.2.0 - relstage: deprecated - -hdf5_serial/1.8.16: - - with: gcc/{4.7.4,5.3.0,6.1.0} - relstage: deprecated - - with: intel/{15.3,16.2} - relstage: deprecated - -hdf5_serial/1.8.17: - - with: gcc/{4.7.4,4.9.4,5.4.0,6.2.0} - relstage: deprecated - - with: intel/16.3 - relstage: deprecated - -hdf5_serial/1.8.18: - - with: gcc/{4.8.5,5.5.0,6.3.0,6.4.0,7.2.0,7.3.0} - relstage: deprecated - -hdf5_serial/1.8.19: - - with: gcc/4.8.5 - relstage: deprecated - -hdf5_serial/1.8.20: - - with: gcc/{4.8.5,8.2.0} - relstage: deprecated - - with: intel/18.4 - relstage: deprecated - -hdf5_serial/1.8.21: - - with: gcc/{5.5.0,6.5.0,7.4.0,8.3.0} - relstage: deprecated - - with: pgi/18.5 - relstage: deprecated - -hdf5_serial/1.10.0: - - with: gcc/6.1.0 - relstage: deprecated - - with: intel/16.3 - relstage: deprecated - -hdf5_serial/1.10.1: - - with: gcc/{4.8.5,4.9.4,5.4.0,5.5.0,6.3.0,6.4.0,7.1.0,7.2.0,7.3.0} - relstage: deprecated - - with: intel/{17.1,17.4} - relstage: deprecated - - with: pgi/{17.3,17.7} - relstage: deprecated - -hdf5_serial/1.10.2: - - with: gcc/5.5.0 - relstage: deprecated - - with: intel/{18.2,18.3} - relstage: deprecated - -hdf5_serial/1.10.3: - - with: gcc/4.8.5 - relstage: deprecated - -hdf5_serial/1.10.4: - - with: gcc/7.3.0 - relstage: deprecated - -hdf5_serial/1.10.5: - - with: gcc/5.5.0 - relstage: deprecated - - with: intel/19.3 - relstage: deprecated - -hdf5_serial/1.10.6: - - with: gcc/{7.5.0,8.4.0,9.3.0,10.2.0} +--- +# yamllint disable rule:line-length +format: 1 +hdf5_serial: + defaults: + group: Compiler + overlay: base relstage: stable + systems: [rhel7, rhel8, rhel9] + urls: + - url: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${V_MAJOR}.${V_MINOR}/hdf5-$V/src/hdf5-$V.tar.bz2 + shasums: + hdf5-1.8.10-patch1.tar.bz2: 292afb3615ad9e68f4d5d18ebb11e4a73f2aece39f2da3875a457ff1e109fc41 + hdf5-1.8.12.tar.bz2: 10a369a4fc207bb09245f57c758e587420e06dfc0e445e337a58b0848b75a949 + hdf5-1.8.13.tar.bz2: c2f5a412107aba6f99fd7a4a9db6ce5f5fc8171ec931472784e5839d26aa17ef + hdf5-1.8.14.tar.bz2: 53722cb9f5977af2908f92fc1a3f8c597800a5cb448cfe5c75060d6335bb9bab + hdf5-1.8.15-patch1.tar.bz2: a5afc630c4443547fff15e9637b5b10404adbed4c00206d89517d32d6668fb32 + hdf5-1.8.15.1.tar.bz2: 289307fd70cef6715e0a28371635c8038153a4f25069319e34b0bc675a23e8ed + hdf5-1.8.16.tar.bz2: 13aaae5ba10b70749ee1718816a4b4bfead897c2fcb72c24176e759aec4598c6 + hdf5-1.8.17.tar.bz2: fc35dd8fd8d398de6b525b27cc111c21fc79795ad6db1b1f12cb15ed1ee8486a + hdf5-1.8.18.tar.bz2: 01c6deadf4211f86922400da82c7a8b5b50dc8fc1ce0b5912de3066af316a48c + hdf5-1.8.19.tar.bz2: 59c03816105d57990329537ad1049ba22c2b8afe1890085f0c022b75f1727238 + hdf5-1.8.20.tar.bz2: a4f2db7e0a078aa324f64e0216a80731731f73025367fa94d158c9b1d3fbdf6f + hdf5-1.8.21.tar.bz2: e5b1b1dee44a64b795a91c3321ab7196d9e0871fe50d42969761794e3899f40d + hdf5-1.10.0.tar.bz2: 31ff70dc7c7317066ab3bda3eec4498a8b099c69c1271b008ed3df388e743d28 + hdf5-1.10.1.tar.bz2: 9c5ce1e33d2463fb1a42dd04daacbc22104e57676e2204e3d66b1ef54b88ebf2 + hdf5-1.10.2.tar.bz2: 1cad5b7bfdf128dfc53cd16fba48f6e7ae4e93c75c371d9ec8dfc4df0c1fcb71 + hdf5-1.10.3.tar.bz2: c65cdcce4724a57fd3f8da9f0d109b497be30092acb9fac634d1291190d905a9 + hdf5-1.10.4.tar.bz2: 1267ff06aaedc04ca25f7c6026687ea2884b837043431195f153401d942b28df + hdf5-1.10.5.tar.bz2: 68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44 + hdf5-1.10.6.tar.bz2: 09d6301901685201bb272a73e21c98f2bf7e044765107200b01089104a47c3bd + hdf5-1.10.6_slurm.tar.bz2: d5a89e26beae0bc03ad18a0b0d1d3d75f87c32047879d25da11970cb5c4662a3 + hdf5-1.10.7.tar.bz2: 02018fac7e5efc496d9539a303cfb41924a5dadffab05df9812096e273efa55e + hdf5-1.10.8.tar.bz2: 66ec544b195a4cb9f6ffed034fd82e52429d6112747c2996ab69853f606e546b + hdf5-1.10.11.tar.bz2: 0afc77da5c46217709475bbefbca91c0cb6f1ea628ccd8c36196cf6c5a4de304 + hdf5-1.12.0.tar.bz2: 97906268640a6e9ce0cde703d5a71c9ac3092eded729591279bf2e3ca9765f61 + hdf5-1.12.2.tar.bz2: 3016ea56a175d2ca7f2568c8016420f7a2aad8f95e214fe7fa5485f4b80fbe51 + hdf5-1.13.1.tar.bz2: e16973ec893e2d5aa9c8dc73e196db9b99a605578e7317b421c713936f8bf57d -hdf5_serial/1.10.7: - - with: gcc/{10.2.0,10.3.0,11.2.0} - relstage: stable + versions: + 1.8.12: + config: + group_deps: + compiler: + gcc: [4.7.4, 4.8.3, 4.8.4, 4.9.2] + intel: [15.2] + relstage: deprecated -hdf5_serial/1.10.8: - - with: gcc/{6.5.0,7.5.0,8.5.0,9.5.0,10.3.0,11.3.0,12.1.0} - relstage: stable + 1.8.13: + config: + group_deps: + compiler: + gcc: [4.7.4] + relstage: deprecated -hdf5_serial/1.12.0: - - with: gcc/10.2.0 - relstage: stable + 1.8.14: + config: + group_deps: + compiler: + gcc: [4.7.4, 4.8.5, 4.9.3] + intel: [15.2] + relstage: deprecated -hdf5_serial/1.12.2: - - with: gcc/{6.5.0,7.5.0,8.5.0,9.5.0,10.3.0,11.3.0,12.1.0} - relstage: stable + 1.8.15-patch1: + config: + group_deps: + compiler: + gcc: [5.2.0] + relstage: deprecated + 1.8.16: + config: + group_deps: + compiler: + gcc: [4.7.4, 5.3.0, 6.1.0] + intel: [15.3, 16.2] + relstage: deprecated + + 1.8.17: + config: + group_deps: + compiler: + gcc: [4.7.4, 4.9.4, 5.4.0, 6.2.0] + intel: [16.3] + relstage: deprecated + + 1.8.18: + config: + group_deps: + compiler: + gcc: [4.8.5, 5.5.0, 6.3.0, 6.4.0, 7.2.0, 7.3.0] + relstage: deprecated + + 1.8.19: + config: + group_deps: + compiler: + gcc: [4.8.5] + relstage: deprecated + + 1.8.20: + config: + group_deps: + compiler: + gcc: [4.8.5, 8.2.0] + intel: [18.4] + relstage: deprecated + + 1.8.21: + config: + group_deps: + compiler: + gcc: [5.5.0, 6.5.0, 7.4.0, 8.3.0] + pgi: [18.5] + relstage: deprecated + + 1.10.0: + config: + group_deps: + compiler: + gcc: [6.1.0] + intel: [16.3] + relstage: deprecated + + 1.10.1: + config: + group_deps: + compiler: + gcc: [4.8.5, 4.9.4, 5.4.0, 5.5.0, 6.3.0, 6.4.0, 7.1.0, 7.2.0, 7.3.0] + intel: [17.1, 17.4] + pgi: [17.3, 17.7] + relstage: deprecated + + 1.10.2: + config: + group_deps: + compiler: + gcc: [5.5.0] + intel: [18.2, 18.3] + relstage: deprecated + + 1.10.3: + config: + group_deps: + compiler: + gcc: [4.8.5] + relstage: deprecated + + 1.10.4: + config: + group_deps: + compiler: + gcc: [7.3.0] + relstage: deprecated + + 1.10.5: + config: + group_deps: + compiler: + gcc: [5.5.0] + intel: [19.3] + relstage: deprecated + + 1.10.6: + config: + group_deps: + compiler: + gcc: [7.5.0, 8.4.0, 9.3.0, 10.2.0] + relstage: stable + + 1.10.7: + config: + group_deps: + compiler: + gcc: [10.2.0, 10.3.0, 11.2.0] + relstage: stable + + 1.10.8: + config: + group_deps: + compiler: + gcc: [6.5.0, 7.5.0, 8.5.0, 9.5.0, 10.3.0, 11.3.0, 12.1.0] + relstage: stable + + 1.10.11: + config: + group_deps: + compiler: + gcc: [10.4.0] + relstage: unstable + + 1.12.0: + config: + group_deps: + compiler: + gcc: [10.2.0] + relstage: stable + + 1.12.2: + config: + group_deps: + compiler: + gcc: [6.5.0, 7.5.0, 8.5.0, 9.5.0, 10.3.0, 11.3.0, 12.1.0] + relstage: stable From 36a18a3a09d4ddc51f6324c69fe5eea4b74b181b Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 14:51:00 +0100 Subject: [PATCH 012/158] hdf5_serial: YAML config file and build script added --- Compiler/hdf5_serial/build-yaml | 52 +++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100755 Compiler/hdf5_serial/build-yaml diff --git a/Compiler/hdf5_serial/build-yaml b/Compiler/hdf5_serial/build-yaml new file mode 100755 index 0000000..79ce963 --- /dev/null +++ b/Compiler/hdf5_serial/build-yaml @@ -0,0 +1,52 @@ +#!/usr/bin/env modbuild + +pbuild::install_docfiles ACKNOWLEDGMENTS +pbuild::install_docfiles COPYING +#pbuild::install_docfiles MANIFEST +pbuild::install_docfiles README.md + +pbuild::pre_configure() { + pbuild::add_configure_args "--enable-shared" + pbuild::add_configure_args "--enable-cxx" + pbuild::add_configure_args "--enable-unsupported" + pbuild::add_configure_args "--enable-threadsafe" + pbuild::add_configure_args "--with-pic" + case "${COMPILER}" in + clang-macos ) + # we do not have Fortran in Xcode + pbuild::add_configure_args "--disable-fortran" + if [[ "${V_MAJOR}.${V_MINOR}" == "1.8" ]]; then + pbuild::add_configure_args "--disable-fortran2003" + fi + ;; + pgi ) + # PGI uses GCC's include files, some object files and + # the STL implementation! + # The PGI C pre-processor is broken and doesn't work + # for HDF5. We use the pre-processor of the underlying + # GCC... + # This is a bit hackish! + # + # The following eval sets GCCDIR! Which is something + # like: + # /opt/psi/Programming/gcc/7.3.0/bin/../lib/gcc/x86_64-pc-linux-gnu/7.3.0 + # + eval $(pgcc -show 2>/dev/null | \ + awk '/^GCCDIR[[:space:]]*=/{gsub(/[[:space:]]/,""); print $0}') + pbuild::add_configure_args "CPP=${GCCDIR%%/..*}/cpp" + pbuild::add_configure_args "CFLAGS=-fPIC" + pbuild::add_configure_args "CXXFLAGS=-fPIC" + pbuild::add_configure_args "FCFLAGS=-fPIC" + pbuild::add_configure_args "--enable-fortran" + if [[ "${V_MAJOR}.${V_MINOR}" == "1.8" ]]; then + pbuild::add_configure_args "--enable-fortran2003" + fi + ;; + * ) + pbuild::add_configure_args "--enable-fortran" + if [[ "${V_MAJOR}.${V_MINOR}" == "1.8" ]]; then + pbuild::add_configure_args "--enable-fortran2003" + fi + ;; + esac +} From 5e69f5bc1520621cacfb7b0fc081210095cb4c12 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 14:52:57 +0100 Subject: [PATCH 013/158] openmpi: use of uninitialised variables fixed --- Compiler/openmpi/build | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index ab75d48..ba87cf3 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -21,35 +21,35 @@ pbuild::pre_configure() { pbuild::add_configure_args "--enable-static" pbuild::add_configure_args "--with-slurm=yes" - if [[ -n "${CUDA_VERSION}" ]]; then + if [[ -v CUDA_VERSION ]]; then pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" fi - if [[ -n "${HWLOC_VERSION}" ]]; then + if [[ -v HWLOC_VERSION ]]; then unset HWLOC_VERSION pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" else pbuild::add_configure_args "--with-hwloc=internal" fi - if [[ -n "${LIBEVENT_VERSION}" ]]; then + if [[ -v LIBEVENT_VERSION ]]; then pbuild::add_configure_args "--with-libevent=${LIBEVENT_PREFIX}" fi - if [[ -n "${PMIX_VERSION}" ]]; then + if [[ -v PMIX_VERSION ]]; then unset PMIX_VERSION pbuild::add_configure_args "--with-pmix=${PMIX_PREFIX}" fi - if [[ -n "${LIBFABRIC_VERSION}" ]]; then + if [[ -v LIBFABRIC_VERSION ]]; then pbuild::add_configure_args "--with-ofi=${LIBFABRIC_PREFIX}" fi - if [[ -n "${UCX_VERSION}" ]]; then + if [[ -v UCX_VERSION ]]; then pbuild::add_configure_args "--with-ucx=${UCX_PREFIX}" fi - if [[ -n "${INTEL_VERSION}" ]]; then + if [[ -v INTEL_VERSION ]]; then pbuild::add_configure_args "CC=icc" pbuild::add_configure_args "CXX=icpc" pbuild::add_configure_args "FC=ifort" @@ -95,7 +95,7 @@ pbuild::post_install() { pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so' fi - if [[ -n "${CUDA_VERSION}" ]]; then + if [[ -v CUDA_VERSION ]]; then echo "opal_warn_on_missing_libcuda = 0" >> ${PREFIX}/etc/openmpi-mca-params.conf fi From 7702e4c3134caab717f2f9a4da0298d70ec16e6b Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 14:54:28 +0100 Subject: [PATCH 014/158] openmpi_slurm: build with compilers gcc/{9.5.0,12.3.0,13.1.0} added --- Compiler/openmpi/files/variants.merlin6 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Compiler/openmpi/files/variants.merlin6 b/Compiler/openmpi/files/variants.merlin6 index d74c05c..6e58f0b 100644 --- a/Compiler/openmpi/files/variants.merlin6 +++ b/Compiler/openmpi/files/variants.merlin6 @@ -40,7 +40,7 @@ openmpi/4.1.1-1_slurm unstable gcc/10.2.0 cuda/11.3.0 b:ucx/1.10.0_slurm openmpi/4.1.3_slurm stable gcc/{9.3.0,10.3.0,11.2.0} cuda/11.5.1 b:ucx/1.12.1_slurm openmpi/4.1.4_slurm stable gcc/10.4.0 cuda/11.5.1 b:ucx/1.12.1_slurm -openmpi/4.1.5_slurm unstable gcc/{10.4.0,11.4.0} b:cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 +openmpi/4.1.5_slurm unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} b:cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 openmpi/4.1.5_slurm unstable intelcc/22.2 b:cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 openmpi/4.0.5-1_dgx deprecated gcc/{8.4.0,9.3.0,10.2.0} cuda/11.2.2 b:ucx/1.10.0-1_dgx From 4aa7e25919da90cf9cdbdf2fae00ec873f16572c Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 14:55:00 +0100 Subject: [PATCH 015/158] openmpi: build version 4.1.5 added --- Compiler/openmpi/files/variants.rhel6 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Compiler/openmpi/files/variants.rhel6 b/Compiler/openmpi/files/variants.rhel6 index 32db4a6..c81d7d8 100644 --- a/Compiler/openmpi/files/variants.rhel6 +++ b/Compiler/openmpi/files/variants.rhel6 @@ -52,3 +52,5 @@ openmpi/4.0.5 stable gcc/{7.5.0,8.4.0,9.3.0,10.2.0} ucx/1.8.1 openmpi/4.0.5 stable gcc/10.3.0 openmpi/4.1.4 stable gcc/10.4.0 + +openmpi/4.1.5 unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0} From 270be3ca2551aa75a853074f43420ef462870ea7 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 14:55:52 +0100 Subject: [PATCH 016/158] openmpi: YAML config file added --- Compiler/openmpi/files/config.yaml | 209 +++++++++++++++++++++++++++++ 1 file changed, 209 insertions(+) create mode 100644 Compiler/openmpi/files/config.yaml diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml new file mode 100644 index 0000000..a3ec3c1 --- /dev/null +++ b/Compiler/openmpi/files/config.yaml @@ -0,0 +1,209 @@ +--- +# yamllint disable rule:line-length +format: 1 +openmpi: + defaults: + group: Compiler + overlay: base + relstage: stable + systems: [rhel7, rhel8, rhel9] + urls: + - url: https://download.open-mpi.org/release/open-mpi/v${V_MAJOR}.${V_MINOR}/openmpi-${V_PKG}.tar.bz + shasums: + openmpi-1.10.0.tar.bz2: 26b432ce8dcbad250a9787402f2c999ecb6c25695b00c9c6ee05a306c78b6490 + openmpi-1.10.4.tar.bz2: fb3c0c4c77896185013b6091b306d29ba592eb40d8395533da5c8bc300d922db + openmpi-1.10.7.tar.bz2: a089ece151fec974905caa35b0a59039b227bdea4e7933069e94bee4ed0e5a90 + openmpi-1.4.3.tar.bz2: 220b72b1c7ee35469ff74b4cfdbec457158ac6894635143a33e9178aa3981015 + openmpi-1.4.5.tar.bz2: a3857bc69b7d5258cf7fc1ed1581d9ac69110f5c17976b949cb7ec789aae462d + openmpi-1.6.5.tar.bz2: fe37bab89b5ef234e0ac82dc798282c2ab08900bf564a1ec27239d3f1ad1fc85 + openmpi-1.8.0.tar.bz2: 8ce8a0fb60d39469adba0adc4d0b94b3055ef6f800d536dbcb788f334b55db0d + openmpi-1.8.1.tar.bz2: 171427ebc007943265f33265ec32e15e786763952e2bfa2eac95e3e192c1e18f + openmpi-1.8.2.tar.bz2: ab70770faf1bac15ef44301fe2186b02f857646545492dd7331404e364a7d131 + openmpi-1.8.4.tar.bz2: 23158d916e92c80e2924016b746a93913ba7fae9fff51bf68d5c2a0ae39a2f8a + openmpi-1.8.8.tar.bz2: a28382d1e6a36f4073412dc00836ff2524e42b674da9caf6ca7377baad790b94 + openmpi-2.0.0.tar.bz2: 08b64cf8e3e5f50a50b4e5655f2b83b54653787bd549b72607d9312be44c18e0 + openmpi-2.0.1.tar.bz2: fed74f4ae619b7ebcc18150bb5bdb65e273e14a8c094e78a3fea0df59b9ff8ff + openmpi-2.1.0.tar.bz2: b169e15f5af81bf3572db764417670f508c0df37ce86ff50deb56bd3acb43957 + openmpi-2.1.1.tar.bz2: bd7badd4ff3afa448c0d7f3ca0ee6ce003b957e9954aa87d8e4435759b5e4d16 + openmpi-2.1.2.tar.bz2: 3cc5804984c5329bdf88effc44f2971ed244a29b256e0011b8deda02178dd635 + openmpi-2.1.5.tar.bz2: b807ccab801f27c3159a5edf29051cd3331d3792648919f9c4cee48e987e7794 + openmpi-2.1.6.tar.bz2: 98b8e1b8597bbec586a0da79fcd54a405388190247aa04d48e8c40944d4ca86e + openmpi-3.0.0.tar.bz2: f699bff21db0125d8cccfe79518b77641cd83628725a1e1ed3e45633496a82d7 + openmpi-3.0.1.tar.bz2: 663450d1ee7838b03644507e8a76edfb1fba23e601e9e0b5b2a738e54acd785d + openmpi-3.0.5.tar.bz2: f8976b95f305efc435aa70f906b82d50e335e34cffdbf5d78118a507b1c6efe8 + openmpi-3.1.1.tar.bz2: 3f11b648dd18a8b878d057e9777f2c43bf78297751ad77ae2cef6db0fe80c77c + openmpi-3.1.2.tar.bz2: c654ed847f34a278c52a15c98add40402b4a90f0c540779f1ae6c489af8a76c5 + openmpi-3.1.3.tar.bz2: 8be04307c00f51401d3fb9d837321781ea7c79f2a5a4a2e5d4eaedc874087ab6 + openmpi-3.1.4.tar.bz2: 17a69e0054db530c7dc119f75bd07d079efa147cf94bf27e590905864fe379d6 + openmpi-3.1.5.tar.bz2: fbf0075b4579685eec8d56d34d4d9c963e6667825548554f5bf308610af72133 + openmpi-3.1.6.tar.bz2: 50131d982ec2a516564d74d5616383178361c2f08fdd7d1202b80bdf66a0d279 + openmpi-4.0.0.tar.bz2: 2f0b8a36cfeb7354b45dda3c5425ef8393c9b04115570b615213faaa3f97366b + openmpi-4.0.1.tar.bz2: cce7b6d20522849301727f81282201d609553103ac0b09162cf28d102efb9709 + openmpi-4.0.2.tar.bz2: 900bf751be72eccf06de9d186f7b1c4b5c2fa9fa66458e53b77778dffdfe4057 + openmpi-4.0.3.tar.bz2: 1402feced8c3847b3ab8252165b90f7d1fa28c23b6b2ca4632b6e4971267fd03 + openmpi-4.0.4.tar.bz2: 47e24eb2223fe5d24438658958a313b6b7a55bb281563542e1afc9dec4a31ac4 + openmpi-4.0.5.tar.bz2: c58f3863b61d944231077f344fe6b4b8fbb83f3d1bc93ab74640bf3e5acac009 + openmpi-4.0.6.tar.bz2: 94b7b59ae9860f3bd7b5f378a698713e7b957070fdff2c43453b6cbf8edb410c + openmpi-4.0.7.tar.bz2: 7d3ecc8389161eb721982c855f89c25dca289001577a01a439ae97ce872be997 + openmpi-4.1.0.tar.bz2: 73866fb77090819b6a8c85cb8539638d37d6877455825b74e289d647a39fd5b5 + openmpi-4.1.1rc2.tar.bz2: f7d572621c93934b329281ee159c89124905ef05900d1a817efb7d262442d0f3 + openmpi-4.1.1.tar.bz2: e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda + openmpi-4.1.3.tar.bz2: 3d81d04c54efb55d3871a465ffb098d8d72c1f48ff1cbaf2580eb058567c0a3b + openmpi-4.1.4.tar.bz2: 92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d + openmpi-4.1.5.tar.bz2: a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3 + + versions: + + 4.1.5_slurm: + config: + relstage: unstable + group_deps: + compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0], intelcc: [22.2]} + build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5] + runtime_deps: [cuda/12.1.1] + + 4.1.4_slurm: + config: + relstage: stable + group_deps: + compiler: {gcc: [10.4.0]} + runtime_deps: [cuda/11.5.1] + build_requires: [ucx/1.12.1_slurm] + + 4.1.3_slurm: + config: + relstage: stable + group_deps: + compiler: {gcc: [9.3.0, 10.3.0, 11.2.0]} + runtime_deps: [cuda/11.5.1] + build_requires: [ucx/1.12.1_slurm] + + 4.1.1-1_slurm: + config: + relstage: unstable + group_deps: + compiler: {gcc: [10.2.0]} + runtime_deps: [cuda/11.3.0] + build_requires: [ucx/1.10.0_slurm] + + 4.1.1_slurm: + config: + relstage: unstable + group_deps: + compiler: {gcc: [10.2.0]} + runtime_deps: [cuda/11.3.0] + build_requires: [ucx/1.11.2_slurm] + + 4.1.0-1_dgx: + config: + relstage: deprecated + group_deps: + compiler: {gcc: [10.2.0]} + runtime_deps: [cuda/11.2.2] + build_requires: [ucx/1.10.0-1_dgx] + + 4.0.7-1_slurm: + config: + relstage: stable + group_deps: + compiler: {gcc: [10.2.0]} + runtime_deps: [cuda/11.4.3] + build_requires: [ucx/1.11.2-1_slurm] + + 4.0.7_slurm: + config: + relstage: stable + group_deps: + compiler: {gcc: [10.2.0]} + runtime_deps: [cuda/11.5.1] + build_requires: [ucx/1.11.2-2_slurm] + + 4.0.5-2_slurm: + config: + relstage: stable + group_deps: + compiler: {gcc: [10.2.0]} + runtime_deps: [cuda/11.3.0] + build_requires: [ucx/1.11.0_slurm] + + 4.0.5-1_slurm: + config: + relstage: stable + group_deps: + compiler: {gcc: [8.4.0, 9.3.0, 10.2.0, 10.3.0]} + runtime_deps: [cuda/11.2.2] + build_requires: [ucx/1.10.0-1_slurm] + + 4.0.5-1_dgx: + config: + relstage: deprecated + group_deps: + compiler: {gcc: [8.4.0, 9.3.0, 10.2.0]} + runtime_deps: [cuda/11.2.2] + build_requires: [ucx/1.10.0-1_dgx] + + 4.0.5_slurm: + config: + relstage: stable + variants: + - group_deps: + compiler: {gcc: [gcc/9.2.0]} + runtime_deps: [cuda/11.0.3] + - group_deps: + compiler: {gcc: [8.4.0, 9.3.0], intel: [20.4]} + runtime_deps: [cuda/11.1.0] + + 4.0.4_slurm_libpmix: + config: + relstage: deprecated + group_deps: + compiler: {gcc: [9.3.0]} + + 4.0.4_slurm: + config: + relstage: deprecated + group_deps: + compiler: {gcc: [4.9.4, 5.5.0, 6.5.0, 7.5.0, 8.4.0, 9.3.0], intel: [15.2, 17.4, 18.4, 20.1]} + + 4.0.3_slurm: + config: + relstage: deprecated + group_deps: + compiler: {gcc: [4.9.4, 5.5.0, 6.5.0, 7.5.0, 8.4.0, 9.3.0], intel: [15.2, 17.4, 18.4, 20.1]} + + 3.1.6_slurm: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.9.4, 5.5.0, 6.5.0], intel: [15.2, 17.4, 18.4, 20.1]} + - group_deps: + compiler: {gcc: [7.5.0, 8.4.0, 9.3.0]} + relstage: stable + - group_deps: + compiler: {intel: [20.4]} + runtime_deps: [cuda/11.1.0] + + 3.1.4_merlin6: + config: + relstage: deprecated + group_deps: + compiler: {gcc: [7.4.0, 8.3.0]} + + 3.1.5_merlin6;3.1.5-1_merlin6: + config: + relstage: deprecated + group_deps: + compiler: {gcc: [7.3.0, 7.4.0, 8.3.0, 9.2.0], intel: [15.2, 17.4, 18.4]} + + 3.0.5_slurm: + config: + relstage: deprecated + group_deps: + compiler: {gcc: [4.9.4, 5.5.0, 6.5.0, 7.4.0, 8.3.0, 9.2.0], intel: [15.2, 17.4, 18.4]} + + 2.1.6_slurm: + config: + relstage: deprecated + group_deps: + compiler: {gcc: [4.9.4, 5.5.0, 6.5.0, 7.4.0, 8.3.0, 9.2.0], intel: [15.2, 17.4, 18.4]} From 89fc2670d3d8ea83b01c00cd9c66968384e25e8f Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:01:20 +0100 Subject: [PATCH 017/158] H5hut: build v2.0.0rc6 with openmpi/4.1.4 --- HDF5/H5hut/files/variants.rhel6 | 1 + 1 file changed, 1 insertion(+) diff --git a/HDF5/H5hut/files/variants.rhel6 b/HDF5/H5hut/files/variants.rhel6 index 97c47d1..27e09a6 100644 --- a/HDF5/H5hut/files/variants.rhel6 +++ b/HDF5/H5hut/files/variants.rhel6 @@ -23,3 +23,4 @@ H5hut/2.0.0rc6 deprecated gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 hdf5/1.1 H5hut/2.0.0rc6 stable gcc/10.3.0 openmpi/4.0.5 hdf5/1.10.7 b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.12 b:parmetis/4.0.3 H5hut/2.0.0rc6 stable gcc/10.4.0 openmpi/4.1.4 hdf5/1.10.8 b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.17 +H5hut/2.0.0rc6 unstable gcc/10.4.0 openmpi/4.1.5 hdf5/1.10.8 b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.17 From d1208d51f5206a4412fba0ff5abf91186186dfb4 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:02:49 +0100 Subject: [PATCH 018/158] H5hut/2.0.0rc6_slurm: build with current GCC and openmpi/4.1.5_slurm --- HDF5/H5hut/files/variants.merlin6 | 1 + 1 file changed, 1 insertion(+) diff --git a/HDF5/H5hut/files/variants.merlin6 b/HDF5/H5hut/files/variants.merlin6 index 6ccc2b5..262952c 100644 --- a/HDF5/H5hut/files/variants.merlin6 +++ b/HDF5/H5hut/files/variants.merlin6 @@ -2,3 +2,4 @@ H5hut/2.0.0rc6_slurm stable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm hdf5/1. H5hut/2.0.0rc6_slurm stable gcc/10.3.0 openmpi/4.0.5-1_slurm hdf5/1.10.7_slurm b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.12 b:parmetis/4.0.3_slurm H5hut/2.0.0rc6_slurm stable gcc/10.4.0 openmpi/4.1.4_slurm hdf5/1.10.8_slurm b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.17 +H5hut/2.0.0rc6_slurm unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} openmpi/4.1.5_slurm hdf5/1.10.8_slurm b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.17 From d8a6b4dc8a06c0fddabafa738f826ffe115ff54a Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:06:08 +0100 Subject: [PATCH 019/158] trilinos/13.4.0: added --- HDF5/trilinos/files/variants.merlin6 | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/HDF5/trilinos/files/variants.merlin6 b/HDF5/trilinos/files/variants.merlin6 index 1747888..8da63f5 100644 --- a/HDF5/trilinos/files/variants.merlin6 +++ b/HDF5/trilinos/files/variants.merlin6 @@ -1,2 +1,6 @@ -trilinos/12.18.1_slurm stable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm hdf5/1.10.6_slurm b:cmake/3.15.5 b:OpenBLAS/0.3.10 b:parmetis/4.0.3_slurm -trilinos/13.0.1_slurm stable gcc/10.4.0 openmpi/4.1.4_slurm hdf5/1.10.8_slurm b:cmake/3.20.5 b:OpenBLAS/0.3.21 b:parmetis/4.0.3_slurm +trilinos/12.18.1_slurm stable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm hdf5/1.10.6_slurm b:cmake/3.15.5 b:OpenBLAS/0.3.10 b:parmetis/4.0.3_slurm +trilinos/13.0.1_slurm stable gcc/10.3.0 openmpi/4.0.5-1_slurm hdf5/1.10.7_slurm b:cmake/3.20.5 b:OpenBLAS/0.3.15 b:parmetis/4.0.3_slurm +trilinos/13.0.1_slurm stable gcc/10.4.0 openmpi/4.1.4_slurm hdf5/1.10.8_slurm b:cmake/3.20.5 b:OpenBLAS/0.3.21 b:parmetis/4.0.3_slurm +trilinos/13.4.0_slurm unstable gcc/10.3.0 openmpi/4.0.5-1_slurm hdf5/1.10.7_slurm b:cmake/3.20.5 b:OpenBLAS/0.3.15 b:parmetis/4.0.3_slurm +trilinos/13.4.0_slurm unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} openmpi/4.1.5_slurm hdf5/1.10.8_slurm b:cmake/3.20.5 b:OpenBLAS/0.3.23 b:parmetis/4.0.3_slurm + From cfced7ddb8c2b4caed3a30cbe0cbe90c4b900514 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:06:16 +0100 Subject: [PATCH 020/158] trilinos/13.4.0: added --- HDF5/trilinos/files/variants.rhel6 | 1 + 1 file changed, 1 insertion(+) diff --git a/HDF5/trilinos/files/variants.rhel6 b/HDF5/trilinos/files/variants.rhel6 index ee61ecc..2dac5f5 100644 --- a/HDF5/trilinos/files/variants.rhel6 +++ b/HDF5/trilinos/files/variants.rhel6 @@ -18,4 +18,5 @@ trilinos/12.18.1 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 hdf5/1.10 trilinos/13.0.1 stable gcc/{7.5.0,8.4.0,9.3.0,10.3.0} openmpi/4.0.5 hdf5/1.10.7 b:cmake/3.15.5 b:OpenBLAS/0.3.15 b:parmetis/4.0.3 trilinos/13.0.1 stable gcc/10.4.0 openmpi/4.1.4 hdf5/1.10.8 b:cmake/3.15.5 b:OpenBLAS/0.3.21 b:parmetis/4.0.3 +trilinos/13.4.0 unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0} openmpi/4.1.5 hdf5/1.10.8 b:cmake/3.20.5 b:OpenBLAS/0.3.23 b:parmetis/4.0.3 From 2ab0509dfa8984387652019b525aeb23bec1227a Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:07:03 +0100 Subject: [PATCH 021/158] trilinos; version 13.x support added --- HDF5/trilinos/build | 128 +++++++++++++++++++++++++++++--------------- 1 file changed, 84 insertions(+), 44 deletions(-) diff --git a/HDF5/trilinos/build b/HDF5/trilinos/build index 34afa1c..af23e67 100755 --- a/HDF5/trilinos/build +++ b/HDF5/trilinos/build @@ -1,9 +1,9 @@ #!/usr/bin/env modbuild pbuild::set_download_url \ - "https://github.com/$P/$P/tarball/$P-release-${V//./-}" \ + "https://github.com/trilinos/Trilinos/archive/refs/tags/$P-release-${V_PKG//./-}.tar.gz" \ "$P-${V_PKG}.tar.gz" - +# https://github.com/trilinos/Trilinos/archive/refs/tags/trilinos-release-13-4-0.tar.gz pbuild::set_sha256sum \ "trilinos-12.12.1.tar.gz:c8f2029fa36230b9f384c56139aaa33111227bcf653e73f7daf3c9efdecc1d2d" @@ -28,59 +28,99 @@ pbuild::configure() { config_args+=( "-DLAPACK_INCLUDE_DIRS:PATH=${LAPACK_INCLUDE_DIRS}" ) config_args+=( "-DLAPACK_LIBRARY_NAMES:STRING=${LAPACK_LIBRARY_NAMES}" ) fi - - if (( V_MAJOR == 12 && V_MINOR >= 12)); then - config_args+=( "-DTrilinos_ENABLE_SEACAS:BOOL=OFF" ) - config_args+=( "-DTrilinos_ENABLE_OpenMP:BOOL=OFF" ) - config_args+=( "-DKokkos_ENABLE_Serial:BOOL=ON" ) - config_args+=( "-DKokkos_ENABLE_OpenMP:BOOL=OFF" ) - config_args+=( "-DKokkos_ENABLE_Pthread:BOOL=OFF" ) - config_args+=( "-DKokkos_ENABLE_Cuda:BOOL=OFF" ) - config_args+=( "-DKokkos_ENABLE_Cuda_UVM:BOOL=OFF" ) - config_args+=( "-DTpetra_INST_SERIAL:BOOL=ON" ) - config_args+=( "-DTrilinos_ENABLE_TESTS:BOOL=OFF" ) - config_args+=( "-DTrilinos_ENABLE_MueLu:BOOL=ON" ) - fi - PARMETIS_INCLUDE_DIRS="${PARMETIS_PREFIX}/include" PARMETIS_LIBRARIES="${PARMETIS_PREFIX}/lib/libparmetis.a" METIS_INCLUDE_DIRS="${PARMETIS_PREFIX}/include/metis" METIS_LIBRARIES="${PARMETIS_PREFIX}/lib/libmetis.a" + + if pbuild::version_lt 12.12.0; then + config_args+=( "-DTPL_ENABLE_DLlib:BOOL=OFF" ) + config_args+=( "-DTPL_ENABLE_QT:BOOL=OFF" ) + config_args+=( "-DTPL_ENABLE_MPI:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_BLAS:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_LAPACK:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_METIS:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_ParMETIS:BOOL=ON" ) + config_args+=( "-DTPL_METIS_INCLUDE_DIRS:PATH=$METIS_INCLUDE_DIRS" ) + config_args+=( "-DTPL_METIS_LIBRARIES:PATH=$METIS_LIBRARIES" ) + config_args+=( "-DTPL_ParMETIS_INCLUDE_DIRS:PATH=$PARMETIS_INCLUDE_DIRS" ) + config_args+=( "-DTPL_ParMETIS_LIBRARIES:PATH=$PARMETIS_LIBRARIES" ) + config_args+=( "-DTrilinos_ENABLE_Amesos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Amesos2:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_AztecOO:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Belos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Epetra:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_EpetraExt:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Galeri:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Ifpack:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Isorropia:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_ML:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_MueLu:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_NOX:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Optika:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_Teuchos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Tpetra:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_TESTS:BOOL=OFF" ) + elif pbuild::version_ge 12.12.0; then + + config_args+=( "-DGtest_SKIP_INSTALL:BOOL=ON" ) + config_args+=( "-DMueLu_ENABLE_Kokkos_Refactor:STRING=ON" ) + config_args+=( "-DMueLu_ENABLE_Kokkos_Refactor_Use_By_Default:STRING=ON" ) + config_args+=( "-DTpetra_ENABLE_DEPRECATED_CODE:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON" ) + config_args+=( "-DTpetra_ENABLE_TESTS:BOOL=OFF" ) + config_args+=( "-DTpetra_ENABLE_EXAMPLES:BOOL=OFF" ) + config_args+=( "-DTpetra_INST_INT_INT:BOOL=OFF" ) + config_args+=( "-DTpetra_INST_INT_LONG:BOOL=ON" ) + config_args+=( "-DTpetra_INST_INT_LONG_LONG:BOOL=OFF" ) + + config_args+=( "-DKokkos_ENABLE_Serial:BOOL=ON" ) + config_args+=( "-DKokkos_ENABLE_OpenMP:BOOL=OFF" ) + config_args+=( "-DKokkos_ENABLE_Pthread:BOOL=OFF" ) + config_args+=( "-DKokkos_ENABLE_Cuda:BOOL=OFF" ) + config_args+=( "-DKokkos_ENABLE_Cuda_UVM:BOOL=OFF" ) + config_args+=( "-DKokkos_ENABLE_Cuda_Lambda:BOOL=OFF" ) + config_args+=( "-DTpetra_INST_SERIAL:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_DLlib:BOOL=OFF" ) + config_args+=( "-DTPL_ENABLE_QT:BOOL=OFF" ) + config_args+=( "-DTPL_ENABLE_MPI:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_BLAS:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_LAPACK:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_METIS:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_ParMETIS:BOOL=ON" ) + config_args+=( "-DTPL_METIS_INCLUDE_DIRS:PATH=$METIS_INCLUDE_DIRS" ) + config_args+=( "-DTPL_METIS_LIBRARIES:PATH=$METIS_LIBRARIES" ) + config_args+=( "-DTPL_ParMETIS_INCLUDE_DIRS:PATH=$PARMETIS_INCLUDE_DIRS" ) + config_args+=( "-DTPL_ParMETIS_LIBRARIES:PATH=$PARMETIS_LIBRARIES" ) + config_args+=( "-DTrilinos_ENABLE_SEACAS:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_OpenMP:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_MueLu:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Amesos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Amesos2:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_AztecOO:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Belos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Epetra:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_EpetraExt:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Galeri:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Ifpack:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Isorropia:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_ML:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_MueLu:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_NOX:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Optika:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_Teuchos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Tpetra:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_TESTS:BOOL=OFF" ) + fi + cmake \ -D CMAKE_BUILD_TYPE:STRING=Release \ -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX \ -DCMAKE_CXX_FLAGS:STRING="-DMPICH_IGNORE_CXX_SEEK -fPIC" \ -DCMAKE_C_FLAGS:STRING="-DMPICH_IGNORE_CXX_SEEK -fPIC" \ - -DCMAKE_CXX_STANDARD:STRING="11" \ + -DCMAKE_CXX_STANDARD:STRING="14" \ -DCMAKE_Fortran_FLAGS:STRING="-fPIC" \ - -DTPL_ENABLE_DLlib:BOOL=OFF \ - -DTPL_ENABLE_QT:BOOL=OFF \ - -DTPL_ENABLE_MPI:BOOL=ON \ - -DTPL_ENABLE_BLAS:BOOL=ON \ - -DTPL_ENABLE_LAPACK:BOOL=ON \ - -DTPL_ENABLE_METIS:BOOL=ON \ - -DTPL_ENABLE_ParMETIS:BOOL=ON \ - -DTPL_METIS_INCLUDE_DIRS:PATH=$METIS_INCLUDE_DIRS \ - -DTPL_METIS_LIBRARIES:PATH=$METIS_LIBRARIES \ - -DTPL_ParMETIS_INCLUDE_DIRS:PATH=$PARMETIS_INCLUDE_DIRS \ - -DTPL_ParMETIS_LIBRARIES:PATH=$PARMETIS_LIBRARIES \ - -DTrilinos_ENABLE_Amesos:BOOL=ON \ - -DTrilinos_ENABLE_Amesos2:BOOL=ON \ - -DTrilinos_ENABLE_AztecOO:BOOL=ON \ - -DTrilinos_ENABLE_Belos:BOOL=ON \ - -DTrilinos_ENABLE_Epetra:BOOL=ON \ - -DTrilinos_ENABLE_EpetraExt:BOOL=ON \ - -DTrilinos_ENABLE_Galeri:BOOL=ON \ - -DTrilinos_ENABLE_Ifpack:BOOL=ON \ - -DTrilinos_ENABLE_Isorropia:BOOL=ON \ - -DTrilinos_ENABLE_ML:BOOL=ON \ - -DTrilinos_ENABLE_MueLu:BOOL=ON \ - -DTrilinos_ENABLE_NOX:BOOL=ON \ - -DTrilinos_ENABLE_Optika:BOOL=OFF \ - -DTrilinos_ENABLE_Teuchos:BOOL=ON \ - -DTrilinos_ENABLE_Tpetra:BOOL=ON \ - -DTrilinos_ENABLE_TESTS:BOOL=OFF \ "${config_args[@]}" \ "${SRC_DIR}" || exit 1 } From e822c1b7a2457992e3dcf16f4c1326cd4bd8a903 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:09:04 +0100 Subject: [PATCH 022/158] trilinos: build with YAML --- HDF5/trilinos/build-xml | 123 ++++++++++++++++++++++++++++++++ HDF5/trilinos/files/config.yaml | 33 +++++++++ 2 files changed, 156 insertions(+) create mode 100755 HDF5/trilinos/build-xml create mode 100644 HDF5/trilinos/files/config.yaml diff --git a/HDF5/trilinos/build-xml b/HDF5/trilinos/build-xml new file mode 100755 index 0000000..df930b9 --- /dev/null +++ b/HDF5/trilinos/build-xml @@ -0,0 +1,123 @@ +#!/usr/bin/env modbuild + + +declare -rx AR=ar + +pbuild::configure() { + declare config_args=() + if [[ "${OS}" == "Linux" ]]; then + BLAS_PREFIX="${OPENBLAS_PREFIX}" + BLAS_INCLUDE_DIRS="${BLAS_PREFIX}/include" + BLAS_LIBRARY_DIRS="${BLAS_PREFIX}/lib64" + BLAS_LIBRARY_NAMES="openblas" + LAPACK_PREFIX="${OPENBLAS_PREFIX}" + + LAPACK_INCLUDE_DIRS="${LAPACK_PREFIX}/include" + LAPACK_LIBRARY_DIRS="${LAPACK_PREFIX}/lib64" + LAPACK_LIBRARY_NAMES="openblas" + config_args+=( "-DBLAS_LIBRARY_DIRS:PATH=${BLAS_LIBRARY_DIRS}" ) + config_args+=( "-DBLAS_INCLUDE_DIRS:PATH=${BLAS_LIBRARY_DIRS}" ) + config_args+=( "-DBLAS_LIBRARY_NAMES:STRING=${BLAS_LIBRARY_NAMES}" ) + config_args+=( "-DLAPACK_LIBRARY_DIRS:PATH=${LAPACK_LIBRARY_DIRS}" ) + config_args+=( "-DLAPACK_INCLUDE_DIRS:PATH=${LAPACK_INCLUDE_DIRS}" ) + config_args+=( "-DLAPACK_LIBRARY_NAMES:STRING=${LAPACK_LIBRARY_NAMES}" ) + fi + PARMETIS_INCLUDE_DIRS="${PARMETIS_PREFIX}/include" + PARMETIS_LIBRARIES="${PARMETIS_PREFIX}/lib/libparmetis.a" + METIS_INCLUDE_DIRS="${PARMETIS_PREFIX}/include" + METIS_LIBRARIES="${PARMETIS_PREFIX}/lib/libmetis.a" + + + if pbuild::version_lt 12.12.0; then + config_args+=( "-DTPL_ENABLE_DLlib:BOOL=OFF" ) + config_args+=( "-DTPL_ENABLE_QT:BOOL=OFF" ) + config_args+=( "-DTPL_ENABLE_MPI:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_BLAS:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_LAPACK:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_METIS:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_ParMETIS:BOOL=ON" ) + config_args+=( "-DTPL_METIS_INCLUDE_DIRS:PATH=$METIS_INCLUDE_DIRS" ) + config_args+=( "-DTPL_METIS_LIBRARIES:PATH=$METIS_LIBRARIES" ) + config_args+=( "-DTPL_ParMETIS_INCLUDE_DIRS:PATH=$PARMETIS_INCLUDE_DIRS" ) + config_args+=( "-DTPL_ParMETIS_LIBRARIES:PATH=$PARMETIS_LIBRARIES" ) + config_args+=( "-DTrilinos_ENABLE_Amesos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Amesos2:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_AztecOO:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Belos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Epetra:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_EpetraExt:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Galeri:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Ifpack:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Isorropia:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_ML:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_MueLu:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_NOX:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Optika:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_Teuchos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Tpetra:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_TESTS:BOOL=OFF" ) + elif pbuild::version_ge 12.12.0; then + + config_args+=( "-DGtest_SKIP_INSTALL:BOOL=ON" ) + config_args+=( "-DMueLu_ENABLE_Kokkos_Refactor:STRING=ON" ) + config_args+=( "-DMueLu_ENABLE_Kokkos_Refactor_Use_By_Default:STRING=ON" ) + config_args+=( "-DTpetra_ENABLE_DEPRECATED_CODE:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON" ) + config_args+=( "-DTpetra_ENABLE_TESTS:BOOL=OFF" ) + config_args+=( "-DTpetra_ENABLE_EXAMPLES:BOOL=OFF" ) + config_args+=( "-DTpetra_INST_INT_INT:BOOL=OFF" ) + config_args+=( "-DTpetra_INST_INT_LONG:BOOL=ON" ) + config_args+=( "-DTpetra_INST_INT_LONG_LONG:BOOL=OFF" ) + + config_args+=( "-DKokkos_ENABLE_Serial:BOOL=ON" ) + config_args+=( "-DKokkos_ENABLE_OpenMP:BOOL=OFF" ) + config_args+=( "-DKokkos_ENABLE_Pthread:BOOL=OFF" ) + config_args+=( "-DKokkos_ENABLE_Cuda:BOOL=OFF" ) + config_args+=( "-DKokkos_ENABLE_Cuda_UVM:BOOL=OFF" ) + config_args+=( "-DKokkos_ENABLE_Cuda_Lambda:BOOL=OFF" ) + config_args+=( "-DTpetra_INST_SERIAL:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_DLlib:BOOL=OFF" ) + config_args+=( "-DTPL_ENABLE_QT:BOOL=OFF" ) + config_args+=( "-DTPL_ENABLE_MPI:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_BLAS:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_LAPACK:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_METIS:BOOL=ON" ) + config_args+=( "-DTPL_ENABLE_ParMETIS:BOOL=ON" ) + config_args+=( "-DTPL_METIS_INCLUDE_DIRS:PATH=$METIS_INCLUDE_DIRS" ) + config_args+=( "-DTPL_METIS_LIBRARIES:PATH=$METIS_LIBRARIES" ) + config_args+=( "-DTPL_ParMETIS_INCLUDE_DIRS:PATH=$PARMETIS_INCLUDE_DIRS" ) + config_args+=( "-DTPL_ParMETIS_LIBRARIES:PATH=$PARMETIS_LIBRARIES" ) + config_args+=( "-DTrilinos_ENABLE_SEACAS:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_OpenMP:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_MueLu:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Amesos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Amesos2:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_AztecOO:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Belos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Epetra:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_EpetraExt:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Galeri:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Ifpack:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Isorropia:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_ML:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_MueLu:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_NOX:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Optika:BOOL=OFF" ) + config_args+=( "-DTrilinos_ENABLE_Teuchos:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_Tpetra:BOOL=ON" ) + config_args+=( "-DTrilinos_ENABLE_TESTS:BOOL=OFF" ) + fi + + cmake \ + -D CMAKE_BUILD_TYPE:STRING=Release \ + -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX \ + -DCMAKE_CXX_FLAGS:STRING="-DMPICH_IGNORE_CXX_SEEK -fPIC" \ + -DCMAKE_C_FLAGS:STRING="-DMPICH_IGNORE_CXX_SEEK -fPIC" \ + -DCMAKE_CXX_STANDARD:STRING="17" \ + -DCMAKE_Fortran_FLAGS:STRING="-fPIC" \ + "${config_args[@]}" \ + "${SRC_DIR}" || exit 1 +} + +pbuild::install_docfiles Copyright.txt LICENSE README RELEASE_NOTES + diff --git a/HDF5/trilinos/files/config.yaml b/HDF5/trilinos/files/config.yaml new file mode 100644 index 0000000..c253e01 --- /dev/null +++ b/HDF5/trilinos/files/config.yaml @@ -0,0 +1,33 @@ +--- +# yamllint disable rule:line-length +format: 1 +trilinos: + defaults: + group: HDF5 + overlay: base + relstage: stable + systems: [rhel7, rhel8, rhel9] + urls: + - url: https://github.com/trilinos/Trilinos/archive/refs/tags/$P-release-${V_MAJOR}-${V_MINOR}-${V_PATCHLVL}.tar.gz + name: $P-${V_PKG}.tar.gz + + versions: + 14.4.0: + variants: + - relstage: unstable + overlay: devel + group_deps: + compiler: {gcc: [10.4.0]} + mpi: {openmpi: [4.1.5]} + hdf5: {hdf5: [1.10.8]} + build_requires: [cmake/3.25.2, OpenBLAS/0.3.23, parmetis/4.0.3] + + 12.12.1: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [7.3.0]} + mpi: {openmpi: [1.10.7, 2.1.2, 3.0.0]} + hdf5: {hdf5: [1.10.1]} + build_requires: [hdf5/1.10.1, cmake/3.6.3, OpenBLAS/0.2.20, parmetis/4.0.3] From ccc78e3573835bf2fd60b0ab038247c0baeec753 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:12:49 +0100 Subject: [PATCH 023/158] nettle: build with YAML --- Libraries/nettle/build-xml | 6 ++++++ Libraries/nettle/files/config.yaml | 16 ++++++++++++++++ 2 files changed, 22 insertions(+) create mode 100755 Libraries/nettle/build-xml create mode 100644 Libraries/nettle/files/config.yaml diff --git a/Libraries/nettle/build-xml b/Libraries/nettle/build-xml new file mode 100755 index 0000000..a99bec2 --- /dev/null +++ b/Libraries/nettle/build-xml @@ -0,0 +1,6 @@ +#!/usr/bin/env modbuild + +# use system gcc to compile +declare -rx CC=gcc + +pbuild::add_configure_args "--disable-shared" diff --git a/Libraries/nettle/files/config.yaml b/Libraries/nettle/files/config.yaml new file mode 100644 index 0000000..ad0a590 --- /dev/null +++ b/Libraries/nettle/files/config.yaml @@ -0,0 +1,16 @@ +format: 1 +nettle: + defaults: + group: Libraries + relstage: stable + docfiles: [] + urls: + - url: https://ftp.gnu.org/gnu/nettle/nettle-${V_PKG}.tar.gz + shasums: + nettle-3.9.1.tar.gz: ccfeff981b0ca71bbd6fbcb054f407c60ffb644389a5be80d6716d5b550c6ce3 + versions: + 3.9.1: + config: + relstage: unstable + build_requires: [gmp/6.1.2-1] + From e8ee8aee67dacd066b15d089598e5dc9b7c1737c Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:14:23 +0100 Subject: [PATCH 024/158] libidn2: new build-block added --- Libraries/libidn2/build | 2 ++ Libraries/libidn2/files/config.yaml | 26 ++++++++++++++++++++++++++ Libraries/libidn2/files/variants | 1 + Libraries/libidn2/modulefile | 13 +++++++++++++ 4 files changed, 42 insertions(+) create mode 100755 Libraries/libidn2/build create mode 100644 Libraries/libidn2/files/config.yaml create mode 100644 Libraries/libidn2/files/variants create mode 100644 Libraries/libidn2/modulefile diff --git a/Libraries/libidn2/build b/Libraries/libidn2/build new file mode 100755 index 0000000..6e021f3 --- /dev/null +++ b/Libraries/libidn2/build @@ -0,0 +1,2 @@ +#!/usr/bin/env modbuild + diff --git a/Libraries/libidn2/files/config.yaml b/Libraries/libidn2/files/config.yaml new file mode 100644 index 0000000..3cbfa1c --- /dev/null +++ b/Libraries/libidn2/files/config.yaml @@ -0,0 +1,26 @@ +format: 1 +libidn2: + defaults: + group: Libraries + relstage: stable + docfiles: + - ABOUT-NLS + - AUTHORS + - CONTRIBUTING.md + - COPYING + - COPYING.LESSERv3 + - COPYING.unicode + - COPYINGv2 + - ChangeLog + - INSTALL + - NEWS + - README + - README.md + urls: + - url: https://ftp.gnu.org/gnu/libidn/libidn2-${V_PKG}.tar.gz + shasums: + libidn2-2.3.4.tar.gz: 93caba72b4e051d1f8d4f5a076ab63c99b77faee019b72b9783b267986dbb45f + versions: + 2.3.4: + config: + relstage: unstable diff --git a/Libraries/libidn2/files/variants b/Libraries/libidn2/files/variants new file mode 100644 index 0000000..a1fcd25 --- /dev/null +++ b/Libraries/libidn2/files/variants @@ -0,0 +1 @@ +libpng/1.6.34 unstable diff --git a/Libraries/libidn2/modulefile b/Libraries/libidn2/modulefile new file mode 100644 index 0000000..8a52e93 --- /dev/null +++ b/Libraries/libidn2/modulefile @@ -0,0 +1,13 @@ +#%Module1.0 + +module-whatis "PNG reference library" +module-url "http://www.libpng.org/pub/png/libpng.html" +module-license "Open source" +module-maintainer "Achim Gsell " + +module-help " +libpng is the official PNG reference library. It supports almost all +PNG features, is extensible, and has been extensively tested for over +23 years. +" + From f2be15edffc30803ded87d0efa37e026c8f42d9f Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:19:55 +0100 Subject: [PATCH 025/158] MITHRA: pbuild::install() added --- MPI/MITHRA/build | 3 +++ 1 file changed, 3 insertions(+) diff --git a/MPI/MITHRA/build b/MPI/MITHRA/build index b0012bb..7cc7bdb 100755 --- a/MPI/MITHRA/build +++ b/MPI/MITHRA/build @@ -26,6 +26,9 @@ pbuild::configure() { : } +pbuild::install() { + make -e PREFIX="${PREFIX}" install +} # Local Variables: # mode: sh # sh-basic-offset: 8 From cc828638f264aca58dcb31608fc61248b485ee21 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:20:51 +0100 Subject: [PATCH 026/158] MITHRA/2.0: build with openmpi/{4.1.5,4.1.5_slurm} added --- MPI/MITHRA/files/variants.rhel6 | 1 + MPI/MITHRA/files/variants.slurm | 1 + 2 files changed, 2 insertions(+) diff --git a/MPI/MITHRA/files/variants.rhel6 b/MPI/MITHRA/files/variants.rhel6 index 6e1c60b..5fe91c4 100644 --- a/MPI/MITHRA/files/variants.rhel6 +++ b/MPI/MITHRA/files/variants.rhel6 @@ -2,3 +2,4 @@ MITHRA/2020.8.27 deprecated gcc/8.4.0 openmpi/3.1.6 MITHRA/2.0 stable gcc/8.4.0 openmpi/3.1.6 MITHRA/2.0 stable gcc/10.3.0 openmpi/4.0.5 MITHRA/2.0 stable gcc/10.4.0 openmpi/4.1.4 +MITHRA/2.0 unstable gcc/10.4.0 openmpi/4.1.5 diff --git a/MPI/MITHRA/files/variants.slurm b/MPI/MITHRA/files/variants.slurm index 20035f6..827ce72 100644 --- a/MPI/MITHRA/files/variants.slurm +++ b/MPI/MITHRA/files/variants.slurm @@ -2,3 +2,4 @@ MITHRA/2020.8.27_slurm deprecated gcc/8.4.0 openmpi/3.1.6_slurm MITHRA/2.0_slurm stable gcc/8.4.0 openmpi/3.1.6_slurm MITHRA/2.0_slurm stable gcc/10.3.0 openmpi/4.0.5-1_slurm MITHRA/2.0_slurm stable gcc/10.4.0 openmpi/4.1.4_slurm +MITHRA/2.0_slurm unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} openmpi/4.1.5_slurm From 5c9ada56101a5159bd452519d5693b30f9b4bba6 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:47:15 +0100 Subject: [PATCH 027/158] amrex: typo fixed in var.name OPENMPI_VERSION --- MPI/amrex/build | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/MPI/amrex/build b/MPI/amrex/build index 5c04f24..a1e395d 100755 --- a/MPI/amrex/build +++ b/MPI/amrex/build @@ -10,7 +10,7 @@ pbuild::install_docfiles 'license.txt' pbuild::install_docfiles 'README.txt' pbuild::pre_prep() { - echo "OPENMPI_VERSION=${OPENMPI_VEERSION}" 1>&2 + echo "OPENMPI_VERSION=${OPENMPI_VERSION}" 1>&2 if pbuild::version_gt "${OPENMPI_VERSION}" '4.0.0'; then pbuild::add_patch "files/AMReX_ParallelDescriptor.patch" fi From 5de25379cc6973f83875f324954f74d562bf8e3d Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:48:27 +0100 Subject: [PATCH 028/158] amrex/3.15.5,3.15.5_slurm: added with openmpi/4.1.5,4.1.5_slurm --- MPI/amrex/files/variants.merlin6 | 1 + MPI/amrex/files/variants.rhel6 | 1 + 2 files changed, 2 insertions(+) diff --git a/MPI/amrex/files/variants.merlin6 b/MPI/amrex/files/variants.merlin6 index c2f93ac..78772a7 100644 --- a/MPI/amrex/files/variants.merlin6 +++ b/MPI/amrex/files/variants.merlin6 @@ -1,4 +1,5 @@ amrex/18.07_3d_slurm stable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:cmake/3.15.5 amrex/18.07_3d_slurm stable gcc/10.3.0 openmpi/4.0.5-1_slurm b:cmake/3.20.5 amrex/18.07_3d_slurm stable gcc/10.4.0 openmpi/4.1.4_slurm b:cmake/3.20.5 +amrex/18.07.1_3d_slurm unstable gcc/{10.4.0,11.4.0,12.3.0,13.1.0} openmpi/4.1.5_slurm b:cmake/3.20.5 diff --git a/MPI/amrex/files/variants.rhel6 b/MPI/amrex/files/variants.rhel6 index 39b3be3..01343a8 100644 --- a/MPI/amrex/files/variants.rhel6 +++ b/MPI/amrex/files/variants.rhel6 @@ -17,4 +17,5 @@ amrex/18.07_3d stable gcc/{7.3.0,8.2.0} mpich/3.2.1 b:cmake/3.9.6 amrex/18.07_3d stable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6 b:cmake/3.15.5 amrex/18.07_3d stable gcc/{7.5.0,8.4.0,9.3.0,10.3.0} openmpi/4.0.5 b:cmake/3.15.5 amrex/18.07_3d stable gcc/10.4.0 openmpi/4.1.4 b:cmake/3.15.5 +amrex/18.07.1_3d unstable gcc/10.4.0 openmpi/4.1.5 b:cmake/3.15.5 From 3285f9e031cb9e6bda93d9a6734ce5d0df242c8b Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:52:42 +0100 Subject: [PATCH 029/158] boost/1.81.0_slurm,1.82.0_slurm,1.81.0: added with openmpi/4.1.5_slurm,4.1.5 --- MPI/boost/files/variants.merlin6 | 3 +++ MPI/boost/files/variants.rhel6 | 1 + 2 files changed, 4 insertions(+) diff --git a/MPI/boost/files/variants.merlin6 b/MPI/boost/files/variants.merlin6 index c90fec5..e3c4b2a 100644 --- a/MPI/boost/files/variants.merlin6 +++ b/MPI/boost/files/variants.merlin6 @@ -9,3 +9,6 @@ boost/1.76.0_slurm stable gcc/{10.2.0,10.3.0} openmpi/4.0.5-1_slur boost/1.79.0_slurm stable gcc/{9.3.0,10.3.0} openmpi/4.1.3_slurm b:zlib/1.2.11 boost/1.79.0_slurm stable gcc/10.4.0 openmpi/4.1.4_slurm b:zlib/1.2.13 boost/1.79.0_slurm unstable intel/22.1 impi/22.1 b:zlib/1.2.11 + +boost/1.81.0_slurm unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} openmpi/4.1.5_slurm b:zlib/1.2.13 +boost/1.82.0_slurm unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} openmpi/4.1.5_slurm b:zlib/1.2.13 diff --git a/MPI/boost/files/variants.rhel6 b/MPI/boost/files/variants.rhel6 index 8bd4f52..b8bbc04 100644 --- a/MPI/boost/files/variants.rhel6 +++ b/MPI/boost/files/variants.rhel6 @@ -14,3 +14,4 @@ boost/1.73.0 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:zlib/1.2.11 boost/1.76.0 stable gcc/{7.5.0,8.4.0,9.3.0,10.3.0} openmpi/4.0.5 b:zlib/1.2.11 boost/1.79.0 stable gcc/10.4.0 openmpi/4.1.4 b:zlib/1.2.13 +boost/1.82.0 unstable gcc/10.4.0 openmpi/4.1.5 b:zlib/1.2.13 From ac745330090d8efb5d0651ed116737fac3abc6d2 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:54:40 +0100 Subject: [PATCH 030/158] ftw/3.3.10_merlin6: compile with gcc/11.4.0,12.3.0,13.1.0 added --- MPI/fftw/files/variants.merlin6 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/MPI/fftw/files/variants.merlin6 b/MPI/fftw/files/variants.merlin6 index 30dc0e0..7a4a719 100644 --- a/MPI/fftw/files/variants.merlin6 +++ b/MPI/fftw/files/variants.merlin6 @@ -7,4 +7,4 @@ fftw/3.3.9_merlin6 unstable gcc/{8.4.0,9.3.0,10.2.0,10.3.0,11.2.0} openmpi/4.0.5 fftw/3.3.10 unstable gcc/{7.5.0,8.4.0,9.3.0,10.3.0} openmpi/4.0.5 fftw/3.3.10_merlin6 unstable gcc/{8.4.0,9.3.0,10.2.0,10.3.0,11.2.0} openmpi/4.0.5-1_slurm -fftw/3.3.10_merlin6 unstable gcc/10.4.0 openmpi/4.1.5_slurm +fftw/3.3.10_merlin6 unstable gcc/{10.4.0,11.4.0,12.3.0,13.1.0} openmpi/4.1.5_slurm From 4cf4676583dc6eb544ff1cc6ce3ffca4c1e28c0f Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:56:51 +0100 Subject: [PATCH 031/158] hdf5: YAML build added --- MPI/hdf5/build-yaml | 56 ++++++++ MPI/hdf5/files/config.yaml | 287 +++++++++++++++++++++++++++++++++++++ 2 files changed, 343 insertions(+) create mode 100755 MPI/hdf5/build-yaml create mode 100644 MPI/hdf5/files/config.yaml diff --git a/MPI/hdf5/build-yaml b/MPI/hdf5/build-yaml new file mode 100755 index 0000000..188d8f6 --- /dev/null +++ b/MPI/hdf5/build-yaml @@ -0,0 +1,56 @@ +#!/usr/bin/env modbuild + +pbuild::install_docfiles ACKNOWLEDGMENTS +pbuild::install_docfiles COPYING +pbuild::install_docfiles MANIFEST +pbuild::install_docfiles README* + +pbuild::pre_configure() { + pbuild::add_configure_args "CC=${MPICC}" + pbuild::add_configure_args "CXX=${MPICXX}" + + pbuild::add_configure_args "--enable-shared" + pbuild::add_configure_args "--enable-parallel" + pbuild::add_configure_args "--enable-cxx" + pbuild::add_configure_args "--enable-unsupported" + #pbuild::add_configure_args "--enable-threadsafe" + pbuild::add_configure_args "--with-pic" + + local enable_fortran='yes' + + case "${COMPILER}" in + clang-macos ) + enable_fortran='no' + # we do not have Fortran in Xcode + ;; + pgi ) + # PGI uses GCC's include files, some object files and + # the STL implementation! + # The PGI C pre-processor is broken and doesn't work + # for HDF5. We use the pre-processor of the underlying + # GCC... + # This is a bit hackish! + # + # The following eval sets GCCDIR! Which is something + # like: + # /opt/psi/Programming/gcc/7.3.0/bin/../lib/gcc/x86_64-pc-linux-gnu/7.3.0 + # + eval $(pgcc -show 2>/dev/null | \ + awk '/^GCCDIR[[:space:]]*=/{gsub(/[[:space:]]/,""); print $0}') + pbuild::add_configure_args "CPP=${GCCDIR%%/..*}/cpp" + pbuild::add_configure_args "CFLAGS=-fPIC" + pbuild::add_configure_args "CXXFLAGS=-fPIC" + pbuild::add_configure_args "FCFLAGS=-fPIC" + ;; + esac + + if [[ "${enable_fortran}" == 'yes' ]]; then + pbuild::add_configure_args "F77=${MPIF77}" + pbuild::add_configure_args "F90=${MPIF90}" + pbuild::add_configure_args "FC=${MPIFC}" + pbuild::add_configure_args "FORTRAN=${MPIFORTRAN}" + pbuild::add_configure_args "--enable-fortran" + fi + +} + diff --git a/MPI/hdf5/files/config.yaml b/MPI/hdf5/files/config.yaml new file mode 100644 index 0000000..45c1ab5 --- /dev/null +++ b/MPI/hdf5/files/config.yaml @@ -0,0 +1,287 @@ +--- +# yamllint disable rule:line-length +format: 1 +hdf5: + defaults: + group: MPI + overlay: base + relstage: stable + systems: [rhel7, rhel8, rhel9] + urls: + - url: https://support.hdfgroup.org/ftp/HDF5/releases/$P-${V_MAJOR}.${V_MINOR}/$P-${V_PKG}/src/$P-${V_PKG}.tar.bz2 + shasums: + hdf5-1.8.10-patch1.tar.bz2: 292afb3615ad9e68f4d5d18ebb11e4a73f2aece39f2da3875a457ff1e109fc41 + hdf5-1.8.12.tar.bz2: 10a369a4fc207bb09245f57c758e587420e06dfc0e445e337a58b0848b75a949 + hdf5-1.8.13.tar.bz2: c2f5a412107aba6f99fd7a4a9db6ce5f5fc8171ec931472784e5839d26aa17ef + hdf5-1.8.14.tar.bz2: 53722cb9f5977af2908f92fc1a3f8c597800a5cb448cfe5c75060d6335bb9bab + hdf5-1.8.15-patch1.tar.bz2: a5afc630c4443547fff15e9637b5b10404adbed4c00206d89517d32d6668fb32 + hdf5-1.8.15.1.tar.bz2: 289307fd70cef6715e0a28371635c8038153a4f25069319e34b0bc675a23e8ed + hdf5-1.8.16.tar.bz2: 13aaae5ba10b70749ee1718816a4b4bfead897c2fcb72c24176e759aec4598c6 + hdf5-1.8.17.tar.bz2: fc35dd8fd8d398de6b525b27cc111c21fc79795ad6db1b1f12cb15ed1ee8486a + hdf5-1.8.18.tar.bz2: 01c6deadf4211f86922400da82c7a8b5b50dc8fc1ce0b5912de3066af316a48c + hdf5-1.8.19.tar.bz2: 59c03816105d57990329537ad1049ba22c2b8afe1890085f0c022b75f1727238 + hdf5-1.8.20.tar.bz2: a4f2db7e0a078aa324f64e0216a80731731f73025367fa94d158c9b1d3fbdf6f + hdf5-1.8.21.tar.bz2: e5b1b1dee44a64b795a91c3321ab7196d9e0871fe50d42969761794e3899f40d + hdf5-1.10.0.tar.bz2: 31ff70dc7c7317066ab3bda3eec4498a8b099c69c1271b008ed3df388e743d28 + hdf5-1.10.1.tar.bz2: 9c5ce1e33d2463fb1a42dd04daacbc22104e57676e2204e3d66b1ef54b88ebf2 + hdf5-1.10.2.tar.bz2: 1cad5b7bfdf128dfc53cd16fba48f6e7ae4e93c75c371d9ec8dfc4df0c1fcb71 + hdf5-1.10.3.tar.bz2: c65cdcce4724a57fd3f8da9f0d109b497be30092acb9fac634d1291190d905a9 + hdf5-1.10.4.tar.bz2: 1267ff06aaedc04ca25f7c6026687ea2884b837043431195f153401d942b28df + hdf5-1.10.5.tar.bz2: 68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44 + hdf5-1.10.6.tar.bz2: 09d6301901685201bb272a73e21c98f2bf7e044765107200b01089104a47c3bd + hdf5-1.10.6_slurm.tar.bz2: d5a89e26beae0bc03ad18a0b0d1d3d75f87c32047879d25da11970cb5c4662a3 + hdf5-1.10.7.tar.bz2: 02018fac7e5efc496d9539a303cfb41924a5dadffab05df9812096e273efa55e + hdf5-1.10.8.tar.bz2: 66ec544b195a4cb9f6ffed034fd82e52429d6112747c2996ab69853f606e546b + hdf5-1.10.11.tar.bz2: 0afc77da5c46217709475bbefbca91c0cb6f1ea628ccd8c36196cf6c5a4de304 + hdf5-1.12.0.tar.bz2: 97906268640a6e9ce0cde703d5a71c9ac3092eded729591279bf2e3ca9765f61 + hdf5-1.12.2.tar.bz2: 3016ea56a175d2ca7f2568c8016420f7a2aad8f95e214fe7fa5485f4b80fbe51 + hdf5-1.13.1.tar.bz2: e16973ec893e2d5aa9c8dc73e196db9b99a605578e7317b421c713936f8bf57d + + versions: + 1.8.12: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.7.4, 4.8.3, 4.8.4, 4.9.2]} + mpi: {openmpi: [1.6.5, 1.8.2, 1.8.4]} + - group_deps: + compiler: {gcc: [4.8.2]} + mpi: {openmpi: [1.6.5]} + - group_deps: + compiler: {gcc: [4.7.4, 4.8.4, gcc/4.9.2, 5.1.0], intel: [15.2]} + mpit: {mpich: [3.1.4]} + - group_deps: + compiler: {gcc: [4.8.5]} + mpi: {openmpi: [1.8.8]} + - group_deps: + compiler: {gcc: [5.1.0], intel: [15.2]} + mpi: {openmpi: [1.6.5]} + - group_deps: + compiler: {gcc: [5.1.0], intel: [15.2, 15.3]} + mpi: {openmpi: [1.8.4]} + 1.8.13: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.7.4, 4.8.3, 4.8.4]} + mpi: {openmpi: [1.6.5, 1.8.2, 1.8.4]} + 1.8.14: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.7.4, 4.8.3, 4.8.4, 4.9.2]} + mpi: {openmpi: [1.6.5, 1.8.2, 1.8.4]} + - group_deps: + compiler: {gcc: [4.7.4, 4.8.4, 4.9.2, 5.1.0], intel: [15.2]} + mpi: {mpich: [3.1.4]} + - group_deps: + compiler: {gcc: [5.1.0], intel: [15.2]} + mpi: {openmpi: [1.6.5]} + - group_deps: + compiler: {gcc: [5.1.0], intel: [15.2, 15.3]} + mpi: {openmpi: [1.8.4]} + + 1.8.15-patch1: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.7.4, 4.8.4, 4.9.2, 5.1.0]} + mpi: {mpich: [3.1.4], openmpi: [1.6.5, 1.8.4]} + - group_deps: + compiler: {gcc: [4.8.5, 4.9.3, 5.2.0]} + mpi: {openmpi: [1.10.0]} + - group_deps: + compiler: {intel: [15.3]} + mpi: {openmpi: [1.6.5]} + + 1.8.15.1: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.9.3, 5.2.0]} + mpi: {openmpi: [1.8.8]} + + 1.8.16: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.8.5, 4.9.3]} + mpi: {openmpi: [1.8.8]} + - group_deps: + compiler: {gcc: [4.9.2]} + mpi: {openmpi: [1.8.4]} + - group_deps: + compiler: {gcc: [4.8.5, 5.3.0, 6.1.0]} + mpi: {openmpi: [1.10.2]} + + 1.8.17: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.8.5, 4.9.3]} + mpi: {openmpi: [1.8.8]} + - group_deps: + compiler: {gcc: [4.8.5, 5.3.0, 6.1.0, 6.2.0]} + mpi: {openmpi: [1.10.2]} + - group_deps: + compiler: {gcc: [4.8.5, 4.9.4, 5.4.0, 6.2.0]} + mpi: {openmpi: [1.10.4]} + + 1.8.18: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.8.5, 4.9.4, 5.4.0, 6.2.0]} + mpi: {openmpi: [1.10.4]} + + 1.8.20: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.8.5]} + mpi: {openmpi: [1.10.4]} + + - group_deps: + compiler: {gcc: [7.3.0]} + mpi: {openmpi: [1.10.7, 2.1.5, 3.1.3], mpich: [3.2.1]} + + - group_deps: + compiler: {intel: [18.4]} + mpi: {impi: [18.4]} + + 1.10.0: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [4.8.5, 5.3.0, 6.1.0]} + mpi: {openmpi: [1.10.2]} + + 1.10.1: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [7.3.0]} + mpi: {openmpi: [1.10.7, 2.1.2, 3.0.0, 3.0.1]} + - group_deps: + compiler: {intel: [17.4]} + mpi: {openmpi: [1.10.7, 2.1.2, 3.0.0]} + - group_deps: + compiler: {pgi: [18.5]} + mpi: {pgi-mpi: [18.5]} + + 1.10.2: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [7.3.0]} + mpi: {openmpi: [3.0.1]} + + 1.10.3: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [7.3.0]} + mpi: {openmpi: [3.1.2]} + - group_deps: + compiler: {intel: [17.4]} + mpi: {intel-mpi: [17.4]} + + 1.10.4: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [5.5.0, 7.3.0, 8.2.0]} + mpi: {openmpi: [3.1.3]} + - group_deps: + compiler: {gcc: [7.3.0]} + mpi: {mpich: [3.3]} + + 1.10.5: + config: + relstage: deprecated + variants: + - group_deps: + compiler: {gcc: [7.4.0, 8.3.0]} + mpi: {openmpi: [3.1.4]} + + 1.10.6: + variants: + - group_deps: + compiler: {gcc: [7.5.0, 8.4.0, 9.3.0, 10.1.0]} + mpi: {openmpi: [3.1.6]} + + 1.10.6_slurm: + variants: + - group_deps: + compiler: {gcc: [7.5.0, 8.4.0, 9.3.0]} + mpi: {openmpi: [3.1.6_slurm]} + + 1.10.7: + variants: + - group_deps: + compiler: {gcc: [7.5.0, 8.4.0, 9.3.0, 10.2.0, 10.3.0]} + mpi: {openmpi: [4.0.5]} + + 1.10.7_slurm: + variants: + - group_deps: + compiler: {gcc: [10.3.0]} + mpi: {openmpi: [4.0.5-1_slurm]} + + 1.10.8: + variants: + - group_deps: + compiler: {gcc: [10.4.0]} + mpi: {openmpi: [4.1.4]} + - relstage: unstable + group_deps: + compiler: {gcc: [10.4.0]} + mpi: {openmpi: [4.1.5]} + + 1.10.8_slurm: + variants: + - group_deps: + compiler: {gcc: [10.4.0]} + mpi: {openmpi: [4.1.4_slurm]} + - relstage: unstable + group_deps: + compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} + mpi: {openmpi: [4.1.5_slurm]} + + 1.10.11: + variants: + - relstage: unstable + group_deps: + compiler: {gcc: [12.3.0]} + mpi: {openmpi: [4.1.5]} + + 1.12.0: + variants: + - group_deps: + compiler: {gcc: [7.5.0, 8.4.0, 9.3.0, 10.2.0]} + mpi: {openmpi: [4.0.5]} + - relstage: unstable + group_deps: + compiler: {pgi: [21.5]} + mpi: {pgi-mpi: [21.5]} + + 1.13.1_slurm: + variants: + - relstage: unstable + group_deps: + compiler: {gcc: [11.2.0]} + mpi: {openmpi: [4.1.3_slurm]} From db5fd74afbb65636b90229dc7091aab85ecdace2 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:58:12 +0100 Subject: [PATCH 032/158] hdf5/1.10.8: build with openmpi/4.1.5_slurm,4.1.5 added --- MPI/hdf5/files/variants.merlin6 | 1 + MPI/hdf5/files/variants.rhel6 | 1 + 2 files changed, 2 insertions(+) diff --git a/MPI/hdf5/files/variants.merlin6 b/MPI/hdf5/files/variants.merlin6 index 675c4e5..b2a0a13 100644 --- a/MPI/hdf5/files/variants.merlin6 +++ b/MPI/hdf5/files/variants.merlin6 @@ -1,4 +1,5 @@ hdf5/1.10.6_slurm stable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm hdf5/1.10.7_slurm stable gcc/10.3.0 openmpi/4.0.5-1_slurm hdf5/1.10.8_slurm stable gcc/10.4.0 openmpi/4.1.4_slurm +hdf5/1.10.8_slurm unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} openmpi/4.1.5_slurm hdf5/1.13.1_slurm unstable gcc/11.2.0 openmpi/4.1.3_slurm diff --git a/MPI/hdf5/files/variants.rhel6 b/MPI/hdf5/files/variants.rhel6 index 02b83bd..6b44112 100644 --- a/MPI/hdf5/files/variants.rhel6 +++ b/MPI/hdf5/files/variants.rhel6 @@ -60,5 +60,6 @@ hdf5/1.10.7 stable gcc/{7.5.0,8.4.0,9.3.0,10.2.0} openmpi/4.0.5 hdf5/1.10.7 stable gcc/10.3.0 openmpi/4.0.5 hdf5/1.10.8 stable gcc/10.4.0 openmpi/4.1.4 +hdf5/1.10.8 unstable gcc/10.4.0 openmpi/4.1.5 hdf5/1.12.0 stable gcc/{7.5.0,8.4.0,9.3.0,10.2.0} openmpi/4.0.5 From 5e2412ec9fa4826ea4f7ba9fde2afd015844b599 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 15:59:28 +0100 Subject: [PATCH 033/158] parmetis: YAML config file added --- MPI/parmetis/files/config.yaml | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 MPI/parmetis/files/config.yaml diff --git a/MPI/parmetis/files/config.yaml b/MPI/parmetis/files/config.yaml new file mode 100644 index 0000000..ed6d400 --- /dev/null +++ b/MPI/parmetis/files/config.yaml @@ -0,0 +1,29 @@ +parmetis/3.2.0 deprecated gcc/{4.7.4,4.8.3,4.8.4,4.9.2} openmpi/{1.6.5,1.8.2,1.8.4} + +parmetis/3.2.0 deprecated gcc/{4.8.5,5.3.0,6.1.0,6.2.0} openmpi/1.10.2 + +parmetis/3.2.0 deprecated gcc/6.2.0 openmpi/{1.10.4,2.0.1} + +parmetis/3.2.0 deprecated gcc/7.3.0 openmpi/3.0.1 + +parmetis/3.2.0 deprecated intel/15.3 openmpi/1.8.4 + +parmetis/4.0.3 deprecated gcc/4.8.2 openmpi/1.6.5 b:cmake/3.4.1 +parmetis/4.0.3 deprecated gcc/{4.8.5,4.9.4,5.3.0,5.4.0,6.1.0,6.2.0} openmpi/1.10.2 b:cmake/3.4.1 + +parmetis/4.0.3 deprecated gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.6.3 + +parmetis/4.0.3 deprecated gcc/6.2.0 openmpi/2.0.1 b:cmake/3.6.3 + +parmetis/4.0.3 deprecated gcc/7.3.0 openmpi/{1.10.7,2.1.2,3.0.0,3.0.1,3.1.2,3.1.3} b:cmake/3.6.3 +parmetis/4.0.3 deprecated gcc/7.4.0 openmpi/3.1.4 b:cmake/3.9.6 + +parmetis/4.0.3 deprecated intel/17.4 openmpi/{1.10.7,2.1.2,3.0.0} b:cmake/3.6.3 + +parmetis/4.0.3 stable gcc/7.3.0 mpich/3.3 b:cmake/3.9.6 + +parmetis/4.0.3 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:cmake/3.9.6 + +parmetis/4.0.3 stable gcc/{7.5.0,8.4.0,9.3.0,10.3.0} openmpi/4.0.5 b:cmake/3.15.5 +parmetis/4.0.3 stable gcc/10.4.0 openmpi/4.1.4 b:cmake/3.15.5 +parmetis/4.0.3 unstable gcc/10.4.0 openmpi/4.1.5 b:cmake/3.15.5 From f24b477b7c18f2bc15fc49f6ca3df62507be0e50 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:00:12 +0100 Subject: [PATCH 034/158] parmetis/4.0.3_slurm,4.0.3: build with openmpi/4.1.5_slurm,4.1.5 added --- MPI/parmetis/files/variants.merlin6 | 1 + MPI/parmetis/files/variants.rhel6 | 1 + 2 files changed, 2 insertions(+) diff --git a/MPI/parmetis/files/variants.merlin6 b/MPI/parmetis/files/variants.merlin6 index 4845c56..c2cb010 100644 --- a/MPI/parmetis/files/variants.merlin6 +++ b/MPI/parmetis/files/variants.merlin6 @@ -2,4 +2,5 @@ parmetis/4.0.3_slurm stable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:cmake/ parmetis/4.0.3_slurm stable gcc/10.3.0 openmpi/4.0.5-1_slurm b:cmake/3.20.5 parmetis/4.0.3_slurm stable gcc/10.4.0 openmpi/4.1.4_slurm b:cmake/3.20.5 +parmetis/4.0.3_slurm unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} openmpi/4.1.5_slurm b:cmake/3.20.5 diff --git a/MPI/parmetis/files/variants.rhel6 b/MPI/parmetis/files/variants.rhel6 index 9ff9d6a..ed6d400 100644 --- a/MPI/parmetis/files/variants.rhel6 +++ b/MPI/parmetis/files/variants.rhel6 @@ -26,3 +26,4 @@ parmetis/4.0.3 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:cmake/3.9. parmetis/4.0.3 stable gcc/{7.5.0,8.4.0,9.3.0,10.3.0} openmpi/4.0.5 b:cmake/3.15.5 parmetis/4.0.3 stable gcc/10.4.0 openmpi/4.1.4 b:cmake/3.15.5 +parmetis/4.0.3 unstable gcc/10.4.0 openmpi/4.1.5 b:cmake/3.15.5 From 09082dbdd2c489d015b6896b2d6853c6e9605bd2 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:03:38 +0100 Subject: [PATCH 035/158] Python: update build-script to compile 3.9.17 and 3.9.18 --- Programming/Python/build | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/Programming/Python/build b/Programming/Python/build index 6b04a83..bace901 100755 --- a/Programming/Python/build +++ b/Programming/Python/build @@ -12,6 +12,8 @@ pbuild::set_sha256sum 'Python-3.7.4.tgz:d63e63e14e6d29e17490abbe6f7d17afb3db182d pbuild::add_to_group 'Programming' +pbuild::compile_in_sourcetree + pbuild::pre_configure() { local -a cflags=() local -a ldflags=() @@ -26,7 +28,7 @@ pbuild::pre_configure() { ldflags+=("-L${OPENSSL_LIBRARY_DIR}") else pbuild::add_configure_args "--with-openssl=${OPENSSL_DIR}" - pbuild::add_configure_args "--enable-optimizations" + #pbuild::add_configure_args "--enable-optimizations" fi pbuild::add_configure_args "CFLAGS=${cflags[*]}" pbuild::add_configure_args "LDFLAGS=${ldflags[*]}" @@ -39,12 +41,16 @@ pbuild::pre_configure_Linux() { } pbuild::post_install_Linux() { - install "${OPENSSL_LIBRARY_DIR}"/libcrypto.so.* "${PREFIX}/lib" - install "${OPENSSL_LIBRARY_DIR}"/libssl.so.* "${PREFIX}/lib" - install "${TCLTK_LIBRARY_DIR}"/libtcl*.so "${PREFIX}/lib" - install "${TCLTK_LIBRARY_DIR}"/libtk*.so "${PREFIX}/lib" - install "${XZ_LIBRARY_DIR}"/liblzma.so.* "${PREFIX}/lib" - install /usr/lib64/libffi.so.* "${PREFIX}/lib" + if version_le 3.9.10; then + install "${OPENSSL_LIBRARY_DIR}"/libcrypto.so.* "${PREFIX}/lib" + install "${OPENSSL_LIBRARY_DIR}"/libssl.so.* "${PREFIX}/lib" + install "${TCLTK_LIBRARY_DIR}"/libtcl*.so "${PREFIX}/lib" + install "${TCLTK_LIBRARY_DIR}"/libtk*.so "${PREFIX}/lib" + install "${XZ_LIBRARY_DIR}"/liblzma.so.* "${PREFIX}/lib" + install /usr/lib64/libffi.so.* "${PREFIX}/lib" + else + : + fi } pbuild::post_install() { @@ -88,6 +94,9 @@ pbuild::post_install() { std::info "Building virtualenv\n" pip${V_MAJOR} install virtualenv + + std::info "Building virtualenv\n" + pip${V_MAJOR} install ansible ansible-core==2.15.4 } From 120ad33e260aa24fcd6402eb99ed955688e420d4 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:04:04 +0100 Subject: [PATCH 036/158] Python: version 3.9.17 and 3.9.18 added --- Programming/Python/files/variants.rhel6 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Programming/Python/files/variants.rhel6 b/Programming/Python/files/variants.rhel6 index 5fe2089..3ac0bff 100644 --- a/Programming/Python/files/variants.rhel6 +++ b/Programming/Python/files/variants.rhel6 @@ -13,3 +13,5 @@ Python/3.8.4 deprecated Python/3.8.8 deprecated Python/3.8.12 stable Python/3.9.10 stable +Python/3.9.17 unstable b:openssl/1.1.1v b:TclTk/8.6.9 b:xz/5.2.4 +Python/3.9.18 unstable b:openssl/1.1.1w b:TclTk/8.6.9 b:xz/5.2.4 From ea7ce4aff428e6210355889acf6020de8f068222 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:06:03 +0100 Subject: [PATCH 037/158] binutils/2.41: version added --- Programming/binutils/files/variants.rhel6 | 1 + Programming/binutils/files/variants.rhel7 | 1 + 2 files changed, 2 insertions(+) create mode 120000 Programming/binutils/files/variants.rhel7 diff --git a/Programming/binutils/files/variants.rhel6 b/Programming/binutils/files/variants.rhel6 index dca4760..f0434ad 100644 --- a/Programming/binutils/files/variants.rhel6 +++ b/Programming/binutils/files/variants.rhel6 @@ -1,3 +1,4 @@ binutils/2.25 stable binutils/2.29 stable binutils/2.37 stable +binutils/2.41 unstable diff --git a/Programming/binutils/files/variants.rhel7 b/Programming/binutils/files/variants.rhel7 new file mode 120000 index 0000000..8b9b44c --- /dev/null +++ b/Programming/binutils/files/variants.rhel7 @@ -0,0 +1 @@ +variants.rhel6 \ No newline at end of file From 4ceb3e2af2dd9d272e642df24eab47cfdcf00294 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:06:54 +0100 Subject: [PATCH 038/158] cmake: YAML build added --- Programming/cmake/build-yaml | 28 +++++++++++++ Programming/cmake/files/config.yaml | 65 +++++++++++++++++++---------- 2 files changed, 70 insertions(+), 23 deletions(-) create mode 100755 Programming/cmake/build-yaml diff --git a/Programming/cmake/build-yaml b/Programming/cmake/build-yaml new file mode 100755 index 0000000..6d7e5da --- /dev/null +++ b/Programming/cmake/build-yaml @@ -0,0 +1,28 @@ +#!/usr/bin/env modbuild + +pbuild::set_download_url "https://cmake.org/files/v${V_MAJOR}.${V_MINOR}/$P-$V.tar.gz" +pbuild::add_to_group 'Programming' + +declare bootstrap_flags='' + +pbuild::pre_configure() { + bootstrap_flags+='--system-curl' +} + +pbuild::configure() { + "${SRC_DIR}/bootstrap" --prefix="${PREFIX}" ${bootstrap_flags} --verbose +} + +pbuild::post_install_Linux() { + mkdir -p "${PREFIX}/libexec" + cp -v "${GCC_DIR}"/lib64/libgcc_s.so.* "${PREFIX}/libexec" + cp -v "${GCC_DIR}"/lib64/libstdc++.so.* "${PREFIX}/libexec" + chrpath -d /opt/psi/Programming/cmake/3.15.5/bin/ccmake + patchelf --set-rpath '$ORIGIN/../libexec' --force-rpath "${PREFIX}/bin/ccmake" + chrpath -d /opt/psi/Programming/cmake/3.15.5/bin/cmake + patchelf --set-rpath '$ORIGIN/../libexec' --force-rpath "${PREFIX}/bin/cmake" + chrpath -d /opt/psi/Programming/cmake/3.15.5/bin/cpack + patchelf --set-rpath '$ORIGIN/../libexec' --force-rpath "${PREFIX}/bin/cpack" + chrpath -d /opt/psi/Programming/cmake/3.15.5/bin/ctest + patchelf --set-rpath '$ORIGIN/../libexec' --force-rpath "${PREFIX}/bin/ctest" +} diff --git a/Programming/cmake/files/config.yaml b/Programming/cmake/files/config.yaml index fccae50..4beb6c5 100644 --- a/Programming/cmake/files/config.yaml +++ b/Programming/cmake/files/config.yaml @@ -1,23 +1,42 @@ -overlay: base -relstage: stable -cmake/2.8.12.2: -cmake/3.1.3: -cmake/3.3.2: -cmake/3.4.1: -cmake/3.6.3: -cmake/3.9.6: -cmake/3.10.3: -- dependencies: b:gcc/7.3.0 -cmake/3.13.3: -- dependencies: b:gcc/7.3.0 -cmake/3.14.0: -- dependencies: b:gcc/7.3.0 -cmake/3.15.5: -- dependencies: b:gcc/7.3.0 b:patchelf/0.8.1 -cmake/3.19.2: -- dependencies: b:gcc/8.4.0 b:patchelf/0.8.1 -cmake/3.20.5: -- dependencies: b:gcc/8.4.0 b:patchelf/0.8.1 -cmake/3.23.2: -- dependencies: b:gcc/8.4.0 b:patchelf/0.8.1 - relstage: stable +format: 1 +cmake: + defaults: + overlay: base + relstage: stable + urls: + - url: https://cmake.org/files/v${V_MAJOR}.${V_MINOR}/$P-$V.tar.gz + + shasums: + cmake-2.8.12.2.tar.gz: 8c6574e9afabcb9fc66f463bb1f2f051958d86c85c37fccf067eb1a44a120e5e + cmake-3.1.3.tar.gz: 45f4d3fa8a2f61cc092ae461aac4cac1bab4ac6706f98274ea7f314dd315c6d0 + cmake-3.3.2.tar.gz: e75a178d6ebf182b048ebfe6e0657c49f0dc109779170bad7ffcb17463f2fc22 + cmake-3.4.1.tar.gz: d41462bdd80dc37f0d5608167b354bb3af8c068eee640be04c907154c5c113e2 + cmake-3.6.3.tar.gz: 7d73ee4fae572eb2d7cd3feb48971aea903bb30a20ea5ae8b4da826d8ccad5fe + cmake-3.8.1.tar.gz: ce5d9161396e06501b00e52933783150a87c33080d4bdcef461b5b7fd24ac228 + cmake-3.9.6.tar.gz: 7410851a783a41b521214ad987bb534a7e4a65e059651a2514e6ebfc8f46b218 + cmake-3.10.2.tar.gz: 80d0faad4ab56de07aa21a7fc692c88c4ce6156d42b0579c6962004a70a3218b + cmake-3.10.3.tar.gz: 0c3a1dcf0be03e40cf4f341dda79c96ffb6c35ae35f2f911845b72dab3559cf8 + cmake-3.13.3.tar.gz: 665f905036b1f731a2a16f83fb298b1fb9d0f98c382625d023097151ad016b25 + cmake-3.14.0.tar.gz: aa76ba67b3c2af1946701f847073f4652af5cbd9f141f221c97af99127e75502 + cmake-3.15.5.tar.gz: fbdd7cef15c0ced06bb13024bfda0ecc0dedbcaaaa6b8a5d368c75255243beb4 + cmake-3.19.2.tar.gz: e3e0fd3b23b7fb13e1a856581078e0776ffa2df4e9d3164039c36d3315e0c7f0 + cmake-3.20.5.tar.gz: 12c8040ef5c6f1bc5b8868cede16bb7926c18980f59779e299ab52cbc6f15bb0 + cmake-3.23.2.tar.gz: f316b40053466f9a416adf981efda41b160ca859e97f6a484b447ea299ff26aa + cmake-3.25.2.tar.gz: c026f22cb931dd532f648f087d587f07a1843c6e66a3dfca4fb0ea21944ed33c + cmake-3.26.3.tar.gz: bbd8d39217509d163cb544a40d6428ac666ddc83e22905d3e52c925781f0f659 + + versions: + 2.8.12.2;3.1.3;3.3.2;3.4.1;3.6.3;3.9.6: + 3.8.1: + config: + relstage: removed + 3.10.3;3.13.3;3.14.0: + config: + build_requires: [gcc/7.3.0] + 3.15.5;3.19.2;3.20.5;3.23.2;3.25.2: + config: + build_requires: [gcc/7.3.0, patchelf/0.8.1] + 3.26.3: + config: + build_requires: [gcc/7.3.0, patchelf/0.8.1] + relstage: unstable \ No newline at end of file From 9f1dc01baff64e70a0147f1cd011dc1989d94fb3 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:08:26 +0100 Subject: [PATCH 039/158] emacs/29.1: version added --- Tools/emacs/files/variants | 1 + 1 file changed, 1 insertion(+) diff --git a/Tools/emacs/files/variants b/Tools/emacs/files/variants index ed4f327..d1fd572 100644 --- a/Tools/emacs/files/variants +++ b/Tools/emacs/files/variants @@ -3,3 +3,4 @@ emacs/25.3 stable b:libungif/4.1.4 b:tiff/4.0.9 emacs/26.1 stable b:libungif/4.1.4 b:tiff/4.0.9 b:nettle/3.4 gnutls/3.5.19 emacs/26.3 stable b:libungif/4.1.4 b:tiff/4.0.9 b:nettle/3.4 gnutls/3.5.19 emacs/27.2 stable b:libungif/4.1.4 b:tiff/4.0.9 b:nettle/3.4 gnutls/3.5.19 +emacs/29.1 unstable b:libungif/4.1.4 b:tiff/4.0.9 b:nettle/3.4 gnutls/3.5.19 From edc31e3daebd685c72b75a401b795514f766e698 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:09:06 +0100 Subject: [PATCH 040/158] emacs: YAML build added --- Tools/emacs/build-xml | 34 ++++++++++++++++++++++++++++++++++ Tools/emacs/files/config.yaml | 16 ++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100755 Tools/emacs/build-xml create mode 100644 Tools/emacs/files/config.yaml diff --git a/Tools/emacs/build-xml b/Tools/emacs/build-xml new file mode 100755 index 0000000..a853bc4 --- /dev/null +++ b/Tools/emacs/build-xml @@ -0,0 +1,34 @@ +#!/usr/bin/env modbuild + +CC='' +CXX='' +eval $(modulecmd bash use System) + +pbuild::pre_configure() { + case ${OS} in + Darwin ) + pbuild::add_configure_args '--with-ns' '--with-jpeg=no' + ;; + Linux ) + # with 24.5 configure complains about missing libjpeg even it + # is installed! + pbuild::add_configure_args '--with-jpeg=no' + ;; + *) + ;; + esac + install -m 0755 -d "${PREFIX}" +} + +pbuild::post_install() { + mkdir -p "${PREFIX}/bin" + install -m 0755 "${BUILDBLOCK_DIR}/Emacs" "${PREFIX}/bin" + install -m 0755 "${BUILDBLOCK_DIR}/Emacsclient" "${PREFIX}/bin" + #cp -a "${GNUTLS_LIBRARY_DIR}"/libgnutls.so.* "${PREFIX}/lib" + #cp -a "${NETTLE_LIBRARY_DIR}"/libnettle.so.* "${PREFIX}/lib" +} + +pbuild::post_install_Darwin() { + cp -a "${BUILD_DIR}/nextstep/Emacs.app" "${PREFIX}" +} + diff --git a/Tools/emacs/files/config.yaml b/Tools/emacs/files/config.yaml new file mode 100644 index 0000000..78ebdb8 --- /dev/null +++ b/Tools/emacs/files/config.yaml @@ -0,0 +1,16 @@ +format: 1 +emacs: + defaults: + group: Tools + relstage: stable + docfiles: + urls: + - url: https://ftp.gnu.org/gnu/emacs/$P-${V_PKG}.tar.xz + shasums: + emacs-29.1.tar.xz: d2f881a5cc231e2f5a03e86f4584b0438f83edd7598a09d24a21bd8d003e2e01 + versions: + 29.1: + config: + relstage: unstable + runtime_deps: [gnutls/3.5.19] + build_requires: [libidn2/2.3.4, libungif/4.1.4, tiff/4.0.9, nettle/3.4] From 4fb06b58d655284a0dafe9369e3029e380862878 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:10:34 +0100 Subject: [PATCH 041/158] git: YAML build script added --- Tools/git/build-yaml | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100755 Tools/git/build-yaml diff --git a/Tools/git/build-yaml b/Tools/git/build-yaml new file mode 100755 index 0000000..ebc480e --- /dev/null +++ b/Tools/git/build-yaml @@ -0,0 +1,29 @@ +#!/usr/bin/env modbuild + +pbuild::pre_configure_Darwin() { + export NO_APPLE_COMMON_CRYPTO=1 +} + +pbuild::pre_configure() { + #pbuild::add_configure_args "LIBS=-lintl" + pbuild::add_configure_args "--with-tcltk" + pbuild::add_configure_args "--with-iconv=${GETTEXT_PREFIX}" + pbuild::add_configure_args "--with-perl=${PERL_PREFIX}/bin/perl" + : +} + +pbuild::post_compile() { + make -C contrib/subtree prefix="${PREFIX}" +} + +pbuild::post_install() { + make install-doc V=1 XMLTO_EXTRA='--skip-validation' + make -C contrib/subtree prefix="${PREFIX}" install + make -C contrib/subtree prefix="${PREFIX}" install-doc XMLTO="xmlto --skip-validation" +} + +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: From f819546e5f3a9b858bd16925d418de960a1e338e Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:11:23 +0100 Subject: [PATCH 042/158] git: YAML config file fixed --- Tools/git/files/config.yaml | 74 +++++++++++++++++++------------------ 1 file changed, 38 insertions(+), 36 deletions(-) diff --git a/Tools/git/files/config.yaml b/Tools/git/files/config.yaml index e046f99..5405f8a 100644 --- a/Tools/git/files/config.yaml +++ b/Tools/git/files/config.yaml @@ -1,36 +1,38 @@ -overlay: base -relstage: stable -group: Tools -shasums: - git/2.37.0: fc3ffe6c65c1f7c681a1ce6bb91703866e432c762731d4b57c566d696f6d62c3 - git/2.33.1: 02047f8dc8934d57ff5e02aadd8a2fe8e0bcf94a7158da375e48086cc46fce1d - git/2.30.0: d24c4fa2a658318c2e66e25ab67cc30038a35696d2d39e6b12ceccf024de1e5e - git/2.22.0: a4b7e4365bee43caa12a38d646d2c93743d755d1cea5eab448ffb40906c9da0b - git/2.21.0: 85eca51c7404da75e353eba587f87fea9481ba41e162206a6f70ad8118147bee - git/2.8.1: e6626b43ba4bc63ad4918df4c275f50bd7f8af2ab54bde60496ad75e91e927fc - git/2.3.3: c189e4a48d8805482f450db666330c79bcefae37e0d035c7717517126ddf4305 - -git/2.37.2: - - dependencies: TclTk/8.6.9 - build_requires: go/1.19 perl/5.30.0 asciidoc/8.6.9-1 xmlto/0.0.28 gettext/0.19.8 - overlay: devel - relstage: unstable -git/2.37.0: - - dependencies: TclTk/8.6.9 - build_requires: perl/5.30.0 asciidoc/8.6.9-1 xmlto/0.0.28 gettext/0.19.8 -git/2.33.1: - - dependencies: TclTk/8.6.9 - build_requires: perl/5.30.0 asciidoc/8.6.9-1 xmlto/0.0.28 gettext/0.19.8 -git/2.30.0: - - dependencies: TclTk/8.6.9 - build_requires: perl/5.30.0 asciidoc/8.6.9-1 xmlto/0.0.28 gettext/0.19.8 -git/2.22.0: - - dependencies: TclTk/8.6.9 - build_requires: perl/5.30.0 asciidoc/8.6.9-1 xmlto/0.0.28 gettext/0.19.8 -git/2.21.0: - - dependencies: TclTk/8.6.9 - build_requires: perl/5.30.0 asciidoc/8.6.9-1 xmlto/0.0.28 gettext/0.19.8 -git/2.8.1: - - dependencies: Tcl/8.6.4 Tk/8.6.4 -git/2.3.3: - - dependencies: Tcl/8.6.4 Tk/8.6.4 +--- +# yamllint disable rule:line-length +format: 1 +git: + defaults: + group: Tools + overlay: base + relstage: stable + systems: [rhel6, rhel7, rhel8] + compile_in_sourcetree: true + urls: + - url: https://mirrors.edge.kernel.org/pub/software/scm/git/git-${V_PKG}.tar.xz + shasums: + git-2.39.1.tar.gz: ae8d3427e4ccd677abc931f16183c0ec953e3bfcd866493601351e04a2b97398 + git-2.37.2.tar.gz: 4c428908e3a2dca4174df6ef49acc995a4fdb1b45205a2c79794487a33bc06e5 + git-2.37.0.tar.gz: fc3ffe6c65c1f7c681a1ce6bb91703866e432c762731d4b57c566d696f6d62c3 + git-2.33.1.tar.gz: 02047f8dc8934d57ff5e02aadd8a2fe8e0bcf94a7158da375e48086cc46fce1d + git-2.30.0.tar.xz: 4c428908e3a2dca4174df6ef49acc995a4fdb1b45205a2c79794487a33bc06e5 + git-2.22.0.tar.gz: a4b7e4365bee43caa12a38d646d2c93743d755d1cea5eab448ffb40906c9da0b + git-2.21.0.tar.gz: 85eca51c7404da75e353eba587f87fea9481ba41e162206a6f70ad8118147bee + git-2.8.1.tar.xz: e6626b43ba4bc63ad4918df4c275f50bd7f8af2ab54bde60496ad75e91e927fc + git-2.3.3.tar.gz: c189e4a48d8805482f450db666330c79bcefae37e0d035c7717517126ddf4305 + versions: + 2.42.0: + config: + runtime_deps: [TclTk/8.6.9] + build_requires: [gcc/10.4.0, perl/5.30.0, asciidoc/8.6.9-1, xmlto/0.0.28, gettext/0.19.8] + relstage: unstable + overlay: devel + systems: [rhel7, rhel8, rhel9] + docfiles: [COPYING, README.md] + 2.39.1;2.37.2;2.37.0;2.33.1;2.30.0;2.22.0;2.21.0: + config: + runtime_deps: [TclTk/8.6.9] + build_requires: [gcc/10.4., perl/5.30.0, asciidoc/8.6.9-1, xmlto/0.0.28, gettext/0.19.8] + 2.3.3;2.8.1: + config: + runtime_deps: [Tcl/8.6.9, Tk/8.6.9] From 59e1221e33387d2c6ea2b6c9fe89305285bdbea1 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:12:37 +0100 Subject: [PATCH 043/158] gnuplot: YAML config added/reviewed --- Tools/gnuplot/build-yaml | 11 ++++++ Tools/gnuplot/files/config.yaml | 62 ++++++++++++++++----------------- 2 files changed, 42 insertions(+), 31 deletions(-) create mode 100755 Tools/gnuplot/build-yaml diff --git a/Tools/gnuplot/build-yaml b/Tools/gnuplot/build-yaml new file mode 100755 index 0000000..3a25f73 --- /dev/null +++ b/Tools/gnuplot/build-yaml @@ -0,0 +1,11 @@ +#!/usr/bin/env modbuild + +pbuild::pre_configure() { + pbuild::add_configure_args '--with-latex=no' + pbuild::add_configure_args '--with-qt=no' +} +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Tools/gnuplot/files/config.yaml b/Tools/gnuplot/files/config.yaml index 8a809bd..7bfcef0 100644 --- a/Tools/gnuplot/files/config.yaml +++ b/Tools/gnuplot/files/config.yaml @@ -1,33 +1,33 @@ -overlay: base -relstage: stable -group: Tools -shasums: - gnuplot/5.4.4: 372300b7867f5b3538b25fc5d0ac7734af6e3fe0d202b6db926e4369913f0902 - gnuplot/5.4.3: 51f89bbab90f96d3543f95235368d188eb1e26eda296912256abcd3535bd4d84 - gnuplot/5.4.2: e57c75e1318133951d32a83bcdc4aff17fed28722c4e71f2305cfc2ae1cae7ba - gnuplot/5.4.1: 6b690485567eaeb938c26936e5e0681cf70c856d273cc2c45fabf64d8bc6590e - gnuplot/5.4.0: eb4082f03a399fd1e9e2b380cf7a4f785e77023d8dcc7e17570c1b5570a49c47 - gnuplot/5.2.8: 60a6764ccf404a1668c140f11cc1f699290ab70daa1151bb58fed6139a28ac37 - gnuplot/5.2.7: 97fe503ff3b2e356fe2ae32203fc7fd2cf9cef1f46b60fe46dc501a228b9f4ed - gnuplot/5.2.6: 35dd8f013139e31b3028fac280ee12d4b1346d9bb5c501586d1b5a04ae7a94ee - gnuplot/5.2.4: 1515f000bd373aaa53b16183f274189d4f5e0ae47d22f434857933d16a4770cb - gnuplot/5.0.0: 417d4bc5bc914a60409bb75cf18dd14f48b07f53c6ad3c4a4d3cd9a8d7370faf - gnuplot/4.6.3: df5ffafa25fb32b3ecc0206a520f6bca8680e6dcc961efd30df34c0a1b7ea7f5 - -gnuplot/5.4.5: - systems: rhel7 rhel6 -gnuplot/5.4.4: - systems: rhel7 rhel6 -gnuplot/5.4.3: -gnuplot/5.4.2: -gnuplot/5.4.1: -gnuplot/5.4.0: -gnuplot/5.2.8: -gnuplot/5.2.7: -gnuplot/5.2.6: -gnuplot/5.2.4: -gnuplot/5.2.0: -gnuplot/5.0.0: -gnuplot/4.6.3: +format: 1 +gnuplot: + defaults: + group: Tools + overlay: base + relstage: stable + systems: [rhel8, rhel7, rhel6] + docfiles: [Copyright, NEWS, README] + urls: + - url: https://sourceforge.net/projects/gnuplot/files/$P/$V/$P-${V_PKG}.tar.gz + shasums: + gnuplot-5.4.10.tar.gz: 975d8c1cc2c41c7cedc4e323aff035d977feb9a97f0296dd2a8a66d197a5b27c + gnuplot-5.4.9.tar.gz: a328a021f53dc05459be6066020e9a71e8eab6255d3381e22696120d465c6a97 + gnuplot-5.4.8.tar.gz: 931279c7caad1aff7d46cb4766f1ff41c26d9be9daf0bcf0c79deeee3d91f5cf + gnuplot-5.4.5.tar.gz: 66f679115dd30559e110498fc94d926949d4d370b4999a042e724b8e910ee478 + gnuplot-5.4.4.tar.gz: 372300b7867f5b3538b25fc5d0ac7734af6e3fe0d202b6db926e4369913f0902 + gnuplot-5.4.3.tar.gz: 51f89bbab90f96d3543f95235368d188eb1e26eda296912256abcd3535bd4d84 + gnuplot-5.4.2.tar.gz: e57c75e1318133951d32a83bcdc4aff17fed28722c4e71f2305cfc2ae1cae7ba + gnuplot-5.4.1.tar.gz: 6b690485567eaeb938c26936e5e0681cf70c856d273cc2c45fabf64d8bc6590e + gnuplot-5.4.0.tar.gz: eb4082f03a399fd1e9e2b380cf7a4f785e77023d8dcc7e17570c1b5570a49c47 + gnuplot-5.2.8.tar.gz: 60a6764ccf404a1668c140f11cc1f699290ab70daa1151bb58fed6139a28ac37 + gnuplot-5.2.7.tar.gz: 97fe503ff3b2e356fe2ae32203fc7fd2cf9cef1f46b60fe46dc501a228b9f4ed + gnuplot-5.2.6.tar.gz: 35dd8f013139e31b3028fac280ee12d4b1346d9bb5c501586d1b5a04ae7a94ee + gnuplot-5.2.4.tar.gz: 1515f000bd373aaa53b16183f274189d4f5e0ae47d22f434857933d16a4770cb + gnuplot-5.0.0.tar.gz: 417d4bc5bc914a60409bb75cf18dd14f48b07f53c6ad3c4a4d3cd9a8d7370faf + gnuplot-4.6.3.tar.gz: df5ffafa25fb32b3ecc0206a520f6bca8680e6dcc961efd30df34c0a1b7ea7f5 + versions: + 5.4.{0,1,2,3,4,5,8,9};5.2.{0,4,6,7,8};5.0.0;4.6.3: + 5.4.10: + config: + relstage: unstable From 91ba9217efb51daf537ade91f41c3e1678164822 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:13:46 +0100 Subject: [PATCH 044/158] gnutls: modulefiles fixed --- Tools/gnutls/modulefile | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/Tools/gnutls/modulefile b/Tools/gnutls/modulefile index 8ce71d5..a46fdb5 100644 --- a/Tools/gnutls/modulefile +++ b/Tools/gnutls/modulefile @@ -1,18 +1,21 @@ #%Module1.0 -module-whatis "Toolkit for the TLS and SSL protocol" -module-url "https://openssl.org/" -module-license "Apache style" +module-whatis "secure communications library implementing the SSL, TLS and DTLS protocols" +module-url "https://www.gnutls.org" +module-license "GNU Lesser General Public License version 2.1" module-maintainer "Achim Gsell " module-help " -OpenSSL is an open source project that provides a robust, commercial-grade, -and full-featured toolkit for the Transport Layer Security (TLS) and Secure -Sockets Layer (SSL) protocols. It is also a general-purpose cryptography -library. For more information about the team and community around the -project, or to start making your own contributions, start with the community -page. To get the latest news, download the source, and so on, please see the -sidebar or the buttons at the top of every page. +GnuTLS is a secure communications library implementing the SSL, TLS and +DTLS protocols and technologies around them. It provides a simple C +language application programming interface (API) to access the secure +communications protocols as well as APIs to parse and write X.509, +PKCS #12, and other required structures. + +The project strives to provide a secure communications back-end, simple +to use and integrated with the rest of the base Linux libraries. A back- +end designed to work and be secure out of the box, keeping the complexity +of TLS and PKI out of application code. " -append-path PKG_CONFIG_PATH $PREFIX/lib/pkgconfig +#append-path PKG_CONFIG_PATH $PREFIX/lib/pkgconfig From 8df7ef213da6fcd0ddac4ff6c713646b8d4343a7 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:14:25 +0100 Subject: [PATCH 045/158] gnutls: YAML build files added --- Tools/gnutls/build-xml | 8 ++++++++ Tools/gnutls/files/config.yaml | 17 +++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100755 Tools/gnutls/build-xml create mode 100644 Tools/gnutls/files/config.yaml diff --git a/Tools/gnutls/build-xml b/Tools/gnutls/build-xml new file mode 100755 index 0000000..906f85b --- /dev/null +++ b/Tools/gnutls/build-xml @@ -0,0 +1,8 @@ +#!/usr/bin/env modbuild + +#module use 'Libraries' + +pbuild::add_configure_args "--with-included-unistring" +pbuild::add_configure_args "--with-included-libtasn1" +pbuild::add_configure_args "--without-p11-kit" + diff --git a/Tools/gnutls/files/config.yaml b/Tools/gnutls/files/config.yaml new file mode 100644 index 0000000..f22314f --- /dev/null +++ b/Tools/gnutls/files/config.yaml @@ -0,0 +1,17 @@ +format: 1 +gnutls: + defaults: + group: Tools + relstage: stable + docfiles: + urls: + - url: https://www.gnupg.org/ftp/gcrypt/gnutls/v3.7/gnutls-${V_PKG}.tar.xz + shasums: + gnutls-3.5.19.tar.xz: 1936eb64f03aaefd6eb16cef0567457777618573826b94d03376bb6a4afadc44 + versions: + 3.5.19: + 3.7.10: + config: + relstage: unstable + build_requires: [nettle/3.9.1, gmp/6.1.2-1] + From 8ed71918811b105b90a208e2affaba34c6f626b2 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 14 Nov 2023 16:15:20 +0100 Subject: [PATCH 046/158] openssl: rhel7 variants file added --- Tools/openssl/files/variants.rhel7 | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 Tools/openssl/files/variants.rhel7 diff --git a/Tools/openssl/files/variants.rhel7 b/Tools/openssl/files/variants.rhel7 new file mode 100644 index 0000000..0712f7e --- /dev/null +++ b/Tools/openssl/files/variants.rhel7 @@ -0,0 +1,11 @@ +openssl/1.0.2h deprecated +openssl/1.0.2j stable +openssl/1.0.2m stable +openssl/1.0.2o stable +openssl/1.0.2r stable +openssl/1.1.1g stable +openssl/1.1.1k stable +openssl/1.1.1l stable +openssl/1.1.1m stable +openssl/1.1.1v unstable +openssl/1.1.1w unstable From eab7fac248bba353bae06169e64c76d57c0d4571 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Nov 2023 17:02:47 +0100 Subject: [PATCH 047/158] openmpi/4.1.5: YAML config reviewed --- Compiler/openmpi/files/config.yaml | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index a3ec3c1..1bac1f8 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -7,6 +7,7 @@ openmpi: overlay: base relstage: stable systems: [rhel7, rhel8, rhel9] + docfiles: [AUTHORS, LICENSE, NEWS, README] urls: - url: https://download.open-mpi.org/release/open-mpi/v${V_MAJOR}.${V_MINOR}/openmpi-${V_PKG}.tar.bz shasums: @@ -54,13 +55,21 @@ openmpi: versions: - 4.1.5_slurm: - config: - relstage: unstable - group_deps: - compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0], intelcc: [22.2]} - build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5] - runtime_deps: [cuda/12.1.1] + 4.1.5: + variants: + - systems: [merlin-*, ra-*] + suffix: _slurm + group_deps: + compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} + build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5] + runtime_deps: [cuda/12.1.1] + - systems: [merlin-*, ra-*] + suffix: _slurm + relstage: unstable + group_deps: + compiler: {intelcc: [22.2]} + build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5] + runtime_deps: [cuda/12.1.1] 4.1.4_slurm: config: From 81d0d552c3acd1fd22caeacd749fd75953ae0870 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Nov 2023 17:03:22 +0100 Subject: [PATCH 048/158] openmpi: YAM build script added --- Compiler/openmpi/build-xml | 100 +++++++++++++++++++++++++++++++++++++ 1 file changed, 100 insertions(+) create mode 100755 Compiler/openmpi/build-xml diff --git a/Compiler/openmpi/build-xml b/Compiler/openmpi/build-xml new file mode 100755 index 0000000..31bf3b5 --- /dev/null +++ b/Compiler/openmpi/build-xml @@ -0,0 +1,100 @@ +#!/usr/bin/env modbuild + +pbuild::install_docfiles 'AUTHORS' 'LICENSE' 'NEWS' 'README' + +pbuild::pre_configure() { + pbuild::add_configure_args "--prefix=${PREFIX}" + pbuild::add_configure_args "--enable-mpi-cxx" + pbuild::add_configure_args "--enable-mpi-cxx-seek" + pbuild::add_configure_args "--enable-orterun-prefix-by-default" + pbuild::add_configure_args "--enable-shared" + pbuild::add_configure_args "--enable-static" + pbuild::add_configure_args "--with-slurm=yes" + + if [[ -v CUDA_VERSION ]]; then + pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" + fi + + if [[ -v HWLOC_VERSION ]]; then + unset HWLOC_VERSION + pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" + else + pbuild::add_configure_args "--with-hwloc=internal" + fi + + if [[ -v LIBEVENT_VERSION ]]; then + pbuild::add_configure_args "--with-libevent=${LIBEVENT_PREFIX}" + fi + + if [[ -v PMIX_VERSION ]]; then + unset PMIX_VERSION + pbuild::add_configure_args "--with-pmix=${PMIX_PREFIX}" + fi + + if [[ -v LIBFABRIC_VERSION ]]; then + pbuild::add_configure_args "--with-ofi=${LIBFABRIC_PREFIX}" + fi + + if [[ -v UCX_VERSION ]]; then + pbuild::add_configure_args "--with-ucx=${UCX_PREFIX}" + fi + + if [[ -v INTEL_VERSION ]]; then + pbuild::add_configure_args "CC=icc" + pbuild::add_configure_args "CXX=icpc" + pbuild::add_configure_args "FC=ifort" + pbuild::add_configure_args "F90=ifort" + pbuild::add_configure_args "F77=ifort" + pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" + fi + + if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6; then + pbuild::add_configure_args "--with-gpfs=/usr/lpp/mmfs" + pbuild::add_configure_args "--with-pmi" + # pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/" + + if pbuild::use_flag "libpmix"; then + pbuild::add_configure_args "--enable-install-libpmix" + fi + fi + + local version + (( version = (${V_MAJOR} * 100 + ${V_MINOR}) * 100 + V_PATCHLVL )) + if (( V_MAJOR < 4 )); then + pbuild::add_configure_args "--enable-mpi-f90" + pbuild::add_configure_args "--enable-mpi-profile" + pbuild::add_configure_args "--enable-smp-locks" + elif (( V_MAJOR >= 4 )); then + pbuild::add_configure_args "--enable-mpi-fortran" + pbuild::add_configure_args "--without-verbs" + fi + +} + +pbuild::post_install() { + if ! pbuild::use_flag slurm && ! pbuild::use_flag dgx && ! pbuild::use_flag merlin6; then + mkdir -p "${PREFIX}/lib/fallback" + local -r binary=$(ls "${PREFIX}"/lib/libmpi.so.*.*.*) + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuc[mpst].so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuct_ib.so.0' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libnuma.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libibverbs.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/librdmacm.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so' + fi + + if [[ -v CUDA_VERSION ]]; then + echo "opal_warn_on_missing_libcuda = 0" >> ${PREFIX}/etc/openmpi-mca-params.conf + fi + + for FILE in $(find $PREFIX -type f \( ! -name "*.a" -and ! -name "*.mod" \) -exec grep -IL . "{}" \;) + do + OLD_RPATH=$(objdump -a -x $FILE | grep RPATH | awk '{print $2}') + NEW_RPATH=$(echo $OLD_RPATH | sed 's/:\/usr\/lib64:/:/g') + if [[ "${OLD_RPATH}" != "${NEW_RPATH}" ]]; then + patchelf --force-rpath --set-rpath "${NEW_RPATH}" "${FILE}" + fi + done +} From aed90f976de9a225307443a7233ff214dd46ed2b Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Nov 2023 17:05:47 +0100 Subject: [PATCH 049/158] openmpi/4.1.5_slurm: release stage changed to stable in legacy config file --- Compiler/openmpi/files/variants.merlin6 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Compiler/openmpi/files/variants.merlin6 b/Compiler/openmpi/files/variants.merlin6 index 6e58f0b..3b81657 100644 --- a/Compiler/openmpi/files/variants.merlin6 +++ b/Compiler/openmpi/files/variants.merlin6 @@ -40,7 +40,7 @@ openmpi/4.1.1-1_slurm unstable gcc/10.2.0 cuda/11.3.0 b:ucx/1.10.0_slurm openmpi/4.1.3_slurm stable gcc/{9.3.0,10.3.0,11.2.0} cuda/11.5.1 b:ucx/1.12.1_slurm openmpi/4.1.4_slurm stable gcc/10.4.0 cuda/11.5.1 b:ucx/1.12.1_slurm -openmpi/4.1.5_slurm unstable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} b:cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 +openmpi/4.1.5_slurm stable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} b:cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 openmpi/4.1.5_slurm unstable intelcc/22.2 b:cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 openmpi/4.0.5-1_dgx deprecated gcc/{8.4.0,9.3.0,10.2.0} cuda/11.2.2 b:ucx/1.10.0-1_dgx From 3ba53543d3a0f9379407cd2429ca5427df81bd45 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Nov 2023 17:07:26 +0100 Subject: [PATCH 050/158] pmix(4.2.4: released as stable --- Libraries/pmix/files/variants.merlin6 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Libraries/pmix/files/variants.merlin6 b/Libraries/pmix/files/variants.merlin6 index beb6bdd..def96fc 100644 --- a/Libraries/pmix/files/variants.merlin6 +++ b/Libraries/pmix/files/variants.merlin6 @@ -3,4 +3,4 @@ pmix/2.2.5 unstable libevent/2.1.12 pmix/3.2.3 unstable libevent/2.1.12 pmix/4.1.2 unstable libevent/2.1.12 b:hwloc/2.7.1 pmix/4.2.3 unstable libevent/2.1.12 b:hwloc/2.9.1 -pmix/4.2.4 unstable b:gcc/10.4.0 libevent/2.1.12 b:hwloc/2.9.1 +pmix/4.2.4 stable b:gcc/10.4.0 libevent/2.1.12 b:hwloc/2.9.1 From 3a317858fb84e2cfe6af069969e44e2381befb99 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Nov 2023 17:08:00 +0100 Subject: [PATCH 051/158] pmix: YAML build files added --- Libraries/pmix/build-xml | 24 ++++++++++++++++ Libraries/pmix/files/config.yaml | 48 ++++++++++++++++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100755 Libraries/pmix/build-xml create mode 100644 Libraries/pmix/files/config.yaml diff --git a/Libraries/pmix/build-xml b/Libraries/pmix/build-xml new file mode 100755 index 0000000..1ebd0fd --- /dev/null +++ b/Libraries/pmix/build-xml @@ -0,0 +1,24 @@ +#!/usr/bin/env modbuild + +pbuild::pre_configure() { + if [[ -v HWLOC_PREFIX ]]; then + pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" + fi + + if [[ -v LIBEVENT_PREFIX ]]; then + pbuild::add_configure_args "--with-libevent=${LIBEVENT_PREFIX}" + fi + + if [[ -v INTEL_VERSION ]]; then + pbuild::add_configure_args "CC=icc" + pbuild::add_configure_args "CXX=icpc" + pbuild::add_configure_args "FC=ifort" + pbuild::add_configure_args "F77=ifort" + pbuild::add_configure_args "F90=ifort" + # pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel" + fi + + # pbuild::add_configure_args "--enable-pmi-backward-compatibility" + pbuild::add_configure_args "--enable-shared" + pbuild::add_configure_args "--enable-static" +} diff --git a/Libraries/pmix/files/config.yaml b/Libraries/pmix/files/config.yaml new file mode 100644 index 0000000..4585449 --- /dev/null +++ b/Libraries/pmix/files/config.yaml @@ -0,0 +1,48 @@ +format: 1 +pmix: + defaults: + group: Libraries + relstage: stable + compile_in_sourcetree: yes + docfiles: + - AUTHORS + - README.md + - LICENSE + - NEWS + - VERSION + urls: + - url: "https://github.com/openpmix/openpmix/releases/download/v${V_PKG}/$P-${V_PKG}.tar.gz" + shasums: + pmix-1.2.5.tar.gz: d7337601c5b985743e6b6f79ec1a34dfc2aefbb2d04d40b2c0d5bd7100d268ed + pmix-2.2.5.tar.gz: db24480fa5be080e1ddcb273098992b69f8f21e4cd6b8df1682e836b303a2a6f + pmix-3.2.3.tar.gz: 1325a1355d0794196bb47665053fdbc588f9183aa5385f3581b668427316306e + pmix-4.1.2.tar.gz: a7a6d5b322c261999ce0a6395c0ac7dc359c0ff61380ed4c6935430fb9f5f6e6 + pmix-4.2.3.tar.gz: fd45e18e483e42089d4059df9753d9be3cfb68297a05981b1d937e09f7716d5a + pmix-4.2.4.tar.gz: f1fe5fe817ac447ce8d3d88486a1c0d22227efd186e11062aa1f7b0f093089c6 + versions: + 1.2.5: + config: + relstage: removed + docfiles: + - README + - LICENSE + - NEWS + - VERSION + 2.2.5;3.2.3: + config: + relstage: unstable + 4.1.2: + config: + relstage: unstable + runtime_deps: [libevent/2.1.12] + build_requires: [hwloc/2.7.1] + 4.2.3: + config: + relstage: unstable + runtime_deps: [libevent/2.1.12] + build_requires: [hwloc/2.9.1] + 4.2.4: + config: + relstage: stable + runtime_deps: [libevent/2.1.12] + build_requires: [gcc/10.4.0, hwloc/2.9.1] From 7ae60052f1d2e46425725f864ba87145caf2972f Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Nov 2023 17:09:35 +0100 Subject: [PATCH 052/158] hwloc/2.7.1,2.9.1: relased as stable --- Libraries/hwloc/files/variants.merlin6 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Libraries/hwloc/files/variants.merlin6 b/Libraries/hwloc/files/variants.merlin6 index e754fa1..919640f 100644 --- a/Libraries/hwloc/files/variants.merlin6 +++ b/Libraries/hwloc/files/variants.merlin6 @@ -1,2 +1,2 @@ -hwloc/2.7.1 unstable b:cuda/11.5.1 -hwloc/2.9.1 unstable b:cuda/12.1.1 +hwloc/2.7.1 stable b:cuda/11.5.1 +hwloc/2.9.1 stable b:cuda/12.1.1 From d680940d29a15b482764981e6ad22434c2aab23f Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Nov 2023 17:10:04 +0100 Subject: [PATCH 053/158] hwloc: YAML build files added --- Libraries/hwloc/build-xml | 8 ++++++++ Libraries/hwloc/files/config.yaml | 20 ++++++++++++++++++++ 2 files changed, 28 insertions(+) create mode 100755 Libraries/hwloc/build-xml create mode 100644 Libraries/hwloc/files/config.yaml diff --git a/Libraries/hwloc/build-xml b/Libraries/hwloc/build-xml new file mode 100755 index 0000000..f2b8b67 --- /dev/null +++ b/Libraries/hwloc/build-xml @@ -0,0 +1,8 @@ +#!/usr/bin/env modbuild + +pbuild::pre_configure() { + pbuild::add_configure_args "--enable-netloc" + pbuild::add_configure_args "--enable-plugins" +} + + diff --git a/Libraries/hwloc/files/config.yaml b/Libraries/hwloc/files/config.yaml new file mode 100644 index 0000000..418f57f --- /dev/null +++ b/Libraries/hwloc/files/config.yaml @@ -0,0 +1,20 @@ +format: 1 +hwloc: + defaults: + group: Libraries + relstage: stable + docfiles: [README, AUTHORS, NEWS, COPYING, VERSION] + urls: + - url: https://download.open-mpi.org/release/${P}/v${V_MAJOR}.${V_MINOR}/${P}-${V}.tar.gz + shasums: + hwloc-2.7.1.tar.gz: 4cb0a781ed980b03ad8c48beb57407aa67c4b908e45722954b9730379bc7f6d5 + hwloc-2.9.1.tar.gz: a440e2299f7451dc10a57ddbfa3f116c2a6c4be1bb97c663edd3b9c7b3b3b4cf + versions: + 2.7.1: + config: + relstage: stable + build_requires: cuda/11.5.1 + 2.9.1: + config: + relstage: stable + build_requires: cuda/12.1.1 From 4251796e7aaf3010c2c079c929e420add48399cc Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Nov 2023 17:11:26 +0100 Subject: [PATCH 054/158] libfabric/1.18.0: relased as stable --- Libraries/libfabric/files/variants | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Libraries/libfabric/files/variants b/Libraries/libfabric/files/variants index ab94958..4f4731e 100644 --- a/Libraries/libfabric/files/variants +++ b/Libraries/libfabric/files/variants @@ -1 +1 @@ -libfabric/1.18.0 unstable b:gcc/10.4.0 +libfabric/1.18.0 stable b:gcc/10.4.0 From 529a9352e4ad753435ca2543794f7e12aada56f9 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Nov 2023 17:11:59 +0100 Subject: [PATCH 055/158] libfabric: YAML build files added --- Libraries/libfabric/build-xml | 2 ++ Libraries/libfabric/files/config.yaml | 20 ++++++++++++++++++++ 2 files changed, 22 insertions(+) create mode 100755 Libraries/libfabric/build-xml create mode 100644 Libraries/libfabric/files/config.yaml diff --git a/Libraries/libfabric/build-xml b/Libraries/libfabric/build-xml new file mode 100755 index 0000000..6e021f3 --- /dev/null +++ b/Libraries/libfabric/build-xml @@ -0,0 +1,2 @@ +#!/usr/bin/env modbuild + diff --git a/Libraries/libfabric/files/config.yaml b/Libraries/libfabric/files/config.yaml new file mode 100644 index 0000000..981efdc --- /dev/null +++ b/Libraries/libfabric/files/config.yaml @@ -0,0 +1,20 @@ +format: 1 +libfabric: + defaults: + group: Libraries + relstage: stable + compile_in_sourcetree: yes + docfiles: + - AUTHORS + - README + - COPYING + - NEWS.md + urls: + - url: https://github.com/ofiwg/libfabric/releases/download/v$V/$P-$V.tar.bz2 + shasums: + libfabric-1.13.0.tar.bz2: 0c68264ae18de5c31857724c754023351614330bd61a50b40cef2b5e8f63ab28 + libfabric-1.18.0.tar.bz2: 912fb7c7b3cf2a91140520962b004a1c5d2f39184adbbd98ae5919b0178afd43 + versions: + 1.18.0: + config: + build_requires: [gcc/10.4.0] From e2341cc0e44e4fbe16ec6b872586b0f4690e2c27 Mon Sep 17 00:00:00 2001 From: sala Date: Thu, 30 Nov 2023 10:41:04 +0100 Subject: [PATCH 056/158] Ra standard py311 --- .../jupyterhub-4.0.2_lab3_py3.11/README.md | 14 +++++++ .../jupyterhub-4.0.2_lab3_py3.11.yml | 20 ++++++++++ .../ra-standard_py311/README.md | 28 ++++++++++++++ .../ra-standard_py311/ra-standard_py311.yml | 37 +++++++++++++++++++ .../conda-env-defs/ra-standard_py36/README.md | 1 + .../ra-standard_py36/ra-standard_py36.yml | 29 +++++++++++++++ 6 files changed, 129 insertions(+) create mode 100644 Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/README.md create mode 100644 Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/jupyterhub-4.0.2_lab3_py3.11.yml create mode 100644 Programming/anaconda/2019.07/conda-env-defs/ra-standard_py311/README.md create mode 100644 Programming/anaconda/2019.07/conda-env-defs/ra-standard_py311/ra-standard_py311.yml create mode 100644 Programming/anaconda/2019.07/conda-env-defs/ra-standard_py36/README.md create mode 100644 Programming/anaconda/2019.07/conda-env-defs/ra-standard_py36/ra-standard_py36.yml diff --git a/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/README.md b/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/README.md new file mode 100644 index 0000000..3eaf2a9 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/README.md @@ -0,0 +1,14 @@ +Installation done on pmod7 + +``` +conda env create -f jupyterhub-4.0.2_lab3_py3.11 + +conda activatejupyterhub-4.0.2_lab3_py3.11 +``` + +The current production versions of the spawners (e.g. batchspawner-1.0.0) are +not compatible with jupyterhub-1.0.0. So, one is forced to deploy the +development versions. This is coded in the yaml file as pip dependency, +pointing to the latest commit available + +Also, jupyterlab 4 and jupyter-server 2.11 are not yet supported diff --git a/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/jupyterhub-4.0.2_lab3_py3.11.yml b/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/jupyterhub-4.0.2_lab3_py3.11.yml new file mode 100644 index 0000000..79533cc --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/jupyterhub-4.0.2_lab3_py3.11.yml @@ -0,0 +1,20 @@ +name: jupyterhub-4.0.2_lab3_py3.11 +channels: + - conda-forge +dependencies: + - jupyterhub=4.0.2 + - jupyterlab=3.6.3 + - nb_conda + - nb_conda_kernels + - jupyter_contrib_nbextensions + - ipywidgets=7.6.3 + - pip + - jupytext + - python=3.11.6 + - jupyterlab-git + - git + - psycopg2 + - jupyter_server<2.11 +# - sqlalchemy=1.4.39 + - pip: + - git+https://github.com/jupyterhub/batchspawner.git@e89bf6a diff --git a/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py311/README.md b/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py311/README.md new file mode 100644 index 0000000..9f5799d --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py311/README.md @@ -0,0 +1,28 @@ +Standard Ra environment based on python 3.11. It includes: + - pandas + - numpy + - scipy + - scikit-learn + - matplotlib + - seaborn + - tensorflow + - pytables + - ipython + - keras + - ipywidgets + - plotly + - python-graphviz + - statsmodels + - scikit-image + - numba + - hdf5 + - h5py + - dask + - dask-jobqueue + - ipympl # needed for jupyterlab interactive plotting + - toml + - tabulate + - click + - conda-forge::jupyter-resource-usage + - conda-forge::julia + diff --git a/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py311/ra-standard_py311.yml b/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py311/ra-standard_py311.yml new file mode 100644 index 0000000..1dca6ce --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py311/ra-standard_py311.yml @@ -0,0 +1,37 @@ +# Clean environment based on pure conda-forge packages +name: ra-standard_py311 +#channels: +# - conda-forge +dependencies: + - python=3.11 + - pandas + - xlrd + - numpy + - scipy + - scikit-learn + - matplotlib + - seaborn + - tensorflow + - pytables + - ipython + - keras + - nb_conda_kernels + - ipywidgets + - plotly + - python-graphviz + - statsmodels + - scikit-image + - numba + - hdf5 + - h5py + - dask + - dask-jobqueue + - ipympl # needed for jupyterlab interactive plotting + - toml + - tabulate + - click + - conda-forge::jupyter-resource-usage + - conda-forge::julia + #- paulscherrerinstitute::bitshuffle + - paulscherrerinstitute::scicat_client + #- paulscherrerinstitute::jungfrau_utils diff --git a/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py36/README.md b/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py36/README.md new file mode 100644 index 0000000..c14361f --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py36/README.md @@ -0,0 +1 @@ +**THIS IS A TEST** \ No newline at end of file diff --git a/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py36/ra-standard_py36.yml b/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py36/ra-standard_py36.yml new file mode 100644 index 0000000..5718dc3 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/ra-standard_py36/ra-standard_py36.yml @@ -0,0 +1,29 @@ +# Clean environment based on pure conda-forge packages +name: ra-standard_py36 +#channels: +# - conda-forge +dependencies: + - python=3.6 + - pandas + - xlrd + - numpy + - scipy + - scikit-learn + - matplotlib + - seaborn + - tensorflow + - pytables + - ipython + - keras + - nb_conda_kernels + - ipywidgets + - plotly + - python-graphviz + - statsmodels + - scikit-image + - numba + - hdf5 + - h5py + - dask + - dask-jobqueue + - paulscherrerinstitute::bitshuffle \ No newline at end of file From 4b951b51501d02e12dbc642206662c8ff869c026 Mon Sep 17 00:00:00 2001 From: sala Date: Wed, 10 Jan 2024 10:52:02 +0100 Subject: [PATCH 057/158] Quick fix for notebook widgets --- .../jupyterhub-4.0.2_lab3_py3.11.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/jupyterhub-4.0.2_lab3_py3.11.yml b/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/jupyterhub-4.0.2_lab3_py3.11.yml index 79533cc..f913dff 100644 --- a/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/jupyterhub-4.0.2_lab3_py3.11.yml +++ b/Programming/anaconda/2019.07/conda-env-defs/jupyterhub-4.0.2_lab3_py3.11/jupyterhub-4.0.2_lab3_py3.11.yml @@ -8,6 +8,8 @@ dependencies: - nb_conda_kernels - jupyter_contrib_nbextensions - ipywidgets=7.6.3 +# needed for widgets! + - ipympl - pip - jupytext - python=3.11.6 From dd82e0afb48e751e1284534d2cc4e3e89158b568 Mon Sep 17 00:00:00 2001 From: gsell Date: Mon, 18 Mar 2024 09:19:22 +0100 Subject: [PATCH 058/158] Update README.md --- Compiler/fluka4/README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Compiler/fluka4/README.md b/Compiler/fluka4/README.md index 8de9062..855ee91 100644 --- a/Compiler/fluka4/README.md +++ b/Compiler/fluka4/README.md @@ -21,7 +21,9 @@ GEOVIEWER_VERSION=3.2 GCC_VERSION=9.5.0 PYTHON_VERSION=3.9.10 TCLTK_VERSION=8.6.9 +```` +``` PREFIX="${PMODULES_ROOT}/Compiler/fluka4/${FLUKA4_VERSION}/gcc/${GCC_VERSION}" DISTFILES_DIR='/afs/psi.ch/software/Pmodules/distfiles' FLUKA_TAR="${DISTFILES_DIR}/fluka-4-${FLUKA4_VERSION}.x86-Linux-gfor${GCC_VERSION/.*}.tgz" From 3ec82facc0af133fc4fd97712e81aa40e7006d36 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 19 Mar 2024 16:19:10 +0100 Subject: [PATCH 059/158] openssl: release version 1.1.1v and w as stable --- Tools/openssl/files/variants.rhel7 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Tools/openssl/files/variants.rhel7 b/Tools/openssl/files/variants.rhel7 index 0712f7e..616da08 100644 --- a/Tools/openssl/files/variants.rhel7 +++ b/Tools/openssl/files/variants.rhel7 @@ -7,5 +7,5 @@ openssl/1.1.1g stable openssl/1.1.1k stable openssl/1.1.1l stable openssl/1.1.1m stable -openssl/1.1.1v unstable -openssl/1.1.1w unstable +openssl/1.1.1v stable +openssl/1.1.1w stable From ebc579e85519d402bce57ffc5cdc079e31fcd754 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 19 Mar 2024 16:22:07 +0100 Subject: [PATCH 060/158] git: config for version 2.43.1 added --- Tools/git/files/config.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/Tools/git/files/config.yaml b/Tools/git/files/config.yaml index 5405f8a..06f4ade 100644 --- a/Tools/git/files/config.yaml +++ b/Tools/git/files/config.yaml @@ -21,6 +21,14 @@ git: git-2.8.1.tar.xz: e6626b43ba4bc63ad4918df4c275f50bd7f8af2ab54bde60496ad75e91e927fc git-2.3.3.tar.gz: c189e4a48d8805482f450db666330c79bcefae37e0d035c7717517126ddf4305 versions: + 2.43.1: + config: + runtime_deps: [TclTk/8.6.9] + build_requires: [gcc/10.4.0, perl/5.30.0, asciidoc/8.6.9-1, xmlto/0.0.28, gettext/0.19.8, openssl/1.1.1w] + relstage: unstable + overlay: devel + systems: [rhel7, rhel8, rhel9] + docfiles: [COPYING, README.md] 2.42.0: config: runtime_deps: [TclTk/8.6.9] From c79c62502f862d7cd64d7f61df984f3741f05e90 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 19 Mar 2024 16:23:19 +0100 Subject: [PATCH 061/158] cmake: deprecated function removed --- Programming/cmake/build-yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/Programming/cmake/build-yaml b/Programming/cmake/build-yaml index 6d7e5da..277b777 100755 --- a/Programming/cmake/build-yaml +++ b/Programming/cmake/build-yaml @@ -1,8 +1,5 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://cmake.org/files/v${V_MAJOR}.${V_MINOR}/$P-$V.tar.gz" -pbuild::add_to_group 'Programming' - declare bootstrap_flags='' pbuild::pre_configure() { From 55063a7966cd3d95c2e87f03c9d611fe4fdbbe86 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 19 Mar 2024 16:24:25 +0100 Subject: [PATCH 062/158] cmake: version 3.27.8 added; cleanup/review config --- Programming/cmake/files/config.yaml | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/Programming/cmake/files/config.yaml b/Programming/cmake/files/config.yaml index 4beb6c5..4efa3b7 100644 --- a/Programming/cmake/files/config.yaml +++ b/Programming/cmake/files/config.yaml @@ -1,6 +1,7 @@ format: 1 cmake: defaults: + group: Programming overlay: base relstage: stable urls: @@ -24,19 +25,23 @@ cmake: cmake-3.23.2.tar.gz: f316b40053466f9a416adf981efda41b160ca859e97f6a484b447ea299ff26aa cmake-3.25.2.tar.gz: c026f22cb931dd532f648f087d587f07a1843c6e66a3dfca4fb0ea21944ed33c cmake-3.26.3.tar.gz: bbd8d39217509d163cb544a40d6428ac666ddc83e22905d3e52c925781f0f659 + cmake-3.27.8.tar.gz: fece24563f697870fbb982ea8bf17482c9d5f855d8c9bf0b82463d76c9e8d0cc versions: - 2.8.12.2;3.1.3;3.3.2;3.4.1;3.6.3;3.9.6: - 3.8.1: - config: - relstage: removed - 3.10.3;3.13.3;3.14.0: - config: - build_requires: [gcc/7.3.0] - 3.15.5;3.19.2;3.20.5;3.23.2;3.25.2: + 3.27.8: config: build_requires: [gcc/7.3.0, patchelf/0.8.1] + relstage: unstable 3.26.3: config: build_requires: [gcc/7.3.0, patchelf/0.8.1] - relstage: unstable \ No newline at end of file + 3.15.5;3.19.2;3.20.5;3.23.2;3.25.2: + config: + build_requires: [gcc/7.3.0, patchelf/0.8.1] + 3.10.3;3.13.3;3.14.0: + config: + build_requires: [gcc/7.3.0] + 3.8.1: + config: + relstage: removed + 2.8.12.2;3.1.3;3.3.2;3.4.1;3.6.3;3.9.6: From 78ac33d14f0963c41604127ee55e4b03c26e2dfa Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 19 Mar 2024 16:38:07 +0100 Subject: [PATCH 063/158] Python YAML config and build script added --- Programming/Python/build-xml | 88 ++++++++++++++++++++++++++++ Programming/Python/files/config.yaml | 58 ++++++++++++++++++ 2 files changed, 146 insertions(+) create mode 100755 Programming/Python/build-xml create mode 100644 Programming/Python/files/config.yaml diff --git a/Programming/Python/build-xml b/Programming/Python/build-xml new file mode 100755 index 0000000..fcd556e --- /dev/null +++ b/Programming/Python/build-xml @@ -0,0 +1,88 @@ +#!/usr/bin/env modbuild + +pbuild::pre_configure() { + local -a cflags=() + local -a ldflags=() + + cflags+=("-fPIC") + cflags+=("-I${XZ_INCLUDE_DIR}") + + ldflags+=("-L${XZ_LIBRARY_DIR}") + + if (( V_MAJOR == 2 || (V_MAJOR == 3 && V_MINOR <= 6) )); then + cflags+=("-I${OPENSSL_INCLUDE_DIR}" "-I${OPENSSL_INCLUDE_DIR}/openssl") + ldflags+=("-L${OPENSSL_LIBRARY_DIR}") + else + pbuild::add_configure_args "--with-openssl=${OPENSSL_DIR}" + #pbuild::add_configure_args "--enable-optimizations" + fi + pbuild::add_configure_args "CFLAGS=${cflags[*]}" + pbuild::add_configure_args "LDFLAGS=${ldflags[*]}" + pbuild::add_configure_args "--enable-shared" +} + +pbuild::pre_configure_Linux() { + pbuild::add_configure_args "--with-tcltk-includes=-I${TCLTK_INCLUDE_DIR}" + pbuild::add_configure_args "--with-tcltk-libs=-L${TCLTK_LIBRARY_DIR} -ltcl8.6 -ltk8.6" +} + +pbuild::post_install_Linux() { + if version_le 3.9.10; then + install "${OPENSSL_LIBRARY_DIR}"/libcrypto.so.* "${PREFIX}/lib" + install "${OPENSSL_LIBRARY_DIR}"/libssl.so.* "${PREFIX}/lib" + install "${TCLTK_LIBRARY_DIR}"/libtcl*.so "${PREFIX}/lib" + install "${TCLTK_LIBRARY_DIR}"/libtk*.so "${PREFIX}/lib" + install "${XZ_LIBRARY_DIR}"/liblzma.so.* "${PREFIX}/lib" + install /usr/lib64/libffi.so.* "${PREFIX}/lib" + else + : + fi +} + +pbuild::post_install() { + export PATH="${PREFIX}/bin:${PATH}" + export LD_LIBRARY_PATH="${PREFIX}/lib:${LD_LIBRARY_PATH}" + export CFLAGS="-I${OPENSSL_INCLUDE_DIR} -I${OPENSSL_INCLUDE_DIR}/openssl" + export CPPFLAGS="-I${OPENSSL_INCLUDE_DIR} -I${OPENSSL_INCLUDE_DIR}/openssl" + export LDFLAGS="-L${OPENSSL_LIBRARY_DIR}" + ln -fs "${PREFIX}/bin/python${V%%.*}" "${PREFIX}/bin/python" + ln -fs "${PREFIX}/include/python${V%.*}m" "${PREFIX}/include/python" + ln -fs "${PREFIX}/include/python${V%.*}m" "${PREFIX}/include/python${V%.*}" + + if (( V_MAJOR == 2 || (V_MAJOR == 3 && V_MINOR <= 7) )); then + cd "${BUILDBLOCK_DIR}" + "${PREFIX}/bin/python" 'get-pip.py' + fi + + std::info "Building numpy\n" + pip${V_MAJOR} install numpy + + std::info "Building scipy\n" + pip${V_MAJOR} install scipy + + std::info "Building matplotlib\n" + pip${V_MAJOR} install matplotlib + + std::info "Building ipython\n" + pip${V_MAJOR} install ipython + + std::info "Building sympy\n" + pip${V_MAJOR} install sympy + + std::info "Building nose\n" + pip${V_MAJOR} install nose + + std::info "Building h5py\n" + pip${V_MAJOR} install h5py + + std::info "Building pandas\n" + pip${V_MAJOR} install pandas + + #std::info "Building virtualenv\n" + #pip${V_MAJOR} install virtualenv + + #std::info "Building ansible\n" + #pip${V_MAJOR} install ansible ansible-core==2.15.4 +} + + diff --git a/Programming/Python/files/config.yaml b/Programming/Python/files/config.yaml new file mode 100644 index 0000000..4041769 --- /dev/null +++ b/Programming/Python/files/config.yaml @@ -0,0 +1,58 @@ +format: 1 +Python: + defaults: + group: Programming + overlay: base + relstage: stable + urls: + - url: https://www.python.org/ftp/python/${V_PKG}/$P-${V_PKG}.tgz + + shasums: + Python-2.7.12.tgz: 3cb522d17463dfa69a155ab18cffa399b358c966c0363d6c8b5b3bf1384da4b6 + Python-2.7.14.tgz: 304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8 + Python-2.7.16.tgz: 01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5 + Python-2.7.17.tgz: f22059d09cdf9625e0a7284d24a13062044f5bf59d93a7f3382190dfa94cecde + Python-2.7.18.tgz: da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814 + Python-3.6.11.tgz: 96621902f89746fffc22f39749c07da7c2917b232e72352e6837d41850f7b90c + Python-3.6.3.tgz: ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91 + Python-3.7.3.tgz: d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff + Python-3.7.4.tgz: d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3 + Python-3.7.8.tgz: 0e25835614dc221e3ecea5831b38fa90788b5389b99b675a751414c858789ab0 + Python-3.8.12.tgz: 316aa33f3b7707d041e73f246efedb297a70898c4b91f127f66dc8d80c596f1a + Python-3.8.4.tgz: 32c4d9817ef11793da4d0d95b3191c4db81d2e45544614e8449255ca9ae3cc18 + Python-3.8.8.tgz: 76c0763f048e4f9b861d24da76b7dd5c7a3ba7ec086f40caedeea359263276f7 + Python-3.9.10.tgz: 1aa9c0702edbae8f6a2c95f70a49da8420aaa76b7889d3419c186bfc8c0e571e + Python-3.9.17.tgz: 8ead58f669f7e19d777c3556b62fae29a81d7f06a7122ff9bc57f7dd82d7e014 + Python-3.9.18.tgz: 504ce8cfd59addc04c22f590377c6be454ae7406cb1ebf6f5a350149225a9354 + versions: + 3.9.18-1: + config: + relstage: unstable + build_requires: [openssl/1.1.1w, TclTk/8.6.9, xz/5.2.4] + 3.9.18: + config: + relstage: unstable + build_requires: [openssl/1.1.1w, TclTk/8.6.9, xz/5.2.4] + 3.9.17: + config: + relstage: unstable + build_requires: [openssl/1.1.1v, TclTk/8.6.9, xz/5.2.4] + 3.9.10: + 3.8.12: + 3.8.8;3.8.4: + config: + relstage: deprecated + 3.7.8: + config: + relstage: stable + 3.7.4;3.7.3: + config: + relstage: deprecated + 3.6.3: + 3.4.3;3.4.0: + config: + relstage: deprecated + 2.7.17;2.7.16: + 2.7.14;2.7.12;2.7.11: + config: + relstage: deprecated From 92696ce24293bbf8fa2eef266612e13edc15fa00 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 19 Mar 2024 16:39:08 +0100 Subject: [PATCH 064/158] bash: YAML config and build script added --- System/bash/build-xml | 2 ++ System/bash/files/config.yaml | 19 +++++++++++++++++++ 2 files changed, 21 insertions(+) create mode 100755 System/bash/build-xml create mode 100644 System/bash/files/config.yaml diff --git a/System/bash/build-xml b/System/bash/build-xml new file mode 100755 index 0000000..6e021f3 --- /dev/null +++ b/System/bash/build-xml @@ -0,0 +1,2 @@ +#!/usr/bin/env modbuild + diff --git a/System/bash/files/config.yaml b/System/bash/files/config.yaml new file mode 100644 index 0000000..b1ff680 --- /dev/null +++ b/System/bash/files/config.yaml @@ -0,0 +1,19 @@ +format: 1 +bash: + defaults: + relstage: stable + group: System + overlay: base + urls: + - url: https://ftp.gnu.org/gnu/$P/$P-$V.tar.gz + + shasums: + bash-4.3.30.tar.gz: 317881019bbf2262fb814b7dd8e40632d13c3608d2f237800a8828fbb8a640dd + bash-5.1.tar.gz: cc012bc860406dcf42f64431bcd3d2fa7560c02915a601aba9cd597a39329baa + bash-5.1.16.tar.gz: 5bac17218d3911834520dad13cd1f85ab944e1c09ae1aba55906be1f8192f558 + bash-5.2.21.tar.gz: c8e31bdc59b69aaffc5b36509905ba3e5cbb12747091d27b4b977f078560d5b8 + versions: + 4.3.30;5.1;5.1.16: + 5.2.21: + config: + relstage: unstable From 4120533cad0b19d1b5106aa7abea03d098a91127 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 19 Mar 2024 17:10:46 +0100 Subject: [PATCH 065/158] patchelf: YAML config and build script added --- System/patchelf/build-xml | 6 ++++++ System/patchelf/files/config.yaml | 22 ++++++++++++++++++++++ 2 files changed, 28 insertions(+) create mode 100755 System/patchelf/build-xml create mode 100644 System/patchelf/files/config.yaml diff --git a/System/patchelf/build-xml b/System/patchelf/build-xml new file mode 100755 index 0000000..bd8e687 --- /dev/null +++ b/System/patchelf/build-xml @@ -0,0 +1,6 @@ +#!/usr/bin/env modbuild + +pbuild::post_prep() { + cd "${SRC_DIR}" + ./bootstrap.sh +} diff --git a/System/patchelf/files/config.yaml b/System/patchelf/files/config.yaml new file mode 100644 index 0000000..8a4dab5 --- /dev/null +++ b/System/patchelf/files/config.yaml @@ -0,0 +1,22 @@ +format: 1 +patchelf: + defaults: + group: System + overlay: base + relstage: stable + urls: + - url: https://github.com/NixOS/$P/archive/$V.tar.gz + name: $P-$V.tar.gz + shasums: + patchelf-0.8.1.tar.bz2: 12367e9ce9c315a26e14f11db8542e2e0f3a877aff52590912111268cb775bef7ce713368eb3759df6823f457a7b6d0419fd02c231d40db5dd0b853f41caf254 + patchelf-0.11.tar.gz: b156bad513d5bac33aaf61d5f04d5a78efc81abf8c0ccb851f605e1137c21e671b4933263a47543daf5064db5e83c9afa836b1aea143fca7d8e6a18ebf96beb8 + patchelf-0.12.tar.gz: 2563a5b22b90392d5755d9a08022daf8570fa1b741becbbca92548d0a2f82f7ee21175a2c34816a4653c89c2219bf59b1440304b0fa2d49842e398ab18b9923c + patchelf-0.14.5.tar.gz: 1b7eca84f6fe2d6f6d4469ca1ccdf35dc920d2052ba94b7daeba6c8cb41fdaff20b1e5bac7c8a7650ff12bf4156da87f84d32e75b09958636dc992a1b7b1a59d + + versions: + 0.8.1;0.11;0.12;0.14.5: + 0.18.0: + config: + relstage: unstable + build_requires: [gcc/12.3.0] + From 190c57cf82e5815631ed396927f89cc0c612fbdc Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Tue, 2 Apr 2024 12:08:01 +0200 Subject: [PATCH 066/158] Set MotionCor2 path based on the loaded cuda version. Fixes #275. --- EM/relion/modulefile | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/EM/relion/modulefile b/EM/relion/modulefile index 9042d98..bd88c8d 100644 --- a/EM/relion/modulefile +++ b/EM/relion/modulefile @@ -44,4 +44,22 @@ setenv RELION_RESMAP_EXECUTABLE /opt/psi/EM/ResMap/1.1.4/bin/ResMap # Version-specific variables setenv RELION_QSUB_TEMPLATE /opt/psi/EM/relion/$V/scripts/multi_gpu.sh -setenv RELION_MOTIONCOR2_EXECUTABLE /opt/psi/EM/MotionCor2/1.4.0/bin/MotionCor2 + +# See MC2 compatibility matrix: https://intranet.psi.ch/en/bio/motioncor2 +if {[string match "8.0*" $env(CUDA_VERSION)]} { + setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.3.2/bin/MotionCor2_1.3.2-Cuda80" +} elseif {[string match "11.0*" $env(CUDA_VERSION)]} { + setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.4.0/bin/MotionCor2" +} else { + setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.6.4/bin/MotionCor2" +} + +# relion 5 features +if {[file exists /opt/psi/EM/relion/$V/conda_env/$V]} { + setenv RELION_TOPAZ_EXECUTABLE /opt/psi/EM/relion/$V/conda_env/$V/bin/topaz + setenv RELION_PYTHON_EXECUTABLE /opt/psi/EM/relion/$V/conda_env/$V/bin/python +} +if {[file exists /opt/psi/EM/relion/$V/torch]} { + setenv RELION_TORCH_HOME_PATH /opt/psi/EM/relion/$V/torch +} + From d9d6ec9f988db01c177ee37a60fda2b1d641a8a8 Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Wed, 3 Apr 2024 16:13:27 +0200 Subject: [PATCH 067/158] relion5.0 update --- EM/relion/README.md | 2 ++ EM/relion/build | 52 ++++++++++++++++++++++++++++++++++++++++ EM/relion/files/variants | 4 +++- EM/relion/modulefile | 6 +++-- 4 files changed, 61 insertions(+), 3 deletions(-) diff --git a/EM/relion/README.md b/EM/relion/README.md index a03e1ac..095d00f 100644 --- a/EM/relion/README.md +++ b/EM/relion/README.md @@ -11,3 +11,5 @@ and MKL, but this would require additional openmpi variants. After running ./build, install relion scripts from the repository at https://git.psi.ch/lsm-hpce/relion-scripts + +From version 5.0-beta on, a conda env is required. conda env is build in the folder $SRC\_DIR/conda\_envs. Also, weights for BLUSH, MODEL-ANGELO and CLASS-RANKER are downloaded in the installation step. diff --git a/EM/relion/build b/EM/relion/build index 22c5302..6e3c435 100755 --- a/EM/relion/build +++ b/EM/relion/build @@ -2,11 +2,23 @@ pbuild::add_to_group 'EM' pbuild::use_cmake +PROFILE="no" +SP="no" pbuild::prep() { + local BRANCH if [[ "$V" =~ beta$ ]]; then BRANCH="ver${V_MAJOR}.${V_MINOR}" + + elif [[ "$V" =~ profile$ ]]; then + BRANCH="${V_PKG}" + PROFILE="yes" + + elif [[ "$V" =~ sp$ ]]; then + BRANCH="ver${V_MAJOR}.${V_MINOR}" + SP="yes" + else BRANCH="${V_PKG}" fi @@ -15,6 +27,46 @@ pbuild::prep() { } pbuild::pre_configure() { + + # Section will be switched on for -profile version + #----------------------------------------------------------- + if [[ "$PROFILE" == "yes" ]]; then + pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=BENCHMARKING" + fi + #------------------------------------------------------------ + + + # Section will be switched on for single-precision version + # Safe memory usage for multibody refinements + #------------------------------------------------------------ + if [[ "$SP" == "yes" ]]; then + pbuild::add_configure_args "-DDoublePrec_CPU=OFF" + fi + #------------------------------------------------------------ + + + + # The following section will only work for versions >= 5.0-beta + # ------------------------------------------------------------- + if [[ "$V_MAJOR" -ge "5" ]]; then + + #download blush weights + wget ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/blush_v1.0.ckpt.gz -P "$PREFIX/torch/hub/checkpoints/relion_blush" \ + && gunzip "$PREFIX/torch/hub/checkpoints/relion_blush/blush_v1.0.ckpt.gz" + mv "$PREFIX/torch/hub/checkpoints/relion_blush/blush_v1.0.ckpt" "$PREFIX/torch/hub/checkpoints/relion_blush/v1.0.ckpt" + touch "$PREFIX/torch/hub/checkpoints/relion_blush/v1.0_installed.txt" + + #Set Torch Home + pbuild::add_configure_args "-DTORCH_HOME_PATH=$PREFIX/torch" + + #Conda + conda env create -f "$SRC_DIR/environment.yml" -p "$PREFIX/conda_env/$P_$V" + pbuild::add_configure_args "-DPYTHON_EXE_PATH=$PREFIX/conda_env/$P_$V/bin/python" + fi + + #--------------------------------------------------------------- + + # CMake-based build pbuild::add_configure_args "-DFORCE_OWN_FFTW=ON" diff --git a/EM/relion/files/variants b/EM/relion/files/variants index c7e3efa..bbe791e 100644 --- a/EM/relion/files/variants +++ b/EM/relion/files/variants @@ -13,4 +13,6 @@ relion/3.1.3 stable gcc/9.2.0 openmpi/4.0.5_slurm cuda/11.0.3 b:cmake/3.15.5 b:t relion/4.0-beta deprecated gcc/9.2.0 openmpi/4.0.5_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 relion/4.0.0 unstable gcc/11.2.0 openmpi/4.1.3_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 relion/4.0.1 unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 - +relion/4.0.1-profile unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 +relion/5.0-beta unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 anaconda/2019.07 +relion/5.0-sp unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 anaconda/2019.07 diff --git a/EM/relion/modulefile b/EM/relion/modulefile index 9042d98..44b6f71 100644 --- a/EM/relion/modulefile +++ b/EM/relion/modulefile @@ -3,7 +3,7 @@ module-whatis "3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)" module-url "https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" module-license "GPLv2 license" -module-maintainer "Spencer Bliven " +module-maintainer "Greta Assmann " module-help " RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a @@ -41,7 +41,9 @@ setenv RELION_SUMMOVIE_EXECUTABLE /opt/psi/EM/Summovie/1.0.2/bin/sum_movie_openm setenv RELION_CTFFIND_EXECUTABLE /opt/psi/EM/ctffind4/4.1.8/bin/ctffind setenv RELION_GCTF_EXECUTABLE /opt/psi/EM/Gctf/1.06/bin/Gctf setenv RELION_RESMAP_EXECUTABLE /opt/psi/EM/ResMap/1.1.4/bin/ResMap - +setenv RELION_TOPAZ_EXECUTABLE /opt/psi/EM/relion/5.0-sp/conda_env/5.0-beta/bin/topaz +setenv RELION_PYTHON_EXECUTABLE /opt/psi/EM/relion/5.0-sp/conda_env/5.0-beta/bin/python +setenv RELION_TORCH_HOME_PATH /opt/psi/EM/relion/5.0-sp/torch # Version-specific variables setenv RELION_QSUB_TEMPLATE /opt/psi/EM/relion/$V/scripts/multi_gpu.sh setenv RELION_MOTIONCOR2_EXECUTABLE /opt/psi/EM/MotionCor2/1.4.0/bin/MotionCor2 From 993a57c8da85e970fe30d36c733d2808144f4934 Mon Sep 17 00:00:00 2001 From: Germann Elsa Sylvia Date: Thu, 11 Apr 2024 15:36:30 +0200 Subject: [PATCH 068/158] ADD: nvhidia 4.3 and 23.5 SDKK related openmpi and qe/7.3.1 CPU&GPU --- Compiler/openmpi/build | 7 +++ Compiler/openmpi/files/config.yaml | 10 +++- MPI/hdf5/build | 5 ++ MPI/qe/build | 35 +++++++------- MPI/qe/files/config.yaml | 32 +++++++++++++ Programming/nvhpc/Readme.md | 5 ++ Programming/nvhpc/build | 23 ++++++++++ Programming/nvhpc/files/config.yaml | 33 ++++++++++++++ Programming/nvhpc/modulefile | 71 +++++++++++++++++++++++++++++ 9 files changed, 202 insertions(+), 19 deletions(-) create mode 100644 MPI/qe/files/config.yaml create mode 100644 Programming/nvhpc/Readme.md create mode 100755 Programming/nvhpc/build create mode 100644 Programming/nvhpc/files/config.yaml create mode 100644 Programming/nvhpc/modulefile diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index ba87cf3..c66ef35 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -58,6 +58,13 @@ pbuild::pre_configure() { pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" fi + if [[ -v NVHPC_VERSION ]]; then + pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" + pbuild::add_configure_args "CFLAGS=-fPIC -DPIC" + pbuild::add_configure_args "CXXFLAGS=-fPIC -DPIC" + pbuild::add_configure_args "FCFLAGS=-Mstandard -fPIC -DPIC" + fi + if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6; then pbuild::add_configure_args "--with-gpfs=/usr/lpp/mmfs" pbuild::add_configure_args "--with-pmi" diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index 1bac1f8..ce0e73d 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -9,7 +9,7 @@ openmpi: systems: [rhel7, rhel8, rhel9] docfiles: [AUTHORS, LICENSE, NEWS, README] urls: - - url: https://download.open-mpi.org/release/open-mpi/v${V_MAJOR}.${V_MINOR}/openmpi-${V_PKG}.tar.bz + - url: https://download.open-mpi.org/release/open-mpi/v${V_MAJOR}.${V_MINOR}/openmpi-${V_PKG}.tar.bz2 shasums: openmpi-1.10.0.tar.bz2: 26b432ce8dcbad250a9787402f2c999ecb6c25695b00c9c6ee05a306c78b6490 openmpi-1.10.4.tar.bz2: fb3c0c4c77896185013b6091b306d29ba592eb40d8395533da5c8bc300d922db @@ -54,6 +54,14 @@ openmpi: openmpi-4.1.5.tar.bz2: a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3 versions: + 4.1.4: + variants: + - systems: [merlin-*, ra-*] + relstage: unstable + suffix: _slurm + group_deps: + compiler: {nvhpc: [24.3_cuda_12.3, 23.5_cuda_12.1]} + build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5] 4.1.5: variants: diff --git a/MPI/hdf5/build b/MPI/hdf5/build index 59d4910..eeccb3c 100755 --- a/MPI/hdf5/build +++ b/MPI/hdf5/build @@ -45,6 +45,11 @@ pbuild::pre_configure() { pbuild::add_configure_args "CXXFLAGS=-fPIC" pbuild::add_configure_args "FCFLAGS=-fPIC" ;; + nvhpc ) + pbuild::add_configure_args "CFLAGS=-fPIC" + pbuild::add_configure_args "CXXFLAGS=-fPIC" + pbuild::add_configure_args "FCFLAGS=-fPIC" + ;; esac if [[ "${enable_fortran}" == 'yes' ]]; then diff --git a/MPI/qe/build b/MPI/qe/build index 03073fd..5610e09 100755 --- a/MPI/qe/build +++ b/MPI/qe/build @@ -1,23 +1,22 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://github.com/QEF/q-e/archive/$P-$V.tar.gz" - -pbuild::add_to_group 'MPI' - -pbuild::install_docfiles License README.md CONTRIBUTING.md - -pbuild::compile_in_sourcetree - pbuild::pre_configure() { - pbuild::add_configure_args "-enable-openmp" -} - -pbuild::compile() { - make all - make install -} - -pbuild::install() { - : + pbuild::add_configure_args "-DQE_ENABLE_OPENMP=ON" + pbuild::add_configure_args "-DQE_ENABLE_MPI=ON" + # Recommended by the Quantum Espresso Developers + pbuild::add_configure_args "-DCMAKE_C_COMPILER=mpicc" + pbuild::add_configure_args "-DCMAKE_Fortran_COMPILER=mpif90" + pbuild::add_configure_args "-DCMAKE_SYSTEM_PROCESSOR=x86_64" + + case "${COMPILER}" in + nvhpc ) + pbuild::add_configure_args "-DQE_ENABLE_CUDA=ON" + pbuild::add_configure_args "-DQE_ENABLE_MPI_GPU_AWARE=ON" + pbuild::add_configure_args "-DQE_ENABLE_OPENACC=ON" + pbuild::add_configure_args "-DNVFORTRAN_CUDA_VERSION=12.1" + pbuild::add_configure_args "-DNVFORTRAN_CUDA_CC=60" + ;; + esac + } diff --git a/MPI/qe/files/config.yaml b/MPI/qe/files/config.yaml new file mode 100644 index 0000000..cc6cdd6 --- /dev/null +++ b/MPI/qe/files/config.yaml @@ -0,0 +1,32 @@ +--- +# yamllint disable rule:line-length +format: 1 +qe: + defaults: + group: MPI + overlay: base + relstage: stable + systems: [rhel7, rhel8, rhel9] + docfiles: [AUTHORS, LICENSE, NEWS, README] + configure_with: cmake + urls: + - url: https://gitlab.com/QEF/q-e/-/archive/qe-${V_PKG}/q-e-qe-${V_PKG}.tar.bz2 + shasums: + qe-7.3.1.tar.bz2: 4955e4ca5e47a0faafefc72442155bef02ff94c8b796698ad81d4804a1cf6d88 + + versions: + 7.3.1: + variants: + - systems: [merlin-*, ra-*] + group_deps: + compiler: {gcc: [13.1.0]} + mpi: {openmpi: [4.1.5_slurm]} + relstage: unstable + build_requires: [cmake/3.26.3, git/2.39.1, lapack/3.10.0, OpenBLAS/0.3.23, hdf5/1.13.1_slurm] + - systems: [merlin-*, ra-*] + group_deps: + compiler: {nvhpc: [23.5_cuda_12.1]} + mpi: {openmpi: [4.1.4_slurm]} + relstage: unstable + build_requires: [cmake/3.26.3, git/2.39.1] + runtime_deps: [libfabric/1.18.0] diff --git a/Programming/nvhpc/Readme.md b/Programming/nvhpc/Readme.md new file mode 100644 index 0000000..5c1be1d --- /dev/null +++ b/Programming/nvhpc/Readme.md @@ -0,0 +1,5 @@ +After installing PGI, the localrc file of the pgi installation needs to be modified by issuing the following commands in the directory where the localrc file is located: + + module add gcc/ # currently 7.3.0 + ./makelocalrc -x -gcc $(which gcc) -gpp $(which g++) -g77 $(which gfortran) + diff --git a/Programming/nvhpc/build b/Programming/nvhpc/build new file mode 100755 index 0000000..2252749 --- /dev/null +++ b/Programming/nvhpc/build @@ -0,0 +1,23 @@ +#!/usr/bin/env modbuild + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + export NVHPC_SILENT="true" + export NVHPC_INSTALL_DIR=$PREFIX + export NVHPC_INSTALL_TYPE="network" + ./install +} + +pbuild::post_install() { + cd $PREFIX/Linux_x86_64/$V_MAJOR.$V_MINOR/compilers/bin + rm -rf localrc* + ./makelocalrc -x $PWD +} + diff --git a/Programming/nvhpc/files/config.yaml b/Programming/nvhpc/files/config.yaml new file mode 100644 index 0000000..7c58b14 --- /dev/null +++ b/Programming/nvhpc/files/config.yaml @@ -0,0 +1,33 @@ +--- +# yamllint disable rule:line-length +format: 1 +nvhpc: + defaults: + group: Programming + overlay: base + relstage: stable + systems: [rhel7, rhel8, rhel9] + docfiles: [AUTHORS, LICENSE, NEWS, README] + compile_in_sourcetree: true + shasums: + nvhpc-24.3.tar.gz: 4fb8949ba8cef73b28818bd9375c9420ec48fab1c64e71315a7c1984f5329d6b + nvhpc-23.5.tar.gz: 3196309b38df6f0a27e18b80f6a40e23cab8195cad43fc6bbd569af7d8ca5742 + + versions: + 24.3: + variants: + - systems: [merlin-*, ra-*] + suffix: _cuda_12.3 + urls: + - url: https://developer.download.nvidia.com/hpc-sdk/${V_PKG}/nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz + suffix: _cuda_12.3 + relstage: unstable + build_requires: [gcc/10.4.0] + 23.5: + variants: + - systems: [merlin-*, ra-*] + suffix: _cuda_12.1 + urls: + - url: https://developer.download.nvidia.com/hpc-sdk/${V_PKG}/nvhpc_2023_235_Linux_x86_64_cuda_12.1.tar.gz + relstage: unstable + build_requires: [gcc/10.4.0] diff --git a/Programming/nvhpc/modulefile b/Programming/nvhpc/modulefile new file mode 100644 index 0000000..1835016 --- /dev/null +++ b/Programming/nvhpc/modulefile @@ -0,0 +1,71 @@ +#%Module1.0 + +# Copyright (c) 2021, NVIDIA CORPORATION. All rights reserved. +# +# NVIDIA CORPORATION and its licensors retain all intellectual property +# and proprietary rights in and to this software, related documentation +# and any modifications thereto. Any use, reproduction, disclosure or +# distribution of this software and related documentation without an express +# license agreement from NVIDIA CORPORATION is strictly prohibited. + +module-whatis "NVIDIA HPC SDK: A Comprehensive Suite of Compilers, Libraries and Tools for HPC" +module-url "https://developer.nvidia.com/hpc-sdk" +module-license "# Copyright (c) 2023 NVIDIA CORPORATION. All rights reserved. + # + # NVIDIA CORPORATION and its licensors retain all intellectual property + # and proprietary rights in and to this software, related documentation + # and any modifications thereto. Any use, reproduction, disclosure or + # distribution of this software and related documentation without an express + # license agreement from NVIDIA CORPORATION is strictly prohibited." +module-maintainer "Elsa Germann " + +module-addgroup "Compiler" + +set nvhome $PREFIX +set target Linux_x86_64 +set version $V_MAJOR.3 + +set nvcudadir $nvhome/$target/$version/cuda +set nvcompdir $nvhome/$target/$version/compilers +set nvmathdir $nvhome/$target/$version/math_libs +set nvcommdir $nvhome/$target/$version/comm_libs + +setenv NVHPC $nvhome +setenv NVHPC_ROOT $nvhome/$target/$version +setenv CUDA_HOME $nvcudadir +setenv CC $nvcompdir/bin/nvc +setenv CXX $nvcompdir/bin/nvc++ +setenv FC $nvcompdir/bin/nvfortran +setenv F90 $nvcompdir/bin/nvfortran +setenv F77 $nvcompdir/bin/nvfortran +setenv CPP cpp + +prepend-path PATH $nvcudadir/bin +prepend-path PATH $nvcompdir/bin +prepend-path PATH $nvcompdir/extras/qd/bin + +prepend-path LD_LIBRARY_PATH $nvcudadir/lib64 +prepend-path LD_LIBRARY_PATH $nvcudadir/extras/CUPTI/lib64 +prepend-path LD_LIBRARY_PATH $nvcompdir/extras/qd/lib +prepend-path LD_LIBRARY_PATH $nvcompdir/lib +prepend-path LD_LIBRARY_PATH $nvmathdir/lib64 +prepend-path LD_LIBRARY_PATH $nvcommdir/nccl/lib +prepend-path LD_LIBRARY_PATH $nvcommdir/nvshmem/lib +prepend-path LD_LIBRARY_PATH /opt/psi/Programming/gcc/10.4.0/lib64 + +prepend-path LIBRARY_PATH /opt/psi/Programming/gcc/10.4.0/lib64 +prepend-path LIBRARY_PATH $nvmathdir/lib64 +prepend-path LIBRARY_PATH $nvcudadir/lib64 +prepend-path LIBRARY_PATH $nvcudadir/extras/CUPTI/lib64 +prepend-path LIBRARY_PATH $nvcompdir/extras/qd/lib +prepend-path LIBRARY_PATH $nvcompdir/lib +prepend-path LIBRARY_PATH $nvmathdir/lib64 +prepend-path LIBRARY_PATH $nvcommdir/nccl/lib +prepend-path LIBRARY_PATH $nvcommdir/nvshmem/lib + +prepend-path CPATH $nvmathdir/include +prepend-path CPATH $nvcommdir/nccl/include +prepend-path CPATH $nvcommdir/nvshmem/include +prepend-path CPATH $nvcompdir/extras/qd/include/qd + +prepend-path MANPATH $nvcompdir/man From 57db11bdbfe024d45f4b0b16c12c09c9ce66797f Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Sat, 27 Apr 2024 22:56:27 +0200 Subject: [PATCH 069/158] datacatalog/2.2.0 This migrates to installing from github. --- Tools/datacatalog/README.md | 28 ++++++++++++++++++++++++ Tools/datacatalog/build | 30 +++++++++++++------------- Tools/datacatalog/files/variants.Linux | 8 ++++--- Tools/datacatalog/modulefile | 13 +++++++---- 4 files changed, 57 insertions(+), 22 deletions(-) diff --git a/Tools/datacatalog/README.md b/Tools/datacatalog/README.md index 7d08119..7df942a 100644 --- a/Tools/datacatalog/README.md +++ b/Tools/datacatalog/README.md @@ -4,6 +4,18 @@ This module provides tools to interface with the Data Catalog (discovery.psi.ch). +## Version Numbers + +Prior to version 2, each command had it's own version. The pmodule version +roughly tracked the datasetIngestor version. However, some pmodules were +updated manually with more recent binaries, so in general there is no way to +check the versions contained in older pmodules other than running each command +and parsing the output. + +From v2.2.0 all CLI commands share a common version, and the pmodules will +reflect this. The SciCat GUI is still versioned independently, but this is +planned to be brought in sync with the CLI and pmodule soon. + ## Installation Run `./build ` to install the latest version. This downloads the @@ -18,3 +30,19 @@ the conda module is not activated. See Programming/anaconda/2019.07/conda-env-defs/scicat_client for environment installation details. +### SciCat GUI + +The SciCat GUI is installed manually to `bin`. As of 2.2.0, no standard release +cycle is used for the GUI. It should be built from source in the [rollout +repo](https://git.psi.ch/MELANIE/rollout/-/tree/master/Software/00-General/SciCatArchiverGUI) +and manually coppied. + +An issue in 2.2.0 and earlier prevents the GUI from running on RHEL 8. This was +fixed with a manual wrapper script which produces an error on RHEL 8. + +# TODO + +- [ ] The post_prep section of the build script should be removed following + fixing [#55](https://github.com/paulscherrerinstitute/scicat-cli/issues/55) +- [ ] SciCat should be downloaded and installed in the build script + diff --git a/Tools/datacatalog/build b/Tools/datacatalog/build index 77e2ff3..f039f9e 100755 --- a/Tools/datacatalog/build +++ b/Tools/datacatalog/build @@ -1,32 +1,32 @@ #!/usr/bin/env modbuild pbuild::add_to_group 'Tools' +pbuild::set_download_url https://github.com/paulscherrerinstitute/scicat-cli/releases/download/v${V_PKG}/scicat-cli_.${V_PKG}_Linux_x86_64.tar.gz -pbuild::prep() { - : +pbuild::post_prep() { + # PModules 1.0.0 fails on tar bundles without top-level directories. This + # tries to work around this. It could be removed if the cli release process + # changes (https://github.com/paulscherrerinstitute/scicat-cli/issues/55) + if [[ ! -f "${SRC_DIR}/datasetIngestor" ]]; then + local file="$PMODULES_DISTFILESDIR/scicat-cli_.${V_PKG}_Linux_x86_64.tar.gz" + tar --directory="${SRC_DIR}" -xv --strip-components 0 -f "${file}" + fi } pbuild::configure() { - : + : } pbuild::compile() { - : + : } pbuild::install() { - mkdir -p "$PREFIX/bin" + mkdir -p "$PREFIX/bin" - /usr/bin/curl -o "$PREFIX/bin/datasetIngestor" https://intranet.psi.ch/pub/Daas/WebHome/datasetIngestor - chmod +x "$PREFIX/bin/datasetIngestor" + cp $SRC_DIR/dataset{Ingestor,Retriever,Archiver} "$PREFIX/bin" - /usr/bin/curl -o "$PREFIX/bin/datasetRetriever" https://intranet.psi.ch/pub/Daas/WebHome/datasetRetriever - chmod +x "$PREFIX/bin/datasetRetriever" - - /usr/bin/curl -o "$PREFIX/bin/datasetArchiver" https://intranet.psi.ch/pub/Daas/WebHome/datasetArchiver - chmod +x "$PREFIX/bin/datasetArchiver" - - # Hardcoded; could be made version-specific in the future if needed - ln -s "${PMODULES_ROOT}/Programming/anaconda/2019.07/conda/envs/scicat_client-0.1.0/bin/scicat_client" "$PREFIX/bin/scicat_client" + # Hardcoded; could be made version-specific in the future if needed + ln -s "${PMODULES_ROOT}/Programming/anaconda/2019.07/conda/envs/scicat_client-0.1.0/bin/scicat_client" "$PREFIX/bin/scicat_client" } diff --git a/Tools/datacatalog/files/variants.Linux b/Tools/datacatalog/files/variants.Linux index bd3c881..03713ef 100644 --- a/Tools/datacatalog/files/variants.Linux +++ b/Tools/datacatalog/files/variants.Linux @@ -1,7 +1,9 @@ -datacatalog/1.1.10 stable -datacatalog/1.1.9 removed -datacatalog/1.1.15 removed datacatalog/1.1.3 removed datacatalog/1.1.4 removed datacatalog/1.1.7 removed datacatalog/1.1.8 removed +datacatalog/1.1.9 removed +datacatalog/1.1.15 removed +datacatalog/1.1.10 deprecated +datacatalog/1.1.11 deprecated +datacatalog/2.2.0 stable diff --git a/Tools/datacatalog/modulefile b/Tools/datacatalog/modulefile index fb6329c..d52cf13 100644 --- a/Tools/datacatalog/modulefile +++ b/Tools/datacatalog/modulefile @@ -1,11 +1,16 @@ #%Module1.0 module-whatis "SciCat datacatalog related tools" -module-url "https://melanie.gitpages.psi.ch/SciCatPages/" -module-license "GPL-V3" -module-maintainer "Stephan Egli " +module-url "https://scicatproject.github.io/documentation/Ingestor/ingestManual.html" +module-license "BSD 3" +module-maintainer "Spencer Bliven " module-help " Data catalog ingest and retrieve tools. -" +Source code for the command line tools (datasetIngestor and datasetRetreiver) +is available at https://github.com/paulscherrerinstitute/scicat-cli. Source +code for the SciCat GUI is available from PSI at +https://git.psi.ch/MELANIE/rollout + +" From 7bb0fc99596dd4cdb6001e521f7d7c2784888fd6 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Tue, 21 May 2024 17:34:24 +0200 Subject: [PATCH 070/158] Marking old versions as deprecated These can be removed after some time. They don't work anyways. --- Tools/datacatalog/files/variants.Linux | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Tools/datacatalog/files/variants.Linux b/Tools/datacatalog/files/variants.Linux index 03713ef..4b06b63 100644 --- a/Tools/datacatalog/files/variants.Linux +++ b/Tools/datacatalog/files/variants.Linux @@ -1,8 +1,8 @@ datacatalog/1.1.3 removed datacatalog/1.1.4 removed -datacatalog/1.1.7 removed -datacatalog/1.1.8 removed -datacatalog/1.1.9 removed +datacatalog/1.1.7 deprecated +datacatalog/1.1.8 deprecated +datacatalog/1.1.9 deprecated datacatalog/1.1.15 removed datacatalog/1.1.10 deprecated datacatalog/1.1.11 deprecated From 18e0912f98dc805f60abc73e8979fff8f98d36b9 Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Fri, 24 May 2024 11:54:22 +0200 Subject: [PATCH 071/158] add tomodrgn --- EM/tomodrgn/README.md | 13 +++++++++++++ EM/tomodrgn/build | 34 ++++++++++++++++++++++++++++++++++ EM/tomodrgn/environment.yaml | 18 ++++++++++++++++++ EM/tomodrgn/files/config.yaml | 11 +++++++++++ EM/tomodrgn/modulefile | 34 ++++++++++++++++++++++++++++++++++ 5 files changed, 110 insertions(+) create mode 100644 EM/tomodrgn/README.md create mode 100755 EM/tomodrgn/build create mode 100644 EM/tomodrgn/environment.yaml create mode 100644 EM/tomodrgn/files/config.yaml create mode 100644 EM/tomodrgn/modulefile diff --git a/EM/tomodrgn/README.md b/EM/tomodrgn/README.md new file mode 100644 index 0000000..f4d5526 --- /dev/null +++ b/EM/tomodrgn/README.md @@ -0,0 +1,13 @@ + Installation remarks for Tomodrgn: + +1.) function in tomodrgn/analysis.py is not valid with matplotlib v3.8 anymore, this is why the function is substituted in the build script: +sed -i 's/cbar.draw_all/cbar._draw_all/' tomodrgn/analysis.py + +2.) the tomodrgn quicktest script can be exectued by : +python /opt/psi/EM/tomodrgn/0.2.2/tomodrgn/testing/quicktest.py +REMARK: This file was changed in order to provide the argument --datadir /opt/psi/EM/tomodrgn/0.2.2/tomodrgn/testing/, otherwise it will look for the "data" folder in the current working dir. + +3.) quicktest is run without the two arguments: --num-workers (dafault =0) and --prefetch-factor (default should be None, but is actually 2), which throws an error,was fixed by changing the default of --prefetch-factor to None in the file /opt/psi/EM/tomodrgn/0.2.2/miniconda/envs/tomodrgn_0.2.2/lib/python3.9/site-packages/tomodrgn/commands/train_vae.py + + + diff --git a/EM/tomodrgn/build b/EM/tomodrgn/build new file mode 100755 index 0000000..aec16fa --- /dev/null +++ b/EM/tomodrgn/build @@ -0,0 +1,34 @@ +#!/usr/bin/env modbuild + + +pbuild::configure() { + #MINICONDA INSTALL + mkdir -p "$PREFIX/miniconda" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" + + + #CREATE ENV , make sure to source the "correct" conda.sh + "$PREFIX/miniconda/condabin/conda" env create --name "tomodrgn_$V" -f "$BUILDBLOCK_DIR/environment.yaml" + source "$PREFIX/miniconda/etc/profile.d/conda.sh" + conda activate "tomodrgn_$V" + + #CP SOURCE CODE + mkdir "$PREFIX/tomodrgn" + cd "$PREFIX/tomodrgn" + cp -r "$SRC_DIR"/* . + #FIX MATPLOTLIB VERSION issue + sed -i 's/cbar.draw_all/cbar._draw_all/' tomodrgn/analysis.py + #INSTALL IN ENV + pip install . + +} + +#DO NOTHING +pbuild::compile(){ + : +} + +pbuild::install(){ + : +} diff --git a/EM/tomodrgn/environment.yaml b/EM/tomodrgn/environment.yaml new file mode 100644 index 0000000..1ed6b23 --- /dev/null +++ b/EM/tomodrgn/environment.yaml @@ -0,0 +1,18 @@ +channels: + - pytorch + - conda-forge + - defaults +dependencies: + - pytorch-gpu>=1.11.0 + - cudatoolkit>=11.0 + - pandas + - seaborn + - scikit-learn + - umap-learn + - ipython_genutils + - notebook + - pip + - pip: + - ipyvolume>=0.6.0 + - pythreejs>=2.4.2 + diff --git a/EM/tomodrgn/files/config.yaml b/EM/tomodrgn/files/config.yaml new file mode 100644 index 0000000..273ff2e --- /dev/null +++ b/EM/tomodrgn/files/config.yaml @@ -0,0 +1,11 @@ +format: 1 +tomodrgn: + deaults: + group: EM + overlay: base + relstage: unstable + urls: + - url: https://github.com/bpowell122/tomodrgn/archive/refs/tags/v${V_PKG}.tar.gz + name: tomodrgn-${V_PKG}.tar.gz + versions: + 0.2.2: diff --git a/EM/tomodrgn/modulefile b/EM/tomodrgn/modulefile new file mode 100644 index 0000000..4871b84 --- /dev/null +++ b/EM/tomodrgn/modulefile @@ -0,0 +1,34 @@ +#%Module1.0 + +module-whatis "TomoDRGN - analyzing structural heterogeneity in cryo-electron sub-tomograms" +module-url "https://github.com/bpowell122/tomodrgn" +module-license "-" +module-maintainer "Greta Assmann " + +module-help "https://github.com/bpowell122/tomodrgn" + + +# Check for supported shell types +set shelltype [module-info shelltype] +switch -- $shelltype { + "sh" { + puts stdout "source \"\${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n" + } + default { + puts stderr "Shells of type '$shelltype' are NOT supported!" + } +} + + +switch [module-info mode] { + "load" { + # Relies on the anaconda module being loaded since we need to update the path + puts stdout "conda activate $P_$V;\n" + } + "unload" - + "remove" { + puts stdout "conda deactivate;\n" + } +} + + From 51070a669015838a083b550274fb9e22ef07e832 Mon Sep 17 00:00:00 2001 From: usov_i Date: Tue, 28 May 2024 12:04:49 +0200 Subject: [PATCH 072/158] Update README.md --- Programming/matlab/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Programming/matlab/README.md b/Programming/matlab/README.md index 48166e5..b84005e 100644 --- a/Programming/matlab/README.md +++ b/Programming/matlab/README.md @@ -1,3 +1,3 @@ Installation guidelines: -https://gitlab.psi.ch/Pmodules/buildblocks/wikis/Matlab \ No newline at end of file +https://gitlab.psi.ch/Pmodules/buildblocks/wikis/matlab/2024a \ No newline at end of file From c2c925856cc409d4fcec99229eb63ed2ad6c414c Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Mon, 3 Jun 2024 10:42:46 +0200 Subject: [PATCH 073/158] Release datacatalog 2.2.1 Features: - SciCat GUI works on RHEL8 - Updates download URL and untar procedure --- Tools/datacatalog/README.md | 7 +++---- Tools/datacatalog/build | 12 +----------- Tools/datacatalog/files/variants.Linux | 1 + 3 files changed, 5 insertions(+), 15 deletions(-) diff --git a/Tools/datacatalog/README.md b/Tools/datacatalog/README.md index 7df942a..1ab8cc7 100644 --- a/Tools/datacatalog/README.md +++ b/Tools/datacatalog/README.md @@ -6,7 +6,7 @@ This module provides tools to interface with the Data Catalog (discovery.psi.ch) ## Version Numbers -Prior to version 2, each command had it's own version. The pmodule version +Prior to version 2, each command had its own version. The pmodule version roughly tracked the datasetIngestor version. However, some pmodules were updated manually with more recent binaries, so in general there is no way to check the versions contained in older pmodules other than running each command @@ -42,7 +42,6 @@ fixed with a manual wrapper script which produces an error on RHEL 8. # TODO -- [ ] The post_prep section of the build script should be removed following - fixing [#55](https://github.com/paulscherrerinstitute/scicat-cli/issues/55) -- [ ] SciCat should be downloaded and installed in the build script +- [ ] SciCat should be downloaded and installed in the build script. (This is + planned after the GUI is migrated to github and CI/CD implemented.) diff --git a/Tools/datacatalog/build b/Tools/datacatalog/build index f039f9e..d3a7ddb 100755 --- a/Tools/datacatalog/build +++ b/Tools/datacatalog/build @@ -1,17 +1,7 @@ #!/usr/bin/env modbuild pbuild::add_to_group 'Tools' -pbuild::set_download_url https://github.com/paulscherrerinstitute/scicat-cli/releases/download/v${V_PKG}/scicat-cli_.${V_PKG}_Linux_x86_64.tar.gz - -pbuild::post_prep() { - # PModules 1.0.0 fails on tar bundles without top-level directories. This - # tries to work around this. It could be removed if the cli release process - # changes (https://github.com/paulscherrerinstitute/scicat-cli/issues/55) - if [[ ! -f "${SRC_DIR}/datasetIngestor" ]]; then - local file="$PMODULES_DISTFILESDIR/scicat-cli_.${V_PKG}_Linux_x86_64.tar.gz" - tar --directory="${SRC_DIR}" -xv --strip-components 0 -f "${file}" - fi -} +pbuild::set_download_url https://github.com/paulscherrerinstitute/scicat-cli/releases/download/v${V_PKG}/scicat-cli_v${V_PKG}_Linux_x86_64.tar.gz pbuild::configure() { : diff --git a/Tools/datacatalog/files/variants.Linux b/Tools/datacatalog/files/variants.Linux index 4b06b63..36cd865 100644 --- a/Tools/datacatalog/files/variants.Linux +++ b/Tools/datacatalog/files/variants.Linux @@ -7,3 +7,4 @@ datacatalog/1.1.15 removed datacatalog/1.1.10 deprecated datacatalog/1.1.11 deprecated datacatalog/2.2.0 stable +datacatalog/2.2.1 stable From 6a28c61c089fcb50dc03d9836bc71c1c3f669f3e Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Wed, 24 Jul 2024 11:51:17 +0200 Subject: [PATCH 074/158] add cryocare module --- EM/cryocare/README.md | 11 +++++++++++ EM/cryocare/build | 23 +++++++++++++++++++++++ EM/cryocare/environment.yaml | 10 ++++++++++ EM/cryocare/files/config.yaml | 8 ++++++++ EM/cryocare/modulefile | 34 ++++++++++++++++++++++++++++++++++ 5 files changed, 86 insertions(+) create mode 100644 EM/cryocare/README.md create mode 100755 EM/cryocare/build create mode 100644 EM/cryocare/environment.yaml create mode 100644 EM/cryocare/files/config.yaml create mode 100644 EM/cryocare/modulefile diff --git a/EM/cryocare/README.md b/EM/cryocare/README.md new file mode 100644 index 0000000..8570033 --- /dev/null +++ b/EM/cryocare/README.md @@ -0,0 +1,11 @@ + Installation remarks for cryocare: + + - pip installation from https://pypi.org/project/cryoCARE/, (see environment.yaml) + - creation of conda env with miniconda + +Usage with Relion: module does not need to be activated , BUT : +- executables need to be provided in the relion GUI +- the modulefile in RELION needs to add the cryocare bin to the LD_LIBRARY_PATH, otherwise the libraries will not be found + + + diff --git a/EM/cryocare/build b/EM/cryocare/build new file mode 100755 index 0000000..d3169b1 --- /dev/null +++ b/EM/cryocare/build @@ -0,0 +1,23 @@ +#!/usr/bin/env modbuild + + +pbuild::configure() { + #MINICONDA INSTALL + mkdir -p "$PREFIX/miniconda" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" + + + #CREATE ENV , make sure to source the "correct" conda.sh + "$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml" + +} + +#DO NOTHING +pbuild::compile(){ + : +} + +pbuild::install(){ + : +} diff --git a/EM/cryocare/environment.yaml b/EM/cryocare/environment.yaml new file mode 100644 index 0000000..06b66c2 --- /dev/null +++ b/EM/cryocare/environment.yaml @@ -0,0 +1,10 @@ +channels: + - conda-forge + - defaults +dependencies: + - python=3.8 + - cudatoolkit=11.0 + - cudnn=8.0 + - pip: + - tensorflow==2.4 + - cryoCARE diff --git a/EM/cryocare/files/config.yaml b/EM/cryocare/files/config.yaml new file mode 100644 index 0000000..5efcd34 --- /dev/null +++ b/EM/cryocare/files/config.yaml @@ -0,0 +1,8 @@ +format: 1 +cryocare: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 0.3.0: diff --git a/EM/cryocare/modulefile b/EM/cryocare/modulefile new file mode 100644 index 0000000..2c0f37a --- /dev/null +++ b/EM/cryocare/modulefile @@ -0,0 +1,34 @@ +#%Module1.0 + +module-whatis "Cryocare - Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data" +module-url "https://github.com/juglab/cryoCARE_T2T" +module-license "BSD 2-Clause Simplified License" +module-maintainer "Greta Assmann " + +module-help "https://arxiv.org/abs/1810.05420" + + +# Check for supported shell types +set shelltype [module-info shelltype] +switch -- $shelltype { + "sh" { + puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n" + } + default { + puts stderr "Shells of type '$shelltype' are NOT supported!" + } +} + + +switch [module-info mode] { + "load" { + # Relies on the anaconda module being loaded since we need to update the path + puts stdout "conda activate ${P}_${V};\n" + } + "unload" - + "remove" { + puts stdout "conda deactivate;\n" + } +} + + From 78e59c22b5c977acd936181aa9841bf5d9af799b Mon Sep 17 00:00:00 2001 From: talamo_i Date: Tue, 20 Aug 2024 14:27:19 +0200 Subject: [PATCH 075/158] Resolve "openmpi 4.1.6 without libfabric" --- Compiler/openmpi/build | 17 ----- Compiler/openmpi/build-xml | 100 ----------------------------- Compiler/openmpi/files/config.yaml | 10 +++ 3 files changed, 10 insertions(+), 117 deletions(-) delete mode 100755 Compiler/openmpi/build-xml diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index c66ef35..31bf3b5 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -1,17 +1,7 @@ #!/usr/bin/env modbuild -# pbuild::set_download_url \ - # "http://www.open-mpi.org/software/ompi/v${V_MAJOR}.${V_MINOR}/downloads/openmpi-${V_PKG}.tar.bz2" - -pbuild::set_download_url \ - "https://download.open-mpi.org/release/open-mpi/v${V_MAJOR}.${V_MINOR}/openmpi-${V_PKG}.tar.bz2" - -pbuild::set_sha256sum "openmpi-3.1.2.tar.bz2:c654ed847f34a278c52a15c98add40402b4a90f0c540779f1ae6c489af8a76c5" - -pbuild::add_to_group 'Compiler' pbuild::install_docfiles 'AUTHORS' 'LICENSE' 'NEWS' 'README' - pbuild::pre_configure() { pbuild::add_configure_args "--prefix=${PREFIX}" pbuild::add_configure_args "--enable-mpi-cxx" @@ -58,13 +48,6 @@ pbuild::pre_configure() { pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" fi - if [[ -v NVHPC_VERSION ]]; then - pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" - pbuild::add_configure_args "CFLAGS=-fPIC -DPIC" - pbuild::add_configure_args "CXXFLAGS=-fPIC -DPIC" - pbuild::add_configure_args "FCFLAGS=-Mstandard -fPIC -DPIC" - fi - if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6; then pbuild::add_configure_args "--with-gpfs=/usr/lpp/mmfs" pbuild::add_configure_args "--with-pmi" diff --git a/Compiler/openmpi/build-xml b/Compiler/openmpi/build-xml deleted file mode 100755 index 31bf3b5..0000000 --- a/Compiler/openmpi/build-xml +++ /dev/null @@ -1,100 +0,0 @@ -#!/usr/bin/env modbuild - -pbuild::install_docfiles 'AUTHORS' 'LICENSE' 'NEWS' 'README' - -pbuild::pre_configure() { - pbuild::add_configure_args "--prefix=${PREFIX}" - pbuild::add_configure_args "--enable-mpi-cxx" - pbuild::add_configure_args "--enable-mpi-cxx-seek" - pbuild::add_configure_args "--enable-orterun-prefix-by-default" - pbuild::add_configure_args "--enable-shared" - pbuild::add_configure_args "--enable-static" - pbuild::add_configure_args "--with-slurm=yes" - - if [[ -v CUDA_VERSION ]]; then - pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" - fi - - if [[ -v HWLOC_VERSION ]]; then - unset HWLOC_VERSION - pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" - else - pbuild::add_configure_args "--with-hwloc=internal" - fi - - if [[ -v LIBEVENT_VERSION ]]; then - pbuild::add_configure_args "--with-libevent=${LIBEVENT_PREFIX}" - fi - - if [[ -v PMIX_VERSION ]]; then - unset PMIX_VERSION - pbuild::add_configure_args "--with-pmix=${PMIX_PREFIX}" - fi - - if [[ -v LIBFABRIC_VERSION ]]; then - pbuild::add_configure_args "--with-ofi=${LIBFABRIC_PREFIX}" - fi - - if [[ -v UCX_VERSION ]]; then - pbuild::add_configure_args "--with-ucx=${UCX_PREFIX}" - fi - - if [[ -v INTEL_VERSION ]]; then - pbuild::add_configure_args "CC=icc" - pbuild::add_configure_args "CXX=icpc" - pbuild::add_configure_args "FC=ifort" - pbuild::add_configure_args "F90=ifort" - pbuild::add_configure_args "F77=ifort" - pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" - fi - - if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6; then - pbuild::add_configure_args "--with-gpfs=/usr/lpp/mmfs" - pbuild::add_configure_args "--with-pmi" - # pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/" - - if pbuild::use_flag "libpmix"; then - pbuild::add_configure_args "--enable-install-libpmix" - fi - fi - - local version - (( version = (${V_MAJOR} * 100 + ${V_MINOR}) * 100 + V_PATCHLVL )) - if (( V_MAJOR < 4 )); then - pbuild::add_configure_args "--enable-mpi-f90" - pbuild::add_configure_args "--enable-mpi-profile" - pbuild::add_configure_args "--enable-smp-locks" - elif (( V_MAJOR >= 4 )); then - pbuild::add_configure_args "--enable-mpi-fortran" - pbuild::add_configure_args "--without-verbs" - fi - -} - -pbuild::post_install() { - if ! pbuild::use_flag slurm && ! pbuild::use_flag dgx && ! pbuild::use_flag merlin6; then - mkdir -p "${PREFIX}/lib/fallback" - local -r binary=$(ls "${PREFIX}"/lib/libmpi.so.*.*.*) - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuc[mpst].so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuct_ib.so.0' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libnuma.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libibverbs.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/librdmacm.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so' - fi - - if [[ -v CUDA_VERSION ]]; then - echo "opal_warn_on_missing_libcuda = 0" >> ${PREFIX}/etc/openmpi-mca-params.conf - fi - - for FILE in $(find $PREFIX -type f \( ! -name "*.a" -and ! -name "*.mod" \) -exec grep -IL . "{}" \;) - do - OLD_RPATH=$(objdump -a -x $FILE | grep RPATH | awk '{print $2}') - NEW_RPATH=$(echo $OLD_RPATH | sed 's/:\/usr\/lib64:/:/g') - if [[ "${OLD_RPATH}" != "${NEW_RPATH}" ]]; then - patchelf --force-rpath --set-rpath "${NEW_RPATH}" "${FILE}" - fi - done -} diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index ce0e73d..a15cd1b 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -52,8 +52,18 @@ openmpi: openmpi-4.1.3.tar.bz2: 3d81d04c54efb55d3871a465ffb098d8d72c1f48ff1cbaf2580eb058567c0a3b openmpi-4.1.4.tar.bz2: 92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d openmpi-4.1.5.tar.bz2: a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3 + openmpi-4.1.6.tar.bz2: f740994485516deb63b5311af122c265179f5328a0d857a567b85db00b11e415 versions: + 4.1.6: + variants: + - systems: [merlin-*, ra-*] + suffix: _slurm + group_deps: + compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} + build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] + runtime_deps: [cuda/12.1.1] + 4.1.4: variants: - systems: [merlin-*, ra-*] From c4f4291c949f74675334c70fa62eb6ba5ce52d2d Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Mon, 2 Sep 2024 16:25:54 +0200 Subject: [PATCH 076/158] gcc: new versions added --- Programming/gcc/build | 70 ++-------------- Programming/gcc/files/config.yaml | 132 ++++++++++++++++++++++++++++++ 2 files changed, 140 insertions(+), 62 deletions(-) create mode 100644 Programming/gcc/files/config.yaml diff --git a/Programming/gcc/build b/Programming/gcc/build index 4497b6c..6cd3a30 100755 --- a/Programming/gcc/build +++ b/Programming/gcc/build @@ -1,68 +1,14 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://ftp.gnu.org/gnu/gcc/$P-$V/$P-$V.tar.gz" - -pbuild::add_to_group 'Programming' -pbuild::install_docfiles 'COPYING' 'COPYING.LIB' 'COPYING.RUNTIME' 'COPYING3' 'COPYING3.LIB' 'NEWS' 'README' - -#pbuild::pre_prep_Darwin() { -# if (( V_MAJOR == 8 )); then -# pbuild::add_patch "files/headers-10.14.4-fix.patch" +#pbuild::pre_prep() { +# if (( V_MAJOR == 10 && V_MINOR == 2 )); then +# pbuild::add_patch "files/gcc-10.2.0-cpp-__has_include.patch" # fi #} -pbuild::post_prep_Darwin() { - if (( V_MAJOR == 8 )); then - local -r OS_REL=$(uname -r) - local -r patch_fname="${BUILDBLOCK_DIR}/8/headers-10.14.4-fix.patch" - patch -p1 < <(sed "s/darwin18.5/${OS,,}${OS_REL%.*}/" ${patch_fname}) - fi -} - -pbuild::pre_prep() { - if (( V_MAJOR == 4 && V_MINOR <= 8 )) || \ - (( V_MAJOR == 4 && V_MINOR == 9 && V_PATCHLVL < 4)); then - pbuild::add_patch_Darwin "${V_MAJOR}/non-dead-strip.patch" - pbuild::add_patch_Darwin "${V_MAJOR}/configure-as.patch" - fi - if (( V_MAJOR == 5 )) || (( V_MAJOR == 6 )); then - pbuild::add_patch_Darwin "${V_MAJOR}/PR57438_avoiding_empty_function_bodies_and_trailing_labels.patch" - fi - if (( V_MAJOR == 10 && V_MINOR == 2 )); then - pbuild::add_patch "files/gcc-10.2.0-cpp-__has_include.patch" - fi -} - -pbuild::pre_configure() { - pbuild::add_configure_args "--with-gmp=${GMP_PREFIX}" - pbuild::add_configure_args "--with-mpfr=${MPFR_PREFIX}" - pbuild::add_configure_args "--with-mpc=${MPC_PREFIX}" - pbuild::add_configure_args "--enable-lto" - pbuild::add_configure_args "--disable-multilib" - pbuild::add_configure_args "--with-pkgversion='PSI Environment Module'" - pbuild::add_configure_args "--with-build-config=bootstrap-debug" -} - -pbuild::pre_configure_Linux() { - if (( V_MAJOR >= 8 )); then - pbuild::add_configure_args "--enable-languages=c,c++,objc,obj-c++,lto,fortran,go" - fi -} - -pbuild::pre_configure_Darwin() { - local -r prefix='/usr' - pbuild::add_configure_args "--enable-languages=c,c++,objc,obj-c++,lto,fortran" - pbuild::add_configure_args "--with-as=${prefix}/bin/as" - pbuild::add_configure_args "--with-ld=${prefix}/bin/ld" - pbuild::add_configure_args "--with-ar=${prefix}/bin/ar" - pbuild::add_configure_args "AR_FOR_TARGET=${prefix}/bin/ar" - pbuild::add_configure_args "AS_FOR_TARGET=${prefix}/bin/as" - pbuild::add_configure_args "LD_FOR_TARGET=${prefix}/bin/ld" - pbuild::add_configure_args "NM_FOR_TARGET=${prefix}/bin/nm" - pbuild::add_configure_args "OBJDUMP_FOR_TARGET=${prefix}/bin/objdump" - pbuild::add_configure_args "RANLIB_FOR_TARGET=${prefix}/bin/ranlib" - pbuild::add_configure_args "STRIP_FOR_TARGET=${prefix}/bin/strip" - pbuild::add_configure_args "OTOOL=${prefix}/bin/otool" - pbuild::add_configure_args "OTOOL64=${prefix}/bin/otool" -} +#pbuild::pre_configure_Linux() { +# if (( V_MAJOR >= 8 )); then +# pbuild::add_configure_args "--enable-languages=c,c++,objc,obj-c++,lto,fortran,go" +# fi +#} diff --git a/Programming/gcc/files/config.yaml b/Programming/gcc/files/config.yaml new file mode 100644 index 0000000..9ea5a50 --- /dev/null +++ b/Programming/gcc/files/config.yaml @@ -0,0 +1,132 @@ +--- +format: 1 +gcc: + defaults: + group: Programming + relstage: stable + docfiles: + - COPYING + - COPYING.LIB + - COPYING.RUNTIME + - COPYING3 + - COPYING3.LIB + - NEWS + - README + configure_args: + - --with-gmp=${GMP_PREFIX} + - --with-mpfr=${MPFR_PREFIX} + - --with-mpc=${MPC_PREFIX} + - --enable-lto + - --disable-multilib + - --with-pkgversion=PSI Environment Module + - --with-build-config=bootstrap-debug + urls: + - url: https://ftp.gnu.org/gnu/gcc/$P-$V/$P-$V.tar.gz + + shasums: + gcc-14.2.0.tar.gz: 3a2b10cab86e32358fdac871546d57e2700e9bdb5875ef33fff5b601265b9e32 + gcc-13.3.0.tar.gz: 3a2b10cab86e32358fdac871546d57e2700e9bdb5875ef33fff5b601265b9e32 + gcc-13.1.0.tar.gz: bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2 + gcc-12.4.0.tar.gz: 5a30de2be740062bb3ddd3fd13c9b1bb4584d8f85616d33f23a713439d714148 + gcc-12.3.0.tar.gz: 11275aa7bb34cd8ab101d01b341015499f8d9466342a2574ece93f954d92273b + gcc-12.1.0.tar.gz: e88a004a14697bbbaba311f38a938c716d9a652fd151aaaa4cf1b5b99b90e2de + gcc-11.4.0.tar.gz: af828619dd1970734dda3cfb792ea3f2cba61b5a00170ba8bce4910749d73c07 + gcc-11.3.0.tar.gz: 98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed + gcc-11.2.0.tar.gz: f0837f1bf8244a5cc23bd96ff6366712a791cfae01df8e25b137698aca26efc1 + gcc-10.4.0.tar.gz: ab1974017834430de27fd803ade4389602a7d6ca1362496c57bef384b2a4cb07 + gcc-10.3.0.tar.gz: 8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16 + gcc-10.2.0.tar.gz: 27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d + gcc-10.1.0.tar.gz: 954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900 + gcc-9.5.0.tar.gz: 15b34072105272a3eb37f6927409f7ce9aa0dd1498efebc35f851d6e6f029a4d + gcc-9.3.0.tar.gz: 5258a9b6afe9463c2e56b9e8355b1a4bee125ca828b8078f910303bc2ef91fa6 + gcc-9.2.0.tar.gz: a931a750d6feadacbeecb321d73925cd5ebb6dfa7eff0802984af3aef63759f4 + gcc-9.1.0.tar.gz: be303f7a8292982a35381489f5a9178603cbe9a4715ee4fa4a815d6bcd2b658d + gcc-8.5.0.tar.gz: 6e6e0628573d2185727a2dd83211d04a2b2748e4a262099099b9c8064634c9ee + gcc-8.4.0.tar.gz: 41e8b145832fc0b2b34c798ed25fb54a881b0cee4cd581b77c7dc92722c116a8 + gcc-8.3.0.tar.gz: ea71adc1c3d86330874b8df19611424b143308f0d6612d542472600532c96d2d + gcc-8.2.0.tar.gz: 1b0f36be1045ff58cbb9c83743835367b860810f17f0195a4e093458b372020f + gcc-8.1.0.tar.gz: af300723841062db6ae24e38e61aaf4fbf3f6e5d9fd3bf60ebbdbf95db4e9f09 + gcc-7.5.0.tar.gz: 4f518f18cfb694ad7975064e99e200fe98af13603b47e67e801ba9580e50a07f + gcc-7.4.0.tar.gz: cb8df68237b0bea3307217697ad749a0a0565584da259e8a944ef6cfc4dc4d3d + gcc-7.3.0.tar.gz: fa06e455ca198ddc11ea4ddf2a394cf7cfb66aa7e0ab98cc1184189f1d405870 + gcc-7.2.0.tar.gz: 0153a003d3b433459336a91610cca2995ee0fb3d71131bd72555f2231a6efcfc + gcc-7.1.0.tar.gz: 3c187ef42e4cf657eec0ed641aac7f7e46261bcb1cea31b72dcf2dedddbbdea5 + gcc-6.5.0.tar.gz: 4eed92b3c24af2e774de94e96993aadbf6761cdf7a0345e59eb826d20a9ebf73 + gcc-6.4.0.tar.gz: 4715f02413f8a91d02d967521c084990c99ce1a671b8a450a80fbd4245f4b728 + gcc-6.3.0.tar.gz: 02f9302a559fa2251595ca0bc1e937219eff2995a3802d7b31676fec2402beb4 + gcc-6.2.0.tar.gz: ba8c49e54f1b3e04434d6261e5718ed843d1ba3e54a070740913acfbd815e577 + gcc-6.1.0.tar.gz: 724a61d190f27d5028791587149c6a6d6a312d6659a61636be5be86b6e809b59 + gcc-5.5.0.tar.gz: 3aabce75d6dd206876eced17504b28d47a724c2e430dbd2de176beb948708983 + gcc-5.4.0.tar.gz: 37089e80c3f2e9a0663d7ccc51c2a6c7dbbf3275bc1e4ed1ed3b1460cd5b3030 + gcc-5.3.0.tar.gz: b7f5f56bd7db6f4fcaa95511dbf69fc596115b976b5352c06531c2fc95ece2f4 + gcc-5.2.0.tar.gz: 87f3f1b3deebee26b6b71068c37201541586647c1ee64a505b06fc4129d6376a + gcc-5.1.0.tar.gz: 335275817b5ed845fee787e75efd76a6e240bfabbe0a0c20a81a04777e204617 + gcc-4.9.4.tar.gz: 1680f92781b92cbdb57d7e4f647c650678c594154cb0d707fd9a994424a9860d + gcc-4.9.3.tar.gz: e6c63b40877bc756cc7cfe6ca98013eb15f02ec6c8c2cf68e24533ad1203aaba + gcc-4.9.2.tar.gz: 3e573826ec8b0d62d47821408fbc58721cd020df3e594cd492508de487a43b5e + gcc-4.9.1.tar.gz: 51c3be8eb5f029929f05117c15c77be2d2f4290eb3c3edbdb54a59a5cd58bf0f + gcc-4.9.0.tar.gz: f945544c12435a54f60a463c5aa16e458b82cbb374e26eafe56bb95dbc308ca1 + gcc-4.8.5.tar.gz: 1dbc5cd94c9947fe5dffd298e569de7f44c3cedbd428fceea59490d336d8295a + gcc-4.8.4.tar.gz: 655fe692ddd333c29c5a1418f50f63a42cdd9e9eb7ebdb7f621e33c4b8799e31 + gcc-4.8.3.tar.gz: 5a46edbee29b6fed9006c02899db7cb7eff5f2d5837678484e1ff7da3b4beb6f + gcc-4.8.2.tar.gz: 2ea77114344a06c45dd5791275311e91d306545aa5ec9db31d24174f6965e880 + gcc-4.7.4.tar.gz: ddbaa583c5d4e4f0928bf15d9f6b6c283349e16eedc47bde71e1b813f6f37819 + gcc-4.7.3.tar.gz: 34a273937eb63ee710784b65bcf9fb3cfcd79d02848f80c75f8254abd14c79c8 + gcc-4.6.4.tar.gz: 53de33db01815914b3905a7d2cefac1ecf24ad081b82d93e4f526d8e62ff736f + versions: + 14.2.0: + config: + relstage: unstable + build_requires: [gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] + configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] + variants: + - overlay: base + systems: [rhel.*] + - overlay: PSI + systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] + use_overlays: [PSI] + runtime_deps: [cray/23.12, PrgEnv-gnu/8.5.0] + + 13.3.0: + config: + relstage: unstable + build_requires: [gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] + configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] + variants: + - overlay: base + systems: [rhel.*] + - overlay: PSI + systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] + use_overlays: [PSI] + runtime_deps: [cray/23.12, PrgEnv-gnu/8.5.0] + + 13.2.0: + config: + relstage: unstable + build_requires: [gmp/6.3.0, mpfr/4.2.1, mpc/1.3.1-1] + configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] + + 12.4.0: + config: + relstage: unstable + build_requires: [gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] + configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] + variants: + - overlay: base + systems: [rhel.*] + - overlay: PSI + systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] + use_overlays: [PSI] + runtime_deps: [cray/23.12, PrgEnv-gnu/8.5.0] + + 12.3.0: + config: + relstage: stable + build_requires: [gmp/6.2.1, mpfr/4.2.0, mpc/1.3.1] + configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] + variants: + - overlay: PSI + systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] + use_overlays: [PSI] + runtime_deps: [cray/23.12, PrgEnv-gnu/8.5.0] + From 9b77d1339f40fb6a017b7c88e509490c0212e5fd Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 3 Sep 2024 11:28:21 +0200 Subject: [PATCH 077/158] gcc: YAML config for gmp, mpfr, mpc, gcc --- Libraries/gmp/build | 10 ------ Libraries/gmp/files/config.yaml | 37 +++++++++++++++++++++ Libraries/mpc/build | 9 ------ Libraries/mpc/files/config.yaml | 30 +++++++++++++++++ Libraries/mpfr/build | 10 ------ Libraries/mpfr/files/config.yaml | 35 ++++++++++++++++++++ Programming/gcc/files/config.yaml | 53 ++++--------------------------- 7 files changed, 108 insertions(+), 76 deletions(-) create mode 100644 Libraries/gmp/files/config.yaml create mode 100644 Libraries/mpc/files/config.yaml create mode 100644 Libraries/mpfr/files/config.yaml diff --git a/Libraries/gmp/build b/Libraries/gmp/build index 5f4ffcc..6e021f3 100755 --- a/Libraries/gmp/build +++ b/Libraries/gmp/build @@ -1,12 +1,2 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://gmplib.org/download/$P/$P-$V_PKG.tar.bz2" -pbuild::add_to_group 'Libraries' - -# use system gcc to compile -declare -rx CC=gcc -declare -rx CPP=/usr/bin/cpp - -pbuild::add_configure_args "--disable-shared" -pbuild::add_configure_args "--with-pic" - diff --git a/Libraries/gmp/files/config.yaml b/Libraries/gmp/files/config.yaml new file mode 100644 index 0000000..4af444c --- /dev/null +++ b/Libraries/gmp/files/config.yaml @@ -0,0 +1,37 @@ +format: 1 +gmp: + defaults: + group: Libraries + overlay: base + relstage: stable + configure_args: + - --disable-shared + - --with-pic + - CC=gcc + - CPP=/usr/bin/cpp + docfiles: [] + urls: + - url: https://gmplib.org/download/$P/$P-$V_PKG.tar.bz2 + shasums: + gmp-6.3.0.tar.bz2: ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb + gmp-6.2.1.tar.bz2: eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c + gmp-6.2.0.tar.bz2: f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea + gmp-6.1.2.tar.gz: 97904147e7216a58cf5870a810aa1347488fe714d710f53d42f72247be7b77f7 + gmp-6.1.2.tar.bz2: 5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2 + gmp-6.1.2.tar.bz2.sig: 7de6a71ccadc8e1d761713a9fce2ef67de2dcc8cbaee51d464d360df07f5e951 + gmp-6.1.2-1.tar.gz: 97904147e7216a58cf5870a810aa1347488fe714d710f53d42f72247be7b77f7 + gmp-6.1.2-1.tar.bz2: 97904147e7216a58cf5870a810aa1347488fe714d710f53d42f72247be7b77f7 + gmp-6.1.1.tar.lz: 2ac8d815c670bbfecc2e796b9bcd4869eecd31299868248b0b221bc64a2570b2 + gmp-6.1.1.tar.bz2: a8109865f2893f1373b0a8ed5ff7429de8db696fc451b1036bd7bdf95bbeffd6 + gmp-6.1.0.tar.bz2: 498449a994efeba527885c10405993427995d3f86b8768d8cdf8d9dd7c6b73e8 + gmp-6.0.0.tar.bz2: 7f8e9a804b9c6d07164cf754207be838ece1219425d64e28cfa3e70d5c759aaf + gmp-5.1.3.tar.bz2: 752079520b4690531171d0f4532e40f08600215feefede70b24fabdc6f1ab160 + gmp-5.1.1.tar.bz2: a0d4779f48b36519dfaceb5f987a7c76fcac223258bebea3bb2244310970afad + + versions: + 6.2.1;6.3.0: + + 5.1.1;6.0.0;6.1.0;6.1.1;6.1.2;6.1.2-1;6.2.0: + config: + relstage: deprecated + diff --git a/Libraries/mpc/build b/Libraries/mpc/build index 3257c64..6e021f3 100755 --- a/Libraries/mpc/build +++ b/Libraries/mpc/build @@ -1,11 +1,2 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "http://ftp.gnu.org/gnu/${P}/${P}-${V_PKG}.tar.gz" -pbuild::add_to_group 'Libraries' - -pbuild::pre_configure() { - pbuild::add_configure_args "--with-gmp=${GMP_PREFIX}" - pbuild::add_configure_args "--with-mpfr=${MPFR_PREFIX}" - pbuild::add_configure_args "--disable-shared" -} - diff --git a/Libraries/mpc/files/config.yaml b/Libraries/mpc/files/config.yaml new file mode 100644 index 0000000..aa6b00b --- /dev/null +++ b/Libraries/mpc/files/config.yaml @@ -0,0 +1,30 @@ +format: 1 +mpc: + defaults: + group: Libraries + overlay: base + relstage: stable + configure_args: + - --disable-shared + - --with-pic + - --with-gmp=${GMP_PREFIX} + - --with-mpfr=${MPFR_PREFIX} + docfiles: [] + urls: + - url: http://ftp.gnu.org/gnu/${P}/${P}-${V_PKG}.tar.gz + + shasums: + mpc-1.3.1.tar.gz: ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8 + mpc-1.2.1.tar.gz: 17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459 + mpc-1.1.0.tar.gz: 6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e + mpc-1.0.3.tar.gz: 617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3 + mpc-1.0.2.tar.gz: b561f54d8a479cee3bc891ee52735f18ff86712ba30f036f8b8537bae380c488 + mpc-1.0.1.tar.gz: ed5a815cfea525dc778df0cb37468b9c1b554aaf30d9328b1431ca705b7400ff + + versions: + 1.2.1;1.3.1-1: + + 1.0.{2,3};1.0.3-2;1.1.0-{1..4};1.3.1: + config: + relstage: deprecated + diff --git a/Libraries/mpfr/build b/Libraries/mpfr/build index 425992c..6e021f3 100755 --- a/Libraries/mpfr/build +++ b/Libraries/mpfr/build @@ -1,12 +1,2 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "http://www.mpfr.org/$P-${V_PKG}/$P-${V_PKG}.tar.xz" -pbuild::add_to_group 'Libraries' - -#module use 'Libraries' - -pbuild::pre_configure() { - pbuild::add_configure_args "--with-gmp=${GMP_PREFIX}" - pbuild::add_configure_args "--with-pic" - pbuild::add_configure_args "--disable-shared" -} diff --git a/Libraries/mpfr/files/config.yaml b/Libraries/mpfr/files/config.yaml new file mode 100644 index 0000000..2773a97 --- /dev/null +++ b/Libraries/mpfr/files/config.yaml @@ -0,0 +1,35 @@ +format: 1 +mpfr: + defaults: + group: Libraries + overlay: base + relstage: stable + configure_args: + - --disable-shared + - --with-pic + - --with-gmp=${GMP_PREFIX} + docfiles: [] + urls: + - url: http://www.mpfr.org/$P-${V_PKG}/$P-${V_PKG}.tar.xz + + shasums: + mpfr-4.2.1.tar.xz: 277807353a6726978996945af13e52829e3abd7a9a5b7fb2793894e18f1fcbb2 + mpfr-4.2.0.tar.xz: 06a378df13501248c1b2db5aa977a2c8126ae849a9d9b7be2546fb4a9c26d993 + mpfr-4.1.0.tar.xz: 0c98a3f1732ff6ca4ea690552079da9c597872d30e96ec28414ee23c95558a7f + mpfr-4.0.2.tar.xz: 1d3be708604eae0e42d578ba93b390c2a145f17743a744d8f3f8c2ad5855a38a + mpfr-4.0.2.tar.bz2: c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc + mpfr-4.0.1.tar.xz: 67874a60826303ee2fb6affc6dc0ddd3e749e9bfcb4c8655e3953d0458a6e16e + mpfr-4.0.0.tar.bz2: 6aa31fbf3bd1f9f95bcfa241590a9d11cb0f874e2bb93b99c9e2de8eaea6d5fd + mpfr-3.1.5.tar.bz2: ca498c1c7a74dd37a576f353312d1e68d490978de4395fa28f1cbd46a364e658 + mpfr-3.1.4.tar.gz: 0d4de7e1476f79d24c38d5bc04a06fcc9a1bb9cf35fd654ceada29af03ad1844 + mpfr-3.1.3.tar.bz2: f63bb459157cacd223caac545cb816bcdb5a0de28b809e7748b82e9eb89b0afd + mpfr-3.1.2.tar.bz2: 79c73f60af010a30a5c27a955a1d2d01ba095b72537dab0ecaad57f5a7bb1b6b + mpfr-3.1.1.tar.bz2: 7b66c3f13dc8385f08264c805853f3e1a8eedab8071d582f3e661971c9acd5fd + + versions: + 4.1.0;4.2.0;4.2.1: + + 3.1.{2..5};4.0.{0..1};4.0.1-1;4.0.2;4.0.2-{1..2}: + config: + relstage: deprecated + diff --git a/Programming/gcc/files/config.yaml b/Programming/gcc/files/config.yaml index 9ea5a50..b6db02f 100644 --- a/Programming/gcc/files/config.yaml +++ b/Programming/gcc/files/config.yaml @@ -73,60 +73,19 @@ gcc: gcc-4.7.4.tar.gz: ddbaa583c5d4e4f0928bf15d9f6b6c283349e16eedc47bde71e1b813f6f37819 gcc-4.7.3.tar.gz: 34a273937eb63ee710784b65bcf9fb3cfcd79d02848f80c75f8254abd14c79c8 gcc-4.6.4.tar.gz: 53de33db01815914b3905a7d2cefac1ecf24ad081b82d93e4f526d8e62ff736f + versions: - 14.2.0: - config: - relstage: unstable - build_requires: [gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] - configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] - variants: - - overlay: base - systems: [rhel.*] - - overlay: PSI - systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] - use_overlays: [PSI] - runtime_deps: [cray/23.12, PrgEnv-gnu/8.5.0] - - 13.3.0: - config: - relstage: unstable - build_requires: [gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] - configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] - variants: - - overlay: base - systems: [rhel.*] - - overlay: PSI - systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] - use_overlays: [PSI] - runtime_deps: [cray/23.12, PrgEnv-gnu/8.5.0] - - 13.2.0: - config: - relstage: unstable - build_requires: [gmp/6.3.0, mpfr/4.2.1, mpc/1.3.1-1] - configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] - - 12.4.0: - config: - relstage: unstable - build_requires: [gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] - configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] - variants: - - overlay: base - systems: [rhel.*] - - overlay: PSI - systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] - use_overlays: [PSI] - runtime_deps: [cray/23.12, PrgEnv-gnu/8.5.0] - - 12.3.0: + 12.4.0;12.3.0;13.2.0;13.3.0;14.2.0: config: relstage: stable - build_requires: [gmp/6.2.1, mpfr/4.2.0, mpc/1.3.1] + build_requires: [gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] variants: + - overlay: base + systems: [rhel.*] - overlay: PSI systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] use_overlays: [PSI] runtime_deps: [cray/23.12, PrgEnv-gnu/8.5.0] + From 0542111f2d13bd8e697c9dad0abc2398a02e15ca Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 3 Sep 2024 11:32:12 +0200 Subject: [PATCH 078/158] gcc: old config files removed --- Libraries/gmp/files/variants | 8 -------- Libraries/mpc/files/variants | 11 ----------- Libraries/mpfr/files/variants | 13 ------------- 3 files changed, 32 deletions(-) delete mode 100644 Libraries/gmp/files/variants delete mode 100644 Libraries/mpc/files/variants delete mode 100644 Libraries/mpfr/files/variants diff --git a/Libraries/gmp/files/variants b/Libraries/gmp/files/variants deleted file mode 100644 index 349dcfc..0000000 --- a/Libraries/gmp/files/variants +++ /dev/null @@ -1,8 +0,0 @@ -gmp/5.1.1 stable -gmp/6.0.0 stable -gmp/6.1.0 stable -gmp/6.1.1 stable -gmp/6.1.2 stable -gmp/6.1.2-1 stable -gmp/6.2.0 stable -gmp/6.2.1 stable diff --git a/Libraries/mpc/files/variants b/Libraries/mpc/files/variants deleted file mode 100644 index cd04296..0000000 --- a/Libraries/mpc/files/variants +++ /dev/null @@ -1,11 +0,0 @@ -mpc/1.0.2 stable b:gmp/5.1.1 b:mpfr/3.1.2 -mpc/1.0.3 stable b:gmp/6.1.0 b:mpfr/3.1.4 -mpc/1.0.3-1 stable b:gmp/6.1.1 b:mpfr/3.1.4 -mpc/1.0.3-2 stable b:gmp/6.1.2 b:mpfr/3.1.5 -mpc/1.1.0 stable b:gmp/6.1.2 b:mpfr/4.0.0 -mpc/1.1.0-1 stable b:gmp/6.1.2 b:mpfr/4.0.1 -mpc/1.1.0-2 stable b:gmp/6.1.2-1 b:mpfr/4.0.1-1 -mpc/1.1.0-3 stable b:gmp/6.1.2-1 b:mpfr/4.0.2 -mpc/1.1.0-4 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 -mpc/1.2.1 stable b:gmp/6.2.1 b:mpfr/4.1.0 -mpc/1.3.1 stable b:gmp/6.2.1 b:mpfr/4.2.0 diff --git a/Libraries/mpfr/files/variants b/Libraries/mpfr/files/variants deleted file mode 100644 index 6f88c53..0000000 --- a/Libraries/mpfr/files/variants +++ /dev/null @@ -1,13 +0,0 @@ -mpfr/3.1.2 stable b:gmp/5.1.1 -mpfr/3.1.3 stable b:gmp/6.0.0 -mpfr/3.1.4 stable b:gmp/6.1.0 -mpfr/3.1.4-1 stable b:gmp/6.1.1 -mpfr/3.1.5 stable b:gmp/6.1.2 -mpfr/4.0.0 stable b:gmp/6.1.2 -mpfr/4.0.1 stable b:gmp/6.1.2 -mpfr/4.0.1-1 stable b:gmp/6.1.2-1 -mpfr/4.0.2 stable b:gmp/6.1.2-1 -mpfr/4.0.2-1 stable b:gmp/6.2.0 -mpfr/4.0.2-2 stable b:gmp/6.2.0 -mpfr/4.1.0 stable b:gmp/6.2.1 -mpfr/4.2.0 stable b:gmp/6.2.1 From 76ccc68c856c4252ea3fa09ffead5fa00feb9b52 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 3 Sep 2024 17:26:12 +0200 Subject: [PATCH 079/158] gcc: cleanup and YAML config --- Programming/gcc/build | 12 - Programming/gcc/files/config.yaml | 263 +++++++++++++++++- .../files/gcc-10.2.0-cpp-__has_include.patch | 40 --- Programming/gcc/files/variants.macos10.14 | 22 -- Programming/gcc/files/variants.rhel6 | 50 ---- Programming/gcc/files/variants.yaml | 39 --- 6 files changed, 258 insertions(+), 168 deletions(-) delete mode 100644 Programming/gcc/files/gcc-10.2.0-cpp-__has_include.patch delete mode 100644 Programming/gcc/files/variants.macos10.14 delete mode 100644 Programming/gcc/files/variants.rhel6 delete mode 100644 Programming/gcc/files/variants.yaml diff --git a/Programming/gcc/build b/Programming/gcc/build index 6cd3a30..6e021f3 100755 --- a/Programming/gcc/build +++ b/Programming/gcc/build @@ -1,14 +1,2 @@ #!/usr/bin/env modbuild -#pbuild::pre_prep() { -# if (( V_MAJOR == 10 && V_MINOR == 2 )); then -# pbuild::add_patch "files/gcc-10.2.0-cpp-__has_include.patch" -# fi -#} - - -#pbuild::pre_configure_Linux() { -# if (( V_MAJOR >= 8 )); then -# pbuild::add_configure_args "--enable-languages=c,c++,objc,obj-c++,lto,fortran,go" -# fi -#} diff --git a/Programming/gcc/files/config.yaml b/Programming/gcc/files/config.yaml index b6db02f..360df85 100644 --- a/Programming/gcc/files/config.yaml +++ b/Programming/gcc/files/config.yaml @@ -20,6 +20,7 @@ gcc: - --disable-multilib - --with-pkgversion=PSI Environment Module - --with-build-config=bootstrap-debug + - --enable-languages=c,c++,objc,obj-c++,lto,fortran,go' urls: - url: https://ftp.gnu.org/gnu/gcc/$P-$V/$P-$V.tar.gz @@ -75,17 +76,269 @@ gcc: gcc-4.6.4.tar.gz: 53de33db01815914b3905a7d2cefac1ecf24ad081b82d93e4f526d8e62ff736f versions: - 12.4.0;12.3.0;13.2.0;13.3.0;14.2.0: + 12.3.0;12.4.0;13.2.0;13.3.0;14.2.0: config: relstage: stable - build_requires: [gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] - configure_args+: ['--enable-languages=c,c++,objc,obj-c++,lto,fortran,go'] + build_requires: [gcc/10.4.0, gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] variants: - overlay: base systems: [rhel.*] - overlay: PSI systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] - use_overlays: [PSI] - runtime_deps: [cray/23.12, PrgEnv-gnu/8.5.0] + - overlay: base + systems: [rhel.*] + gcc/12.1.0: + config: + relstage: deprecated + build_requires: [gcc/11.3.0, gmp/6.2.1, mpfr/4.1.0, mpc/1.2.1] + variants: + - overlay: base + systems: [rhel.*] + 11.4.0: + config: + restage: stable + build_requires: [gcc/10.3.0, gmp/6.2.1, mpfr/4.2.0, mpc/1.3.1] + variants: + - overlay: base + systems: [rhel.*] + + 11.3.0: + config: + restage: stable + build_requires: [gcc/10.3.0, gmp/6.2.1, mpfr/4.1.0, mpc/1.2.1] + variants: + - overlay: base + systems: [rhel.*] + + 11.2.0: + config: + restage: deprecated + build_requires: [gcc/10.3.0, gmp/6.2.1, mpfr/4.1.0, mpc/1.2.1] + variants: + - overlay: base + systems: [rhel.*] + + 10.4.0: + config: + restage: stable + build_requires: [gmp/6.2.1, mpfr/4.1.0, mpc/1.2.1] + variants: + - overlay: base + systems: [rhel.*] + + 10.3.0: + config: + restage: stable + build_requires: [gmp/6.2.1, mpfr/4.1.0, mpc/1.2.1] + variants: + - overlay: base + systems: [rhel.*] + + 10.1.0;10.2.0: + config: + restage: deprecated + build_requires: [gmp/6.2.0, mpfr/4.0.2-1, mpc/1.1.0-4] + variants: + - overlay: base + systems: [rhel.*] + + 9.3.0: + config: + restage: stable + build_requires: [gmp/6.2.0, mpfr/4.0.2-1, mpc/1.1.0-4] + variants: + - overlay: base + systems: [rhel.*] + + 9.2.0: + config: + restage: deprecated + build_requires: [gmp/6.1.2-1, mpfr/4.0.2, mpc/1.1.0-3, isl/0.21] + variants: + - overlay: base + systems: [rhel.*] + + 9.1.0: + config: + restage: deprecated + build_requires: [gmp/6.1.2-1, mpfr/4.0.2, mpc/1.1.0-3] + variants: + - overlay: base + systems: [rhel.*] + + 8.4.0: + config: + restage: stable + build_requires: [gmp/6.2.0, mpfr/4.0.2-1, mpc/1.1.0-4] + variants: + - overlay: base + systems: [rhel.*] + + 8.3.0: + config: + restage: stable + build_requires: [gmp/6.1.2-1, mpfr/4.0.2, mpc/1.1.0-3] + variants: + - overlay: base + systems: [rhel.*] + + 8.1.0;8.2.0: + config: + restage: deprecated + build_requires: [gmp/6.1.2, mpfr/4.0.1, mpc/1.1.0] + variants: + - overlay: base + systems: [rhel.*] + + 7.5.0: + config: + restage: stable + build_requires: [gmp/6.2.0, mpfr/4.0.2-1, mpc/1.1.0-4] + variants: + - overlay: base + systems: [rhel.*] + + 7.4.0: + config: + restage: stable + build_requires: [gmp/6.1.2-1, mpfr/4.0.1-1, mpc/1.1.0-2] + variants: + - overlay: base + systems: [rhel.*] + + 7.3.0: + config: + restage: deprecated + build_requires: [gmp/6.1.2, mpfr/4.0.0, mpc/1.1.0] + variants: + - overlay: base + systems: [rhel.*] + + 7.2.0: + config: + restage: deprecated + build_requires: [gmp/6.1.2, mpfr/3.1.5, mpc/1.0.3-2] + variants: + - overlay: base + systems: [rhel.*] + + 7.1.0: + config: + restage: deprecated + build_requires: [gmp/6.1.2, mpfr/3.1.5, mpc/1.0.3] + variants: + - overlay: base + systems: [rhel.*] + + 6.5.0: + config: + restage: stable + build_requires: [gmp/6.1.2-1, mpfr/4.0.1-1, mpc/1.1.0-2] + variants: + - overlay: base + systems: [rhel.*] + + 6.4.0: + config: + restage: stable + build_requires: [gmp/6.1.2, mpfr/3.1.5, mpc/1.0.3] + variants: + - overlay: base + systems: [rhel.*] + + 6.3.0: + config: + restage: deprecated + build_requires: [gmp/6.1.2, mpfr/3.1.5, mpc/1.0.3-2] + variants: + - overlay: base + systems: [rhel.*] + + 6.2.0: + config: + restage: deprecated + build_requires: [gmp/6.1.1, mpfr/3.1.4, mpc/1.0.3] + variants: + - overlay: base + systems: [rhel.*] + + 6.1.0: + config: + restage: deprecated + build_requires: [gmp/6.1.0, mpfr/3.1.4, mpc/1.0.3] + variants: + - overlay: base + systems: [rhel.*] + + 5.5.0: + config: + restage: stable + build_requires: [gmp/6.1.2-1, mpfr/4.0.1, mpc/1.1.0-1] + variants: + - overlay: base + systems: [rhel.*] + + 5.4.0: + config: + restage: stable + build_requires: [gmp/6.1.2, mpfr/3.1.5, mpc/1.0.3-2] + variants: + - overlay: base + systems: [rhel.*] + + 5.2.0;5.3.0: + config: + restage: deprecated + build_requires: [gmp/6.0.0, mpfr/3.1.3, mpc/1.0.3] + variants: + - overlay: base + systems: [rhel.*] + + 5.1.0: + config: + restage: deprecated + build_requires: [gmp/5.1.1, mpfr/3.1.2, mpc/1.0.2] + variants: + - overlay: base + systems: [rhel.*] + + 4.9.4: + config: + restage: stable + build_requires: [gmp/6.1.1, mpfr/3.1.4, mpc/1.0.3] + variants: + - overlay: base + systems: [rhel.*] + + 4.9.3: + config: + restage: stable + build_requires: [gmp/6.1.0, mpfr/3.1.4, mpc/1.0.3] + variants: + - overlay: base + systems: [rhel.*] + + 4.9.0;4.9.2: + config: + restage: stable + build_requires: [gmp/5.1.1, mpfr/3.1.2, mpc/1.0.2] + variants: + - overlay: base + systems: [rhel.*] + 4.8.5: + config: + restage: stable + build_requires: [gmp/6.0.0, mpfr/3.1.3, mpc/1.0.3] + variants: + - overlay: base + systems: [rhel.*] + + 4.7.4;4.8.2;4.8.3;4.8.4: + config: + restage: stable + build_requires: [gmp/5.1.1, mpfr/3.1.2, mpc/1.0.2] + variants: + - overlay: base + systems: [rhel.*] diff --git a/Programming/gcc/files/gcc-10.2.0-cpp-__has_include.patch b/Programming/gcc/files/gcc-10.2.0-cpp-__has_include.patch deleted file mode 100644 index fa1fb8a..0000000 --- a/Programming/gcc/files/gcc-10.2.0-cpp-__has_include.patch +++ /dev/null @@ -1,40 +0,0 @@ -From b7bb13d4a5fcb593dc745ca3b6180f8babb54893 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Tiziano=20M=C3=BCller?= -Date: Mon, 27 Jul 2020 15:40:38 +0200 -Subject: [PATCH] libcpp: fix __has_include handling with traditional-cpp - -fixes #95889 ---- - libcpp/init.c | 3 +++ - libcpp/traditional.c | 4 +++- - 2 files changed, 6 insertions(+), 1 deletion(-) - -diff --git a/libcpp/init.c b/libcpp/init.c -index 0aac5acd0a35..b0cf71192589 100644 ---- a/libcpp/init.c -+++ b/libcpp/init.c -@@ -400,6 +400,9 @@ static const struct builtin_macro builtin_array[] = - B("__LINE__", BT_SPECLINE, true), - B("__INCLUDE_LEVEL__", BT_INCLUDE_LEVEL, true), - B("__COUNTER__", BT_COUNTER, true), -+ /* Make sure to update the list of built-in -+ function-like macros in traditional.c: -+ fun_like_macro() when adding more following */ - B("__has_attribute", BT_HAS_ATTRIBUTE, true), - B("__has_cpp_attribute", BT_HAS_ATTRIBUTE, true), - B("__has_builtin", BT_HAS_BUILTIN, true), -diff --git a/libcpp/traditional.c b/libcpp/traditional.c -index 77adb3bf595f..b087072c9b4c 100644 ---- a/libcpp/traditional.c -+++ b/libcpp/traditional.c -@@ -330,7 +330,9 @@ fun_like_macro (cpp_hashnode *node) - { - if (cpp_builtin_macro_p (node)) - return (node->value.builtin == BT_HAS_ATTRIBUTE -- || node->value.builtin == BT_HAS_BUILTIN); -+ || node->value.builtin == BT_HAS_BUILTIN -+ || node->value.builtin == BT_HAS_INCLUDE -+ || node->value.builtin == BT_HAS_INCLUDE_NEXT); - return node->value.macro->fun_like; - } - diff --git a/Programming/gcc/files/variants.macos10.14 b/Programming/gcc/files/variants.macos10.14 deleted file mode 100644 index 93046f5..0000000 --- a/Programming/gcc/files/variants.macos10.14 +++ /dev/null @@ -1,22 +0,0 @@ -gcc/4.7.4 stable b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.8.3 deprecated b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.8.4 deprecated b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.8.5 stable b:gmp/6.0.0 b:mpfr/3.1.3 b:mpc/1.0.3 -gcc/4.9.0 deprecated b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.9.2 deprecated b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.9.3 stable b:gmp/6.1.0 b:mpfr/3.1.4 b:mpc/1.0.3 -gcc/4.9.4 stable b:gmp/6.1.1 b:mpfr/3.1.4 b:mpc/1.0.3 - -gcc/5.1.0 deprecated b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/5.2.0 deprecated b:gmp/6.0.0 b:mpfr/3.1.3 b:mpc/1.0.3 -gcc/5.3.0 stable b:gmp/6.0.0 b:mpfr/3.1.3 b:mpc/1.0.3 -gcc/5.4.0 stable b:gmp/6.1.2 b:mpfr/3.1.5 b:mpc/1.0.3-2 - -gcc/6.1.0 stable b:gmp/6.1.0 b:mpfr/3.1.4 b:mpc/1.0.3 -gcc/6.2.0 stable b:gmp/6.1.1 b:mpfr/3.1.4 b:mpc/1.0.3 -gcc/6.3.0 stable b:gmp/6.1.2 b:mpfr/3.1.5 b:mpc/1.0.3-2 - -gcc/7.3.0 stable b:gmp/6.1.2 b:mpfr/4.0.0 b:mpc/1.1.0 - -gcc/8.3.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.2 b:mpc/1.1.0-3 - diff --git a/Programming/gcc/files/variants.rhel6 b/Programming/gcc/files/variants.rhel6 deleted file mode 100644 index 71f29c9..0000000 --- a/Programming/gcc/files/variants.rhel6 +++ /dev/null @@ -1,50 +0,0 @@ -gcc/4.7.4 stable b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.8.2 stable b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.8.3 stable b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.8.4 stable b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.8.5 stable b:gmp/6.0.0 b:mpfr/3.1.3 b:mpc/1.0.3 -gcc/4.9.0 deprecated b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.9.2 stable b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/4.9.3 stable b:gmp/6.1.0 b:mpfr/3.1.4 b:mpc/1.0.3 -gcc/4.9.4 stable b:gmp/6.1.1 b:mpfr/3.1.4 b:mpc/1.0.3 - -gcc/5.1.0 deprecated b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 -gcc/5.2.0 deprecated b:gmp/6.0.0 b:mpfr/3.1.3 b:mpc/1.0.3 -gcc/5.3.0 stable b:gmp/6.0.0 b:mpfr/3.1.3 b:mpc/1.0.3 -gcc/5.4.0 stable b:gmp/6.1.2 b:mpfr/3.1.5 b:mpc/1.0.3-2 -gcc/5.5.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.1 b:mpc/1.1.0-1 - -gcc/6.1.0 stable b:gmp/6.1.0 b:mpfr/3.1.4 b:mpc/1.0.3 -gcc/6.2.0 stable b:gmp/6.1.1 b:mpfr/3.1.4 b:mpc/1.0.3 -gcc/6.3.0 stable b:gmp/6.1.2 b:mpfr/3.1.5 b:mpc/1.0.3-2 -gcc/6.4.0 stable b:gmp/6.1.2 b:mpfr/3.1.5 b:mpc/1.0.3 -gcc/6.5.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.1-1 b:mpc/1.1.0-2 - -gcc/7.1.0 stable b:gmp/6.1.2 b:mpfr/3.1.5 b:mpc/1.0.3 -gcc/7.2.0 stable b:gmp/6.1.2 b:mpfr/3.1.5 b:mpc/1.0.3-2 -gcc/7.3.0 stable b:gmp/6.1.2 b:mpfr/4.0.0 b:mpc/1.1.0 -gcc/7.4.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.1-1 b:mpc/1.1.0-2 -gcc/7.5.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4 - -gcc/8.1.0 stable b:gmp/6.1.2 b:mpfr/4.0.1 b:mpc/1.1.0 -gcc/8.2.0 stable b:gmp/6.1.2 b:mpfr/4.0.1 b:mpc/1.1.0 -gcc/8.3.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.2 b:mpc/1.1.0-3 -gcc/8.4.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4 - -gcc/9.1.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.2 b:mpc/1.1.0-3 -gcc/9.2.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.2 b:mpc/1.1.0-3 b:isl/0.21 -gcc/9.3.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4 - -gcc/10.1.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4 -gcc/10.2.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4 -gcc/10.3.0 stable b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 -gcc/10.4.0 stable b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 - -gcc/11.2.0 stable b:gcc/10.3.0 b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 -gcc/11.3.0 stable b:gcc/10.3.0 b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 -gcc/11.4.0 stable b:gcc/10.3.0 b:gmp/6.2.1 b:mpfr/4.2.0 b:mpc/1.3.1 - -gcc/12.1.0 stable b:gcc/11.3.0 b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 -gcc/12.3.0 stable b:gcc/10.3.0 b:gmp/6.2.1 b:mpfr/4.2.0 b:mpc/1.3.1 - -gcc/13.1.0 stable b:gcc/10.4.0 b:gmp/6.2.1 b:mpfr/4.2.0 b:mpc/1.3.1 diff --git a/Programming/gcc/files/variants.yaml b/Programming/gcc/files/variants.yaml deleted file mode 100644 index 60b14e2..0000000 --- a/Programming/gcc/files/variants.yaml +++ /dev/null @@ -1,39 +0,0 @@ -overlay: base -relstage: stable -gcc/4.7.4: - - dependencies: b:gmp/5.1.1 b:mpfr/3.1.2 b:mpc/1.0.2 - -gcc/4.8.5: - - dependencies: b:gmp/6.0.0 b:mpfr/3.1.3 b:mpc/1.0.3 - -gcc/4.9.4: - - dependencies: b:gmp/6.1.1 b:mpfr/3.1.4 b:mpc/1.0.3 - -gcc/5.5.0: - - dependencies: b:gmp/6.1.2-1 b:mpfr/4.0.1 b:mpc/1.1.0-1 - -gcc/6.5.0: - - dependencies: b:gmp/6.1.2-1 b:mpfr/4.0.1-1 b:mpc/1.1.0-2 - -gcc/7.5.0: - - dependencies: b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4 - -gcc/8.4.0: - - dependencies: b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4 -gcc/8.5.0: - - dependencies: b:gcc/7.5.0 b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 - -gcc/9.3.0: - - dependencies: b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4 -gcc/9.5.0: - - dependencies: b:gcc/8.5.0 b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 -gcc/10.3.0: - - dependencies: b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 - -gcc/11.2.0: - - dependencies: b:gcc/10.3.0 b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 -gcc/11.3.0: - - dependencies: b:gcc/10.3.0 b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 - -gcc/12.1.0: - - dependencies: b:gcc/11.3.0 b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 From 913cabaf7ecc60cec8adc900d31499ee2dc818a8 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 3 Sep 2024 17:31:06 +0200 Subject: [PATCH 080/158] version key fixed --- Programming/gcc/files/config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Programming/gcc/files/config.yaml b/Programming/gcc/files/config.yaml index 360df85..03220ff 100644 --- a/Programming/gcc/files/config.yaml +++ b/Programming/gcc/files/config.yaml @@ -88,7 +88,7 @@ gcc: - overlay: base systems: [rhel.*] - gcc/12.1.0: + 12.1.0: config: relstage: deprecated build_requires: [gcc/11.3.0, gmp/6.2.1, mpfr/4.1.0, mpc/1.2.1] From d3e38214d226ccfc1c4498d57b2fd74e5a51ca88 Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Thu, 5 Sep 2024 09:55:03 +0200 Subject: [PATCH 081/158] update 1 --- Compiler/openmpi/build | 18 ++++++--- Compiler/openmpi/files/config.yaml | 8 ++++ Compiler/openmpi/files/variants.merlin7 | 50 +++++++++++++++++++++++++ Libraries/pmix/build | 20 ++-------- Libraries/pmix/build-xml | 24 ------------ Libraries/pmix/files/config.yaml | 10 ++++- 6 files changed, 81 insertions(+), 49 deletions(-) create mode 100644 Compiler/openmpi/files/variants.merlin7 delete mode 100755 Libraries/pmix/build-xml diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index 31bf3b5..ec78d72 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -4,8 +4,12 @@ pbuild::install_docfiles 'AUTHORS' 'LICENSE' 'NEWS' 'README' pbuild::pre_configure() { pbuild::add_configure_args "--prefix=${PREFIX}" - pbuild::add_configure_args "--enable-mpi-cxx" - pbuild::add_configure_args "--enable-mpi-cxx-seek" + + if (( V_MAJOR < 5 )); then + pbuild::add_configure_args "--enable-mpi-cxx" + pbuild::add_configure_args "--enable-mpi-cxx-seek" + fi + pbuild::add_configure_args "--enable-orterun-prefix-by-default" pbuild::add_configure_args "--enable-shared" pbuild::add_configure_args "--enable-static" @@ -48,10 +52,12 @@ pbuild::pre_configure() { pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" fi - if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6; then + if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6 || pbuild::use_flag merlin7; then pbuild::add_configure_args "--with-gpfs=/usr/lpp/mmfs" - pbuild::add_configure_args "--with-pmi" - # pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/" + if (( V_MAJOR < 5 )); then + pbuild::add_configure_args "--with-pmi" + # pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/" + fi if pbuild::use_flag "libpmix"; then pbuild::add_configure_args "--enable-install-libpmix" @@ -72,7 +78,7 @@ pbuild::pre_configure() { } pbuild::post_install() { - if ! pbuild::use_flag slurm && ! pbuild::use_flag dgx && ! pbuild::use_flag merlin6; then + if ! pbuild::use_flag slurm && ! pbuild::use_flag dgx && ! pbuild::use_flag merlin6 && ! pbuild::use_flag merlin7; then mkdir -p "${PREFIX}/lib/fallback" local -r binary=$(ls "${PREFIX}"/lib/libmpi.so.*.*.*) pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuc[mpst].so' diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index a15cd1b..d3f1759 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -55,6 +55,14 @@ openmpi: openmpi-4.1.6.tar.bz2: f740994485516deb63b5311af122c265179f5328a0d857a567b85db00b11e415 versions: + 5.0.5: + variants: + - systems: [login001*,login002*] + suffix: _merlin7 + group_deps: + compiler: {gcc: [12.3.0]} + build_requires: [pmix/4.2.4, ucx/1.15.1_slurm, hwloc/2.9.1, patchelf/0.14.5] + runtime_deps: [cuda/12.1.1] 4.1.6: variants: - systems: [merlin-*, ra-*] diff --git a/Compiler/openmpi/files/variants.merlin7 b/Compiler/openmpi/files/variants.merlin7 new file mode 100644 index 0000000..3b81657 --- /dev/null +++ b/Compiler/openmpi/files/variants.merlin7 @@ -0,0 +1,50 @@ +openmpi/3.1.4_merlin6 deprecated gcc/{7.4.0,8.3.0} + +openmpi/3.1.5_merlin6 deprecated gcc/{7.3.0,7.4.0,8.3.0,9.2.0} +openmpi/3.1.5_merlin6 deprecated intel/{15.2,17.4,18.4} + +openmpi/3.1.5-1_merlin6 deprecated gcc/{7.3.0,7.4.0,8.3.0,9.2.0} +openmpi/3.1.5-1_merlin6 deprecated intel/{15.2,17.4,18.4} + +openmpi/2.1.6_slurm deprecated gcc/{4.9.4,5.5.0,6.5.0,7.4.0,8.3.0,9.2.0} +openmpi/2.1.6_slurm deprecated intel/{15.2,17.4,18.4} + +openmpi/3.0.5_slurm deprecated gcc/{4.9.4,5.5.0,6.5.0,7.4.0,8.3.0,9.2.0} +openmpi/3.0.5_slurm deprecated intel/{15.2,17.4,18.4} + +openmpi/3.1.6_slurm deprecated gcc/{4.9.4,5.5.0,6.5.0} +openmpi/3.1.6_slurm stable gcc/{7.5.0,8.4.0,9.3.0} +openmpi/3.1.6_slurm deprecated intel/{15.2,17.4,18.4,20.1} +openmpi/3.1.6_slurm deprecated intel/20.4 cuda/11.1.0 + +openmpi/4.0.3_slurm deprecated gcc/{4.9.4,5.5.0,6.5.0,7.5.0,8.4.0,9.3.0} +openmpi/4.0.3_slurm deprecated intel/{15.2,17.4,18.4,20.1} + +openmpi/4.0.4_slurm deprecated gcc/{4.9.4,5.5.0,6.5.0,7.5.0,8.4.0,9.3.0} +openmpi/4.0.4_slurm deprecated intel/{15.2,17.4} +openmpi/4.0.4_slurm deprecated intel/{18.4,20.1} + +openmpi/4.0.5_slurm stable gcc/9.2.0 cuda/11.0.3 +openmpi/4.0.5_slurm stable gcc/{8.4.0,9.3.0} cuda/11.1.0 +openmpi/4.0.5_slurm stable intel/20.4 cuda/11.1.0 + +openmpi/4.0.5-1_slurm stable gcc/{8.4.0,9.3.0,10.2.0,10.3.0} cuda/11.2.2 b:ucx/1.10.0-1_slurm +openmpi/4.0.5-2_slurm stable gcc/10.2.0 cuda/11.3.0 b:ucx/1.11.0_slurm + +openmpi/4.0.7_slurm stable gcc/10.2.0 cuda/11.5.1 b:ucx/1.11.2-2_slurm +openmpi/4.0.7-1_slurm stable gcc/10.2.0 cuda/11.4.3 b:ucx/1.11.2-1_slurm + +openmpi/4.1.1_slurm unstable gcc/10.2.0 cuda/11.3.0 b:ucx/1.11.2_slurm +openmpi/4.1.1-1_slurm unstable gcc/10.2.0 cuda/11.3.0 b:ucx/1.10.0_slurm + +openmpi/4.1.3_slurm stable gcc/{9.3.0,10.3.0,11.2.0} cuda/11.5.1 b:ucx/1.12.1_slurm +openmpi/4.1.4_slurm stable gcc/10.4.0 cuda/11.5.1 b:ucx/1.12.1_slurm + +openmpi/4.1.5_slurm stable gcc/{9.5.0,10.4.0,11.4.0,12.3.0,13.1.0} b:cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 +openmpi/4.1.5_slurm unstable intelcc/22.2 b:cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 + +openmpi/4.0.5-1_dgx deprecated gcc/{8.4.0,9.3.0,10.2.0} cuda/11.2.2 b:ucx/1.10.0-1_dgx +openmpi/4.1.0-1_dgx deprecated gcc/10.2.0 cuda/11.2.2 b:ucx/1.10.0-1_dgx + + +openmpi/4.0.4_slurm_libpmix deprecated gcc/9.3.0 diff --git a/Libraries/pmix/build b/Libraries/pmix/build index a058988..1ebd0fd 100755 --- a/Libraries/pmix/build +++ b/Libraries/pmix/build @@ -1,29 +1,15 @@ #!/usr/bin/env modbuild -echo "https://github.com/openpmix/openpmix/releases/download/v${V_PKG}/$P-${V_PKG}.tar.gz" -pbuild::set_download_url "https://github.com/openpmix/openpmix/releases/download/v${V_PKG}/$P-${V_PKG}.tar.gz" - -pbuild::add_to_group 'Libraries' - -(( version = (${V_MAJOR} * 100 + ${V_MINOR}) * 100 + V_PATCHLVL )) -if (( V_MAJOR > 1 )); then - pbuild::install_docfiles AUTHORS README.md LICENSE NEWS VERSION -else - pbuild::install_docfiles README LICENSE NEWS VERSION -fi - -pbuild::compile_in_sourcetree - pbuild::pre_configure() { - if [[ -n "${HWLOC_PREFIX}" ]]; then + if [[ -v HWLOC_PREFIX ]]; then pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" fi - if [[ -n "${LIBEVENT_PREFIX}" ]]; then + if [[ -v LIBEVENT_PREFIX ]]; then pbuild::add_configure_args "--with-libevent=${LIBEVENT_PREFIX}" fi - if [[ -n "${INTEL_VERSION}" ]]; then + if [[ -v INTEL_VERSION ]]; then pbuild::add_configure_args "CC=icc" pbuild::add_configure_args "CXX=icpc" pbuild::add_configure_args "FC=ifort" diff --git a/Libraries/pmix/build-xml b/Libraries/pmix/build-xml deleted file mode 100755 index 1ebd0fd..0000000 --- a/Libraries/pmix/build-xml +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env modbuild - -pbuild::pre_configure() { - if [[ -v HWLOC_PREFIX ]]; then - pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" - fi - - if [[ -v LIBEVENT_PREFIX ]]; then - pbuild::add_configure_args "--with-libevent=${LIBEVENT_PREFIX}" - fi - - if [[ -v INTEL_VERSION ]]; then - pbuild::add_configure_args "CC=icc" - pbuild::add_configure_args "CXX=icpc" - pbuild::add_configure_args "FC=ifort" - pbuild::add_configure_args "F77=ifort" - pbuild::add_configure_args "F90=ifort" - # pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel" - fi - - # pbuild::add_configure_args "--enable-pmi-backward-compatibility" - pbuild::add_configure_args "--enable-shared" - pbuild::add_configure_args "--enable-static" -} diff --git a/Libraries/pmix/files/config.yaml b/Libraries/pmix/files/config.yaml index 4585449..87c3106 100644 --- a/Libraries/pmix/files/config.yaml +++ b/Libraries/pmix/files/config.yaml @@ -19,6 +19,7 @@ pmix: pmix-4.1.2.tar.gz: a7a6d5b322c261999ce0a6395c0ac7dc359c0ff61380ed4c6935430fb9f5f6e6 pmix-4.2.3.tar.gz: fd45e18e483e42089d4059df9753d9be3cfb68297a05981b1d937e09f7716d5a pmix-4.2.4.tar.gz: f1fe5fe817ac447ce8d3d88486a1c0d22227efd186e11062aa1f7b0f093089c6 + pmix-5.0.3.tar.gz: c98afa8ec5a2495b82fae5eff731c4fc6371e0b0 versions: 1.2.5: config: @@ -33,12 +34,12 @@ pmix: relstage: unstable 4.1.2: config: - relstage: unstable + relstage: stable runtime_deps: [libevent/2.1.12] build_requires: [hwloc/2.7.1] 4.2.3: config: - relstage: unstable + relstage: stable runtime_deps: [libevent/2.1.12] build_requires: [hwloc/2.9.1] 4.2.4: @@ -46,3 +47,8 @@ pmix: relstage: stable runtime_deps: [libevent/2.1.12] build_requires: [gcc/10.4.0, hwloc/2.9.1] + 5.0.3: + config: + relstate: unstable + runtime_deps: [libevent/2.1.12] + build_requires: [hwloc/2.11.1] From a4570581bbcbff9c85e2459935654127d7f1031b Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 5 Sep 2024 10:39:32 +0200 Subject: [PATCH 082/158] openmpi/pmix: build script and config updated for Alps --- Libraries/pmix/build | 32 ++++++++++++++------------------ Libraries/pmix/files/config.yaml | 18 +++++++++++++----- 2 files changed, 27 insertions(+), 23 deletions(-) diff --git a/Libraries/pmix/build b/Libraries/pmix/build index 1ebd0fd..952d750 100755 --- a/Libraries/pmix/build +++ b/Libraries/pmix/build @@ -1,24 +1,20 @@ #!/usr/bin/env modbuild pbuild::pre_configure() { - if [[ -v HWLOC_PREFIX ]]; then - pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" - fi + if [[ -v HWLOC_PREFIX ]]; then + pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" + fi - if [[ -v LIBEVENT_PREFIX ]]; then - pbuild::add_configure_args "--with-libevent=${LIBEVENT_PREFIX}" - fi + if [[ -v LIBEVENT_PREFIX ]]; then + pbuild::add_configure_args "--with-libevent=${LIBEVENT_PREFIX}" + fi - if [[ -v INTEL_VERSION ]]; then - pbuild::add_configure_args "CC=icc" - pbuild::add_configure_args "CXX=icpc" - pbuild::add_configure_args "FC=ifort" - pbuild::add_configure_args "F77=ifort" - pbuild::add_configure_args "F90=ifort" - # pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel" - fi - - # pbuild::add_configure_args "--enable-pmi-backward-compatibility" - pbuild::add_configure_args "--enable-shared" - pbuild::add_configure_args "--enable-static" + if [[ -v INTEL_VERSION ]]; then + pbuild::add_configure_args "CC=icc" + build::add_configure_args "CXX=icpc" + pbuild::add_configure_args "FC=ifort" + pbuild::add_configure_args "F77=ifort" + pbuild::add_configure_args "F90=ifort" + # pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel" + fi } diff --git a/Libraries/pmix/files/config.yaml b/Libraries/pmix/files/config.yaml index 87c3106..1a8cbfe 100644 --- a/Libraries/pmix/files/config.yaml +++ b/Libraries/pmix/files/config.yaml @@ -3,7 +3,10 @@ pmix: defaults: group: Libraries relstage: stable - compile_in_sourcetree: yes + compile_in_sourcetree: true + configure_args: + - --enable-shared + - --enable-static docfiles: - AUTHORS - README.md @@ -11,7 +14,7 @@ pmix: - NEWS - VERSION urls: - - url: "https://github.com/openpmix/openpmix/releases/download/v${V_PKG}/$P-${V_PKG}.tar.gz" + - url: https://github.com/openpmix/openpmix/releases/download/v${V_PKG}/$P-${V_PKG}.tar.gz shasums: pmix-1.2.5.tar.gz: d7337601c5b985743e6b6f79ec1a34dfc2aefbb2d04d40b2c0d5bd7100d268ed pmix-2.2.5.tar.gz: db24480fa5be080e1ddcb273098992b69f8f21e4cd6b8df1682e836b303a2a6f @@ -19,7 +22,7 @@ pmix: pmix-4.1.2.tar.gz: a7a6d5b322c261999ce0a6395c0ac7dc359c0ff61380ed4c6935430fb9f5f6e6 pmix-4.2.3.tar.gz: fd45e18e483e42089d4059df9753d9be3cfb68297a05981b1d937e09f7716d5a pmix-4.2.4.tar.gz: f1fe5fe817ac447ce8d3d88486a1c0d22227efd186e11062aa1f7b0f093089c6 - pmix-5.0.3.tar.gz: c98afa8ec5a2495b82fae5eff731c4fc6371e0b0 + pmix-5.0.3.tar.gz: d9b0b81ba45f58f44573796eb05858061ed7f47ea6b29af8058090023e35dfa9 versions: 1.2.5: config: @@ -49,6 +52,11 @@ pmix: build_requires: [gcc/10.4.0, hwloc/2.9.1] 5.0.3: config: - relstate: unstable + relstage: unstable runtime_deps: [libevent/2.1.12] - build_requires: [hwloc/2.11.1] + build_requires: [gcc/12.3.0, hwloc/2.11.1] + variants: + - systems: [.*.merlin7.psi.ch] + overlay: Alps + use_overlays: [PSI] + - systems: [rhel.*] From e9bb74476437a6247ec554f0d2bd820051f19fd4 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 5 Sep 2024 11:01:22 +0200 Subject: [PATCH 083/158] openmpi: add config for 4.1.6 for Alps --- Compiler/openmpi/build | 18 +++++++++--------- Compiler/openmpi/files/config.yaml | 23 ++++++++++++++++++++++- 2 files changed, 31 insertions(+), 10 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index 31bf3b5..4e5bb07 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -48,15 +48,15 @@ pbuild::pre_configure() { pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" fi - if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6; then - pbuild::add_configure_args "--with-gpfs=/usr/lpp/mmfs" - pbuild::add_configure_args "--with-pmi" - # pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/" - - if pbuild::use_flag "libpmix"; then - pbuild::add_configure_args "--enable-install-libpmix" - fi - fi +# if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6; then +# pbuild::add_configure_args "--with-gpfs=/usr/lpp/mmfs" +# pbuild::add_configure_args "--with-pmi" +# # pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/" +# +# if pbuild::use_flag "libpmix"; then +# pbuild::add_configure_args "--enable-install-libpmix" +# fi +# fi local version (( version = (${V_MAJOR} * 100 + ${V_MINOR}) * 100 + V_PATCHLVL )) diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index a15cd1b..8fc082c 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -57,12 +57,33 @@ openmpi: versions: 4.1.6: variants: - - systems: [merlin-*, ra-*] + - systems: [merlin-.*] suffix: _slurm + relstage: unstable + overlay: private + use_overlays: [private] + group_deps: + compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 12.4.0, 13.1.0]} + build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5] + runtime_deps: [cuda/12.1.1] + configure_args+: + - CFLAGS=-g -O0 + - LDFLAGS=-g + - --with-gpfs=/usr/lpp/mmfs + - --with-pmi=/usr + - systems: [ra-.*] + suffix: _ra group_deps: compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] runtime_deps: [cuda/12.1.1] + - systems: [.*.merlin7.psi.ch] + overlay: Alps + used_overlays: [PSI, Alps] + group_deps: + compiler: {gcc: [12.3.0]} + build_requires: [pmix/5.0.3, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] + runtime_deps: [cuda/12.1.1] 4.1.4: variants: From 4d5fd43427f435c8611ce5322cefd94d4cd407ff Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 6 Sep 2024 18:33:08 +0200 Subject: [PATCH 084/158] OpenBLAS: use YAML config file --- Compiler/OpenBLAS/build | 11 ----------- Compiler/OpenBLAS/build-yaml | 9 --------- Compiler/OpenBLAS/files/config.yaml | 21 ++++++++++++++++++++- 3 files changed, 20 insertions(+), 21 deletions(-) delete mode 100755 Compiler/OpenBLAS/build-yaml diff --git a/Compiler/OpenBLAS/build b/Compiler/OpenBLAS/build index 44020d4..6e021f3 100755 --- a/Compiler/OpenBLAS/build +++ b/Compiler/OpenBLAS/build @@ -1,13 +1,2 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "http://github.com/xianyi/$P/archive/v${V_PKG}.tar.gz" - -pbuild::add_to_group 'Compiler' -pbuild::install_docfiles 'LICENSE' 'README.md' -#pbuild::set_supported_compilers 'gcc' 'intel' 'clang-macos' - -pbuild::pre_configure() { - pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=Release" - pbuild::add_configure_args "-DDYNAMIC_ARCH=ON" -} - diff --git a/Compiler/OpenBLAS/build-yaml b/Compiler/OpenBLAS/build-yaml deleted file mode 100755 index 87289c3..0000000 --- a/Compiler/OpenBLAS/build-yaml +++ /dev/null @@ -1,9 +0,0 @@ -#!/usr/bin/env modbuild - -pbuild::install_docfiles 'LICENSE' 'README.md' - -pbuild::pre_configure() { - pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=Release" - pbuild::add_configure_args "-DDYNAMIC_ARCH=ON" -} - diff --git a/Compiler/OpenBLAS/files/config.yaml b/Compiler/OpenBLAS/files/config.yaml index 8cdf3f0..7d5db3f 100644 --- a/Compiler/OpenBLAS/files/config.yaml +++ b/Compiler/OpenBLAS/files/config.yaml @@ -10,6 +10,12 @@ OpenBLAS: urls: - url: http://github.com/xianyi/$P/archive/v${V_PKG}.tar.gz name: OpenBLAS-${V_PKG}.tar.gz + configure_args: + - -DCMAKE_BUILD_TYPE=Release + - -DDYNAMIC_ARCH=ON + docfiles: + - LICENSE + - README.md shasums: OpenBLAS-0.2.9.tar.gz: e899c70b8771896655765f5c64c00c990f8dd0fe569e96788d8c971a23ecb22a @@ -26,11 +32,24 @@ OpenBLAS: OpenBLAS-0.3.24.tar.gz: ceadc5065da97bd92404cac7254da66cc6eb192679cf1002098688978d4d5132 versions: + 0.3.28: + config: + group_deps: + compiler: + gcc: [12.3.0, 12.4.0, 13.3.0, 14.2.0] + build_requires: [cmake/3.23.2] + relstage: unstable + variants: + - systems: [rhel.*] + overlay: devel + - systems: [login.*.merlin7.psi.ch] + overlay: Alps + use_overlays: [PSI, Alps] 0.3.24: config: group_deps: compiler: - gcc: [12.3.0, 13.1.0] + gcc: [12.3.0, 13.1.0, 13.2.0] build_requires: [cmake/3.23.2] relstage: unstable overlay: devel From f184d5fef9e39b020ea324c2d85cf1ffae56ebe6 Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Thu, 5 Sep 2024 12:14:12 +0200 Subject: [PATCH 085/158] Cuda --- Compiler/openmpi/files/config.yaml | 8 +++++++- Programming/cuda/files/variants.rhel7 | 1 + 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index d836626..0667c0e 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -94,13 +94,19 @@ openmpi: - LDFLAGS=-g - --with-gpfs=/usr/lpp/mmfs - --with-pmi=/usr - - systems: [ra-.*] suffix: _ra group_deps: compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] runtime_deps: [cuda/12.1.1] + - systems: [.*.merlin7.psi.ch] + overlay: Alps + used_overlays: [PSI, Alps] + group_deps: + compiler: {gcc: [12.3.0]} + build_requires: [pmix/5.0.3, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] + runtime_deps: [cuda/12.1.1] - systems: [.*.merlin7.psi.ch] relstage: unstable diff --git a/Programming/cuda/files/variants.rhel7 b/Programming/cuda/files/variants.rhel7 index dc9872f..f9ac67e 100644 --- a/Programming/cuda/files/variants.rhel7 +++ b/Programming/cuda/files/variants.rhel7 @@ -13,3 +13,4 @@ cuda/11.4.3 stable cuda/11.5.1 stable cuda/11.8.0 stable cuda/12.1.1 stable +cuda/12.2.0 unstable From a477e63c9e6852c937692372c46bd7ba72dd04a3 Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Thu, 5 Sep 2024 16:39:28 +0200 Subject: [PATCH 086/158] Update openmpi and libevent --- Compiler/openmpi/build | 8 ++++++++ Libraries/libevent/build | 5 ----- Libraries/libevent/files/config.yaml | 30 ++++++++++++++++++++++++++++ 3 files changed, 38 insertions(+), 5 deletions(-) create mode 100644 Libraries/libevent/files/config.yaml diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index e96f066..ea15ce5 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -1,6 +1,7 @@ #!/usr/bin/env modbuild pbuild::pre_configure() { +<<<<<<< HEAD if (( V_MAJOR < 5 )); then pbuild::add_configure_args "--enable-mpi-cxx" pbuild::add_configure_args "--enable-mpi-cxx-seek" @@ -20,6 +21,13 @@ pbuild::pre_configure() { pbuild::add_configure_args "--enable-mpi-fortran" pbuild::add_configure_args "--without-verbs" fi +======= + pbuild::add_configure_args "--prefix=${PREFIX}" + + pbuild::add_configure_args "--enable-shared" + pbuild::add_configure_args "--enable-orterun-prefix-by-default" + pbuild::add_configure_args "--with-slurm=yes" +>>>>>>> a5c5629 (Update openmpi and libevent) if [[ -v CUDA_VERSION ]]; then pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" diff --git a/Libraries/libevent/build b/Libraries/libevent/build index 1239be0..6e021f3 100755 --- a/Libraries/libevent/build +++ b/Libraries/libevent/build @@ -1,7 +1,2 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://github.com/libevent/libevent/releases/download/release-$V-stable/$P-$V-stable.tar.gz" -pbuild::add_to_group 'Libraries' - -pbuild::install_docfiles 'LICENSE' - diff --git a/Libraries/libevent/files/config.yaml b/Libraries/libevent/files/config.yaml new file mode 100644 index 0000000..23af643 --- /dev/null +++ b/Libraries/libevent/files/config.yaml @@ -0,0 +1,30 @@ +format: 1 +libevent: + defaults: + group: Libraries + relstage: stable + configure_args: + - --enable-shared + - --enable-static + docfiles: + - LICENSE + urls: + - url: https://github.com/libevent/libevent/releases/download/release-$V-stable/$P-$V-stable.tar.gz + shasums: + libevent-2.1.8-stable.tar.gz: 965cc5a8bb46ce4199a47e9b2c9e1cae3b137e8356ffdad6d94d3b9069b71dc2 + libevent-2.1.12-stable.tar.gz: 92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb + versions: + 2.1.12: + config: + runtime_deps: [] + variants: + - systems: [.*.merlin7.psi.ch] + overlay: Alps + use_overlays: [PSI] + build_requires: [] + relstage: unstable + - systems: [rhel.*] + build_requires: [openssl/1.1.1k] + 2.1.8: + config: + build_requires: [openssl/1.0.2r] From 617b9752e9a9d85fca39f056b93631d813403fce Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Fri, 6 Sep 2024 14:54:14 +0200 Subject: [PATCH 087/158] Add older versions of pmix. Removed suffix for Alps Openmpi --- Libraries/pmix/files/config.yaml | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/Libraries/pmix/files/config.yaml b/Libraries/pmix/files/config.yaml index 1a8cbfe..062f675 100644 --- a/Libraries/pmix/files/config.yaml +++ b/Libraries/pmix/files/config.yaml @@ -18,10 +18,13 @@ pmix: shasums: pmix-1.2.5.tar.gz: d7337601c5b985743e6b6f79ec1a34dfc2aefbb2d04d40b2c0d5bd7100d268ed pmix-2.2.5.tar.gz: db24480fa5be080e1ddcb273098992b69f8f21e4cd6b8df1682e836b303a2a6f + pmix-2.2.5.tar.gz: db24480fa5be080e1ddcb273098992b69f8f21e4cd6b8df1682e836b303a2a6f pmix-3.2.3.tar.gz: 1325a1355d0794196bb47665053fdbc588f9183aa5385f3581b668427316306e + pmix-3.2.5.tar.gz: 61385a65b172bfbe8d5363c3cd8f7742cd81049ebb3d8acc0d25806935641584 pmix-4.1.2.tar.gz: a7a6d5b322c261999ce0a6395c0ac7dc359c0ff61380ed4c6935430fb9f5f6e6 pmix-4.2.3.tar.gz: fd45e18e483e42089d4059df9753d9be3cfb68297a05981b1d937e09f7716d5a pmix-4.2.4.tar.gz: f1fe5fe817ac447ce8d3d88486a1c0d22227efd186e11062aa1f7b0f093089c6 + pmix-4.2.9.tar.gz: 00ddb36fb81c31519972079a218c3cdd903510fc3910abaf4d484068fa29e884 pmix-5.0.3.tar.gz: d9b0b81ba45f58f44573796eb05858061ed7f47ea6b29af8058090023e35dfa9 versions: 1.2.5: @@ -35,6 +38,22 @@ pmix: 2.2.5;3.2.3: config: relstage: unstable + runtime_deps: [libevent/2.1.12] + build_requires: [gcc/12.3.0, hwloc/2.11.1] + variants: + - systems: [.*.merlin7.psi.ch] + overlay: Alps + use_overlays: [PSI] + - systems: [rhel.*] + 3.2.5: + config: + relstage: unstable + runtime_deps: [libevent/2.1.12] + build_requires: [gcc/12.3.0, hwloc/2.11.1] + variants: + - systems: [.*.merlin7.psi.ch] + overlay: Alps + use_overlays: [PSI] 4.1.2: config: relstage: stable @@ -50,6 +69,15 @@ pmix: relstage: stable runtime_deps: [libevent/2.1.12] build_requires: [gcc/10.4.0, hwloc/2.9.1] + 4.2.9: + config: + relstage: unstable + runtime_deps: [libevent/2.1.12] + build_requires: [gcc/12.3.0, hwloc/2.11.1] + variants: + - systems: [.*.merlin7.psi.ch] + overlay: Alps + use_overlays: [PSI] 5.0.3: config: relstage: unstable From 63b50624e7d65b658387dfb25546494a3d3779dd Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Tue, 10 Sep 2024 12:43:53 +0200 Subject: [PATCH 088/158] Enable static. Enable UCX --- Compiler/openmpi/build | 1 + Compiler/openmpi/files/config.yaml | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index ea15ce5..73e5a35 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -25,6 +25,7 @@ pbuild::pre_configure() { pbuild::add_configure_args "--prefix=${PREFIX}" pbuild::add_configure_args "--enable-shared" + pbuild::add_configure_args "--enable-static" pbuild::add_configure_args "--enable-orterun-prefix-by-default" pbuild::add_configure_args "--with-slurm=yes" >>>>>>> a5c5629 (Update openmpi and libevent) diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index 0667c0e..b68fc0c 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -68,8 +68,8 @@ openmpi: use_overlays: [PSI] group_deps: compiler: {gcc: [12.3.0]} - build_requires: [pmix/5.0.3, hwloc/2.11.1, patchelf/0.14.5] - # build_requires: [pmix/5.0.3, ucx/1.15.0_slurm, hwloc/2.9.1, patchelf/0.14.5] + # build_requires: [pmix/5.0.3, hwloc/2.11.1, patchelf/0.14.5] + build_requires: [pmix/5.0.3, ucx/1.15.0_slurm, hwloc/2.9.1, patchelf/0.14.5] runtime_deps: [cuda/12.2.0] configure_args+: - --with-ofi=/opt/cray/libfabric/1.15.2.0 From ed4c5cb0281682c2fc6ebc87e798170dab2b066b Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Tue, 10 Sep 2024 14:34:50 +0200 Subject: [PATCH 089/158] Remove UCX support for Alps --- Compiler/openmpi/files/config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index b68fc0c..0667c0e 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -68,8 +68,8 @@ openmpi: use_overlays: [PSI] group_deps: compiler: {gcc: [12.3.0]} - # build_requires: [pmix/5.0.3, hwloc/2.11.1, patchelf/0.14.5] - build_requires: [pmix/5.0.3, ucx/1.15.0_slurm, hwloc/2.9.1, patchelf/0.14.5] + build_requires: [pmix/5.0.3, hwloc/2.11.1, patchelf/0.14.5] + # build_requires: [pmix/5.0.3, ucx/1.15.0_slurm, hwloc/2.9.1, patchelf/0.14.5] runtime_deps: [cuda/12.2.0] configure_args+: - --with-ofi=/opt/cray/libfabric/1.15.2.0 From 41987dcbcc9f651b643552fa195749d088ba82cf Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Tue, 10 Sep 2024 16:48:26 +0200 Subject: [PATCH 090/158] Clean old code --- Compiler/openmpi/build | 9 --------- 1 file changed, 9 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index 73e5a35..e96f066 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -1,7 +1,6 @@ #!/usr/bin/env modbuild pbuild::pre_configure() { -<<<<<<< HEAD if (( V_MAJOR < 5 )); then pbuild::add_configure_args "--enable-mpi-cxx" pbuild::add_configure_args "--enable-mpi-cxx-seek" @@ -21,14 +20,6 @@ pbuild::pre_configure() { pbuild::add_configure_args "--enable-mpi-fortran" pbuild::add_configure_args "--without-verbs" fi -======= - pbuild::add_configure_args "--prefix=${PREFIX}" - - pbuild::add_configure_args "--enable-shared" - pbuild::add_configure_args "--enable-static" - pbuild::add_configure_args "--enable-orterun-prefix-by-default" - pbuild::add_configure_args "--with-slurm=yes" ->>>>>>> a5c5629 (Update openmpi and libevent) if [[ -v CUDA_VERSION ]]; then pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" From dbdc24cdb31705eb349bd193829e381f71af99c3 Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Tue, 10 Sep 2024 17:38:17 +0200 Subject: [PATCH 091/158] Fixes --- Compiler/openmpi/build | 5 ++--- Compiler/openmpi/files/config.yaml | 8 -------- 2 files changed, 2 insertions(+), 11 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index e96f066..d970862 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -104,9 +104,9 @@ pbuild::post_install() { if [[ -v CUDA_VERSION ]]; then echo "opal_warn_on_missing_libcuda = 0" >> ${PREFIX}/etc/openmpi-mca-params.conf fi +} -# for FILE in $(find $PREFIX -type f \( ! -name "*.a" -and ! -name "*.mod" \) -exec grep -IL . -"{}" \;) +# for FILE in $(find $PREFIX -type f \( ! -name "*.a" -and ! -name "*.mod" \) -exec grep -IL . "{}" \;) # do # OLD_RPATH=$(objdump -a -x $FILE | grep RPATH | awk '{print $2}') # NEW_RPATH=$(echo $OLD_RPATH | sed 's/:\/usr\/lib64:/:/g') @@ -114,4 +114,3 @@ pbuild::post_install() { # patchelf --force-rpath --set-rpath "${NEW_RPATH}" "${FILE}" # fi # done - diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index 0667c0e..0d9dfc8 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -100,14 +100,6 @@ openmpi: compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] runtime_deps: [cuda/12.1.1] - - systems: [.*.merlin7.psi.ch] - overlay: Alps - used_overlays: [PSI, Alps] - group_deps: - compiler: {gcc: [12.3.0]} - build_requires: [pmix/5.0.3, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] - runtime_deps: [cuda/12.1.1] - - systems: [.*.merlin7.psi.ch] relstage: unstable overlay: Alps From d9da946fff7b31f92aec048c65acb662e6a417fb Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Wed, 11 Sep 2024 11:41:07 +0200 Subject: [PATCH 092/158] Enable shared and static libraries --- Compiler/openmpi/build | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index d970862..a09afbd 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -1,6 +1,9 @@ #!/usr/bin/env modbuild pbuild::pre_configure() { + pbuild::add_configure_args "--enable-shared" + pbuild::add_configure_args "--enable-static" + if (( V_MAJOR < 5 )); then pbuild::add_configure_args "--enable-mpi-cxx" pbuild::add_configure_args "--enable-mpi-cxx-seek" From 2172928ee3aeff3b57486d8a2a2ed8852f1d5581 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Wed, 11 Sep 2024 17:06:18 +0200 Subject: [PATCH 093/158] openmpi: update build script and config --- Compiler/openmpi/build | 87 ++++++++++++++++++------------ Compiler/openmpi/files/config.yaml | 18 ++++--- 2 files changed, 65 insertions(+), 40 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index a09afbd..796fa90 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -7,11 +7,13 @@ pbuild::pre_configure() { if (( V_MAJOR < 5 )); then pbuild::add_configure_args "--enable-mpi-cxx" pbuild::add_configure_args "--enable-mpi-cxx-seek" - pbuild::add_configure_args "--with-pmi=/usr" - pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/slurmpmi" pbuild::add_configure_args "--enable-orterun-prefix-by-default" fi - if (( V_MAJOR >= 5 )); then + if (( V_MAJOR < 5 )) && pbuild::use_flag 'slurm'; then + pbuild::add_configure_args "--with-pmi=/usr" + pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/slurmpmi" +fi + if (( V_MAJOR >= 5 )); then pbuild::add_configure_args "--enable-prte-prefix-by-default" fi if (( V_MAJOR < 4 )); then @@ -24,43 +26,44 @@ pbuild::pre_configure() { pbuild::add_configure_args "--without-verbs" fi - if [[ -v CUDA_VERSION ]]; then + if [[ -v CUDA_VERSION ]]; then + std::info "Enabling CUDA ${CUDA_VERSION}." pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" fi if [[ -v HWLOC_VERSION ]]; then unset HWLOC_VERSION + std::info "Enabling external hwloc ${HWLOC_PREFIX}." pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" else pbuild::add_configure_args "--with-hwloc=internal" fi if [[ -v LIBEVENT_VERSION ]]; then + std::info "Enabling libevent ${LIBEVENT_VERSION}." pbuild::add_configure_args "--with-libevent=${LIBEVENT_PREFIX}" fi if [[ -v PMIX_VERSION ]]; then - std::info "Enabling PMIX ${PMIX_VERSION}" + std::info "Enabling PMIX ${PMIX_VERSION}." unset PMIX_VERSION pbuild::add_configure_args "--with-pmix=${PMIX_PREFIX}" fi - if [[ ! -v LIBFABRIC_VERSION ]]; then + if pbuild::use_flag merlin7 && [[ ! -v LIBFABRIC_VERSION ]]; then if pkg-config --exists libfabric; then std::info "Get LIBFABRIC_VERSION via pkg-config" LIBFABRIC_PREFIX=$(pkg-config --variable=prefix libfabric) LIBFABRIC_VERSION="$(LIBFABRIC_PREFIX##*/)" fi fi - std::info "LIBFABRIC_PREFIX: ${LIBFABRIC_PREFIX}" - std::info "LIBFABRIC_VERSION=: ${LIBFABRIC_VERSION}" if [[ -v LIBFABRIC_VERSION ]]; then - std::info "Enabling libfabric ${LIBFABRIC_VERSION}" + std::info "Enabling libfabric ${LIBFABRIC_VERSION}." pbuild::add_configure_args "--with-ofi=${LIBFABRIC_PREFIX}" fi if [[ -v UCX_VERSION ]]; then - std::info "Enabling UCX ${UCX_VERSION}" + std::info "Enabling UCX ${UCX_VERSION}." pbuild::add_configure_args "--with-ucx=${UCX_PREFIX}" fi @@ -73,9 +76,12 @@ pbuild::pre_configure() { pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" fi - if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6 || pbuild::use_flag merlin7; then - std::info "Enabling SLURM." - pbuild::add_configure_args "--with-slurm=yes" + if pbuild::use_flag slurm || \ + pbuild::use_flag dgx || \ + pbuild::use_flag merlin6 || \ + pbuild::use_flag merlin7; then + std::info "Enabling SLURM." + pbuild::add_configure_args "--with-slurm=yes" fi if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6; then std::info "Enabling GPFS." @@ -89,31 +95,44 @@ pbuild::pre_configure() { } pbuild::post_install_no_slurm() { - if ! pbuild::use_flag slurm && ! pbuild::use_flag dgx && ! pbuild::use_flag merlin6 && ! pbuild::use_flag merlin7; then - mkdir -p "${PREFIX}/lib/fallback" - local -r binary=$(ls "${PREFIX}"/lib/libmpi.so.*.*.*) - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuc[mpst].so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuct_ib.so.0' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libnuma.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libibverbs.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/librdmacm.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so' - pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so' + if ! pbuild::use_flag slurm && \ + ! pbuild::use_flag dgx && \ + ! pbuild::use_flag merlin6 && \ + ! pbuild::use_flag merlin7; then + mkdir -p "${PREFIX}/lib/fallback" + local -r binary=$(ls "${PREFIX}"/lib/libmpi.so.*.*.*) + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuc[mpst].so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuct_ib.so.0' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libnuma.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libibverbs.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/librdmacm.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so' + pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so' fi } pbuild::post_install() { if [[ -v CUDA_VERSION ]]; then - echo "opal_warn_on_missing_libcuda = 0" >> ${PREFIX}/etc/openmpi-mca-params.conf + echo "opal_warn_on_missing_libcuda = 0" >> ${PREFIX}/etc/openmpi-mca-params.conf fi -} -# for FILE in $(find $PREFIX -type f \( ! -name "*.a" -and ! -name "*.mod" \) -exec grep -IL . "{}" \;) -# do -# OLD_RPATH=$(objdump -a -x $FILE | grep RPATH | awk '{print $2}') -# NEW_RPATH=$(echo $OLD_RPATH | sed 's/:\/usr\/lib64:/:/g') -# if [[ "${OLD_RPATH}" != "${NEW_RPATH}" ]]; then -# patchelf --force-rpath --set-rpath "${NEW_RPATH}" "${FILE}" -# fi -# done + local old_rpath='' + local new_rpath='' + while read file; do + old_rpath=$(objdump -x "${file}" | awk '/RPATH|RUNPATH/ {print $2}') + new_rpath=$(echo "${old_rpath}" | sed 's/:\/usr\/lib64:/:/g') + if [[ "${old_rpath}" != "${new_rpath}" ]]; then + patchelf \ + --force-rpath \ + --set-rpath "${new_rpath}" \ + "${file}" + fi + done < <(find "{PREFIX}" -type f \( ! -name "*.a" -and ! -name "*.mod" \) \ + -exec grep -IL . "{}" \;) + +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index 0d9dfc8..2b21844 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -69,10 +69,9 @@ openmpi: group_deps: compiler: {gcc: [12.3.0]} build_requires: [pmix/5.0.3, hwloc/2.11.1, patchelf/0.14.5] - # build_requires: [pmix/5.0.3, ucx/1.15.0_slurm, hwloc/2.9.1, patchelf/0.14.5] runtime_deps: [cuda/12.2.0] configure_args+: - - --with-ofi=/opt/cray/libfabric/1.15.2.0 + - --with-ofi=${LIBFABRIC_PREFIX} - --enable-mpi1-compatibility - --with-cxi - --with-lustre @@ -86,20 +85,27 @@ openmpi: overlay: private use_overlays: [private] group_deps: - compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 12.4.0, 13.1.0]} - build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5] + compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 12.4.0, 13.2.0, 14.2.0]} + build_requires: + - pmix/4.2.4 + - ucx/1.14.1_slurm + - libfabric/1.18.0 + - hwloc/2.9.1 + - patchelf/0.14.5 runtime_deps: [cuda/12.1.1] configure_args+: - CFLAGS=-g -O0 - LDFLAGS=-g - --with-gpfs=/usr/lpp/mmfs - --with-pmi=/usr + - systems: [ra-.*] suffix: _ra group_deps: compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] runtime_deps: [cuda/12.1.1] + - systems: [.*.merlin7.psi.ch] relstage: unstable overlay: Alps @@ -108,11 +114,11 @@ openmpi: build_requires: [pmix/4.2.9, hwloc/2.11.1, patchelf/0.14.5] runtime_deps: [cuda/12.2.0] configure_args+: - - --with-ofi=/opt/cray/libfabric/1.15.2.0 + - --with-ofi=${LIBFABRIC_PREFIX} - --enable-mpi1-compatibility - --with-lustre use_overlays: [PSI, Alps] - use_flags: [merlin7] + use_flags: [merlin7, slurm] 4.1.4: variants: From c4bea947a4fe09d4ad9f1fd09e47d3298b1c87f6 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 12 Sep 2024 14:03:35 +0200 Subject: [PATCH 094/158] openmpi: error in build script fixed --- Compiler/openmpi/build | 15 +++++++++------ Compiler/openmpi/files/config.yaml | 3 +-- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index 796fa90..a8091f1 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -12,7 +12,7 @@ pbuild::pre_configure() { if (( V_MAJOR < 5 )) && pbuild::use_flag 'slurm'; then pbuild::add_configure_args "--with-pmi=/usr" pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/slurmpmi" -fi + fi if (( V_MAJOR >= 5 )); then pbuild::add_configure_args "--enable-prte-prefix-by-default" fi @@ -61,7 +61,7 @@ fi std::info "Enabling libfabric ${LIBFABRIC_VERSION}." pbuild::add_configure_args "--with-ofi=${LIBFABRIC_PREFIX}" fi - + if [[ -v UCX_VERSION ]]; then std::info "Enabling UCX ${UCX_VERSION}." pbuild::add_configure_args "--with-ucx=${UCX_PREFIX}" @@ -117,19 +117,22 @@ pbuild::post_install() { echo "opal_warn_on_missing_libcuda = 0" >> ${PREFIX}/etc/openmpi-mca-params.conf fi + local fname='' local old_rpath='' local new_rpath='' - while read file; do - old_rpath=$(objdump -x "${file}" | awk '/RPATH|RUNPATH/ {print $2}') + # remove '/usr/lib64' from RPATH/RUNPATH + while read fname; do + old_rpath=$(objdump -x "${fname}" | awk '/RPATH|RUNPATH/ {print $2}') new_rpath=$(echo "${old_rpath}" | sed 's/:\/usr\/lib64:/:/g') if [[ "${old_rpath}" != "${new_rpath}" ]]; then patchelf \ --force-rpath \ --set-rpath "${new_rpath}" \ - "${file}" + "${fname}" fi - done < <(find "{PREFIX}" -type f \( ! -name "*.a" -and ! -name "*.mod" \) \ + done < <(find "${PREFIX}" -type f \( ! -name "*.a" -and ! -name "*.mod" \) \ -exec grep -IL . "{}" \;) +} # Local Variables: # mode: sh diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index 2b21844..c756bff 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -82,8 +82,7 @@ openmpi: - systems: [merlin-.*] suffix: _slurm relstage: unstable - overlay: private - use_overlays: [private] + overlay: base group_deps: compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 12.4.0, 13.2.0, 14.2.0]} build_requires: From 8a14e641181b585bc150c6753d58616508593f37 Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Mon, 16 Sep 2024 15:09:31 +0200 Subject: [PATCH 095/158] Add Lustre support --- Libraries/pmix/files/config.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/Libraries/pmix/files/config.yaml b/Libraries/pmix/files/config.yaml index 062f675..be050d3 100644 --- a/Libraries/pmix/files/config.yaml +++ b/Libraries/pmix/files/config.yaml @@ -87,4 +87,11 @@ pmix: - systems: [.*.merlin7.psi.ch] overlay: Alps use_overlays: [PSI] + # configure_args+: + # - --with-cxi + # - --with-lustre + # - --with-slingshot + # - --with-zlib + # - --with-jansson + # - --with-curl - systems: [rhel.*] From ff79712a590ba1943b07b1cbd23ae1945a97083a Mon Sep 17 00:00:00 2001 From: germann_e Date: Fri, 20 Sep 2024 11:44:10 +0200 Subject: [PATCH 096/158] fluka4: version 4.0 added. Use YAML config file. --- Compiler/flair-geoviewer/build | 9 + Compiler/flair-geoviewer/files/config.yaml | 24 ++ Compiler/flair-geoviewer/modulefile | 18 ++ Compiler/flair/build | 9 + Compiler/flair/files/config.yaml | 23 ++ Compiler/flair/modulefile | 18 ++ Compiler/fluka4/build | 16 ++ Compiler/fluka4/build-brond | 14 ++ Compiler/fluka4/build-cendl | 14 ++ Compiler/fluka4/build-endf | 14 ++ Compiler/fluka4/build-flair | 15 ++ Compiler/fluka4/build-flair-geoviewer | 15 ++ Compiler/fluka4/build-jeff | 14 ++ Compiler/fluka4/build-jendl | 14 ++ Compiler/fluka4/files/config.yaml | 242 ++++++++++++++++++++ Compiler/fluka4/{modulefiles => modulefile} | 0 16 files changed, 459 insertions(+) create mode 100755 Compiler/flair-geoviewer/build create mode 100644 Compiler/flair-geoviewer/files/config.yaml create mode 100644 Compiler/flair-geoviewer/modulefile create mode 100755 Compiler/flair/build create mode 100644 Compiler/flair/files/config.yaml create mode 100644 Compiler/flair/modulefile create mode 100755 Compiler/fluka4/build create mode 100755 Compiler/fluka4/build-brond create mode 100755 Compiler/fluka4/build-cendl create mode 100755 Compiler/fluka4/build-endf create mode 100755 Compiler/fluka4/build-flair create mode 100755 Compiler/fluka4/build-flair-geoviewer create mode 100755 Compiler/fluka4/build-jeff create mode 100755 Compiler/fluka4/build-jendl create mode 100644 Compiler/fluka4/files/config.yaml rename Compiler/fluka4/{modulefiles => modulefile} (100%) diff --git a/Compiler/flair-geoviewer/build b/Compiler/flair-geoviewer/build new file mode 100755 index 0000000..2641772 --- /dev/null +++ b/Compiler/flair-geoviewer/build @@ -0,0 +1,9 @@ +#!/usr/bin/env modbuild +pbuild::compile() { + make +} + +pbuild::install() { + make DESTDIR="${FLAIR_PREFIX}" install +} + diff --git a/Compiler/flair-geoviewer/files/config.yaml b/Compiler/flair-geoviewer/files/config.yaml new file mode 100644 index 0000000..b2a68e8 --- /dev/null +++ b/Compiler/flair-geoviewer/files/config.yaml @@ -0,0 +1,24 @@ +--- +# yamllint disable rule:line-length +format: 1 +flair-geoviewer: + defaults: + group: Compiler + overlay: base + relstage: unstable + compile_in_sourcetree: true + systems: [rhel7, rhel8, rhel9] + docfiles: [AUTHORS, LICENSE, NEWS, README] + urls: + - url: https://flair.web.cern.ch/flair/download/flair-geoviewer-3.3-1.tgz + shasums: + flair-geoviewer-3.3-1.tgz: 3c18747abac21907e90c3ed1759b73ca53c987f12216ba8ee9919a199c0dca26 + + versions: + 3.3.1: + variants: + - systems: [merlin-*, ra-*] + group_deps: + compiler: {gcc: [13.1.0]} + relstage: unstable + build_requires: ['flair/3.3.1', 'TclTk/8.6.9'] diff --git a/Compiler/flair-geoviewer/modulefile b/Compiler/flair-geoviewer/modulefile new file mode 100644 index 0000000..ae7ca95 --- /dev/null +++ b/Compiler/flair-geoviewer/modulefile @@ -0,0 +1,18 @@ +#%Module1.0 + +module-whatis "Flair by CERN: Advanced graphical user interface for particle simulation programs" +module-url "http://flair.web.cern.ch/flair/index.html" +module-license "[http://flair.web.cern.ch/flair/license.html](http://flair.web.cern.ch/flair/license.html)" +module-maintainer "Elsa Germann " +module-help " +/fleə(r)/ n [U,C] natural or instinctive ability to do something well, to select or recognize what is best, more useful, etc. + +flair is an advanced user friendly interface for several Monte Carlo codes. Originally it was developed for FLUKA, where its unique features strongly contributed to the success of both codes FLUKA and flair. From version 3 the interface was separated from the functionality permitting an easy integration of other simulation packages. + +The current line of development is to make flair a unique tool for performing calculations with the same input using FLUKA, Geant4, PENELOPE, and other simulations engines. +Presently is fully supporting the CERN FLUKA version and there is ongoing work to support: + +Moira a Geant4 based application, permitting the user to run with Geant4 FLUKA equivalent inputs with the same geometry, materials, scoring,... + +Other codes like MCNP, PHITS, PENELOPE could be added in the future. +" diff --git a/Compiler/flair/build b/Compiler/flair/build new file mode 100755 index 0000000..c841ef1 --- /dev/null +++ b/Compiler/flair/build @@ -0,0 +1,9 @@ +#!/usr/bin/env modbuild +pbuild::compile() { + make +} + +pbuild::install() { + make DESTDIR="${PREFIX}" install +} + diff --git a/Compiler/flair/files/config.yaml b/Compiler/flair/files/config.yaml new file mode 100644 index 0000000..4476db6 --- /dev/null +++ b/Compiler/flair/files/config.yaml @@ -0,0 +1,23 @@ +--- +# yamllint disable rule:line-length +format: 1 +flair: + defaults: + group: Compiler + overlay: base + relstage: unstable + compile_in_sourcetree: true + systems: [rhel7, rhel8, rhel9] + docfiles: [AUTHORS, LICENSE, NEWS, README] + urls: + - url: http://flair.web.cern.ch/flair/download/flair-3.3-1.tgz + shasums: + flair-3.3-1.tgz: 2bc9b02fd2d9ddb7eed96938314b9c73f0b6a844aa1af15728650eaf81e777bd + + versions: + 3.3.1: + variants: + - systems: [merlin-*, ra-*] + group_deps: + compiler: {gcc: [13.1.0]} + relstage: unstable diff --git a/Compiler/flair/modulefile b/Compiler/flair/modulefile new file mode 100644 index 0000000..ae7ca95 --- /dev/null +++ b/Compiler/flair/modulefile @@ -0,0 +1,18 @@ +#%Module1.0 + +module-whatis "Flair by CERN: Advanced graphical user interface for particle simulation programs" +module-url "http://flair.web.cern.ch/flair/index.html" +module-license "[http://flair.web.cern.ch/flair/license.html](http://flair.web.cern.ch/flair/license.html)" +module-maintainer "Elsa Germann " +module-help " +/fleə(r)/ n [U,C] natural or instinctive ability to do something well, to select or recognize what is best, more useful, etc. + +flair is an advanced user friendly interface for several Monte Carlo codes. Originally it was developed for FLUKA, where its unique features strongly contributed to the success of both codes FLUKA and flair. From version 3 the interface was separated from the functionality permitting an easy integration of other simulation packages. + +The current line of development is to make flair a unique tool for performing calculations with the same input using FLUKA, Geant4, PENELOPE, and other simulations engines. +Presently is fully supporting the CERN FLUKA version and there is ongoing work to support: + +Moira a Geant4 based application, permitting the user to run with Geant4 FLUKA equivalent inputs with the same geometry, materials, scoring,... + +Other codes like MCNP, PHITS, PENELOPE could be added in the future. +" diff --git a/Compiler/fluka4/build b/Compiler/fluka4/build new file mode 100755 index 0000000..d297185 --- /dev/null +++ b/Compiler/fluka4/build @@ -0,0 +1,16 @@ +#!/usr/bin/env modbuild + +pbuild::pre_prep(){ + SRC_DIR="${PREFIX}" + BUILD_DIR="${PREFIX}" +} + +pbuild::compile(){ + cd src + make -j "${JOBS}" +} + +pbuild::install() { + : +} + diff --git a/Compiler/fluka4/build-brond b/Compiler/fluka4/build-brond new file mode 100755 index 0000000..92f7684 --- /dev/null +++ b/Compiler/fluka4/build-brond @@ -0,0 +1,14 @@ +#!/usr/bin/env modbuild + +pbuild::pre_prep(){ + SRC_DIR="${PREFIX}" + BUILD_DIR="${PREFIX}" +} + +pbuild::compile(){ + : +} + +pbuild::install() { + : +} diff --git a/Compiler/fluka4/build-cendl b/Compiler/fluka4/build-cendl new file mode 100755 index 0000000..92f7684 --- /dev/null +++ b/Compiler/fluka4/build-cendl @@ -0,0 +1,14 @@ +#!/usr/bin/env modbuild + +pbuild::pre_prep(){ + SRC_DIR="${PREFIX}" + BUILD_DIR="${PREFIX}" +} + +pbuild::compile(){ + : +} + +pbuild::install() { + : +} diff --git a/Compiler/fluka4/build-endf b/Compiler/fluka4/build-endf new file mode 100755 index 0000000..92f7684 --- /dev/null +++ b/Compiler/fluka4/build-endf @@ -0,0 +1,14 @@ +#!/usr/bin/env modbuild + +pbuild::pre_prep(){ + SRC_DIR="${PREFIX}" + BUILD_DIR="${PREFIX}" +} + +pbuild::compile(){ + : +} + +pbuild::install() { + : +} diff --git a/Compiler/fluka4/build-flair b/Compiler/fluka4/build-flair new file mode 100755 index 0000000..02e6124 --- /dev/null +++ b/Compiler/fluka4/build-flair @@ -0,0 +1,15 @@ +#!/usr/bin/env modbuild + +pbuild::pre_prep(){ + SRC_DIR="${PREFIX}/flair" + BUILD_DIR="${PREFIX}/flair" +} + +pbuild::compile(){ + make -j "${JOBS}" +} + +pbuild::install() { + : +} + diff --git a/Compiler/fluka4/build-flair-geoviewer b/Compiler/fluka4/build-flair-geoviewer new file mode 100755 index 0000000..87c7802 --- /dev/null +++ b/Compiler/fluka4/build-flair-geoviewer @@ -0,0 +1,15 @@ +#!/usr/bin/env modbuild + +pbuild::pre_prep(){ + SRC_DIR="${PREFIX}/geoviewer" + BUILD_DIR="${PREFIX}/geoviewer" +} + +pbuild::compile(){ + make -j "${JOBS}" +} + +pbuild::install() { + make DESTDIR="${PREFIX}/flair" install +} + diff --git a/Compiler/fluka4/build-jeff b/Compiler/fluka4/build-jeff new file mode 100755 index 0000000..92f7684 --- /dev/null +++ b/Compiler/fluka4/build-jeff @@ -0,0 +1,14 @@ +#!/usr/bin/env modbuild + +pbuild::pre_prep(){ + SRC_DIR="${PREFIX}" + BUILD_DIR="${PREFIX}" +} + +pbuild::compile(){ + : +} + +pbuild::install() { + : +} diff --git a/Compiler/fluka4/build-jendl b/Compiler/fluka4/build-jendl new file mode 100755 index 0000000..92f7684 --- /dev/null +++ b/Compiler/fluka4/build-jendl @@ -0,0 +1,14 @@ +#!/usr/bin/env modbuild + +pbuild::pre_prep(){ + SRC_DIR="${PREFIX}" + BUILD_DIR="${PREFIX}" +} + +pbuild::compile(){ + : +} + +pbuild::install() { + : +} diff --git a/Compiler/fluka4/files/config.yaml b/Compiler/fluka4/files/config.yaml new file mode 100644 index 0000000..7b55c27 --- /dev/null +++ b/Compiler/fluka4/files/config.yaml @@ -0,0 +1,242 @@ +--- +# yamllint disable rule:line-length +format: 1 +fluka4: + defaults: + group: Compiler + overlay: base + relstage: unstable + compile_in_sourcetree: true + systems: [.*] + download_dir: /afs/psi.ch/software/Pmodules/protected/fluka + urls: + - url: none + name: fluka-4-${V_PKG}.x86-Linux-gfor9.tgz + shasums: + fluka-4-4.0.x86-Linux-gfor9.tgz: bcc303b96026b91f6d88d7a5ec274e31619562833330be93a992cd3c7e511eba + + versions: + 4.0: + config: + group_deps: + compiler: {gcc: [9.5.0]} + relstage: unstable + build_requires: [] + runtime_deps: ['TclTk/8.6.9', 'Python/3.9.10', 'gnuplot/5.4.10'] + sub_packages: + - name: flair + version: 3.3-1 + build_args: + - --disable-cleanup + - -f + - name: flair-geoviewer + version: 3.3-1 + build_args: + - --disable-cleanup + - -f + - name: jeff + version: 3.3-1-1 + build_args: + - --disable-cleanup + - -f + - name: endf + version: viii0-1.0 + build_args: + - --disable-cleanup + - -f + - name: jendl + version: 4.0u-1.0 + build_args: + - --disable-cleanup + - -f + - name: cendl + version: 31-1.0 + build_args: + - --disable-cleanup + - -f + - name: brond + version: 3.1-1.0 + build_args: + - --disable-cleanup + - -f + + 4.0_beta: + config: + group_deps: + compiler: {gcc: [9.5.0]} + relstage: unstable + build_requires: [] + runtime_deps: ['TclTk/8.6.9', 'Python/3.9.10', 'gnuplot/5.4.10'] + sub_packages: + - name: flair + version: 3.x-3.5 + build_args: + - --disable-cleanup + - -f + - name: flair-geoviewer + version: 3.x-3.5 + build_args: + - --disable-cleanup + - -f + - name: jeff + version: 3.3-1-1 + build_args: + - --disable-cleanup + - -f + - name: endf + version: viii0-1.0 + build_args: + - --disable-cleanup + - -f + - name: jendl + version: 4.0u-1.0 + build_args: + - --disable-cleanup + - -f + - name: cendl + version: 31-1.0 + build_args: + - --disable-cleanup + - -f + - name: brond + version: 3.1-1.0 + build_args: + - --disable-cleanup + - -f + + 4.1_beta1: + config: + group: Tools + build_requires: [] + runtime_deps: ['gcc/9.5.0', 'TclTk/8.6.9', 'Python/3.9.10', 'gnuplot/5.4.10'] + sub_packages: + - name: flair + version: 3.x-5 + build_args: + - --disable-cleanup + - -f + - name: flair-geoviewer + version: 3.x-5 + build_args: + - --disable-cleanup + - -f + - name: jeff + version: 3.3-1-1 + build_args: + - --disable-cleanup + - -f + - name: endf + version: viii0-1.0 + build_args: + - --disable-cleanup + - -f + - name: jendl + version: 4.0u-1.0 + build_args: + - --disable-cleanup + - -f + - name: cendl + version: 31-1.0 + build_args: + - --disable-cleanup + - -f + - name: brond + version: 3.1-1.0 + build_args: + - --disable-cleanup + - -f + +jeff: + type: sub_package + defaults: + urls: + - url: https://flukafiles.web.cern.ch/flukafiles/neutron/fluka_pw_$P-$V.tar.gz + strip_dirs: 0 + shasums: + fluka_pw_jeff-3.3-1-1.tar.gz: 48810cab92bc79b241b306390f88b5fc1333363e85fdd0d9317263ba8e29ed8b + versions: + 3.3-1-1: + +endf: + defaults: + urls: + - url: https://flukafiles.web.cern.ch/flukafiles/neutron/fluka_pw_$P-$V.tgz + strip_dirs: 0 + shasums: + fluka_pw_endf-viii0-1.0.tgz: e26433c9f548c4477b5c47a1929d33ce4a823fa326703d3a52dfa9161f9ae1b9 + versions: + viii0-1.0: + +jendl: + defaults: + urls: + - url: https://flukafiles.web.cern.ch/flukafiles/neutron/fluka_pw_$P-$V.tgz + strip_dirs: 0 + shasums: + fluka_pw_jendl-4.0u-1.0.tgz: 21d5e2676ae26946df98869bd1d95f4f34edb53488fb40e5c1a8ef0c743f5f6e + versions: + 4.0u-1.0: + +cendl: + defaults: + urls: + - url: https://flukafiles.web.cern.ch/flukafiles/neutron/fluka_pw_$P-$V.tgz + strip_dirs: 0 + shasums: + fluka_pw_cendl-31-1.0.tgz: d64916e35bfa6337463d01b3596ccd57b8f8b5c2e8879138ef7be14aff2b49d3 + versions: + 31-1.0: + +brond: + defaults: + urls: + - url: https://flukafiles.web.cern.ch/flukafiles/neutron/fluka_pw_$P-$V.tgz + strip_dirs: 0 + shasums: + fluka_pw_brond-3.1-1.0.tgz: c88ba7cde8ccf1c59b49e1138cc06cfd0b2b84f50a67d1dd9a29f104633b8a72 + versions: + 3.1-1.0: + +flair: + defaults: + urls: + - url: http://flair.web.cern.ch/flair/download/flair-$V.tgz + shasums: + flair-3.3-1.tgz: 2bc9b02fd2d9ddb7eed96938314b9c73f0b6a844aa1af15728650eaf81e777bd + + versions: + 3.3-1: + config: + build_requires: ['gcc/9.5.0', 'Python/3.9.10'] + 3.x-3.5: + config: + build_requires: ['gcc/9.5.0', 'Python/3.9.10'] + urls: + - url: https://cernbox.cern.ch/remote.php/dav/public-files/m87gnQjIkI4dEls/flair-3.x-3.5.tgz + 3.x-5: + config: + build_requires: ['gcc/9.5.0', 'Python/3.9.10'] + urls: + - url: https://cernbox.cern.ch/remote.php/dav/public-files/m87gnQjIkI4dEls/flair-3.x-5.tgz + +flair-geoviewer: + defaults: + urls: + - url: https://flair.web.cern.ch/flair/download/flair-geoviewer-$V.tgz + shasums: + flair-geoviewer-3.3-1.tgz: 3c18747abac21907e90c3ed1759b73ca53c987f12216ba8ee9919a199c0dca26 + + versions: + 3.3-1: + config: + build_requires: ['gcc/9.5.0', 'Python/3.9.10', 'TclTk/8.6.9'] + 3.x-3.5: + config: + build_requires: ['gcc/9.5.0', 'Python/3.9.10', 'TclTk/8.6.9'] + urls: + - url: https://cernbox.cern.ch/remote.php/dav/public-files/m87gnQjIkI4dEls/flair-geoviewer-3.x-3.5.tgz + 3.x-5: + config: + build_requires: ['gcc/9.5.0', 'Python/3.9.10', 'TclTk/8.6.9'] + urls: + - url: https://cernbox.cern.ch/remote.php/dav/public-files/m87gnQjIkI4dEls/flair-geoviewer-3.x-5.tgz diff --git a/Compiler/fluka4/modulefiles b/Compiler/fluka4/modulefile similarity index 100% rename from Compiler/fluka4/modulefiles rename to Compiler/fluka4/modulefile From 521fdfa30933ecc5891dfbbf626283357cb4d1a2 Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Tue, 24 Sep 2024 10:21:36 +0200 Subject: [PATCH 097/158] Add openmpi+intelcc. Update Slurm --- Batchsystem/slurm/build | 9 ++------- Batchsystem/slurm/files/config.yaml | 27 +++++++++++++++++++++++++++ Compiler/openmpi/files/config.yaml | 2 +- Libraries/pmix/files/config.yaml | 14 +++++++------- 4 files changed, 37 insertions(+), 15 deletions(-) create mode 100644 Batchsystem/slurm/files/config.yaml diff --git a/Batchsystem/slurm/build b/Batchsystem/slurm/build index 3800ffa..118fcd0 100755 --- a/Batchsystem/slurm/build +++ b/Batchsystem/slurm/build @@ -1,14 +1,9 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://download.schedmd.com/${P}/${P}-${V}.tar.bz2" - -pbuild::add_to_group 'Batchsystem' -pbuild::install_docfiles 'AUTHORS' 'INSTALL' 'NEWS' 'README.rst' 'RELEASE_NOTES' - pbuild::pre_configure() { - pbuild::add_configure_args "--with-pmix=${PMIX_PREFIX}" + # pbuild::add_configure_args "--with-pmix=${PMIX_PREFIX}" pbuild::add_configure_args "--with-nvml=${CUDA_PREFIX}" pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" - pbuild::add_configure_args "--with-ucx=${UCX_PREFIX}" + # pbuild::add_configure_args "--with-ucx=${UCX_PREFIX}" # pbuild::add_configure_args "--with-netloc=${HWLOC_PREFIX}" } diff --git a/Batchsystem/slurm/files/config.yaml b/Batchsystem/slurm/files/config.yaml new file mode 100644 index 0000000..9de30f2 --- /dev/null +++ b/Batchsystem/slurm/files/config.yaml @@ -0,0 +1,27 @@ +--- +# yamllint disable rule:line-length +format: 1 +slurm: + defaults: + group: Batchsystem + overlay: Alps + relstage: stable + docfiles: [AUTHORS, INSTALL, NEWS, README.rst RELEASE_NOTES] + urls: + - url: https://download.schedmd.com/${P}/${P}-${V}.tar.bz2 + shasums: + slurm-24.05.3.tar.bz2: b0b40513e9b6ae867ddb95d60b950bcb980c15b735b5d0dea37a9a00cc64ae24 + + versions: + 24.05.3: + variants: + - systems: [.*.merlin7.psi.ch] + relstage: unstable + overlay: Alps + use_overlays: [PSI] + group_deps: + compiler: {gcc: [12.3.0]} + build_requires: [cuda/12.2.0, hwloc/2.11.1, patchelf/0.14.5] + configure_args+: + - '--with-pmix=/opt/psi/overlays/Alps/Libraries/pmix/2.2.5:/opt/psi/overlays/Alps/Libraries/pmix/3.2.5:/opt/psi/overlays/Alps/Libraries/pmix/4.2.9:/opt/psi/overlays/Alps/Libraries/pmix/5.0.3' + - '--with-cray_shasta' diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index c756bff..03f28e0 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -67,7 +67,7 @@ openmpi: overlay: Alps use_overlays: [PSI] group_deps: - compiler: {gcc: [12.3.0]} + compiler: {gcc: [12.3.0], intelcc: [22.2]} build_requires: [pmix/5.0.3, hwloc/2.11.1, patchelf/0.14.5] runtime_deps: [cuda/12.2.0] configure_args+: diff --git a/Libraries/pmix/files/config.yaml b/Libraries/pmix/files/config.yaml index be050d3..14db2dc 100644 --- a/Libraries/pmix/files/config.yaml +++ b/Libraries/pmix/files/config.yaml @@ -87,11 +87,11 @@ pmix: - systems: [.*.merlin7.psi.ch] overlay: Alps use_overlays: [PSI] - # configure_args+: - # - --with-cxi - # - --with-lustre - # - --with-slingshot - # - --with-zlib - # - --with-jansson - # - --with-curl + configure_args+: + - --with-lustre + # - --with-cxi + # - --with-slingshot + # - --with-zlib + # - --with-jansson + # - --with-curl - systems: [rhel.*] From 5535d2b4e5bbc86995dbb237c96cbb9699092bde Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Thu, 26 Sep 2024 14:30:21 +0200 Subject: [PATCH 098/158] Hardcode Cray libfabric --- Compiler/openmpi/files/config.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index 03f28e0..f52a321 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -9,8 +9,6 @@ openmpi: configure_args: - --enable-shared - --enable-static - - docfiles: [AUTHORS, LICENSE, NEWS, README] urls: - url: https://download.open-mpi.org/release/open-mpi/v${V_MAJOR}.${V_MINOR}/openmpi-${V_PKG}.tar.bz2 @@ -68,10 +66,10 @@ openmpi: use_overlays: [PSI] group_deps: compiler: {gcc: [12.3.0], intelcc: [22.2]} - build_requires: [pmix/5.0.3, hwloc/2.11.1, patchelf/0.14.5] + build_requires: [pmix/5.0.3, hwloc/2.11.1, libfabric/1.15.2.0, patchelf/0.14.5] runtime_deps: [cuda/12.2.0] configure_args+: - - --with-ofi=${LIBFABRIC_PREFIX} + - --with-ofi=/opt/cray/libfabric/1.15.2.0 - --enable-mpi1-compatibility - --with-cxi - --with-lustre From cc82468009449f3db2a4505c9c31bc6b291efac9 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 26 Sep 2024 14:40:54 +0200 Subject: [PATCH 099/158] openmpi: fixes for Ra, Merlin6 & 7 --- Compiler/openmpi/build | 4 ++++ Compiler/openmpi/files/config.yaml | 13 ++++++++++--- 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index a8091f1..d9bd927 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -13,6 +13,10 @@ pbuild::pre_configure() { pbuild::add_configure_args "--with-pmi=/usr" pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/slurmpmi" fi + if (( V_MAJOR < 5 )) && pbuild::use_flag 'ra'; then + pbuild::add_configure_args "--with-pmi=/usr" + pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/slurm" + fi if (( V_MAJOR >= 5 )); then pbuild::add_configure_args "--enable-prte-prefix-by-default" fi diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index f52a321..5a0e595 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -10,7 +10,7 @@ openmpi: - --enable-shared - --enable-static docfiles: [AUTHORS, LICENSE, NEWS, README] - urls: + Urls: - url: https://download.open-mpi.org/release/open-mpi/v${V_MAJOR}.${V_MINOR}/openmpi-${V_PKG}.tar.bz2 shasums: openmpi-1.10.0.tar.bz2: 26b432ce8dcbad250a9787402f2c999ecb6c25695b00c9c6ee05a306c78b6490 @@ -64,25 +64,28 @@ openmpi: relstage: unstable overlay: Alps use_overlays: [PSI] + use_flags: [merlin7] group_deps: compiler: {gcc: [12.3.0], intelcc: [22.2]} build_requires: [pmix/5.0.3, hwloc/2.11.1, libfabric/1.15.2.0, patchelf/0.14.5] runtime_deps: [cuda/12.2.0] configure_args+: - - --with-ofi=/opt/cray/libfabric/1.15.2.0 + - --with-ofi=${LIBFABRIC_VERSION} - --enable-mpi1-compatibility - --with-cxi - --with-lustre - --with-slingshot 4.1.6: + config: + build_variants: first_match variants: - systems: [merlin-.*] suffix: _slurm relstage: unstable overlay: base group_deps: - compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 12.4.0, 13.2.0, 14.2.0]} + compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 12.4.0, 13.1.0, 13.2.0, 14.2.0]} build_requires: - pmix/4.2.4 - ucx/1.14.1_slurm @@ -98,10 +101,14 @@ openmpi: - systems: [ra-.*] suffix: _ra + use_flags: [ra] group_deps: compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] runtime_deps: [cuda/12.1.1] + configure_args+: + - --with-gpfs=/usr/lpp/mmfs + - --with-pmi=/usr - systems: [.*.merlin7.psi.ch] relstage: unstable From 6b973497c7f9620ff5efe08d24964af065a7e075 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 26 Sep 2024 15:11:28 +0200 Subject: [PATCH 100/158] gcc: changes to build on GraceHopper --- Libraries/mpc/files/config.yaml | 3 ++- Libraries/mpfr/files/config.yaml | 3 ++- Programming/gcc/files/config.yaml | 10 +++++----- 3 files changed, 9 insertions(+), 7 deletions(-) diff --git a/Libraries/mpc/files/config.yaml b/Libraries/mpc/files/config.yaml index aa6b00b..a971912 100644 --- a/Libraries/mpc/files/config.yaml +++ b/Libraries/mpc/files/config.yaml @@ -23,7 +23,8 @@ mpc: versions: 1.2.1;1.3.1-1: - + config: + build_requires: [gmp/6.3.0, mpfr/4.2.1] 1.0.{2,3};1.0.3-2;1.1.0-{1..4};1.3.1: config: relstage: deprecated diff --git a/Libraries/mpfr/files/config.yaml b/Libraries/mpfr/files/config.yaml index 2773a97..3a5e858 100644 --- a/Libraries/mpfr/files/config.yaml +++ b/Libraries/mpfr/files/config.yaml @@ -28,7 +28,8 @@ mpfr: versions: 4.1.0;4.2.0;4.2.1: - + config: + build_requires: [gmp/6.3.0] 3.1.{2..5};4.0.{0..1};4.0.1-1;4.0.2;4.0.2-{1..2}: config: relstage: deprecated diff --git a/Programming/gcc/files/config.yaml b/Programming/gcc/files/config.yaml index 03220ff..7630e47 100644 --- a/Programming/gcc/files/config.yaml +++ b/Programming/gcc/files/config.yaml @@ -20,12 +20,11 @@ gcc: - --disable-multilib - --with-pkgversion=PSI Environment Module - --with-build-config=bootstrap-debug - - --enable-languages=c,c++,objc,obj-c++,lto,fortran,go' urls: - url: https://ftp.gnu.org/gnu/gcc/$P-$V/$P-$V.tar.gz shasums: - gcc-14.2.0.tar.gz: 3a2b10cab86e32358fdac871546d57e2700e9bdb5875ef33fff5b601265b9e32 + gcc-14.2.0.tar.gz: 7d376d445f93126dc545e2c0086d0f647c3094aae081cdb78f42ce2bc25e7293 gcc-13.3.0.tar.gz: 3a2b10cab86e32358fdac871546d57e2700e9bdb5875ef33fff5b601265b9e32 gcc-13.1.0.tar.gz: bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2 gcc-12.4.0.tar.gz: 5a30de2be740062bb3ddd3fd13c9b1bb4584d8f85616d33f23a713439d714148 @@ -79,7 +78,9 @@ gcc: 12.3.0;12.4.0;13.2.0;13.3.0;14.2.0: config: relstage: stable - build_requires: [gcc/10.4.0, gmp/6.3.0, mpfr/4.2.0, mpc/1.3.1] + build_requires: [gcc/10.4.0, gmp/6.3.0, mpfr/4.2.1, mpc/1.3.1-1] + configure_args+: + - --enable-languages=c,c++,objc,obj-c++,lto,fortran,go variants: - overlay: base systems: [rhel.*] @@ -122,11 +123,10 @@ gcc: 10.4.0: config: - restage: stable + relstage: stable build_requires: [gmp/6.2.1, mpfr/4.1.0, mpc/1.2.1] variants: - overlay: base - systems: [rhel.*] 10.3.0: config: From 18e60ef789c061ef64893d7763be05e768e1cd5b Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 26 Sep 2024 15:56:01 +0200 Subject: [PATCH 101/158] git: merge conflict resolved --- Compiler/hdf5_serial/files/config.yaml | 10 ++++++ Compiler/openmpi/files/config.yaml | 11 +++++- MPI/parmetis/files/config.yaml | 50 +++++++++++++------------- Programming/nvhpc/files/config.yaml | 15 ++++---- Tools/git/build | 1 - Tools/git/files/config.yaml | 36 +++++++++++++++++-- Tools/gnuplot/build-yaml | 4 --- Tools/gnuplot/files/config.yaml | 16 +++++++-- 8 files changed, 96 insertions(+), 47 deletions(-) diff --git a/Compiler/hdf5_serial/files/config.yaml b/Compiler/hdf5_serial/files/config.yaml index 00cbb15..4026415 100644 --- a/Compiler/hdf5_serial/files/config.yaml +++ b/Compiler/hdf5_serial/files/config.yaml @@ -202,3 +202,13 @@ hdf5_serial: compiler: gcc: [6.5.0, 7.5.0, 8.5.0, 9.5.0, 10.3.0, 11.3.0, 12.1.0] relstage: stable + + 1.12.3: + config: + group_deps: + compiler: + gcc: [7.5.0, 8.5.0, 9.5.0, 10.4.0, 11.3.0, 12.1.0] + relstage: unstable + urls: + - url: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${V_MAJOR}.${V_MINOR}/hdf5-$V/src/hdf5-$V.tar.bz2 + strip_dirs: 2 diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index a15cd1b..afd076f 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -57,8 +57,17 @@ openmpi: versions: 4.1.6: variants: - - systems: [merlin-*, ra-*] + - systems: [merlin-.*] suffix: _slurm + relstage: unstable + overlay: private + use_overlays: [private] + group_deps: + compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} + build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5] + runtime_deps: [cuda/12.1.1] + - systems: [ra-.*] + suffix: _ra group_deps: compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] diff --git a/MPI/parmetis/files/config.yaml b/MPI/parmetis/files/config.yaml index ed6d400..c351c87 100644 --- a/MPI/parmetis/files/config.yaml +++ b/MPI/parmetis/files/config.yaml @@ -1,29 +1,27 @@ -parmetis/3.2.0 deprecated gcc/{4.7.4,4.8.3,4.8.4,4.9.2} openmpi/{1.6.5,1.8.2,1.8.4} +--- +# yamllint disable rule:line-length +format: 1 +parmetis: + defaults: + group: MPI + overlay: base + relstage: stable + systems: [merlin-*, ra-*] + docfiles: [Changelog, Install.txt, LICENSE.txt] + urls: + - url: http://glaros.dtc.umn.edu/gkhome/fetch/sw/$P/$P-${V_PKG}.tar.gz + name: $P-${V_PKG}.tar.gz -parmetis/3.2.0 deprecated gcc/{4.8.5,5.3.0,6.1.0,6.2.0} openmpi/1.10.2 + shasums: + - parmetis-4.0.3.tar.gz: f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f -parmetis/3.2.0 deprecated gcc/6.2.0 openmpi/{1.10.4,2.0.1} + versions: + 4.0.3_slurm: + variants: + - group_deps: + compiler: + gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0] + mpi: + openmpi: [4.1.5_slurm] + build_requires: [cmake/3.20.5] -parmetis/3.2.0 deprecated gcc/7.3.0 openmpi/3.0.1 - -parmetis/3.2.0 deprecated intel/15.3 openmpi/1.8.4 - -parmetis/4.0.3 deprecated gcc/4.8.2 openmpi/1.6.5 b:cmake/3.4.1 -parmetis/4.0.3 deprecated gcc/{4.8.5,4.9.4,5.3.0,5.4.0,6.1.0,6.2.0} openmpi/1.10.2 b:cmake/3.4.1 - -parmetis/4.0.3 deprecated gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.6.3 - -parmetis/4.0.3 deprecated gcc/6.2.0 openmpi/2.0.1 b:cmake/3.6.3 - -parmetis/4.0.3 deprecated gcc/7.3.0 openmpi/{1.10.7,2.1.2,3.0.0,3.0.1,3.1.2,3.1.3} b:cmake/3.6.3 -parmetis/4.0.3 deprecated gcc/7.4.0 openmpi/3.1.4 b:cmake/3.9.6 - -parmetis/4.0.3 deprecated intel/17.4 openmpi/{1.10.7,2.1.2,3.0.0} b:cmake/3.6.3 - -parmetis/4.0.3 stable gcc/7.3.0 mpich/3.3 b:cmake/3.9.6 - -parmetis/4.0.3 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:cmake/3.9.6 - -parmetis/4.0.3 stable gcc/{7.5.0,8.4.0,9.3.0,10.3.0} openmpi/4.0.5 b:cmake/3.15.5 -parmetis/4.0.3 stable gcc/10.4.0 openmpi/4.1.4 b:cmake/3.15.5 -parmetis/4.0.3 unstable gcc/10.4.0 openmpi/4.1.5 b:cmake/3.15.5 diff --git a/Programming/nvhpc/files/config.yaml b/Programming/nvhpc/files/config.yaml index 7c58b14..877c2dc 100644 --- a/Programming/nvhpc/files/config.yaml +++ b/Programming/nvhpc/files/config.yaml @@ -6,9 +6,9 @@ nvhpc: group: Programming overlay: base relstage: stable - systems: [rhel7, rhel8, rhel9] + systems: ['*.merlin7.*', 'merlin-*', 'ra-*'] docfiles: [AUTHORS, LICENSE, NEWS, README] - compile_in_sourcetree: true + compile_in_sourcetree: true shasums: nvhpc-24.3.tar.gz: 4fb8949ba8cef73b28818bd9375c9420ec48fab1c64e71315a7c1984f5329d6b nvhpc-23.5.tar.gz: 3196309b38df6f0a27e18b80f6a40e23cab8195cad43fc6bbd569af7d8ca5742 @@ -16,18 +16,15 @@ nvhpc: versions: 24.3: variants: - - systems: [merlin-*, ra-*] - suffix: _cuda_12.3 + - suffix: _cuda_12.3 urls: - url: https://developer.download.nvidia.com/hpc-sdk/${V_PKG}/nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz - suffix: _cuda_12.3 - relstage: unstable + relstage: stable build_requires: [gcc/10.4.0] 23.5: variants: - - systems: [merlin-*, ra-*] - suffix: _cuda_12.1 + - suffix: _cuda_12.1 urls: - url: https://developer.download.nvidia.com/hpc-sdk/${V_PKG}/nvhpc_2023_235_Linux_x86_64_cuda_12.1.tar.gz - relstage: unstable + relstage: stable build_requires: [gcc/10.4.0] diff --git a/Tools/git/build b/Tools/git/build index 16961b7..38fb16c 100755 --- a/Tools/git/build +++ b/Tools/git/build @@ -11,7 +11,6 @@ pbuild::pre_configure_Darwin() { export NO_APPLE_COMMON_CRYPTO=1 } - pbuild::pre_configure() { #pbuild::add_configure_args "LIBS=-lintl" pbuild::add_configure_args "--with-tcltk" diff --git a/Tools/git/files/config.yaml b/Tools/git/files/config.yaml index 06f4ade..1885092 100644 --- a/Tools/git/files/config.yaml +++ b/Tools/git/files/config.yaml @@ -6,7 +6,6 @@ git: group: Tools overlay: base relstage: stable - systems: [rhel6, rhel7, rhel8] compile_in_sourcetree: true urls: - url: https://mirrors.edge.kernel.org/pub/software/scm/git/git-${V_PKG}.tar.xz @@ -21,21 +20,38 @@ git: git-2.8.1.tar.xz: e6626b43ba4bc63ad4918df4c275f50bd7f8af2ab54bde60496ad75e91e927fc git-2.3.3.tar.gz: c189e4a48d8805482f450db666330c79bcefae37e0d035c7717517126ddf4305 versions: + 2.45.2: + config: + runtime_deps: [TclTk/8.6.9, openssl/1.1.1w] + build_requires: [gcc/10.4.0, perl/5.30.0, asciidoc/8.6.9-1, xmlto/0.0.28, gettext/0.19.8] + relstage: unstable + overlay: devel + docfiles: [COPYING, README.md] + configure_args: + - --with-tcltk + - --with-iconv=${GETTEXT_PREFIX} + - --with-perl=${PERL_PREFIX}/bin/perl + sub_packages: + - name: git-lfs + version: 3.5.1 + build_args: 2.43.1: config: runtime_deps: [TclTk/8.6.9] build_requires: [gcc/10.4.0, perl/5.30.0, asciidoc/8.6.9-1, xmlto/0.0.28, gettext/0.19.8, openssl/1.1.1w] relstage: unstable overlay: devel - systems: [rhel7, rhel8, rhel9] docfiles: [COPYING, README.md] + configure_args: + - --with-tcltk + - --with-iconv=${GETTEXT_PREFIX} + - --with-perl=${PERL_PREFIX}/bin/perl 2.42.0: config: runtime_deps: [TclTk/8.6.9] build_requires: [gcc/10.4.0, perl/5.30.0, asciidoc/8.6.9-1, xmlto/0.0.28, gettext/0.19.8] relstage: unstable overlay: devel - systems: [rhel7, rhel8, rhel9] docfiles: [COPYING, README.md] 2.39.1;2.37.2;2.37.0;2.33.1;2.30.0;2.22.0;2.21.0: config: @@ -44,3 +60,17 @@ git: 2.3.3;2.8.1: config: runtime_deps: [Tcl/8.6.9, Tk/8.6.9] + +git-lfs: + type: sub_package + defaults: + compile_in_sourcetree: true + versions: + 3.5.1: + config: + variants: + - + kernels: [Linux] + target_cpus: [x86_64] + urls: + - url: https://github.com/git-lfs/git-lfs/releases/download/v3.5.1/git-lfs-linux-amd64-v3.5.1.tar.gz diff --git a/Tools/gnuplot/build-yaml b/Tools/gnuplot/build-yaml index 3a25f73..4d92699 100755 --- a/Tools/gnuplot/build-yaml +++ b/Tools/gnuplot/build-yaml @@ -1,9 +1,5 @@ #!/usr/bin/env modbuild -pbuild::pre_configure() { - pbuild::add_configure_args '--with-latex=no' - pbuild::add_configure_args '--with-qt=no' -} # Local Variables: # mode: sh # sh-basic-offset: 8 diff --git a/Tools/gnuplot/files/config.yaml b/Tools/gnuplot/files/config.yaml index 7bfcef0..9e709c2 100644 --- a/Tools/gnuplot/files/config.yaml +++ b/Tools/gnuplot/files/config.yaml @@ -1,13 +1,14 @@ +--- format: 1 gnuplot: defaults: group: Tools - overlay: base + overlay: base relstage: stable systems: [rhel8, rhel7, rhel6] docfiles: [Copyright, NEWS, README] urls: - - url: https://sourceforge.net/projects/gnuplot/files/$P/$V/$P-${V_PKG}.tar.gz + - url: https://sourceforge.net/projects/gnuplot/files/$P/$V/$P-${V_PKG}.tar.gz shasums: gnuplot-5.4.10.tar.gz: 975d8c1cc2c41c7cedc4e323aff035d977feb9a97f0296dd2a8a66d197a5b27c gnuplot-5.4.9.tar.gz: a328a021f53dc05459be6066020e9a71e8eab6255d3381e22696120d465c6a97 @@ -27,7 +28,16 @@ gnuplot: versions: 5.4.{0,1,2,3,4,5,8,9};5.2.{0,4,6,7,8};5.0.0;4.6.3: 5.4.10: + config: + relstage: stable + 6.0.0: config: relstage: unstable - + systems: [rhel*] + configure_args: ['--with-latex=no', '--with-qt=no'] + 6.0.1: + config: + relstage: unstable + systems: [rhel*] + configure_args: ['--with-latex=no', '--with-qt=no'] From d786b606ee817d9038d16a5c610b969cb2d0ba5e Mon Sep 17 00:00:00 2001 From: Derek Feichtinger Date: Fri, 4 Oct 2024 22:35:30 +0200 Subject: [PATCH 102/158] build files for new miniconda base 2024.08 added 2 conda environments - jupyterhub-4.1.6_lab4_py3.12 - datascience_2024_py3.12 --- .../datascience_2024_py3.12.yml | 29 +++++++++++++++++++ .../jupyterhub-4.1.6_lab4_py3.12.yaml | 28 ++++++++++++++++++ Programming/anaconda/2024.08/config.sh | 6 ++++ Programming/anaconda/build | 28 +++--------------- Programming/anaconda/files/config.yaml | 15 ++++++++++ 5 files changed, 82 insertions(+), 24 deletions(-) create mode 100644 Programming/anaconda/2024.08/conda-env-defs/datascience_2024_py3.12/datascience_2024_py3.12.yml create mode 100644 Programming/anaconda/2024.08/conda-env-defs/jupyterhub-4.1.6_lab4_py3.12/jupyterhub-4.1.6_lab4_py3.12.yaml create mode 100644 Programming/anaconda/2024.08/config.sh create mode 100644 Programming/anaconda/files/config.yaml diff --git a/Programming/anaconda/2024.08/conda-env-defs/datascience_2024_py3.12/datascience_2024_py3.12.yml b/Programming/anaconda/2024.08/conda-env-defs/datascience_2024_py3.12/datascience_2024_py3.12.yml new file mode 100644 index 0000000..0172a3d --- /dev/null +++ b/Programming/anaconda/2024.08/conda-env-defs/datascience_2024_py3.12/datascience_2024_py3.12.yml @@ -0,0 +1,29 @@ +# Clean environment based on pure conda-forge packages +name: datascience_2024_py3.12 +channels: + - conda-forge +dependencies: + - python=3.12 + - pandas + - xlrd + - numpy + - scipy + - scikit-learn + - matplotlib + - seaborn + - tensorflow + - keras + - pytorch + - pytables + - ipython + # keras 2.1.6 not available from conda-forge for py37 + # - keras=2.1.6 + - nb_conda_kernels + - ipywidgets + - plotly + - dask + - dask-jobqueue + - python-graphviz + - bayesian-optimization + - hdf5storage + diff --git a/Programming/anaconda/2024.08/conda-env-defs/jupyterhub-4.1.6_lab4_py3.12/jupyterhub-4.1.6_lab4_py3.12.yaml b/Programming/anaconda/2024.08/conda-env-defs/jupyterhub-4.1.6_lab4_py3.12/jupyterhub-4.1.6_lab4_py3.12.yaml new file mode 100644 index 0000000..65c2f56 --- /dev/null +++ b/Programming/anaconda/2024.08/conda-env-defs/jupyterhub-4.1.6_lab4_py3.12/jupyterhub-4.1.6_lab4_py3.12.yaml @@ -0,0 +1,28 @@ +name: jupyterhub-4.1.6_lab4_py3.12 +channels: + - conda-forge +dependencies: + - python=3.12 + - jupyterhub=4.1.6 + - jupyterlab>4 + - nb_conda + - nb_conda_kernels + - jupyter_contrib_nbextensions + - ipywidgets + - batchspawner + # - jupyter_server<2.11 + # needed for widgets! + - ipympl + - pip + - jupytext + - jupyterlab-git + - git + - psycopg2 + - plotly + - jupyterlab-plotly-extension + - flask + # - sqlalchemy=1.4.39 + ################# PIP packages + # - pip: + # - git+https://github.com/jupyterhub/batchspawner.git@e89bf6a + diff --git a/Programming/anaconda/2024.08/config.sh b/Programming/anaconda/2024.08/config.sh new file mode 100644 index 0000000..afc7cb6 --- /dev/null +++ b/Programming/anaconda/2024.08/config.sh @@ -0,0 +1,6 @@ +# version-specific settings + +# Miniconda version. Defaults to "latest" +# Should match the version distributed with anaconda +CONDA_VERSION="24.5.0-0" + diff --git a/Programming/anaconda/build b/Programming/anaconda/build index 36832c4..8092711 100755 --- a/Programming/anaconda/build +++ b/Programming/anaconda/build @@ -1,30 +1,10 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'Programming' +# pbuild::add_to_group 'Programming' - -source "${BUILDBLOCK_DIR}/${V_PKG}/config.sh" -if [[ x"$CONDA_VERSION" == x ]]; then - echo "ERROR: CONDA_VERSION for this release has not been defined" >&2 - exit 1 -fi - -MINICONDA_EXE="Miniconda3-${CONDA_VERSION}-Linux-x86_64.sh" -DOWNLOAD_URL="https://repo.anaconda.com/miniconda/$MINICONDA_EXE" +MINICONDA_EXE="miniconda-${V_PKG}.sh" INSTALLER="$PMODULES_DISTFILESDIR/$MINICONDA_EXE" -pbuild::pre_prep() { - # Need to implement own downloader since pbuild::set_download_url and pbuild::prep - # currently only support tar files - std::info "DEBUG: in function %s...\n" "$FUNCNAME: FUNCNAME=${FUNCNAME[*]}" - if [[ -r "$INSTALLER" ]]; then - std::info "%s using previously downloaded %s\n" \ - "${module_name}/${module_version}:" "$INSTALLER" - else - curl -fsSLo "$INSTALLER" "$DOWNLOAD_URL" - fi -} - pbuild::configure() { : } @@ -35,9 +15,9 @@ pbuild::compile() { pbuild::install() { # Install conda - bash "$INSTALLER" -b -p "$PREFIX/conda" + bash "$INSTALLER" -b -p "$PREFIX/conda" || std::die 3 "Error calling installer!" #echo "Installing PSI admintools for maintaining conda" std::info "%s Installing admintools ...\n" "${module_name}/${module_version}:" - cp -r "${BUILDBLOCK_DIR}/files/admintools" "$PREFIX/admintools" + # cp -r "${BUILDBLOCK_DIR}/files/admintools" "$PREFIX/admintools" } diff --git a/Programming/anaconda/files/config.yaml b/Programming/anaconda/files/config.yaml new file mode 100644 index 0000000..8784b66 --- /dev/null +++ b/Programming/anaconda/files/config.yaml @@ -0,0 +1,15 @@ +format: 1 +anaconda: + defaults: + group: Programming + overlay: base + relstage: stable + + versions: + 2024.08: + config: + urls: + - url: https://repo.anaconda.com/miniconda/Miniconda3-py39_24.5.0-0-Linux-x86_64.sh + name: miniconda-2024.08.sh + unpacker: none + relstage: unstable From bf31c51c6bb988471d3222c1ea51b0c3e323263b Mon Sep 17 00:00:00 2001 From: caubet_m Date: Wed, 16 Oct 2024 17:07:48 +0200 Subject: [PATCH 103/158] v4.1.6 with intel 22.2 and minor fixes --- Compiler/openmpi/build | 2 +- Compiler/openmpi/files/config.yaml | 11 +++++------ 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index d9bd927..58dfcd0 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -87,7 +87,7 @@ pbuild::pre_configure() { std::info "Enabling SLURM." pbuild::add_configure_args "--with-slurm=yes" fi - if pbuild::use_flag slurm || pbuild::use_flag dgx || pbuild::use_flag merlin6; then + if pbuild::use_flag dgx || pbuild::use_flag merlin6 || pbuild::use_flag "gpfs"; then std::info "Enabling GPFS." pbuild::add_configure_args "--with-gpfs=/usr/lpp/mmfs" fi diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index 5a0e595..23f697f 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -10,7 +10,7 @@ openmpi: - --enable-shared - --enable-static docfiles: [AUTHORS, LICENSE, NEWS, README] - Urls: + urls: - url: https://download.open-mpi.org/release/open-mpi/v${V_MAJOR}.${V_MINOR}/openmpi-${V_PKG}.tar.bz2 shasums: openmpi-1.10.0.tar.bz2: 26b432ce8dcbad250a9787402f2c999ecb6c25695b00c9c6ee05a306c78b6490 @@ -70,7 +70,6 @@ openmpi: build_requires: [pmix/5.0.3, hwloc/2.11.1, libfabric/1.15.2.0, patchelf/0.14.5] runtime_deps: [cuda/12.2.0] configure_args+: - - --with-ofi=${LIBFABRIC_VERSION} - --enable-mpi1-compatibility - --with-cxi - --with-lustre @@ -82,6 +81,7 @@ openmpi: variants: - systems: [merlin-.*] suffix: _slurm + use_flags: [merlin6, gpfs] relstage: unstable overlay: base group_deps: @@ -101,7 +101,7 @@ openmpi: - systems: [ra-.*] suffix: _ra - use_flags: [ra] + use_flags: [ra, gpfs] group_deps: compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]} build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, hwloc/2.9.1, patchelf/0.14.5] @@ -114,11 +114,10 @@ openmpi: relstage: unstable overlay: Alps group_deps: - compiler: {gcc: [12.3.0]} - build_requires: [pmix/4.2.9, hwloc/2.11.1, patchelf/0.14.5] + compiler: {gcc: [12.3.0], intelcc: [22.2]} + build_requires: [pmix/4.2.9, hwloc/2.11.1, libfabric/1.15.2.0, patchelf/0.14.5] runtime_deps: [cuda/12.2.0] configure_args+: - - --with-ofi=${LIBFABRIC_PREFIX} - --enable-mpi1-compatibility - --with-lustre use_overlays: [PSI, Alps] From cbbd8333018f5f7a552473e62774ec578882e141 Mon Sep 17 00:00:00 2001 From: caubet_m Date: Wed, 16 Oct 2024 17:07:57 +0200 Subject: [PATCH 104/158] Mpich merlin7 --- Compiler/mpich/build | 84 ++++++++++++++++++------- Compiler/mpich/files/config.yaml | 46 ++++++++++++++ Compiler/mpich/patch/mpich-v3.3.2.patch | 13 ++++ 3 files changed, 122 insertions(+), 21 deletions(-) create mode 100644 Compiler/mpich/files/config.yaml create mode 100644 Compiler/mpich/patch/mpich-v3.3.2.patch diff --git a/Compiler/mpich/build b/Compiler/mpich/build index 3a4324a..8071064 100755 --- a/Compiler/mpich/build +++ b/Compiler/mpich/build @@ -1,28 +1,70 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "http://www.mpich.org/static/downloads/$V/$P-${V_PKG}.tar.gz" -pbuild::add_to_group 'Compiler' -pbuild::install_docfiles 'COPYRIGHT' 'README' - -module use System - pbuild::pre_configure() { - unset F90 - pbuild::add_configure_args "--enable-cxx" - pbuild::add_configure_args "--enable-fortran" - if pbuild::use_flag merlin; then - MXM_DIR='/opt/mellanox/mxm/' - pbuild::add_configure_args "--with-device=ch3:nemesis:mxm" - pbuild::add_configure_args "--with-mxm=${MXM_DIR}" - pbuild::add_configure_args "--without-x" - #pbuild::add_configure_args "--with-slurm-include=/usr/include/slurm" - #pbuild::add_configure_args "--with-slurm-lib=/usr/lib64" - #pbuild::add_configure_args "--with-pmi=slurm" - #pbuild::add_configure_args "--with-pm=no" - pbuild::add_configure_args "--enable-gl=no" + unset F90 + + pbuild::add_configure_args "--enable-shared" + pbuild::add_configure_args "--enable-static" + + if [[ -v CUDA_VERSION ]]; then + std::info "Enabling CUDA ${CUDA_VERSION}." + pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" + fi + + if [[ -v HWLOC_VERSION ]]; then + unset HWLOC_VERSION + std::info "Enabling external hwloc ${HWLOC_PREFIX}." + pbuild::add_configure_args "--with-hwloc=${HWLOC_PREFIX}" + else + pbuild::add_configure_args "--with-hwloc=embedded" + fi + + if [[ -v PMIX_VERSION ]]; then + std::info "Enabling PMIX ${PMIX_VERSION}." + unset PMIX_VERSION + pbuild::add_configure_args "--with-pmix=${PMIX_PREFIX}" + pbuild::add_configure_args "--with-pmi=pmix" + fi + + if pbuild::use_flag merlin7 && [[ ! -v LIBFABRIC_VERSION ]]; then + if pkg-config --exists libfabric; then + std::info "Get LIBFABRIC_VERSION via pkg-config" + LIBFABRIC_PREFIX=$(pkg-config --variable=prefix libfabric) + LIBFABRIC_VERSION="$(LIBFABRIC_PREFIX##*/)" + fi fi - if [[ "${COMPILER}" == 'gcc' ]] && (( ${COMPILER_VERSION%.*.*} == 10 )); then - pbuild::add_configure_args "FFLAGS=-fallow-argument-mismatch" + if [[ -v LIBFABRIC_VERSION ]]; then + std::info "Enabling libfabric ${LIBFABRIC_VERSION}." + if (( V_MAJOR < 4 )); then + pbuild::add_configure_args "--with-ofi=${LIBFABRIC_PREFIX}" + fi + pbuild::add_configure_args "--with-libfabric=${LIBFABRIC_PREFIX}" + fi + + if [[ -v UCX_VERSION ]]; then + std::info "Enabling UCX ${UCX_VERSION}." + pbuild::add_configure_args "--with-ucx=${UCX_PREFIX}" + fi + + if [[ -v INTEL_VERSION ]]; then + pbuild::add_configure_args "CC=icc" + pbuild::add_configure_args "CXX=icpc" + pbuild::add_configure_args "FC=ifort" + pbuild::add_configure_args "F90=ifort" + pbuild::add_configure_args "F77=ifort" + pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" + fi + + if pbuild::use_flag slurm || \ + pbuild::use_flag merlin6 || \ + pbuild::use_flag merlin7; then + std::info "Enabling SLURM." + pbuild::add_configure_args "--with-slurm" fi } +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Compiler/mpich/files/config.yaml b/Compiler/mpich/files/config.yaml new file mode 100644 index 0000000..f54042b --- /dev/null +++ b/Compiler/mpich/files/config.yaml @@ -0,0 +1,46 @@ +--- +# yamllint disable rule:line-length +format: 1 +mpich: + defaults: + group: Compiler + overlay: base + relstage: stable + configure_args: + - --enable-cxx + - --enable-fortran + docfiles: [COPYRIGHT, README] + urls: + - url: http://www.mpich.org/static/downloads/$V/$P-${V_PKG}.tar.gz + shasums: + mpich-3.3.2.tar.gz: 4bfaf8837a54771d3e4922c84071ef80ffebddbb6971a006038d91ee7ef959b9 + mpich-4.2.3.tar.gz: 7a019180c51d1738ad9c5d8d452314de65e828ee240bcb2d1f80de9a65be88a8 + + versions: + 4.2.3: + variants: + - systems: [.*.merlin7.psi.ch] + relstage: unstable + overlay: Alps + use_overlays: [PSI] + use_flags: [merlin7, slurm] + group_deps: + compiler: {gcc: [12.3.0]} + build_requires: [hwloc/2.11.1, libfabric/1.15.2.0, patchelf/0.14.5] + runtime_deps: [cuda/12.2.0] + configure_args+: + - --with-pm=hydra,gforker + 3.3.2: + variants: + - systems: [.*.merlin7.psi.ch] + relstage: unstable + overlay: Alps + use_overlays: [PSI] + use_flags: [merlin7, slurm] + group_deps: + compiler: {gcc: [8.4.0]} + build_requires: [libfabric/1.15.2.0, patchelf/0.14.5] + patch_files: + - patch/mpich-v3.3.2.patch + configure_args+: + - --with-device=ch3:nemesis:ofi diff --git a/Compiler/mpich/patch/mpich-v3.3.2.patch b/Compiler/mpich/patch/mpich-v3.3.2.patch new file mode 100644 index 0000000..559239b --- /dev/null +++ b/Compiler/mpich/patch/mpich-v3.3.2.patch @@ -0,0 +1,13 @@ +diff --git a/src/pm/hydra/tools/bootstrap/external/slurm_query_node_list.c b/src/pm/hydra/tools/bootstrap/external/slurm_query_node_list.c +index 9b35471f3..7b5dd782f 100644 +--- a/src/pm/hydra/tools/bootstrap/external/slurm_query_node_list.c ++++ b/src/pm/hydra/tools/bootstrap/external/slurm_query_node_list.c +@@ -26,7 +26,7 @@ static struct HYD_node *global_node_list = NULL; + #if defined(HAVE_LIBSLURM) + static HYD_status list_to_nodes(char *str) + { +- hostlist_t hostlist; ++ hostlist_t *hostlist; + char *host; + int k = 0; + HYD_status status = HYD_SUCCESS; From cc8d600d4096bc1bb8c79017a3642eed3388e590 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 18 Oct 2024 09:52:36 +0200 Subject: [PATCH 105/158] hwloc: use YAML config file --- Libraries/hwloc/build | 11 ----------- Libraries/hwloc/build-legacy | 13 +++++++++++++ Libraries/hwloc/build-xml | 8 -------- 3 files changed, 13 insertions(+), 19 deletions(-) create mode 100755 Libraries/hwloc/build-legacy delete mode 100755 Libraries/hwloc/build-xml diff --git a/Libraries/hwloc/build b/Libraries/hwloc/build index c65a014..6e021f3 100755 --- a/Libraries/hwloc/build +++ b/Libraries/hwloc/build @@ -1,13 +1,2 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://download.open-mpi.org/release/${P}/v${V_MAJOR}.${V_MINOR}/${P}-${V}.tar.gz" -pbuild::add_to_group 'Libraries' - -pbuild::install_docfiles 'README' 'AUTHORS' 'NEWS' 'COPYING' 'VERSION' - -pbuild::pre_configure() { - pbuild::add_configure_args "--enable-netloc" - pbuild::add_configure_args "--enable-plugins" -} - - diff --git a/Libraries/hwloc/build-legacy b/Libraries/hwloc/build-legacy new file mode 100755 index 0000000..c65a014 --- /dev/null +++ b/Libraries/hwloc/build-legacy @@ -0,0 +1,13 @@ +#!/usr/bin/env modbuild + +pbuild::set_download_url "https://download.open-mpi.org/release/${P}/v${V_MAJOR}.${V_MINOR}/${P}-${V}.tar.gz" +pbuild::add_to_group 'Libraries' + +pbuild::install_docfiles 'README' 'AUTHORS' 'NEWS' 'COPYING' 'VERSION' + +pbuild::pre_configure() { + pbuild::add_configure_args "--enable-netloc" + pbuild::add_configure_args "--enable-plugins" +} + + diff --git a/Libraries/hwloc/build-xml b/Libraries/hwloc/build-xml deleted file mode 100755 index f2b8b67..0000000 --- a/Libraries/hwloc/build-xml +++ /dev/null @@ -1,8 +0,0 @@ -#!/usr/bin/env modbuild - -pbuild::pre_configure() { - pbuild::add_configure_args "--enable-netloc" - pbuild::add_configure_args "--enable-plugins" -} - - From d459fb0878bbbef485a462a3a54a9c6c554b299c Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 18 Oct 2024 13:41:38 +0200 Subject: [PATCH 106/158] hwloc: version 2.11.1 added --- Libraries/hwloc/files/config.yaml | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/Libraries/hwloc/files/config.yaml b/Libraries/hwloc/files/config.yaml index 418f57f..9369141 100644 --- a/Libraries/hwloc/files/config.yaml +++ b/Libraries/hwloc/files/config.yaml @@ -6,15 +6,20 @@ hwloc: docfiles: [README, AUTHORS, NEWS, COPYING, VERSION] urls: - url: https://download.open-mpi.org/release/${P}/v${V_MAJOR}.${V_MINOR}/${P}-${V}.tar.gz + configure_args: + - --enable-netloc + - --enable-plugins shasums: hwloc-2.7.1.tar.gz: 4cb0a781ed980b03ad8c48beb57407aa67c4b908e45722954b9730379bc7f6d5 hwloc-2.9.1.tar.gz: a440e2299f7451dc10a57ddbfa3f116c2a6c4be1bb97c663edd3b9c7b3b3b4cf versions: - 2.7.1: + 2.11.1: config: - relstage: stable - build_requires: cuda/11.5.1 + relstage: unstable + build_requires: [cuda/12.1.1] 2.9.1: config: - relstage: stable - build_requires: cuda/12.1.1 + build_requires: [cuda/12.1.1] + 2.7.1: + config: + build_requires: [cuda/11.5.1] From 62b6760172a050822414b00d4186be91d8d7e9a1 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 18 Oct 2024 14:08:43 +0200 Subject: [PATCH 107/158] hwloc: shasum added for 2.11.1 --- Libraries/hwloc/files/config.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Libraries/hwloc/files/config.yaml b/Libraries/hwloc/files/config.yaml index 9369141..ba2cd31 100644 --- a/Libraries/hwloc/files/config.yaml +++ b/Libraries/hwloc/files/config.yaml @@ -10,8 +10,9 @@ hwloc: - --enable-netloc - --enable-plugins shasums: - hwloc-2.7.1.tar.gz: 4cb0a781ed980b03ad8c48beb57407aa67c4b908e45722954b9730379bc7f6d5 + hwloc-2.11.1.tar.gz: 9f320925cfd0daeaf3a3d724c93e127ecac63750c623654dca0298504aac4c2c hwloc-2.9.1.tar.gz: a440e2299f7451dc10a57ddbfa3f116c2a6c4be1bb97c663edd3b9c7b3b3b4cf + hwloc-2.7.1.tar.gz: 4cb0a781ed980b03ad8c48beb57407aa67c4b908e45722954b9730379bc7f6d5 versions: 2.11.1: config: From 319dde3b7355ee28ec62f99a48ca3883a7818144 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 18 Oct 2024 17:25:03 +0200 Subject: [PATCH 108/158] git: build-block reviewed --- Tools/git/build | 7 ------- Tools/git/build-git-lfs | 17 +++++++++++++++++ Tools/git/{build-yaml => build-legacy} | 7 +++++++ 3 files changed, 24 insertions(+), 7 deletions(-) create mode 100755 Tools/git/build-git-lfs rename Tools/git/{build-yaml => build-legacy} (78%) diff --git a/Tools/git/build b/Tools/git/build index 38fb16c..ebc480e 100755 --- a/Tools/git/build +++ b/Tools/git/build @@ -1,12 +1,5 @@ #!/usr/bin/env modbuild -pbuild::set_download_url \ - "http://www.kernel.org/pub/software/scm/$P/$P-${V_PKG}.tar.gz" -pbuild::add_to_group 'Tools' - -pbuild::compile_in_sourcetree -pbuild::install_docfiles 'COPYING' 'README.md' - pbuild::pre_configure_Darwin() { export NO_APPLE_COMMON_CRYPTO=1 } diff --git a/Tools/git/build-git-lfs b/Tools/git/build-git-lfs new file mode 100755 index 0000000..ca4de42 --- /dev/null +++ b/Tools/git/build-git-lfs @@ -0,0 +1,17 @@ +#!/usr/bin/env modbuild + +unset -f pbuild::configure +unset -f pbuild::compile +pbuild::install(){ + install -m 0755 git-lfs "${PREFIX}/bin" + install -m 0755 -d "${PREFIX}/share/man/man{1,5,7}" + install -m 0644 man/man1/* "${PREFIX}/share/man/man1" + install -m 0644 man/man5/* "${PREFIX}/share/man/man5" + install -m 0644 man/man7/* "${PREFIX}/share/man/man7" +} + +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Tools/git/build-yaml b/Tools/git/build-legacy similarity index 78% rename from Tools/git/build-yaml rename to Tools/git/build-legacy index ebc480e..38fb16c 100755 --- a/Tools/git/build-yaml +++ b/Tools/git/build-legacy @@ -1,5 +1,12 @@ #!/usr/bin/env modbuild +pbuild::set_download_url \ + "http://www.kernel.org/pub/software/scm/$P/$P-${V_PKG}.tar.gz" +pbuild::add_to_group 'Tools' + +pbuild::compile_in_sourcetree +pbuild::install_docfiles 'COPYING' 'README.md' + pbuild::pre_configure_Darwin() { export NO_APPLE_COMMON_CRYPTO=1 } From f3ad8eb3426d78447ac49ca52a3150fd00784a4b Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 18 Oct 2024 17:33:24 +0200 Subject: [PATCH 109/158] parmetis: build-block reviewed --- MPI/parmetis/build | 16 --------- MPI/parmetis/build-legacy | 71 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 71 insertions(+), 16 deletions(-) create mode 100755 MPI/parmetis/build-legacy diff --git a/MPI/parmetis/build b/MPI/parmetis/build index 6a57b34..3003530 100755 --- a/MPI/parmetis/build +++ b/MPI/parmetis/build @@ -1,21 +1,5 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "http://glaros.dtc.umn.edu/gkhome/fetch/sw/$P/$P-${V_PKG}.tar.gz" - -pbuild::add_to_group 'MPI' - -case ${V_MAJOR} in -3 ) - pbuild::install_docfiles CHANGES INSTALL LICENSE.txt README VERSION - ;; -4 ) - pbuild::install_docfiles Changelog Install.txt LICENSE.txt - ;; -* ) - std::die 4 "Unsupported major version!" - ;; -esac - pbuild::configure() { CC=$MPICC CXX=$MPICXX diff --git a/MPI/parmetis/build-legacy b/MPI/parmetis/build-legacy new file mode 100755 index 0000000..6a57b34 --- /dev/null +++ b/MPI/parmetis/build-legacy @@ -0,0 +1,71 @@ +#!/usr/bin/env modbuild + +pbuild::set_download_url "http://glaros.dtc.umn.edu/gkhome/fetch/sw/$P/$P-${V_PKG}.tar.gz" + +pbuild::add_to_group 'MPI' + +case ${V_MAJOR} in +3 ) + pbuild::install_docfiles CHANGES INSTALL LICENSE.txt README VERSION + ;; +4 ) + pbuild::install_docfiles Changelog Install.txt LICENSE.txt + ;; +* ) + std::die 4 "Unsupported major version!" + ;; +esac + +pbuild::configure() { + CC=$MPICC + CXX=$MPICXX + F77=$MPIF77 + F90=$MPIF90 + FC=$MPIFC + FORTRAN=$MPIFORTRAN + if (( V_MAJOR == 4 )) ; then + cmake \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DMETIS_PATH="${SRC_DIR}/metis" \ + -DGKLIB_PATH="${SRC_DIR}/metis/GKlib" \ + "${SRC_DIR}" \ + || exit 1 + fi +} + +pbuild::compile() { + CC=$MPICC + CXX=$MPICXX + F77=$MPIF77 + F90=$MPIF90 + FC=$MPIFC + FORTRAN=$MPIFORTRAN + if (( V_MAJOR == 3 )) ; then + cd "${SRC_DIR}" + make -e -j3 || exit 1 + + mkdir -p $PREFIX/include/metis + mkdir -p $PREFIX/lib + + cp *.h $PREFIX/include + cp METISLib/*.h $PREFIX/include/metis + cp lib*.a $PREFIX/lib + elif (( V_MAJOR == 4 )); then + make -j3 || exit 1 + make install + + LIBMETIS_A=$(find . -name libmetis.a) + METIS_H=$(find "${SRC_DIR}" -name metis.h) + + install -m 0644 $METIS_H $PREFIX/include + install -m 0644 $LIBMETIS_A $PREFIX/lib + else + std::die 42 "Unsupported version: $V" + fi +} + +pbuild::install() { + : +} + +# vim: filetype=sh From 8022044087d1fbb7ae97294b55d709f726cc26da Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Wed, 13 Nov 2024 13:15:19 +0100 Subject: [PATCH 110/158] getopt: reviewed, YAML config --- System/getopt/build | 8 -------- System/getopt/files/config.yaml | 17 +++++++++++++++++ 2 files changed, 17 insertions(+), 8 deletions(-) create mode 100644 System/getopt/files/config.yaml diff --git a/System/getopt/build b/System/getopt/build index 6f25994..b472075 100755 --- a/System/getopt/build +++ b/System/getopt/build @@ -1,13 +1,5 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "http://frodo.looijaard.name/system/files/software/$P/$P-${V_PKG}.tar.gz" -pbuild::compile_in_sourcetree -pbuild::add_to_group System - -pbuild::pre_configure_Linux() { - pbuild::add_patch "files/Makefile.patch" -} - pbuild::configure() { : } diff --git a/System/getopt/files/config.yaml b/System/getopt/files/config.yaml new file mode 100644 index 0000000..a6f1774 --- /dev/null +++ b/System/getopt/files/config.yaml @@ -0,0 +1,17 @@ +--- +format: 1 +getopt: + defaults: + group: System + overlay: base + relstage: stable + patch_files: [files/Makefile.patch] + compile_in_sourcetree: true + urls: + - url: http://frodo.looijaard.name/system/files/software/$P/$P-${V_PKG}.tar.gz + shasums: + getopt-1.1.6.tar.gz: d0bf1dc642a993e7388a1cddfb9409bed375c21d5278056ccca3a0acd09dc5fe + versions: + 1.1.6: + config: + build_requires: [gettext/0.19.8] From 66117615f1dd5cdcb19ededcea1cc37e4372145b Mon Sep 17 00:00:00 2001 From: caubet_m Date: Wed, 13 Nov 2024 13:25:48 +0100 Subject: [PATCH 111/158] Libfabric rework for Pmodules 1.1.22+ --- Libraries/libfabric/build | 37 +++++++++++++++++++++++--- Libraries/libfabric/files/config.yaml | 28 +++++++++++++++++-- Libraries/libfabric/files/from-git.txt | 2 ++ 3 files changed, 61 insertions(+), 6 deletions(-) create mode 100644 Libraries/libfabric/files/from-git.txt diff --git a/Libraries/libfabric/build b/Libraries/libfabric/build index 0580efc..b6e33ef 100755 --- a/Libraries/libfabric/build +++ b/Libraries/libfabric/build @@ -1,7 +1,36 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://github.com/ofiwg/libfabric/releases/download/v$V/$P-$V.tar.bz2" -pbuild::add_to_group 'Libraries' - -pbuild::install_docfiles 'COPYING' 'AUTHORS' 'README' 'NEWS.md' +# Check 'version-to-gitcommit.txt' +# - If version exists, we will compile directly from GIT cloned commit. +# - If version does not exist, install from GIT repository package (tag). +GITURL=$(grep -E "^${V}" files/from-git.txt | awk '{print $2}') +BRANCH=$(grep -E "^${V}" files/from-git.txt | awk '{print $3}') +CHERRY=$(grep -E "^${V}" files/from-git.txt | awk -F'cherry-pick:' '{print $2}') +CHERRY_COMMIT=$(echo "$CHERRY" | awk -F'|' '{print $1}') +CHERRY_REPO=$(echo "$CHERRY" | awk -F'|' '{print $2}') +if [[ -n ${GITURL} ]]; then + pbuild::pre_prep() { + if [[ ! -f ${PMODULES_DISTFILESDIR}/${P}-${V}.tar.bz2 ]]; then + git clone ${GITURL} ${P} + cd ${P} + if [[ -n ${BRANCH} ]]; then + git fetch -a + git checkout ${BRANCH} + fi + if [[ -n ${CHERRY_REPO} ]]; then + git remote add remotetmp $CHERRY_REPO + git fetch --all + fi + + if [[ -n ${CHERRY_COMMIT} ]]; then + git cherry-pick $CHERRY_COMMIT + fi + + ./autogen.sh + cd .. + tar --exclude-vcs --remove-files -cvf ${PMODULES_DISTFILESDIR}/${P}-${V}.tar ${P} + bzip2 ${PMODULES_DISTFILESDIR}/${P}-${V}.tar + fi + } +fi diff --git a/Libraries/libfabric/files/config.yaml b/Libraries/libfabric/files/config.yaml index 981efdc..cebfb3f 100644 --- a/Libraries/libfabric/files/config.yaml +++ b/Libraries/libfabric/files/config.yaml @@ -3,14 +3,14 @@ libfabric: defaults: group: Libraries relstage: stable - compile_in_sourcetree: yes + compile_in_sourcetree: true docfiles: - AUTHORS - README - COPYING - NEWS.md urls: - - url: https://github.com/ofiwg/libfabric/releases/download/v$V/$P-$V.tar.bz2 + - url: https://github.com/ofiwg/libfabric/releases/download/v${V}/${P}-${V}.tar.bz2 shasums: libfabric-1.13.0.tar.bz2: 0c68264ae18de5c31857724c754023351614330bd61a50b40cef2b5e8f63ab28 libfabric-1.18.0.tar.bz2: 912fb7c7b3cf2a91140520962b004a1c5d2f39184adbbd98ae5919b0178afd43 @@ -18,3 +18,27 @@ libfabric: 1.18.0: config: build_requires: [gcc/10.4.0] + 1.22.0: + config: + relstage: unstable + variants: + - systems: [.*.merlin7.psi.ch] + overlay: Alps + use_overlays: [PSI] + use_flags: [merlin7] + build_requires: [gcc/12.3.0, libfabric/1.15.2.0] + configure_args+: + - --enable-cxi + 2.0.0: + config: + relstage: unstable + urls: + - url: https://github.com/ofiwg/libfabric/releases/download/v${V}alpha/$P-${V}alpha.tar.bz2 + variants: + - systems: [.*.merlin7.psi.ch] + overlay: Alps + use_overlays: [PSI] + use_flags: [merlin7] + build_requires: [gcc/12.3.0, libfabric/1.15.2.0] + configure_args+: + - --enable-cxi diff --git a/Libraries/libfabric/files/from-git.txt b/Libraries/libfabric/files/from-git.txt new file mode 100644 index 0000000..9e55042 --- /dev/null +++ b/Libraries/libfabric/files/from-git.txt @@ -0,0 +1,2 @@ +1.22.0 https://github.com/thomasgillis/libfabric.git dev-cxi +# 1.22.0 https://github.com/ofiwg/libfabric.git main cherry-pick:5793243aec20c4fee126aa3093ff07bb5889f154|https://github.com/raffenet/libfabric.git From ef76df3a07c53657c425850338443a470d2a6d07 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 21 Nov 2024 15:37:15 +0100 Subject: [PATCH 112/158] cuda: review and YAML config file --- Programming/cuda/build | 32 +++------- Programming/cuda/files/config.yaml | 95 ++++++++++++++++++++++++++++++ 2 files changed, 102 insertions(+), 25 deletions(-) create mode 100644 Programming/cuda/files/config.yaml diff --git a/Programming/cuda/build b/Programming/cuda/build index 417baa6..b04936f 100755 --- a/Programming/cuda/build +++ b/Programming/cuda/build @@ -1,29 +1,11 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'Programming' - -pbuild::prep() { - : -} - -pbuild::configure() { - : -} - -pbuild::compile() { - : -} - -pbuild::install() { - : -} - pbuild::post_install() { - if [ -f "/opt/psi/Programming/cuda/${V_PKG}/lib64/stubs/libnvidia-ml.so" ] - then - if [ ! -f "/opt/psi/Programming/cuda/${V_PKG}/lib64/stubs/libnvidia-ml.so.1" ] - then - ln -s /opt/psi/Programming/cuda/$V/lib64/stubs/libnvidia-ml.so /opt/psi/Programming/cuda/${V_PKG}/lib64/stubs/libnvidia-ml.so.1 - fi - fi + cd "${PREFIX}/lib64/stubs" + for lib in lib*; do + local soname="$(patchelf --print-soname "${lib}" 2>/dev/null)" || continue + if [[ ! -e "${soname}" ]]; then + ln -s "${lib}" "${soname}" + fi + done } diff --git a/Programming/cuda/files/config.yaml b/Programming/cuda/files/config.yaml new file mode 100644 index 0000000..1afd260 --- /dev/null +++ b/Programming/cuda/files/config.yaml @@ -0,0 +1,95 @@ +--- +format: 1 +cuda: + defaults: + group: Programming + overlay: base + relstage: stable + build_variants: first_match + build_functions: + configure: [] + compile: [] + install: [pbuild::post_install] + urls: + - &cuda-12_2_2-aarch64 url: https://developer.download.nvidia.com/compute/cuda/12.2.2/local_installers/cuda_12.2.2_535.104.05_linux_sbsa.run + unpacker: none + - &cuda-12_2_2-x86_64 + url: https://developer.download.nvidia.com/compute/cuda/12.2.2/local_installers/cuda_12.2.2_535.104.05_linux.run + unpacker: none + - &cuda-12_2_0-aarch64 + url: https://developer.download.nvidia.com/compute/cuda/12.2.0/local_installers/cuda_12.2.0_535.54.03_linux_sbsa.run + unpacker: none + - &cuda-12_2_0-x86_64 + url: https://developer.download.nvidia.com/compute/cuda/12.2.0/local_installers/cuda_12.2.0_535.54.03_linux.run + unpacker: none + - &cuda-12_1_1-aarch64 + url: https://developer.download.nvidia.com/compute/cuda/12.1.1/local_installers/cuda_12.1.1_530.30.02_linux_sbsa.run + unpacker: none + - &cuda-12_1_1-x86_64 + url: https://developer.download.nvidia.com/compute/cuda/12.1.1/local_installers/cuda_12.1.1_530.30.02_linux.run + unpacker: none + + shasums: + cuda_12.2.2_535.104.05_linux.run: 2b39aae3e7618d9f59a3c8fa1f1bc61f29c0b0e0df75fb05076badb352952ef2 + cuda_12.2.2_535.104.05_linux_sbsa.run: 4113a15e6b27a02638c72edeb5f89de4c9ea312febba12fc4cefff2edc882268 + cuda_12.2.0_535.54.03_linux.run: ecf3d2afadcbac029f0f4505785810d52d006e4b87ba79ff3f984336a2bbf518 + cuda_12.2.0_535.54.03_linux_sbsa.run: 9c90d79bb63952cd30f1f57f9f8fe11e7a8967bba6f824df45d3464b5d37e5d8 + cuda_12.1.1_530.30.02_linux.run: d74022d41d80105319dfa21beea39b77a5b9919539c0487a05caaf2446d6a70e + cuda_12.1.1_530.30.02_linux_sbsa.run: 45ea4cd860f0a26d3db8ce032530f2ee0b55abdd587545213d395a73623b4278 + + versions: + 12.2.2: + variants: + - target_cpus: [aarch64] + systems: [gpu.*.merlin7.psi.ch] + relstage: unstable + overlay: PSI + urls: + - *cuda-12_2_2-aarch64 + - target_cpus: [x86_64] + systems: [.*.merlin7.psi.ch] + relstage: unstable + overlay: PSI + urls: + - *cuda-12_2_2-x86_64 + - target_cpus: [x86_64] + relstage: unstable + urls: + - *cuda-12_2_2-x86_64 + + 12.2.0: + variants: + - target_cpus: [aarch64] + systems: [gpu.*.merlin7.psi.ch] + relstage: unstable + urls: + - *cuda-12_2_0-aarch64 + - target_cpus: [x86_64] + systems: [.*.merlin7.psi.ch] + relstage: unstable + overlay: PSI + urls: + - *cuda-12_2_0-x86_64 + - target_cpus: [x86_64] + relstage: unstable + urls: + - *cuda-12_2_0-x86_64 + + 12.1.1: + variants: + - target_cpus: [aarch64] + systems: [gpu.*.merlin7.psi.ch] + overlay: PSI + relstage: unstable + urls: + - *cuda-12_1_1-aarch64 + + - target_cpus: [x86_64] + systems: [.*.merlin7.psi.ch] + overlay: PSI + urls: + - *cuda-12_1_1-x86_64 + + - target_cpus: [x86_64] + urls: + - *cuda-12_1_1-x86_64 From c9bda4b5eee43673754a81156f9b35066bc211a1 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 22 Nov 2024 10:44:34 +0100 Subject: [PATCH 113/158] cuda: set library pathes on non-gpu systems --- Programming/cuda/modulefile | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/Programming/cuda/modulefile b/Programming/cuda/modulefile index b626491..69c68ce 100644 --- a/Programming/cuda/modulefile +++ b/Programming/cuda/modulefile @@ -13,15 +13,12 @@ harnessing the power of the graphics processing unit (GPU). prepend-path CUDA_PATH "$PREFIX" -# libnvidia-ml.so in GDK package is a stub library that is attached only for build purposes -prepend-path LIBRARY_PATH "$PREFIX/lib64/stubs" -prepend-path LIBRARY_PATH "$PREFIX/targets/x86_64-linux/lib/stubs" +if {[catch {exec /usr/sbin/modinfo -d nvidia} result]} { + # add if the module is *not* loaded => we are on a system without GPU + prepend-path LIBRARY_PATH "$PREFIX/lib64/stubs" + prepend-path LD_LIBRARY_PATH "$PREFIX/lib/stubs" +} prepend-path C_INCLUDE_PATH "$PREFIX/targets/x86_64-linux/include" prepend-path CPLUS_INCLUDE_PATH "$PREFIX/targets/x86_64-linux/include" -# We should always run with libnvidia-ml.so that is installed with your NVIDIA Display Driver. -# By default it's installed in /usr/lib and /usr/lib64. -# Therefore, LD_LIBRARY_PATH must not contain any libnvidia-ml.so reference in the GDK package -# prepend-path LD_LIBRARY_PATH "$PREFIX/lib/stubs" -# prepend-path LD_LIBRARY_PATH "$PREFIX/targets/x86_64-linux/lib/stubs" From ec9f7220638f095c7578e8418e351f0add79a521 Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Fri, 22 Nov 2024 17:16:03 +0100 Subject: [PATCH 114/158] Add gcc 8.5.0 for ALPS --- Programming/gcc/files/config.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/Programming/gcc/files/config.yaml b/Programming/gcc/files/config.yaml index 7630e47..4802bde 100644 --- a/Programming/gcc/files/config.yaml +++ b/Programming/gcc/files/config.yaml @@ -168,6 +168,16 @@ gcc: - overlay: base systems: [rhel.*] + 8.5.0: + config: + relstage: unstable + build_requires: [gmp/6.3.0, mpfr/4.2.1, mpc/1.3.1-1] + configure_args+: + - --enable-languages=c,c++,objc,obj-c++,lto,fortran,go + variants: + - overlay: PSI + systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] + 8.4.0: config: restage: stable From 320261af89e11cee058c38bf68f66638f20a13aa Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 22 Nov 2024 18:42:37 +0100 Subject: [PATCH 115/158] patchelf: 0.18.0 added; YAML config --- System/patchelf/build | 6 ------ System/patchelf/build-xml | 6 ------ System/patchelf/files/config.yaml | 3 ++- 3 files changed, 2 insertions(+), 13 deletions(-) delete mode 100755 System/patchelf/build-xml diff --git a/System/patchelf/build b/System/patchelf/build index 37dad10..bd8e687 100755 --- a/System/patchelf/build +++ b/System/patchelf/build @@ -1,11 +1,5 @@ #!/usr/bin/env modbuild -# :FIXME: needs review - -pbuild::set_download_url "https://github.com/NixOS/$P/archive/$V.tar.gz" "$P-$V.tar.gz" - -pbuild::add_to_group 'System' - pbuild::post_prep() { cd "${SRC_DIR}" ./bootstrap.sh diff --git a/System/patchelf/build-xml b/System/patchelf/build-xml deleted file mode 100755 index bd8e687..0000000 --- a/System/patchelf/build-xml +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env modbuild - -pbuild::post_prep() { - cd "${SRC_DIR}" - ./bootstrap.sh -} diff --git a/System/patchelf/files/config.yaml b/System/patchelf/files/config.yaml index 8a4dab5..320cfd0 100644 --- a/System/patchelf/files/config.yaml +++ b/System/patchelf/files/config.yaml @@ -11,7 +11,8 @@ patchelf: patchelf-0.8.1.tar.bz2: 12367e9ce9c315a26e14f11db8542e2e0f3a877aff52590912111268cb775bef7ce713368eb3759df6823f457a7b6d0419fd02c231d40db5dd0b853f41caf254 patchelf-0.11.tar.gz: b156bad513d5bac33aaf61d5f04d5a78efc81abf8c0ccb851f605e1137c21e671b4933263a47543daf5064db5e83c9afa836b1aea143fca7d8e6a18ebf96beb8 patchelf-0.12.tar.gz: 2563a5b22b90392d5755d9a08022daf8570fa1b741becbbca92548d0a2f82f7ee21175a2c34816a4653c89c2219bf59b1440304b0fa2d49842e398ab18b9923c - patchelf-0.14.5.tar.gz: 1b7eca84f6fe2d6f6d4469ca1ccdf35dc920d2052ba94b7daeba6c8cb41fdaff20b1e5bac7c8a7650ff12bf4156da87f84d32e75b09958636dc992a1b7b1a59d + patchelf-0.14.5.tar.gz: ca6ef65d53842a0e38f43aeb0a476a537c29c8528a5f613bb1ef16e08f6756d9 + patchelf-0.18.0.tar.gz: 1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7 versions: 0.8.1;0.11;0.12;0.14.5: From 3a53e81e8862b3f3890c7ce28dee3ca505ffa3bd Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Thu, 5 Dec 2024 15:33:42 +0100 Subject: [PATCH 116/158] add napari module --- EM/napari/README.md | 12 ++++++++++++ EM/napari/build | 27 +++++++++++++++++++++++++++ EM/napari/environment.yaml | 11 +++++++++++ EM/napari/files/config.yaml | 13 +++++++++++++ EM/napari/modulefile | 34 ++++++++++++++++++++++++++++++++++ 5 files changed, 97 insertions(+) create mode 100644 EM/napari/README.md create mode 100755 EM/napari/build create mode 100644 EM/napari/environment.yaml create mode 100644 EM/napari/files/config.yaml create mode 100644 EM/napari/modulefile diff --git a/EM/napari/README.md b/EM/napari/README.md new file mode 100644 index 0000000..0c1b1b0 --- /dev/null +++ b/EM/napari/README.md @@ -0,0 +1,12 @@ +# napari-boxmanager + +The napari module is built in combination with the crYOLO module : + +From crYOLO/1.9.9 crYOLO exists as two different conda envs, one crYOLO (code itself) env, one napari (visualization) env. +The installation notes recommend to link one into another, on Merlin7 simply two different modules and envs exist. +Users need to load one env in one terminal ( crYOLO itself) and another for visualization (napari). + +## Adding New Versions + +Adding new versions: change the environment file in the build folder accordingly (and the config.yaml file) and run the build script. + diff --git a/EM/napari/build b/EM/napari/build new file mode 100755 index 0000000..789c7bd --- /dev/null +++ b/EM/napari/build @@ -0,0 +1,27 @@ +#!/usr/bin/env modbuild + + +pbuild::configure() { + #MINICONDA INSTALL + mkdir -p "$PREFIX/miniconda" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" + + + #CREATE ENV , make sure to source the "correct" conda.sh + "$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml" + +} + +#DO NOTHING +pbuild::compile(){ + : +} + +pbuild::install(){ + : +} + + + + diff --git a/EM/napari/environment.yaml b/EM/napari/environment.yaml new file mode 100644 index 0000000..422be97 --- /dev/null +++ b/EM/napari/environment.yaml @@ -0,0 +1,11 @@ +channels: + - conda-forge + - anaconda +dependencies: + - python=3.10 + - pyqt + - napari=0.4.17 + - pip + - pip: + - napari-boxmanager + diff --git a/EM/napari/files/config.yaml b/EM/napari/files/config.yaml new file mode 100644 index 0000000..7b4c0ed --- /dev/null +++ b/EM/napari/files/config.yaml @@ -0,0 +1,13 @@ +--- +format: 1 +napari: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 0.4.17: + variants: + - overlay: Alps + systems: [.*.merlin7.psi.ch] + relstage: unstable diff --git a/EM/napari/modulefile b/EM/napari/modulefile new file mode 100644 index 0000000..4855327 --- /dev/null +++ b/EM/napari/modulefile @@ -0,0 +1,34 @@ +#%Module + +module-whatis "Particle selection tool for cryo-em (crYOLO) " +module-url "https://cryolo.readthedocs.io/en/stable/installation.html#install-napari-and-the-boxmanager-plugin" +module-license "SPHIRE-crYOLO Complimentary Science Software License (http://sphire.mpg.de/wiki/doku.php?id=cryolo_license). Non-commercial academic and research purposes only" +module-maintainer "Greta Assmann " + +module-help "Napari-Boxmanager is a tool to use in combination with crYOLO (visualization for particle picking) " + +# Check for supported shell types +set shelltype [module-info shelltype] +switch -- $shelltype { + "sh" { + puts stdout "conda(){ :; };" + puts stdout "set +u" + puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n" + } + default { + puts stderr "Shells of type '$shelltype' are NOT supported!" + } +} + + +switch [module-info mode] { + "load" { + # Relies on the anaconda module being loaded since we need to update the path + puts stdout "conda activate ${P}_${V};\n" + } + "unload" - + "remove" { + puts stdout "conda deactivate;\n" + } +} + From 63734968510b242ac43737750ff97ab6cec8fcfb Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Thu, 5 Dec 2024 16:26:39 +0100 Subject: [PATCH 117/158] 1.9.9 for merlin7 --- EM/crYOLO/README.md | 15 ++++++++------- EM/crYOLO/build | 25 ++++++++++++++++--------- EM/crYOLO/files/config-1.2.3.sh | 10 ---------- EM/crYOLO/files/config.yaml | 13 +++++++++++++ EM/crYOLO/files/variants | 5 ----- EM/crYOLO/modulefile | 18 +++++------------- 6 files changed, 42 insertions(+), 44 deletions(-) delete mode 100644 EM/crYOLO/files/config-1.2.3.sh create mode 100644 EM/crYOLO/files/config.yaml delete mode 100644 EM/crYOLO/files/variants diff --git a/EM/crYOLO/README.md b/EM/crYOLO/README.md index 9845306..0af8110 100644 --- a/EM/crYOLO/README.md +++ b/EM/crYOLO/README.md @@ -1,14 +1,15 @@ # crYOLO crYOLO/1.2.3 was built as a miniconda independent environment. -Subsequent versions are deployed as central conda environments. -This significantly changed the build process. +Subsequent versions (up to 1.6.1) are deployed as central conda environments + +crYOLO/1.9.9 (Merlin7, oct 2024) is installed with an independent miniconda setup again. + +From crYOLO/1.9.9 crYOLO exists as two different conda envs, one crYOLO (code itself) env, one napari (visualization) env. +The installation notes recommend to link one into another, on Merlin7 simply two different modules and envs exist. +Users need to load one env in one terminal ( crYOLO itself) and another for visualization (napari). ## Adding New Versions -To add a new version, first create the conda environment, as described in -../../Programming/anaconda/2019.07/conda-env-defs/cryolo/. - -Next, update files/variants with the new version and run `./build ` to -install the modulefile +Adding new versions: change the environment file in the build folder accordingly (and the config.yaml file) and run the build script. diff --git a/EM/crYOLO/build b/EM/crYOLO/build index 6f1766a..789c7bd 100755 --- a/EM/crYOLO/build +++ b/EM/crYOLO/build @@ -1,20 +1,27 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'EM' -pbuild::prep() { - : -} - pbuild::configure() { + #MINICONDA INSTALL + mkdir -p "$PREFIX/miniconda" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" + + + #CREATE ENV , make sure to source the "correct" conda.sh + "$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml" + +} + +#DO NOTHING +pbuild::compile(){ : } -pbuild::compile() { +pbuild::install(){ : } -pbuild::install() { - : -} + + diff --git a/EM/crYOLO/files/config-1.2.3.sh b/EM/crYOLO/files/config-1.2.3.sh deleted file mode 100644 index 319d977..0000000 --- a/EM/crYOLO/files/config-1.2.3.sh +++ /dev/null @@ -1,10 +0,0 @@ -# crYOLO configuration variables - -# Miniconda installer filename. Defaults to 'latest' -MINICONDA_VERSION='Miniconda2-4.5.12-Linux-x86_64.sh' - -# cryoloBM download url -CRYOLOBM_URL='ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_1_1/cryoloBM-1.1.1.tar.gz' -# cryolo download url. Default: -#CRYOLO_URL='ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_2_3/cryolo-1.2.3.tar.gz' - diff --git a/EM/crYOLO/files/config.yaml b/EM/crYOLO/files/config.yaml new file mode 100644 index 0000000..8b6b49a --- /dev/null +++ b/EM/crYOLO/files/config.yaml @@ -0,0 +1,13 @@ +--- +format: 1 +crYOLO: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 1.9.9: + variants: + - overlay: Alps + systems: [.*.merlin7.psi.ch] + relstage: unstable diff --git a/EM/crYOLO/files/variants b/EM/crYOLO/files/variants deleted file mode 100644 index 3248392..0000000 --- a/EM/crYOLO/files/variants +++ /dev/null @@ -1,5 +0,0 @@ -crYOLO/1.2.3 deprecated cuda/9.0.176 -crYOLO/1.5.6_gpu stable anaconda/2019.07 -crYOLO/1.6.1_gpu stable anaconda/2019.07 -crYOLO/1.6.1_cpu stable anaconda/2019.07 - diff --git a/EM/crYOLO/modulefile b/EM/crYOLO/modulefile index 41cf27a..4a9df37 100644 --- a/EM/crYOLO/modulefile +++ b/EM/crYOLO/modulefile @@ -3,7 +3,7 @@ module-whatis "crYOLO is a fast and accurate particle picking procedure for electron microscopy" module-url "http://sphire.mpg.de/wiki/doku.php?id=pipeline:window:cryolo" module-license "SPHIRE-crYOLO Complimentary Science Software License (http://sphire.mpg.de/wiki/doku.php?id=cryolo_license). Non-commercial academic and research purposes only" -module-maintainer "Spencer Bliven " +module-maintainer "Greta Assmann " module-help " CrYOLO is a fast and accurate particle picking procedure. It's based on @@ -26,28 +26,20 @@ convolutional neural networks and utilizes the popular You Only Look Once set shelltype [module-info shelltype] switch -- $shelltype { "sh" { - puts stdout "source \"\${ANACONDA_PREFIX}\"/admintools/conda_setup.sh;\n" + puts stdout "conda(){ :; };" + puts stdout "set +u" + puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n" } default { puts stderr "Shells of type '$shelltype' are NOT supported!" } } -# Determine useflags and construct conda env name -set list [split $V "_"] -set version [lindex ${list} 0] -set useflags [lrange ${list} 1 end] -set flavour [lindex $useflags 0] -set env_to_activate [string tolower ${P}]-${version}-${flavour} - -#puts stderr "P/V: $P/$V" -#puts stderr "USEFLAG: [lindex $useflags 0]" -#puts stderr "$env_to_activate" switch [module-info mode] { "load" { # Relies on the anaconda module being loaded since we need to update the path - puts stdout "conda activate $env_to_activate;\n" + puts stdout "conda activate ${P}_${V};\n" } "unload" - "remove" { From 8e08282bb9221edc5decdf4e514e937d5af16d36 Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Mon, 16 Dec 2024 14:16:34 +0100 Subject: [PATCH 118/158] new version 5.0.0 on merlin7 --- EM/IMOD/README.md | 4 ++++ EM/IMOD/build | 21 +++++++++++---------- EM/IMOD/files/config.yaml | 15 +++++++++++++++ EM/IMOD/files/variants | 4 ---- EM/IMOD/modulefile | 7 ++++++- 5 files changed, 36 insertions(+), 15 deletions(-) create mode 100644 EM/IMOD/files/config.yaml delete mode 100644 EM/IMOD/files/variants diff --git a/EM/IMOD/README.md b/EM/IMOD/README.md index 034c88d..452197b 100644 --- a/EM/IMOD/README.md +++ b/EM/IMOD/README.md @@ -12,3 +12,7 @@ The installation includes environment scripts which install into `$IMOD_DIR/profile.d`. These are sourced in the modulefile. This means that the module cannot be unloaded cleanly (eg IMOD remains in the PATH after unloading). + +TODO solution: re-write the .sh script that is sourced in the modulefile into the +modulefile directly. Variables and Path extensions will then automatically be +"unset" when unloding. diff --git a/EM/IMOD/build b/EM/IMOD/build index f4fdc4d..2a4b937 100755 --- a/EM/IMOD/build +++ b/EM/IMOD/build @@ -1,18 +1,16 @@ #!/usr/bin/env modbuild -set -e -pbuild::add_to_group 'EM' pbuild::prep() { : ${CUDA_VERSION:?No CUDA_VERSION set} + #local cuda="${CUDA_VERSION%.*}" IF the cua version matches the cuda version in the filename local cuda="${CUDA_VERSION%.*}" - local filename="imod_${V_PKG}_RHEL7-64_CUDA${cuda}.sh" - if [[ $V_RELEASE == *beta* ]]; then - local url="https://bio3d.colorado.edu/ftp/latestIMOD/RHEL7-64_CUDA${cuda}/$filename" - else - local url="https://bio3d.colorado.edu/imod/AMD64-RHEL5/$filename" - fi + #otherwise: + local cuda="12.0" + local filename="imod_${V_PKG}_RHEL8-64_CUDA${cuda}.sh" + # beta release link for Merlin7 ( RH8 for Opensuse) + local url="https://bio3d.colorado.edu/ftp/latestIMOD/RHEL8-64_CUDA${cuda}/$filename" local dst="$PMODULES_DISTFILESDIR/${filename}" if [ -f "$dst" ]; then echo "Found cached $dst" >&2 @@ -35,8 +33,11 @@ pbuild::compile() { pbuild::install() { : ${CUDA_VERSION:?No CUDA_VERSION set} - local cuda="${CUDA_VERSION%.*}" - local filename="imod_${V_PKG}_RHEL7-64_CUDA${cuda}.sh" + #local cuda="${CUDA_VERSION%.*}" + #(if cuda version matches the file name) if not: + local cuda="12.0" + + local filename="imod_${V_PKG}_RHEL8-64_CUDA${cuda}.sh" local dst="$PMODULES_DISTFILESDIR/${filename}" mkdir -p "$PREFIX/profile.d" diff --git a/EM/IMOD/files/config.yaml b/EM/IMOD/files/config.yaml new file mode 100644 index 0000000..c62c171 --- /dev/null +++ b/EM/IMOD/files/config.yaml @@ -0,0 +1,15 @@ +--- +format: 1 +IMOD: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 5.0.0: + variants: + - overlay: Alps + systems: [.*.merlin7.psi.ch] + relstage: unstable + runtime_deps: + - cuda/12.2.0 diff --git a/EM/IMOD/files/variants b/EM/IMOD/files/variants deleted file mode 100644 index 2c4368a..0000000 --- a/EM/IMOD/files/variants +++ /dev/null @@ -1,4 +0,0 @@ -IMOD/4.9.5 stable -IMOD/4.11.20 stable cuda/10.1.105 -IMOD/4.11.24 unstable cuda/10.1.105 -IMOD/4.12.50-beta unstable cuda/10.1.105 diff --git a/EM/IMOD/modulefile b/EM/IMOD/modulefile index d19b9e2..e3f1302 100644 --- a/EM/IMOD/modulefile +++ b/EM/IMOD/modulefile @@ -3,7 +3,7 @@ module-whatis "IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections." module-url "http://bio3d.colorado.edu/imod/" module-license "mostly GPLv2.0, with the exceptions, see http://bio3d.colorado.edu/imod/COPYRIGHT.txt" -module-maintainer "Spencer Bliven / Dmitry Ozerov " +module-maintainer "Greta Assmann - greta.assmann@psi.ch" module-help " IMOD is a set of image processing, modeling and display programs used for tomographic @@ -34,6 +34,11 @@ For tomographic reconstruction, see also: > tomographic reconstruction in IMOD. J. Struct. Biol. 197:102-113. " +# TO DO : rewrite IMOD-linx.sh script directly into the following section instead of sourcing the script + +#this is needed to NOT set the default IMOD_DIR by pmodules, as this is set later in the IMOD-linux.sh +set dont-setenv { IMOD_DIR } + switch [module-info mode] { "load" { puts stdout "source $PREFIX/profile.d/IMOD-linux.sh" From 51547afd7618b1cdf746c38d3fb08fe31d43deca Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Mon, 16 Dec 2024 15:20:00 +0100 Subject: [PATCH 119/158] add topaz merlin7 --- EM/topaz/README.md | 34 ++++++++++++++++++++++++++++++++++ EM/topaz/build | 27 +++++++++++++++++++++++++++ EM/topaz/environment.yaml | 8 ++++++++ EM/topaz/files/config.yaml | 13 +++++++++++++ EM/topaz/modulefile | 34 ++++++++++++++++++++++++++++++++++ 5 files changed, 116 insertions(+) create mode 100644 EM/topaz/README.md create mode 100755 EM/topaz/build create mode 100644 EM/topaz/environment.yaml create mode 100644 EM/topaz/files/config.yaml create mode 100644 EM/topaz/modulefile diff --git a/EM/topaz/README.md b/EM/topaz/README.md new file mode 100644 index 0000000..7b5063d --- /dev/null +++ b/EM/topaz/README.md @@ -0,0 +1,34 @@ +# TOPAZ + +The topaz module is build for using it with the cryosparc software. An executable path to the topaz binary needs to be provided in cryosparc. + +## Adding New Versions + +Adding new versions: change the environment file in the build folder accordingly (and the config.yaml file) and run the build script. +IMPORTANT: Build it on the GPU node , otherwise the pytorch installation will not enable GPU support. + +## HINTS + +Current successful environment.yaml file: + +channels: + - tbepler + - pytorch +dependencies: + - python=3.6 + - cudatoolkit + - topaz + - pytorch + +- specifing cudatoolkit version of 11.8 failed for GPU support (see below) +- specifing higher python/cudatoolkit versions lead to higher pytorch versions, which again failed for topaz to run successful (https://discuss.cryosparc.com/t/topaz-train-typeerror-concat-takes-1-positional-argument-but-2-were-given/11240/18) + +## Versions + +Nov. 2024: 0.2.5 (TOPAZ) with +``` +python3.6 +cudatoolkit 11.3.1 h2bc3f7f_2 +pytorch 1.10.2 py3.6_cuda11.3_cudnn8.2.0_0 +pytorch-mutex 1.0 cuda +``` diff --git a/EM/topaz/build b/EM/topaz/build new file mode 100755 index 0000000..789c7bd --- /dev/null +++ b/EM/topaz/build @@ -0,0 +1,27 @@ +#!/usr/bin/env modbuild + + +pbuild::configure() { + #MINICONDA INSTALL + mkdir -p "$PREFIX/miniconda" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" + + + #CREATE ENV , make sure to source the "correct" conda.sh + "$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml" + +} + +#DO NOTHING +pbuild::compile(){ + : +} + +pbuild::install(){ + : +} + + + + diff --git a/EM/topaz/environment.yaml b/EM/topaz/environment.yaml new file mode 100644 index 0000000..8f19db7 --- /dev/null +++ b/EM/topaz/environment.yaml @@ -0,0 +1,8 @@ +channels: + - tbepler + - pytorch +dependencies: + - python=3.6 + - cudatoolkit + - topaz + - pytorch diff --git a/EM/topaz/files/config.yaml b/EM/topaz/files/config.yaml new file mode 100644 index 0000000..6841a46 --- /dev/null +++ b/EM/topaz/files/config.yaml @@ -0,0 +1,13 @@ +--- +format: 1 +topaz: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 0.2.5: + variants: + - overlay: Alps + systems: [.*.merlin7.psi.ch] + relstage: unstable diff --git a/EM/topaz/modulefile b/EM/topaz/modulefile new file mode 100644 index 0000000..4527b50 --- /dev/null +++ b/EM/topaz/modulefile @@ -0,0 +1,34 @@ +#%Module + +module-whatis "A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph and tomogram denoising using deep denoising models." +module-url "https://github.com/tbepler/topaz" +module-license "https://github.com/tbepler/topaz/blob/master/LICENSE" +module-maintainer "Greta Assmann " + +module-help "Particle Picker for CryoEM. Used with Cryosparc" + +# Check for supported shell types +set shelltype [module-info shelltype] +switch -- $shelltype { + "sh" { + puts stdout "conda(){ :; };" + puts stdout "set +u" + puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n" + } + default { + puts stderr "Shells of type '$shelltype' are NOT supported!" + } +} + + +switch [module-info mode] { + "load" { + # Relies on the anaconda module being loaded since we need to update the path + puts stdout "conda activate ${P}_${V};\n" + } + "unload" - + "remove" { + puts stdout "conda deactivate;\n" + } +} + From 14ad23e52739eced04bc31e5e5571f4293b9d878 Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Thu, 19 Dec 2024 13:00:56 +0100 Subject: [PATCH 120/158] new versoin 1.17.0 and Merlin7 --- EM/PEET/README.md | 13 ++++++++----- EM/PEET/build | 2 +- EM/PEET/files/_config.yaml.disable | 8 -------- EM/PEET/files/config.yaml | 16 ++++++++++++++++ EM/PEET/files/variants | 2 -- EM/PEET/modulefile | 2 +- 6 files changed, 26 insertions(+), 17 deletions(-) delete mode 100644 EM/PEET/files/_config.yaml.disable create mode 100644 EM/PEET/files/config.yaml delete mode 100644 EM/PEET/files/variants diff --git a/EM/PEET/README.md b/EM/PEET/README.md index 9828d75..fb5b585 100644 --- a/EM/PEET/README.md +++ b/EM/PEET/README.md @@ -6,9 +6,7 @@ PEET is shipped as a self-expanding installation script. Run `./build` to install. - -An experimental config.yaml files is included using Pmodules/1.1.10 syntax. -This should probably not be used until yaml support in modbuild stabilizes. +This module is usually used in combination with IMOD (etomo GUI). ## Testing @@ -16,12 +14,17 @@ This should probably not be used until yaml support in modbuild stabilizes. ## Build notes -Building was successful with Pmodules 1.1.8 but not 1.1.9 or 1.1.10. Linking the binary is a bit of a pain. It requires gcc to be loaded to provide relatively recent versions of libstdc++.so.6. I didn't fine what exact version Matlab MCR expects, but 9.5.0 seemed to work. MCR is linked dynamically at runtime through LD_LIBRARY_PATH. This is not set in the modulefile as expected, but rather in wrapper scripts which source particle.cfg. Sed commands in -pbuild::install update this file so that it reads the loaded modules correctly. +pbuild::install update this file so that it reads the loaded modules correctly. +(Remark Nov. 2024: still true for version 1.17.0) +## Versions + +According to the website (INSTALL.TXT) the following Matlab is needed : + +-1.17.0 : 2022b (Merlin7, automatically loads matlab) diff --git a/EM/PEET/build b/EM/PEET/build index 27d7f66..caceb01 100755 --- a/EM/PEET/build +++ b/EM/PEET/build @@ -1,6 +1,5 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'EM' pbuild::prep() { @@ -13,6 +12,7 @@ pbuild::prep() { --fail \ --output "$dst" \ "https://bio3d.colorado.edu/ftp/PEET/linux/Particle_${V_PKG}_linux.sh" + --no-check-certificate fi } diff --git a/EM/PEET/files/_config.yaml.disable b/EM/PEET/files/_config.yaml.disable deleted file mode 100644 index 64da532..0000000 --- a/EM/PEET/files/_config.yaml.disable +++ /dev/null @@ -1,8 +0,0 @@ -overlay: base -relstage: stable -group: EM -shasums: - PEET/1.15.1a: de4e9104f90b9379502a34b58be33eafd5514d554002a94efe2adba6f44785e6 - -PEET/1.15.1a: - - relstage: unstable diff --git a/EM/PEET/files/config.yaml b/EM/PEET/files/config.yaml new file mode 100644 index 0000000..5470687 --- /dev/null +++ b/EM/PEET/files/config.yaml @@ -0,0 +1,16 @@ +--- +format: 1 +PEET: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 1.17.0: + variants: + - overlay: Alps + systems: [.*.merlin7.psi.ch] + relstage: unstable + runtime_deps: + - gcc/12.3.0 + - matlab/2022b diff --git a/EM/PEET/files/variants b/EM/PEET/files/variants deleted file mode 100644 index 05b2b61..0000000 --- a/EM/PEET/files/variants +++ /dev/null @@ -1,2 +0,0 @@ -PEET/1.15.1a stable gcc/9.5.0 matlab/2020b -PEET/1.16.0 stable gcc/9.5.0 matlab/2021b diff --git a/EM/PEET/modulefile b/EM/PEET/modulefile index 7510133..f95a274 100644 --- a/EM/PEET/modulefile +++ b/EM/PEET/modulefile @@ -3,7 +3,7 @@ module-whatis "PEET (Particle Estimation for Electron Tomography) is an open-source package for aligning and averaging particles in 3-D subvolumes extracted from tomograms." module-url "https://bio3d.colorado.edu/PEET/" module-license "GPLv2 license" -module-maintainer "Spencer Bliven " +module-maintainer "Greta Assmann " module-help " PEET (Particle Estimation for Electron Tomography) is an open-source package From 0fe0086db3d947536f1875c75a162af34a30b301 Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Thu, 19 Dec 2024 13:15:34 +0100 Subject: [PATCH 121/158] versoin 2.99.66 merlin7 --- EM/EMAN/README.md | 10 +++++++ EM/EMAN/build | 30 +++++++++++--------- EM/EMAN/environment.yaml | 5 ++++ EM/EMAN/files/config.yaml | 13 +++++++++ EM/EMAN/files/variants | 2 -- EM/EMAN/modulefile | 59 +++++++++++++++++++-------------------- 6 files changed, 73 insertions(+), 46 deletions(-) create mode 100644 EM/EMAN/README.md create mode 100644 EM/EMAN/environment.yaml create mode 100644 EM/EMAN/files/config.yaml delete mode 100644 EM/EMAN/files/variants diff --git a/EM/EMAN/README.md b/EM/EMAN/README.md new file mode 100644 index 0000000..5636bcb --- /dev/null +++ b/EM/EMAN/README.md @@ -0,0 +1,10 @@ +# EMAN + +From version 2.99.53 (Oct. 23) EMAN is built as a conda package. + +Current installation on Merlin7 (Nov 24) is 2.99.66 + + +### Hints + +conda installation on A100 GPU diff --git a/EM/EMAN/build b/EM/EMAN/build index e72e4e4..789c7bd 100755 --- a/EM/EMAN/build +++ b/EM/EMAN/build @@ -1,23 +1,27 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'EM' - -pbuild::prep() { - local EMAN2DL="${PMODULES_TMPDIR:-/tmp}/eman${V}_sphire1.4_sparx.linux64.sh" - - if ! [ -f "$EMAN2DL" ]; then - wget -O "$EMAN2DL" "https://cryoem.bcm.edu/cryoem/static/software/release-${V}/eman${V}_sphire1.4_sparx.linux64.sh" - fi -} pbuild::configure() { + #MINICONDA INSTALL + mkdir -p "$PREFIX/miniconda" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" + + + #CREATE ENV , make sure to source the "correct" conda.sh + "$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml" + +} + +#DO NOTHING +pbuild::compile(){ : } -pbuild::install() { +pbuild::install(){ : } -pbuild::compile() { - bash ${PMODULES_TMPDIR:-/tmp}/eman${V}_sphire1.4_sparx.linux64.sh -u -b -p $PREFIX -} + + + diff --git a/EM/EMAN/environment.yaml b/EM/EMAN/environment.yaml new file mode 100644 index 0000000..ad410e6 --- /dev/null +++ b/EM/EMAN/environment.yaml @@ -0,0 +1,5 @@ +channels: + - cryoem + - conda-forge +dependencies: + - eman-dev diff --git a/EM/EMAN/files/config.yaml b/EM/EMAN/files/config.yaml new file mode 100644 index 0000000..0fce05e --- /dev/null +++ b/EM/EMAN/files/config.yaml @@ -0,0 +1,13 @@ +--- +format: 1 +EMAN: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 2.99.66: + variants: + - overlay: Alps + systems: [.*.merlin7.psi.ch] + relstage: unstable diff --git a/EM/EMAN/files/variants b/EM/EMAN/files/variants deleted file mode 100644 index f50340f..0000000 --- a/EM/EMAN/files/variants +++ /dev/null @@ -1,2 +0,0 @@ -EMAN/2.99.47 unstable cuda/11.2.2 -EMAN/2.2 stable diff --git a/EM/EMAN/modulefile b/EM/EMAN/modulefile index ae15052..a664602 100644 --- a/EM/EMAN/modulefile +++ b/EM/EMAN/modulefile @@ -1,37 +1,34 @@ -#%Module1.0 +#%Module -set dont-setenv {LD_LIBRARY_PATH} +module-whatis "EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes " +module-url "https://blake.bcm.edu/emanwiki/EMAN2" +module-license "GNU gerneral public license: GPLv2" +module-maintainer "Greta Assmann " -module-whatis "EMAN(2) is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes" -module-url "https://blake.bcm.edu/emanwiki/EMAN2" -module-license "GPL license" -module-maintainer "Elsa Germann " +module-help "EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing large data sets (>100,000 particle) very efficiently" -module-help "EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing large data sets (>100,000 particle) very efficiently. +# Check for supported shell types +set shelltype [module-info shelltype] +switch -- $shelltype { + "sh" { + puts stdout "conda(){ :; };" + puts stdout "set +u" + puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n" + } + default { + puts stderr "Shells of type '$shelltype' are NOT supported!" + } +} -Please also note that this is not the (related) EMEN2 electronic notebook, but is EMAN2, a scientific image processing suite. -Please Cite (and read) +switch [module-info mode] { + "load" { + # Relies on the anaconda module being loaded since we need to update the path + puts stdout "conda activate ${P}_${V};\n" + } + "unload" - + "remove" { + puts stdout "conda deactivate;\n" + } +} -EMAN is free software, supported by NIH Grants. It is critical that you cite EMAN2 when you use it in a publication in any significant way, to help us document usage when trying to renew our funding. Feel free to cite any of these: - - Primary EMAN2 paper: - - G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke. (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol. 157, 38-46. PMID: 16859925 - - Subnanometer resolution subtomogram averaging using PPPT methods: - Chen M, Bell JM, Shi X, Sun SY, Wang Z, Ludtke SJ. Nat Methods. (2019) A complete data processing workflow for cryo-ET and subtomogram averaging, Nat. Methods, 16(11):1161-1168, PMC31611690 - - Neural Network Based Tomogram Segmentation - Chen M, Dai W, Sun SY, Jonasch D, He CY, Schmid MF, et al. (2017). Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat. Methods, 14(10), 983–5. PMCID: PMC5623144 - - Neural Network Particle Picker - Bell JM, Chen M, Durmaz T, Fluty AC, Ludtke SJ. (2018). New software tools in EMAN2 inspired by EMDatabank map challenge. J. Struct. Biol. Elsevier;, 204(2), 283–90. - - EMAN2 high resolution refinement methods: - - J.M. Bell, M. Chen, P.R. Baldwin & S.J. Ludtke. (2016) High Resolution Single Particle Refinement in EMAN2.1. Methods. 100, 25-34. PMC4848122 - - Methods for analysis of conformational and compositional variability: - Ludtke, S. J. \"Single-Particle Refinement and Variability Analysis in EMAN2.1.\" in Methods Enzymol 579159-189 (Elsevier, United States, 2016). PMC5101015 -" From 51066a5431114e443298020a1640bdf88d86d083 Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Thu, 19 Dec 2024 13:47:10 +0100 Subject: [PATCH 122/158] new DeepEMhancer merlin7 --- EM/DeepEMhancer/build | 34 +++++++++++++++++++++++++++++++ EM/DeepEMhancer/environment.yaml | 7 +++++++ EM/DeepEMhancer/files/config.yaml | 13 ++++++++++++ EM/DeepEMhancer/modulefile | 34 +++++++++++++++++++++++++++++++ 4 files changed, 88 insertions(+) create mode 100755 EM/DeepEMhancer/build create mode 100644 EM/DeepEMhancer/environment.yaml create mode 100644 EM/DeepEMhancer/files/config.yaml create mode 100644 EM/DeepEMhancer/modulefile diff --git a/EM/DeepEMhancer/build b/EM/DeepEMhancer/build new file mode 100755 index 0000000..cbf5ff7 --- /dev/null +++ b/EM/DeepEMhancer/build @@ -0,0 +1,34 @@ +#!/usr/bin/env modbuild + + +pbuild::configure() { + #MINICONDA INSTALL + mkdir -p "$PREFIX/miniconda" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" + + + #CREATE ENV + "$PREFIX/miniconda/condabin/conda" env create --name "${P}_${V}" -f "$BUILDBLOCK_DIR/environment.yaml" + + + #activate env and download deep learning models + mkdir -p "$PREFIX/deepmodels" + source "$PREFIX/miniconda/etc/profile.d/conda.sh" + conda activate "${P}_${V}" + deepemhancer --download "$PREFIX/deepmodels" + conda deactivate +} + +#DO NOTHING +pbuild::compile(){ + : +} + +pbuild::install(){ + : +} + + + + diff --git a/EM/DeepEMhancer/environment.yaml b/EM/DeepEMhancer/environment.yaml new file mode 100644 index 0000000..9a2d1d9 --- /dev/null +++ b/EM/DeepEMhancer/environment.yaml @@ -0,0 +1,7 @@ +channels: + - rsanchez1369 + - anaconda + - conda-forge +dependencies: + - python=3.10 + - deepEMhancer diff --git a/EM/DeepEMhancer/files/config.yaml b/EM/DeepEMhancer/files/config.yaml new file mode 100644 index 0000000..5b4312b --- /dev/null +++ b/EM/DeepEMhancer/files/config.yaml @@ -0,0 +1,13 @@ +--- +format: 1 +DeepEMhancer: + defaults: + group: EM + overlay: base + relstage: unstable + versions: + 0.16: + variants: + - overlay: Alps + systems: [.*.merlin7.psi.ch] + relstage: unstable diff --git a/EM/DeepEMhancer/modulefile b/EM/DeepEMhancer/modulefile new file mode 100644 index 0000000..657d101 --- /dev/null +++ b/EM/DeepEMhancer/modulefile @@ -0,0 +1,34 @@ +#%Module + +module-whatis "Deep cryo-EM Map Enhancer (DeepEMhancer) " +module-url "https://github.com/rsanchezgarc/deepEMhancer" +module-license "Apache-2.0 License" +module-maintainer "Greta Assmann " + +module-help "DeepEMhancer is a python package designed to perform post-processing of cryo-EM maps as described in DeepEMhancer: a deep learning solution for cryo-EM volume post-processing, by Sanchez-Garcia et al, 2021." + +# Check for supported shell types +set shelltype [module-info shelltype] +switch -- $shelltype { + "sh" { + puts stdout "conda(){ :; };" + puts stdout "set +u" + puts stdout "source \"${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n" + } + default { + puts stderr "Shells of type '$shelltype' are NOT supported!" + } +} + + +switch [module-info mode] { + "load" { + # Relies on the anaconda module being loaded since we need to update the path + puts stdout "conda activate ${P}_${V};\n" + } + "unload" - + "remove" { + puts stdout "conda deactivate;\n" + } +} + From e57683abde7cd3c95f67c3b5baff0e337c9916d8 Mon Sep 17 00:00:00 2001 From: caubet_m Date: Mon, 27 Jan 2025 17:16:45 +0100 Subject: [PATCH 123/158] Openmpi update --- Compiler/openmpi/build | 21 ++++++++--- Compiler/openmpi/files/config.yaml | 52 ++++++++++++++++++++------- Compiler/openmpi/modulefile | 9 +++++ Libraries/libevent/files/config.yaml | 2 +- Libraries/pmix/files/config.yaml | 41 +++++++++++++++++++-- Programming/cuda/files/variants.rhel7 | 2 +- Programming/gcc/files/config.yaml | 2 +- 7 files changed, 105 insertions(+), 24 deletions(-) diff --git a/Compiler/openmpi/build b/Compiler/openmpi/build index 58dfcd0..ba72c49 100755 --- a/Compiler/openmpi/build +++ b/Compiler/openmpi/build @@ -1,9 +1,6 @@ #!/usr/bin/env modbuild pbuild::pre_configure() { - pbuild::add_configure_args "--enable-shared" - pbuild::add_configure_args "--enable-static" - if (( V_MAJOR < 5 )); then pbuild::add_configure_args "--enable-mpi-cxx" pbuild::add_configure_args "--enable-mpi-cxx-seek" @@ -27,12 +24,17 @@ pbuild::pre_configure() { fi if (( V_MAJOR >= 4 )); then pbuild::add_configure_args "--enable-mpi-fortran" + fi + if (( V_MAJOR == 4 )); then pbuild::add_configure_args "--without-verbs" fi if [[ -v CUDA_VERSION ]]; then std::info "Enabling CUDA ${CUDA_VERSION}." pbuild::add_configure_args "--with-cuda=${CUDA_HOME}" + if (( V_MAJOR >= 5 )); then + pbuild::add_configure_args "--with-cuda-libdir=${CUDA_HOME}/lib64/stubs" + fi fi if [[ -v HWLOC_VERSION ]]; then @@ -77,7 +79,9 @@ pbuild::pre_configure() { pbuild::add_configure_args "FC=ifort" pbuild::add_configure_args "F90=ifort" pbuild::add_configure_args "F77=ifort" - pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" + # -O0 was probably added for enabling debugging: + # pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel,-O0" + pbuild::add_configure_args "LDFLAGS=-Wc,-static-intel" fi if pbuild::use_flag slurm || \ @@ -118,7 +122,14 @@ pbuild::post_install_no_slurm() { pbuild::post_install() { if [[ -v CUDA_VERSION ]]; then - echo "opal_warn_on_missing_libcuda = 0" >> ${PREFIX}/etc/openmpi-mca-params.conf + grep -qxF "opal_warn_on_missing_libcuda = 0" ${PREFIX}/etc/openmpi-mca-params.conf || \ + echo "opal_warn_on_missing_libcuda = 0" >> ${PREFIX}/etc/openmpi-mca-params.conf + if (( V_MAJOR == 5 )); then + grep -qxF "mca_base_component_show_load_errors = '^accelerator,rcache,btl/smcuda'" ${PREFIX}/etc/openmpi-mca-params.conf || \ + echo "mca_base_component_show_load_errors = '^accelerator,rcache,btl/smcuda'" >> ${PREFIX}/etc/openmpi-mca-params.conf + grep -qxF "mca_base_component_show_load_errors = '^accelerator,rcache,btl/smcuda'" ${PREFIX}/etc/prte-mca-params.conf || \ + echo "mca_base_component_show_load_errors = '^accelerator,rcache,btl/smcuda'" >> ${PREFIX}/etc/prte-mca-params.conf + fi fi local fname='' diff --git a/Compiler/openmpi/files/config.yaml b/Compiler/openmpi/files/config.yaml index 23f697f..a0e6909 100644 --- a/Compiler/openmpi/files/config.yaml +++ b/Compiler/openmpi/files/config.yaml @@ -8,7 +8,6 @@ openmpi: relstage: stable configure_args: - --enable-shared - - --enable-static docfiles: [AUTHORS, LICENSE, NEWS, README] urls: - url: https://download.open-mpi.org/release/open-mpi/v${V_MAJOR}.${V_MINOR}/openmpi-${V_PKG}.tar.bz2 @@ -58,22 +57,46 @@ openmpi: openmpi-5.0.5.tar.bz2: 6588d57c0a4bd299a24103f4e196051b29e8b55fbda49e11d5b3d32030a32776 versions: + # 5.0.6: + # config: + # configure_args+: + # - --enable-mpi1-compatibility + # - --enable-static=no + # variants: + # - systems: [.*.merlin7.psi.ch] + # relstage: unstable + # overlay: Alps + # use_overlays: [PSI, Alps] + # group_deps: + # compiler: {gcc: [14.2.0,12.3.0,8.5.0], intelcc: [22.2]} + # build_requires: [hwloc/2.11.1, patchelf/0.14.5] + # runtime_deps: [cuda/12.2.0, libfabric/1.15.2.0, pmix/5.0.4] + # configure_args+: + # - --with-cxi + # - --with-lustre + # - --with-slingshot + # use_flags: [merlin7, slurm] + 5.0.5: + config: + configure_args+: + - --enable-mpi1-compatibility + - --enable-static=no variants: - systems: [.*.merlin7.psi.ch] - relstage: unstable + relstage: stable overlay: Alps - use_overlays: [PSI] - use_flags: [merlin7] + use_overlays: [PSI, Alps] group_deps: - compiler: {gcc: [12.3.0], intelcc: [22.2]} - build_requires: [pmix/5.0.3, hwloc/2.11.1, libfabric/1.15.2.0, patchelf/0.14.5] - runtime_deps: [cuda/12.2.0] + compiler: {gcc: [14.2.0, 12.3.0, 8.5.0], + intelcc: [22.2]} + build_requires: [hwloc/2.11.1, patchelf/0.14.5] + runtime_deps: [cuda/12.2.0, libfabric/1.15.2.0, pmix/5.0.3] configure_args+: - - --enable-mpi1-compatibility - --with-cxi - --with-lustre - --with-slingshot + use_flags: [merlin7, slurm] 4.1.6: config: @@ -82,7 +105,7 @@ openmpi: - systems: [merlin-.*] suffix: _slurm use_flags: [merlin6, gpfs] - relstage: unstable + relstage: stable overlay: base group_deps: compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 12.4.0, 13.1.0, 13.2.0, 14.2.0]} @@ -98,6 +121,7 @@ openmpi: - LDFLAGS=-g - --with-gpfs=/usr/lpp/mmfs - --with-pmi=/usr + - --enable-static - systems: [ra-.*] suffix: _ra @@ -109,16 +133,18 @@ openmpi: configure_args+: - --with-gpfs=/usr/lpp/mmfs - --with-pmi=/usr + - --enable-static - systems: [.*.merlin7.psi.ch] - relstage: unstable + relstage: stable overlay: Alps group_deps: - compiler: {gcc: [12.3.0], intelcc: [22.2]} - build_requires: [pmix/4.2.9, hwloc/2.11.1, libfabric/1.15.2.0, patchelf/0.14.5] - runtime_deps: [cuda/12.2.0] + compiler: {gcc: [12.3.0, 13.3.0, 14.2.0], intelcc: [22.2]} + build_requires: [hwloc/2.11.1, patchelf/0.14.5] + runtime_deps: [cuda/12.2.0, libfabric/1.15.2.0, pmix/4.2.9] configure_args+: - --enable-mpi1-compatibility + - --enable-static=no - --with-lustre use_overlays: [PSI, Alps] use_flags: [merlin7, slurm] diff --git a/Compiler/openmpi/modulefile b/Compiler/openmpi/modulefile index d67d904..56befdc 100644 --- a/Compiler/openmpi/modulefile +++ b/Compiler/openmpi/modulefile @@ -44,3 +44,12 @@ if { $libcuda eq "" } { prepend-path LD_LIBRARY_PATH $PREFIX/lib/fallback/cuda } } + +if {[info exists ::env(PMIX_VERSION)]} { + set pmix_major_version [lindex [split $::env(PMIX_VERSION) "."] 0] + setenv SLURM_MPI_TYPE "pmix_v$pmix_major_version" +} + +if { $V_MAJOR >= 5 } { + setenv OMPI_MCA_mca_base_component_show_load_errors = '^accelerator,rcache,btl/smcuda' +} diff --git a/Libraries/libevent/files/config.yaml b/Libraries/libevent/files/config.yaml index 23af643..009dd39 100644 --- a/Libraries/libevent/files/config.yaml +++ b/Libraries/libevent/files/config.yaml @@ -22,7 +22,7 @@ libevent: overlay: Alps use_overlays: [PSI] build_requires: [] - relstage: unstable + relstage: stable - systems: [rhel.*] build_requires: [openssl/1.1.1k] 2.1.8: diff --git a/Libraries/pmix/files/config.yaml b/Libraries/pmix/files/config.yaml index 14db2dc..e5c3cf5 100644 --- a/Libraries/pmix/files/config.yaml +++ b/Libraries/pmix/files/config.yaml @@ -6,7 +6,6 @@ pmix: compile_in_sourcetree: true configure_args: - --enable-shared - - --enable-static docfiles: - AUTHORS - README.md @@ -30,6 +29,8 @@ pmix: 1.2.5: config: relstage: removed + configure_args+: + - --enable-static docfiles: - README - LICENSE @@ -38,6 +39,8 @@ pmix: 2.2.5;3.2.3: config: relstage: unstable + configure_args+: + - --enable-static runtime_deps: [libevent/2.1.12] build_requires: [gcc/12.3.0, hwloc/2.11.1] variants: @@ -48,6 +51,8 @@ pmix: 3.2.5: config: relstage: unstable + configure_args+: + - --enable-static runtime_deps: [libevent/2.1.12] build_requires: [gcc/12.3.0, hwloc/2.11.1] variants: @@ -57,21 +62,29 @@ pmix: 4.1.2: config: relstage: stable + configure_args+: + - --enable-static runtime_deps: [libevent/2.1.12] build_requires: [hwloc/2.7.1] 4.2.3: config: relstage: stable + configure_args+: + - --enable-static runtime_deps: [libevent/2.1.12] build_requires: [hwloc/2.9.1] 4.2.4: config: relstage: stable + configure_args+: + - --enable-static runtime_deps: [libevent/2.1.12] build_requires: [gcc/10.4.0, hwloc/2.9.1] 4.2.9: config: - relstage: unstable + relstage: stable + configure_args+: + - --enable-static runtime_deps: [libevent/2.1.12] build_requires: [gcc/12.3.0, hwloc/2.11.1] variants: @@ -80,7 +93,9 @@ pmix: use_overlays: [PSI] 5.0.3: config: - relstage: unstable + relstage: stable + configure_args+: + - --enable-static=no runtime_deps: [libevent/2.1.12] build_requires: [gcc/12.3.0, hwloc/2.11.1] variants: @@ -95,3 +110,23 @@ pmix: # - --with-jansson # - --with-curl - systems: [rhel.*] + # 5.0.4: + # config: + # relstage: unstable + # configure_args+: + # - --enable-static=no + # runtime_deps: [libevent/2.1.12] + # build_requires: [gcc/12.3.0, hwloc/2.11.1] + # variants: + # - systems: [.*.merlin7.psi.ch] + # overlay: Alps + # use_overlays: [PSI] + # configure_args+: + # - --with-lustre + # - --with-cxi + # - --with-cxi-libdir=/opt/cray/libfabric/1.15.2.0/include + # - --with-slingshot + # - --with-zlib + # # - --with-jansson + # # - --with-curl + # - systems: [rhel.*] diff --git a/Programming/cuda/files/variants.rhel7 b/Programming/cuda/files/variants.rhel7 index f9ac67e..75b1509 100644 --- a/Programming/cuda/files/variants.rhel7 +++ b/Programming/cuda/files/variants.rhel7 @@ -13,4 +13,4 @@ cuda/11.4.3 stable cuda/11.5.1 stable cuda/11.8.0 stable cuda/12.1.1 stable -cuda/12.2.0 unstable +cuda/12.2.0 stable diff --git a/Programming/gcc/files/config.yaml b/Programming/gcc/files/config.yaml index 4802bde..a625fce 100644 --- a/Programming/gcc/files/config.yaml +++ b/Programming/gcc/files/config.yaml @@ -170,7 +170,7 @@ gcc: 8.5.0: config: - relstage: unstable + relstage: stable build_requires: [gmp/6.3.0, mpfr/4.2.1, mpc/1.3.1-1] configure_args+: - --enable-languages=c,c++,objc,obj-c++,lto,fortran,go From a827e8e33d71bae0f11bcdae12fb9b059b883f9d Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Tue, 11 Feb 2025 10:35:56 +0100 Subject: [PATCH 124/158] relion5.0.0 on merlin7 --- EM/relion/README.md | 40 ++++++++++++- EM/relion/build | 73 ++++++++++++------------ EM/relion/environment.yml | 34 +++++++++++ EM/relion/files/config.yaml | 109 ++++++++++++++++++++++++++++++++++++ EM/relion/files/variants | 18 ------ EM/relion/modulefile | 33 +++-------- 6 files changed, 226 insertions(+), 81 deletions(-) create mode 100644 EM/relion/environment.yml create mode 100644 EM/relion/files/config.yaml delete mode 100644 EM/relion/files/variants diff --git a/EM/relion/README.md b/EM/relion/README.md index 095d00f..5af3571 100644 --- a/EM/relion/README.md +++ b/EM/relion/README.md @@ -12,4 +12,42 @@ and MKL, but this would require additional openmpi variants. After running ./build, install relion scripts from the repository at https://git.psi.ch/lsm-hpce/relion-scripts -From version 5.0-beta on, a conda env is required. conda env is build in the folder $SRC\_DIR/conda\_envs. Also, weights for BLUSH, MODEL-ANGELO and CLASS-RANKER are downloaded in the installation step. +## Important info per version! + +### 5.0-beta (OLD, Merlin6) +- From version 5.0-beta on, a conda env is required (done with central anaconda module, needs to be done on pmod7 because of AFS hardlinks) +- the conda env is build in the folder $SRC\_DIR/conda\_envs. Also, weights for BLUSH, MODEL-ANGELO and CLASS-RANKER are downloaded in the installation step. + +### 5.0-1beta (OLD, Merlin6) +- the conda env is made with a miniconda installation, and because of upgrading to Pmodules/1.1.21 , the variants file was dropped and changed into the config.yaml file. +- The build script was also updated accordingly +- Also, cryocare is now available in a wrapper from relion, the cryocare installation executables need to be provided (seperate cryocare module). It is crucial to add the cryocare lib path (from the cryocare conda env) to the LD_LIBRARY_PATH when loading the relion module +- tiff module no longer required, as this conflicts with the system shared tiff libs (not 100% sure why this canged from previous installations though) +### 5.0-2beta (ON MERLIN7) +- no fetching of weights with ftp possible, so cp from other machines into BUILD DIR and using the -DFETCH\_WEIGHTS=OFF option +- link : ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz +- link : ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/classranker\_v1.0.ckpt.gz + +### 5.0.0 A100 +- same as 5.0-2beta (especially when it comes to the weights...) +- copy the fltk and the classranker file into the BUILD Directory. The build script assumes that these two files are in the BUILD\_DIR. +- sha256 errors occured during installation: +``` +ERROR: THESE PACKAGES DO NOT MATCH THE HASHES FROM THE REQUIREMENTS FILE. If you have updated the package versions, please update the hashes. Otherwise, examine the package contents carefully; someone may have tampered with them. + unknown package: + Expected sha256 20abd2cae58e55ca1af8a8dcf43293336a59adf0391f1917bf8518633cfc2cdf + Got e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 +``` +- The download of some packages (.whl files) was blocked by the merlin7 firewall. Google the shasum and find the package name. Try to manually download with curl. If this fails, this is a strong indication for network/firewall issues that need to be adressed by the networking team. .whl files from conda +pip installations are ususally stored in the env in lib/pythonXXX. +- Also, to not clean up build directories: +``` +--no-clean +Don't clean up build directories. +(environment variable: PIP_NO_CLEAN) + +``` +### 5.0.0 for GH + +no successful installation so far - failing for conda env. Elsa G. build some hacky hack that works kind of.. +needs to be investigated further. + diff --git a/EM/relion/build b/EM/relion/build index 6e3c435..e2388ce 100755 --- a/EM/relion/build +++ b/EM/relion/build @@ -1,7 +1,5 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'EM' -pbuild::use_cmake PROFILE="no" SP="no" @@ -23,15 +21,22 @@ pbuild::prep() { BRANCH="${V_PKG}" fi - git clone --depth=1 -b "$BRANCH" https://github.com/3dem/relion.git "$SRC_DIR" || return $? + if [[ -d "$SRC_DIR/.git" ]]; then + cd "$SRC_DIR" + git pull + else + git clone --depth=1 -b "$BRANCH" https://github.com/3dem/relion.git "$SRC_DIR" || return $? + fi } + pbuild::pre_configure() { # Section will be switched on for -profile version #----------------------------------------------------------- if [[ "$PROFILE" == "yes" ]]; then - pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=BENCHMARKING" + # this needs to go into the config.yml file for >5.0-1beta + : #pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=BENCHMARKING" fi #------------------------------------------------------------ @@ -40,55 +45,49 @@ pbuild::pre_configure() { # Safe memory usage for multibody refinements #------------------------------------------------------------ if [[ "$SP" == "yes" ]]; then - pbuild::add_configure_args "-DDoublePrec_CPU=OFF" + # this needs to go into the config.yml file for >5.0-1beta + : #pbuild::add_configure_args "-DDoublePrec_CPU=OFF" fi #------------------------------------------------------------ - # The following section will only work for versions >= 5.0-beta # ------------------------------------------------------------- if [[ "$V_MAJOR" -ge "5" ]]; then - - #download blush weights - wget ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/blush_v1.0.ckpt.gz -P "$PREFIX/torch/hub/checkpoints/relion_blush" \ + #download blush weights, from zenodo + #mkdir -p "${PREFIX}" + wget -q https://zenodo.org/records/10072731/files/blush_v1.0.ckpt.gz -P "$PREFIX/torch/hub/checkpoints/relion_blush" \ && gunzip "$PREFIX/torch/hub/checkpoints/relion_blush/blush_v1.0.ckpt.gz" mv "$PREFIX/torch/hub/checkpoints/relion_blush/blush_v1.0.ckpt" "$PREFIX/torch/hub/checkpoints/relion_blush/v1.0.ckpt" touch "$PREFIX/torch/hub/checkpoints/relion_blush/v1.0_installed.txt" + + #cp classranker that was downloaded on another machine before from BUILDBLOCK_DIR + mkdir -p "$PREFIX/torch/hub/checkpoints/relion_class_ranker" + cp "$BUILDBLOCK_DIR/classranker_v1.0.ckpt.gz" "$PREFIX/torch/hub/checkpoints/relion_class_ranker" + gunzip "$PREFIX/torch/hub/checkpoints/relion_class_ranker/classranker_v1.0.ckpt.gz" + mv "$PREFIX/torch/hub/checkpoints/relion_class_ranker/classranker_v1.0.ckpt" "$PREFIX/torch/hub/checkpoints/relion_class_ranker/v1.0.ckpt" + touch "$PREFIX/torch/hub/checkpoints/relion_class_ranker/v1.0_installed.txt" + + # fltk stuff + mkdir -p "$SRC_DIR/external/fltk" + cp "$BUILDBLOCK_DIR/fltk-1.3.5-source.tar.gz" "$SRC_DIR/external/fltk/" + - #Set Torch Home - pbuild::add_configure_args "-DTORCH_HOME_PATH=$PREFIX/torch" + #INSTALL Miniconda + echo "installing miniconda" + mkdir -p "$PREFIX/miniconda" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh -O "$PREFIX/miniconda/miniconda.sh" + #wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" - #Conda - conda env create -f "$SRC_DIR/environment.yml" -p "$PREFIX/conda_env/$P_$V" - pbuild::add_configure_args "-DPYTHON_EXE_PATH=$PREFIX/conda_env/$P_$V/bin/python" + # Copy manually edited environment.yml file (with cryocare specs) into the folder to substitute the default one + #Conda create env with miniconda installation + "$PREFIX/miniconda/condabin/conda" env create --name "${P}-${V}" -f "$SRC_DIR/environment.yml" + "$PREFIX/miniconda/condabin/conda" env list fi #--------------------------------------------------------------- - # CMake-based build - - pbuild::add_configure_args "-DFORCE_OWN_FFTW=ON" - pbuild::add_configure_args "-DFORCE_OWN_FLTK=ON" - pbuild::add_configure_args "-DFORCE_OWN_TBB=ON" - - # CUDA related (set lowest CC to 6.1 for 1080 compatibility) - pbuild::add_configure_args "-DCUDA=ON" - pbuild::add_configure_args "-DCUDA_ARCH=61" - pbuild::add_configure_args "-DCudaTexture=ON" - - # Since ver3.0 relion cannot have ALTCPU and CUDA activated - # at the same time. Otherwise the configuration exits with - # an error. - if [[ "$V_MAJOR" -le "3" ]]; then - pbuild::add_configure_args "-DALTCPU=ON" - fi - - if [[ -n "$INTEL_VERSION" ]]; then - # Requires intel compiler - pbuild::add_configure_args "-DMKLFFT=ON" - fi } -# vim: ts=4 sw=4 et diff --git a/EM/relion/environment.yml b/EM/relion/environment.yml new file mode 100644 index 0000000..549b89b --- /dev/null +++ b/EM/relion/environment.yml @@ -0,0 +1,34 @@ +name: relion-5.0 +channels: + - conda-forge +dependencies: + - pip + - python=3.9 + - setuptools=59.5.0 + - pip: + - torch==2.0.1 + - torchvision==0.15.2 + - tqdm==4.65.0 + - mrcfile==1.4.3 + - starfile>=0.5.6 + - loguru==0.7.0 + - scikit-learn==1.3.0 + - umap-learn==0.5.3 + - matplotlib==3.7.2 + - morphosamplers==0.0.13 + - pydantic==1.10.18 + - napari[all]==0.4.18 + - tsnecuda==3.0.1 + - PyQt5==5.15.9 + - typer==0.9.0 + - biopython==1.81 + - fastcluster==1.2.6 + - seaborn==0.12.2 + - dill==0.3.7 + - numpy<2 + - git+https://github.com/3dem/relion-classranker@b6e751e5cb4205d8e9b36d0ae38c3687b3395acb + - git+https://github.com/3dem/relion-blush + - git+https://github.com/3dem/DynaMight + - git+https://github.com/3dem/topaz + - git+https://github.com/3dem/model-angelo + - ".[vis]" diff --git a/EM/relion/files/config.yaml b/EM/relion/files/config.yaml new file mode 100644 index 0000000..e51829f --- /dev/null +++ b/EM/relion/files/config.yaml @@ -0,0 +1,109 @@ +--- +format: 1 +relion: + defaults: + group: EM + overlay: base + relstage: unstable + build_variants: first_match + versions: + 5.0.0: + variants: + - overlay: Alps + target_cpus: [x86_64] + systems: [.*.merlin7.psi.ch] + build_requires: + - cmake/3.23.2 + - git/2.37.0 + - openmpi/5.0.5 + relstage: unstable + runtime_deps: + - gcc/12.3.0 + - cuda/12.2.0 + - openmpi/5.0.5 + configure_with: cmake + configure_args: + - "-DTORCH_HOME_PATH=${PREFIX}/torch" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/${P}-${V}/bin/python" + - "-DFORCE_OWN_FFTW=ON" + - "-DFORCE_OWN_FLTK=ON" + - "-DFORCE_OWN_TBB=ON" + - "-DCUDA=ON" + - "-DCUDA_ARCH=80" # dep on the cuda arch of the oldest GPU + - "-DFETCH_WEIGHTS=OFF" + # does not work yet- just an idea... + - overlay: Alps + target_cpus: [aarch64] + systems: [gpu0.*.merlin7.psi.ch] + build_requires: + #- cmake/3.23.2 + #- git/2.37.0 + - openmpi/5.0.5 + - gcc/12.3.0 + - cuda/12.2.0 + relstage: unstable + runtime_deps: + - gcc/12.3.0 + - cuda/12.2.0 + - openmpi/5.0.5 + configure_with: cmake + configure_args: + - "-DTORCH_HOME_PATH=${PREFIX}/torch" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/${P}-${V}/bin/python" + - "-DFORCE_OWN_FFTW=ON" + - "-DFORCE_OWN_FLTK=ON" + - "-DFORCE_OWN_TBB=ON" + - "-DCUDA=ON" + - "-DCUDA_ARCH=90" # dep on the cuda arch of the oldest GPU + - "-DFETCH_WEIGHTS=OFF" + #MERLIN7 old (cray) + 5.0-2beta: + variants: + - overlay: Alps + systems: [gpu.*.merlin7.psi.ch] + build_requires: + - cmake/3.23.2 + - git/2.37.0 + - libfabric/1.22.0 + relstage: unstable + runtime_deps: + - gcc/12.3.0 + # - cudatoolkit/23.9_12.2 + - cuda/12.2.0 + configure_with: cmake + configure_args: + - "-DTORCH_HOME_PATH=${PREFIX}/torch" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/${P}-${V}/bin/python" + - "-DFORCE_OWN_FFTW=ON" + - "-DFORCE_OWN_FLTK=ON" + - "-DFORCE_OWN_TBB=ON" + - "-DCUDA=ON" + - "-DCUDA_ARCH=80" # dep on the cuda arch of the oldest GPU + #- "-DCudaTexture=ON" + - "-DFETCH_WEIGHTS=OFF" + #MERLIN6 + 5.0-1beta: + variants: + - systems: [merlin-.*.psi.ch] + build_requires: + - gcc/10.4.0 + - openmpi/4.1.4_slurm + - cuda/11.5.1 + - cmake/3.23.2 + - git/2.37.0 + relstage: unstable + runtime_deps: + - cuda/11.5.1 + - gcc/10.4.0 + - openmpi/4.1.4_slurm + configure_with: cmake + configure_args: + - "-DTORCH_HOME_PATH=${PREFIX}/torch" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/${P}-${V}/bin/python" + - "-DFORCE_OWN_FFTW=ON" + - "-DFORCE_OWN_FLTK=ON" + - "-DFORCE_OWN_TBB=ON" + - "-DCUDA=ON" + - "-DCUDA_ARCH=61" # dep on the cuda arch of the oldest GPU + - "-DCudaTexture=ON" + diff --git a/EM/relion/files/variants b/EM/relion/files/variants deleted file mode 100644 index bbe791e..0000000 --- a/EM/relion/files/variants +++ /dev/null @@ -1,18 +0,0 @@ -relion/2.1.b1 deprecated gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44 -relion/2.1 deprecated gcc/9.3.0 openmpi/4.0.4_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 -relion/3.0_beta deprecated gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44 -relion/3.0.8 deprecated gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9 -relion/3.0.8-1 stable gcc/9.2.0 openmpi/4.0.5_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 -relion/3.1-beta deprecated gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9 -relion/3.1.0 deprecated gcc/7.5.0 openmpi/4.0.4_slurm cuda/10.0.130 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 -relion/3.1.0-1 deprecated gcc/7.5.0 openmpi/4.0.4_slurm cuda/10.1.105 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 -relion/3.1.1 deprecated gcc/9.3.0 openmpi/4.0.4_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 -relion/3.1.1-1 stable gcc/9.2.0 openmpi/4.0.5_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 -relion/3.1.2 stable gcc/9.2.0 openmpi/4.0.5_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 -relion/3.1.3 stable gcc/9.2.0 openmpi/4.0.5_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 -relion/4.0-beta deprecated gcc/9.2.0 openmpi/4.0.5_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0 -relion/4.0.0 unstable gcc/11.2.0 openmpi/4.1.3_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 -relion/4.0.1 unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 -relion/4.0.1-profile unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 -relion/5.0-beta unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 anaconda/2019.07 -relion/5.0-sp unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 anaconda/2019.07 diff --git a/EM/relion/modulefile b/EM/relion/modulefile index ed09173..1dac00d 100644 --- a/EM/relion/modulefile +++ b/EM/relion/modulefile @@ -25,10 +25,10 @@ Scheres(2012) JSB http://www.sciencedirect.com/science/article/pii/S104784771200 " setenv RELION_QUEUE_USE yes -setenv RELION_QUEUE_NAME gpu +setenv RELION_QUEUE_NAME general-x64 setenv RELION_QSUB_COMMAND sbatch setenv RELION_THREAD_MAX 44 -setenv RELION_QSUB_EXTRA_COUNT 2 +setenv RELION_QSUB_EXTRA_COUNT 4 setenv RELION_QSUB_EXTRA1 "Max Time" setenv RELION_QSUB_EXTRA1_DEFAULT "1-00:00:00" setenv RELION_QSUB_EXTRA1_HELP "Maximum time before the job is killed by slurm. Default: 1-00:00:00" @@ -36,32 +36,15 @@ setenv RELION_QSUB_EXTRA2 "Extra Slurm Args" setenv RELION_QSUB_EXTRA2_DEFAULT "" setenv RELION_QSUB_EXTRA2_HELP "Any additional arguments to pass to slurm" setenv RELION_SCRATCH_DIR /scratch -setenv RELION_UNBLUR_EXECUTABLE /opt/psi/EM/Unblur/1.0.2/bin/unblur_openmp_7_17_15.exe -setenv RELION_SUMMOVIE_EXECUTABLE /opt/psi/EM/Summovie/1.0.2/bin/sum_movie_openmp_7_17_15.exe setenv RELION_CTFFIND_EXECUTABLE /opt/psi/EM/ctffind4/4.1.8/bin/ctffind -setenv RELION_GCTF_EXECUTABLE /opt/psi/EM/Gctf/1.06/bin/Gctf +#also has internal version, depending on what users want... dont know if it works setenv RELION_RESMAP_EXECUTABLE /opt/psi/EM/ResMap/1.1.4/bin/ResMap -setenv RELION_TOPAZ_EXECUTABLE /opt/psi/EM/relion/5.0-sp/conda_env/5.0-beta/bin/topaz -setenv RELION_PYTHON_EXECUTABLE /opt/psi/EM/relion/5.0-sp/conda_env/5.0-beta/bin/python -setenv RELION_TORCH_HOME_PATH /opt/psi/EM/relion/5.0-sp/torch # Version-specific variables -setenv RELION_QSUB_TEMPLATE /opt/psi/EM/relion/$V/scripts/multi_gpu.sh +setenv RELION_QSUB_TEMPLATE /opt/psi/overlays/Alps/EM/relion/$V/scripts/multi_gpu.sh -# See MC2 compatibility matrix: https://intranet.psi.ch/en/bio/motioncor2 -if {[string match "8.0*" $env(CUDA_VERSION)]} { - setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.3.2/bin/MotionCor2_1.3.2-Cuda80" -} elseif {[string match "11.0*" $env(CUDA_VERSION)]} { - setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.4.0/bin/MotionCor2" -} else { - setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.6.4/bin/MotionCor2" -} +setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.6.4/bin/MotionCor2" -# relion 5 features -if {[file exists /opt/psi/EM/relion/$V/conda_env/$V]} { - setenv RELION_TOPAZ_EXECUTABLE /opt/psi/EM/relion/$V/conda_env/$V/bin/topaz - setenv RELION_PYTHON_EXECUTABLE /opt/psi/EM/relion/$V/conda_env/$V/bin/python -} -if {[file exists /opt/psi/EM/relion/$V/torch]} { - setenv RELION_TORCH_HOME_PATH /opt/psi/EM/relion/$V/torch -} +setenv RELION_TOPAZ_EXECUTABLE /opt/psi/overlays/Alps/EM/relion/$V/miniconda/envs/$P-$V/bin/topaz +setenv RELION_PYTHON_EXECUTABLE /opt/psi/overlays/Alps/EM/relion/$V/miniconda/envs/$P-$V/bin/python +setenv RELION_TORCH_HOME_PATH /opt/psi/overlays/Alps/EM/relion/$V/torch/ From a23cb82fe4762a0d585b6aaa235658e0e8bb2b7c Mon Sep 17 00:00:00 2001 From: Greta Assmann Date: Tue, 11 Feb 2025 10:37:41 +0100 Subject: [PATCH 125/158] delete swan file --- EM/relion/.build.swn | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 EM/relion/.build.swn diff --git a/EM/relion/.build.swn b/EM/relion/.build.swn deleted file mode 100644 index e69de29..0000000 From 4bc1213de41b14ab82704145525b0ba0109db89b Mon Sep 17 00:00:00 2001 From: Caubet Serrabou Marc Date: Thu, 27 Feb 2025 10:49:46 +0100 Subject: [PATCH 126/158] Add files/config.yaml --- Tools/ANSYS/build | 2 -- Tools/ANSYS/files/config.yaml | 28 +++++++++++++++++++++++ Tools/ANSYS/files/variants.overlay_alps | 1 + Tools/ANSYS/files/variants.overlay_merlin | 4 ++-- 4 files changed, 31 insertions(+), 4 deletions(-) create mode 100644 Tools/ANSYS/files/config.yaml diff --git a/Tools/ANSYS/build b/Tools/ANSYS/build index b961793..595506c 100755 --- a/Tools/ANSYS/build +++ b/Tools/ANSYS/build @@ -1,7 +1,5 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'Tools' - pbuild::prep() { : } diff --git a/Tools/ANSYS/files/config.yaml b/Tools/ANSYS/files/config.yaml new file mode 100644 index 0000000..7daa5fb --- /dev/null +++ b/Tools/ANSYS/files/config.yaml @@ -0,0 +1,28 @@ +format: 1 +ANSYS: + defaults: + group: Tools + relstage: stable + shasums: + versions: + 2024R2: + variants: + - systems: [.*.merlin7.psi.ch] + relstage: stable + overlay: merlin + use_overlays: [PSI] + use_flags: [merlin7] + 2023R2: + variants: + - systems: [.*.merlin7.psi.ch] + relstage: unstable + overlay: merlin + use_overlays: [PSI] + use_flags: [merlin7] + 2022R2: + variants: + - systems: [.*.merlin7.psi.ch] + relstage: stable + overlay: merlin + use_overlays: [PSI] + use_flags: [merlin7] diff --git a/Tools/ANSYS/files/variants.overlay_alps b/Tools/ANSYS/files/variants.overlay_alps index 8852d90..3353250 100644 --- a/Tools/ANSYS/files/variants.overlay_alps +++ b/Tools/ANSYS/files/variants.overlay_alps @@ -1 +1,2 @@ ANSYS/2022R2 stable +ANSYS/2024R1 stable diff --git a/Tools/ANSYS/files/variants.overlay_merlin b/Tools/ANSYS/files/variants.overlay_merlin index c7ad54d..3b872ee 100644 --- a/Tools/ANSYS/files/variants.overlay_merlin +++ b/Tools/ANSYS/files/variants.overlay_merlin @@ -3,5 +3,5 @@ ANSYS/2020R2 stable ANSYS/2021R1 stable ANSYS/2021R2 stable ANSYS/2022R1 stable -ANSYS/2022R2 unstable -ANSYS/2023R2 unstable +ANSYS/2022R2 stable +ANSYS/2023R2 stable From 20f9945dbb27b3767f0b9d2d29b0ea945bde9e51 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 13 Mar 2025 10:23:47 +0100 Subject: [PATCH 127/158] cuda: new versions and YAML config --- Programming/cuda/build | 3 +++ Programming/cuda/files/config.yaml | 38 ++++++++++++++++++++++++------ 2 files changed, 34 insertions(+), 7 deletions(-) diff --git a/Programming/cuda/build b/Programming/cuda/build index b04936f..9684585 100755 --- a/Programming/cuda/build +++ b/Programming/cuda/build @@ -1,5 +1,8 @@ #!/usr/bin/env modbuild +# install with +# bash ./cuda_12.8.1_570.124.06_linux.run --silent --toolkit --installpath=/opt/psi/Programming/cuda/12.8.1/ --no-opengl-libs --no-man-page +# pbuild::post_install() { cd "${PREFIX}/lib64/stubs" for lib in lib*; do diff --git a/Programming/cuda/files/config.yaml b/Programming/cuda/files/config.yaml index 1afd260..8e03246 100644 --- a/Programming/cuda/files/config.yaml +++ b/Programming/cuda/files/config.yaml @@ -11,7 +11,14 @@ cuda: compile: [] install: [pbuild::post_install] urls: - - &cuda-12_2_2-aarch64 url: https://developer.download.nvidia.com/compute/cuda/12.2.2/local_installers/cuda_12.2.2_535.104.05_linux_sbsa.run + - &cuda-12_8_1-aarch64 + url: https://developer.download.nvidia.com/compute/cuda/12.8.1/local_installers/cuda_12.8.1_570.124.06_linux_sbsa.run + unpacker: none + - &cuda-12_8_1-x86_64 + url: https://developer.download.nvidia.com/compute/cuda/12.8.1/local_installers/cuda_12.8.1_570.124.06_linux.run + unpacker: none + - &cuda-12_2_2-aarch64 + url: https://developer.download.nvidia.com/compute/cuda/12.2.2/local_installers/cuda_12.2.2_535.104.05_linux_sbsa.run unpacker: none - &cuda-12_2_2-x86_64 url: https://developer.download.nvidia.com/compute/cuda/12.2.2/local_installers/cuda_12.2.2_535.104.05_linux.run @@ -30,6 +37,8 @@ cuda: unpacker: none shasums: + cuda_12.8.1_570.124.06_linux.run: 228f6bcaf5b7618d032939f431914fc92d0e5ed39ebe37098a24502f26a19797 + cuda_12.8.1_570.124.06_linux_sbsa.run: 353cbab1b57282a1001071796efd95c1e40ec27a3375e854d12637eaa1c6107c cuda_12.2.2_535.104.05_linux.run: 2b39aae3e7618d9f59a3c8fa1f1bc61f29c0b0e0df75fb05076badb352952ef2 cuda_12.2.2_535.104.05_linux_sbsa.run: 4113a15e6b27a02638c72edeb5f89de4c9ea312febba12fc4cefff2edc882268 cuda_12.2.0_535.54.03_linux.run: ecf3d2afadcbac029f0f4505785810d52d006e4b87ba79ff3f984336a2bbf518 @@ -38,22 +47,40 @@ cuda: cuda_12.1.1_530.30.02_linux_sbsa.run: 45ea4cd860f0a26d3db8ce032530f2ee0b55abdd587545213d395a73623b4278 versions: - 12.2.2: + 12.8.1: variants: - target_cpus: [aarch64] systems: [gpu.*.merlin7.psi.ch] relstage: unstable overlay: PSI urls: - - *cuda-12_2_2-aarch64 + - *cuda-12_8_1-aarch64 - target_cpus: [x86_64] systems: [.*.merlin7.psi.ch] relstage: unstable overlay: PSI + urls: + - *cuda-12_8_1-x86_64 + - target_cpus: [x86_64] + relstage: stable + urls: + - *cuda-12_8_1-x86_64 + 12.2.2: + variants: + - target_cpus: [aarch64] + systems: [gpu.*.merlin7.psi.ch] + relstage: stable + overlay: PSI + urls: + - *cuda-12_2_2-aarch64 + - target_cpus: [x86_64] + systems: [.*.merlin7.psi.ch] + relstage: stable + overlay: PSI urls: - *cuda-12_2_2-x86_64 - target_cpus: [x86_64] - relstage: unstable + relstage: stable urls: - *cuda-12_2_2-x86_64 @@ -61,17 +88,14 @@ cuda: variants: - target_cpus: [aarch64] systems: [gpu.*.merlin7.psi.ch] - relstage: unstable urls: - *cuda-12_2_0-aarch64 - target_cpus: [x86_64] systems: [.*.merlin7.psi.ch] - relstage: unstable overlay: PSI urls: - *cuda-12_2_0-x86_64 - target_cpus: [x86_64] - relstage: unstable urls: - *cuda-12_2_0-x86_64 From 42a6bd0bf811e874377c42efe0b86ada96dc32e4 Mon Sep 17 00:00:00 2001 From: viessm_h Date: Tue, 25 Mar 2025 15:47:11 +0100 Subject: [PATCH 128/158] add relion 5 stable with performance flags --- EM/relion/README.md | 8 ++- EM/relion/build | 98 +++++++++++++++++++++++++++---------- EM/relion/environment.yml | 34 ------------- EM/relion/files/config.yaml | 85 ++++++++++++++++++++++++++------ EM/relion/modulefile | 4 +- 5 files changed, 149 insertions(+), 80 deletions(-) delete mode 100644 EM/relion/environment.yml diff --git a/EM/relion/README.md b/EM/relion/README.md index 5af3571..f1c1701 100644 --- a/EM/relion/README.md +++ b/EM/relion/README.md @@ -23,6 +23,7 @@ https://git.psi.ch/lsm-hpce/relion-scripts - The build script was also updated accordingly - Also, cryocare is now available in a wrapper from relion, the cryocare installation executables need to be provided (seperate cryocare module). It is crucial to add the cryocare lib path (from the cryocare conda env) to the LD_LIBRARY_PATH when loading the relion module - tiff module no longer required, as this conflicts with the system shared tiff libs (not 100% sure why this canged from previous installations though) + ### 5.0-2beta (ON MERLIN7) - no fetching of weights with ftp possible, so cp from other machines into BUILD DIR and using the -DFETCH\_WEIGHTS=OFF option - link : ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz @@ -32,7 +33,7 @@ https://git.psi.ch/lsm-hpce/relion-scripts - same as 5.0-2beta (especially when it comes to the weights...) - copy the fltk and the classranker file into the BUILD Directory. The build script assumes that these two files are in the BUILD\_DIR. - sha256 errors occured during installation: -``` +```text ERROR: THESE PACKAGES DO NOT MATCH THE HASHES FROM THE REQUIREMENTS FILE. If you have updated the package versions, please update the hashes. Otherwise, examine the package contents carefully; someone may have tampered with them. unknown package: Expected sha256 20abd2cae58e55ca1af8a8dcf43293336a59adf0391f1917bf8518633cfc2cdf @@ -40,14 +41,17 @@ ERROR: THESE PACKAGES DO NOT MATCH THE HASHES FROM THE REQUIREMENTS FILE. If you ``` - The download of some packages (.whl files) was blocked by the merlin7 firewall. Google the shasum and find the package name. Try to manually download with curl. If this fails, this is a strong indication for network/firewall issues that need to be adressed by the networking team. .whl files from conda +pip installations are ususally stored in the env in lib/pythonXXX. - Also, to not clean up build directories: -``` +```text --no-clean Don't clean up build directories. (environment variable: PIP_NO_CLEAN) ``` +- adding flags to activate more aggressive compiler optimsations (affixing to `x86-64-v3` which is fully support on all EPYC nodes on Merlin7) + ### 5.0.0 for GH no successful installation so far - failing for conda env. Elsa G. build some hacky hack that works kind of.. needs to be investigated further. +- will attempt to build with more aggressive compiler optimisations as proscribed in: diff --git a/EM/relion/build b/EM/relion/build index e2388ce..d66be30 100755 --- a/EM/relion/build +++ b/EM/relion/build @@ -1,5 +1,6 @@ #!/usr/bin/env modbuild +PERFORMANCE="yes" PROFILE="no" SP="no" @@ -8,21 +9,18 @@ pbuild::prep() { local BRANCH if [[ "$V" =~ beta$ ]]; then BRANCH="ver${V_MAJOR}.${V_MINOR}" - elif [[ "$V" =~ profile$ ]]; then BRANCH="${V_PKG}" PROFILE="yes" - elif [[ "$V" =~ sp$ ]]; then BRANCH="ver${V_MAJOR}.${V_MINOR}" SP="yes" - else BRANCH="${V_PKG}" fi if [[ -d "$SRC_DIR/.git" ]]; then - cd "$SRC_DIR" + cd "$SRC_DIR" git pull else git clone --depth=1 -b "$BRANCH" https://github.com/3dem/relion.git "$SRC_DIR" || return $? @@ -31,63 +29,111 @@ pbuild::prep() { pbuild::pre_configure() { - # Section will be switched on for -profile version #----------------------------------------------------------- if [[ "$PROFILE" == "yes" ]]; then # this needs to go into the config.yml file for >5.0-1beta - : #pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=BENCHMARKING" + if [[ "$V_MAJOR" -lt "5" ]]; then + : pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=BENCHMARKING" + fi fi #------------------------------------------------------------ - # Section will be switched on for single-precision version # Safe memory usage for multibody refinements #------------------------------------------------------------ if [[ "$SP" == "yes" ]]; then # this needs to go into the config.yml file for >5.0-1beta - : #pbuild::add_configure_args "-DDoublePrec_CPU=OFF" + if [[ "$V_MAJOR" -lt "5" ]]; then + : pbuild::add_configure_args "-DDoublePrec_CPU=OFF" + fi fi #------------------------------------------------------------ + # Set performance oriented compiler flags, specific for a given + # architecture. + # ------------------------------------------------------------- + if [[ "$PERFORMANCE" == "yes" && "$PROFILE" == "no" ]]; then + # set compiler flags per arch + echo "> setting performance system compiler flags" + case "$(uname -m)" in + "aarch64") + export CC=gcc + export CFLAGS='-mcpu=neoverse-v2 -O3 -pipe -Wno-error' + export CXX=g++ + export CXXFLAGS='-mcpu=neoverse-v2 -O3 -pipe -Wno-error' + export FCFLAGS='-mcpu=neoverse-v2 -O3 -pipe' + export FFLAGS='-mcpu=neoverse-v2 -O3 -pipe' + export LDFLAGS='-Wl,--as-needed' + ;; + "x86_64") + export CC=gcc + export CFLAGS='-march=x86-64-v3 -mtune=znver1 -O3 -pipe -Wno-error' + export CXX=g++ + export CXXFLAGS='-march=x86-64-v3 -mtune=znver1 -O3 -pipe -Wno-error' + export FCFLAGS='-march=x86-64-v3 -mtune=znver1 -O3 -pipe' + export FFLAGS='-march=x86-64-v3 -mtune=znver1 -O3 -pipe' + export LDFLAGS='-Wl,--as-needed' + ;; + *) + echo ">> Unknown system arch found $(uname -m)! Using basic flags only!" + export CC=gcc + export CFLAGS='-O3 -pipe -Wno-error' + export CXX=g++ + export CXXFLAGS='-O3 -pipe -Wno-error' + export FCFLAGS='-O3 -pipe' + export FFLAGS='-O3 -pipe' + export LDFLAGS='-Wl,--as-needed' + ;; + esac + echo ">> ${CC} ${CFLAGS}" + echo ">> ${CXX} ${CXXFLAGS}" + fi + # ------------------------------------------------------------- + # The following section will only work for versions >= 5.0-beta # ------------------------------------------------------------- if [[ "$V_MAJOR" -ge "5" ]]; then - #download blush weights, from zenodo - #mkdir -p "${PREFIX}" + #download blush weights, from zenodo + echo "> downloading blush weights" + mkdir -p "$PREFIX/torch/hub/checkpoints/relion_blush" wget -q https://zenodo.org/records/10072731/files/blush_v1.0.ckpt.gz -P "$PREFIX/torch/hub/checkpoints/relion_blush" \ && gunzip "$PREFIX/torch/hub/checkpoints/relion_blush/blush_v1.0.ckpt.gz" mv "$PREFIX/torch/hub/checkpoints/relion_blush/blush_v1.0.ckpt" "$PREFIX/torch/hub/checkpoints/relion_blush/v1.0.ckpt" touch "$PREFIX/torch/hub/checkpoints/relion_blush/v1.0_installed.txt" - #cp classranker that was downloaded on another machine before from BUILDBLOCK_DIR + #cp classranker that was downloaded on another machine before from BUILDBLOCK_DIR + echo "> downloading classranker" mkdir -p "$PREFIX/torch/hub/checkpoints/relion_class_ranker" - cp "$BUILDBLOCK_DIR/classranker_v1.0.ckpt.gz" "$PREFIX/torch/hub/checkpoints/relion_class_ranker" - gunzip "$PREFIX/torch/hub/checkpoints/relion_class_ranker/classranker_v1.0.ckpt.gz" + wget -q ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/classranker_v1.0.ckpt.gz -P "$PREFIX/torch/hub/checkpoints/relion_class_ranker" \ + && gunzip "$PREFIX/torch/hub/checkpoints/relion_class_ranker/classranker_v1.0.ckpt.gz" mv "$PREFIX/torch/hub/checkpoints/relion_class_ranker/classranker_v1.0.ckpt" "$PREFIX/torch/hub/checkpoints/relion_class_ranker/v1.0.ckpt" touch "$PREFIX/torch/hub/checkpoints/relion_class_ranker/v1.0_installed.txt" # fltk stuff + echo "> downloading FLTK" mkdir -p "$SRC_DIR/external/fltk" - cp "$BUILDBLOCK_DIR/fltk-1.3.5-source.tar.gz" "$SRC_DIR/external/fltk/" - + wget -q ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz -P "$SRC_DIR/external/fltk/" - #INSTALL Miniconda - echo "installing miniconda" + # Install Miniconda + echo "> installing miniconda" mkdir -p "$PREFIX/miniconda" - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh -O "$PREFIX/miniconda/miniconda.sh" - #wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + if [[ "$(uname -m)" =~ "aarch64" ]]; then + wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh -O "$PREFIX/miniconda/miniconda.sh" + else + wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh" + fi bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/" - # Copy manually edited environment.yml file (with cryocare specs) into the folder to substitute the default one - #Conda create env with miniconda installation - "$PREFIX/miniconda/condabin/conda" env create --name "${P}-${V}" -f "$SRC_DIR/environment.yml" + # Setup conda env; switch into relion repo directory to capture local + # `.[vis]` pip package dependencies + echo "> building conda env" + pushd "$SRC_DIR" + "$PREFIX/miniconda/condabin/conda" env create -q -f environment.yml "$PREFIX/miniconda/condabin/conda" env list + popd fi - + #--------------------------------------------------------------- - - } - diff --git a/EM/relion/environment.yml b/EM/relion/environment.yml deleted file mode 100644 index 549b89b..0000000 --- a/EM/relion/environment.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: relion-5.0 -channels: - - conda-forge -dependencies: - - pip - - python=3.9 - - setuptools=59.5.0 - - pip: - - torch==2.0.1 - - torchvision==0.15.2 - - tqdm==4.65.0 - - mrcfile==1.4.3 - - starfile>=0.5.6 - - loguru==0.7.0 - - scikit-learn==1.3.0 - - umap-learn==0.5.3 - - matplotlib==3.7.2 - - morphosamplers==0.0.13 - - pydantic==1.10.18 - - napari[all]==0.4.18 - - tsnecuda==3.0.1 - - PyQt5==5.15.9 - - typer==0.9.0 - - biopython==1.81 - - fastcluster==1.2.6 - - seaborn==0.12.2 - - dill==0.3.7 - - numpy<2 - - git+https://github.com/3dem/relion-classranker@b6e751e5cb4205d8e9b36d0ae38c3687b3395acb - - git+https://github.com/3dem/relion-blush - - git+https://github.com/3dem/DynaMight - - git+https://github.com/3dem/topaz - - git+https://github.com/3dem/model-angelo - - ".[vis]" diff --git a/EM/relion/files/config.yaml b/EM/relion/files/config.yaml index e51829f..e0242f6 100644 --- a/EM/relion/files/config.yaml +++ b/EM/relion/files/config.yaml @@ -7,38 +7,94 @@ relion: relstage: unstable build_variants: first_match versions: - 5.0.0: + 5.0.0-perf: variants: - - overlay: Alps + - overlay: Alps target_cpus: [x86_64] systems: [.*.merlin7.psi.ch] build_requires: - cmake/3.23.2 - git/2.37.0 - - openmpi/5.0.5 - relstage: unstable + - gcc/12.3.0 + - cuda/12.2.0 + - openmpi/5.0.5 + relstage: stable runtime_deps: - gcc/12.3.0 - cuda/12.2.0 - openmpi/5.0.5 configure_with: cmake configure_args: + - "-DCMAKE_BUILD_TYPE=RELEASE" + - "-DCMAKE_CXX_FLAGS=${CXXFLAGS} -DNDEBUG" + - "-DCMAKE_C_FLAGS=${CFLAGS} -DNDEBUG" - "-DTORCH_HOME_PATH=${PREFIX}/torch" - - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/${P}-${V}/bin/python" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/relion-5.0/bin/python" - "-DFORCE_OWN_FFTW=ON" - "-DFORCE_OWN_FLTK=ON" - - "-DFORCE_OWN_TBB=ON" - "-DCUDA=ON" - "-DCUDA_ARCH=80" # dep on the cuda arch of the oldest GPU - "-DFETCH_WEIGHTS=OFF" - # does not work yet- just an idea... - - overlay: Alps + # does not work yet- just an idea... + - overlay: Alps target_cpus: [aarch64] systems: [gpu0.*.merlin7.psi.ch] build_requires: #- cmake/3.23.2 #- git/2.37.0 - - openmpi/5.0.5 + - openmpi/5.0.5 + - gcc/12.3.0 + - cuda/12.2.0 + relstage: unstable + runtime_deps: + - gcc/12.3.0 + - cuda/12.2.0 + - openmpi/5.0.5 + configure_with: cmake + configure_args: + - "-DCMAKE_BUILD_TYPE=RELEASE" + - "-DCMAKE_CXX_FLAGS=${CXXFLAGS} -DNDEBUG" + - "-DCMAKE_C_FLAGS=${CFLAGS} -DNDEBUG" + - "-DTORCH_HOME_PATH=${PREFIX}/torch" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/relion-5.0/bin/python" + - "-DFORCE_OWN_FFTW=ON" + - "-DFORCE_OWN_FLTK=ON" + - "-DCUDA=ON" + - "-DCUDA_ARCH=90" # dep on the cuda arch of the oldest GPU + - "-DFETCH_WEIGHTS=OFF" + 5.0.0: + variants: + - overlay: Alps + target_cpus: [x86_64] + systems: [.*.merlin7.psi.ch] + build_requires: + - cmake/3.23.2 + - git/2.37.0 + - gcc/12.3.0 + - cuda/12.2.0 + - openmpi/5.0.5 + relstage: unstable + runtime_deps: + - gcc/12.3.0 + - cuda/12.2.0 + - openmpi/5.0.5 + configure_with: cmake + configure_args: + - "-DTORCH_HOME_PATH=${PREFIX}/torch" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/relion-5.0/bin/python" + - "-DFORCE_OWN_FFTW=ON" + - "-DFORCE_OWN_FLTK=ON" + - "-DCUDA=ON" + - "-DCUDA_ARCH=80" # dep on the cuda arch of the oldest GPU + - "-DFETCH_WEIGHTS=OFF" + # does not work yet- just an idea... + - overlay: Alps + target_cpus: [aarch64] + systems: [gpu0.*.merlin7.psi.ch] + build_requires: + #- cmake/3.23.2 + #- git/2.37.0 + - openmpi/5.0.5 - gcc/12.3.0 - cuda/12.2.0 relstage: unstable @@ -49,17 +105,16 @@ relion: configure_with: cmake configure_args: - "-DTORCH_HOME_PATH=${PREFIX}/torch" - - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/${P}-${V}/bin/python" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/relion-5.0/bin/python" - "-DFORCE_OWN_FFTW=ON" - "-DFORCE_OWN_FLTK=ON" - - "-DFORCE_OWN_TBB=ON" - "-DCUDA=ON" - "-DCUDA_ARCH=90" # dep on the cuda arch of the oldest GPU - "-DFETCH_WEIGHTS=OFF" #MERLIN7 old (cray) 5.0-2beta: variants: - - overlay: Alps + - overlay: Alps systems: [gpu.*.merlin7.psi.ch] build_requires: - cmake/3.23.2 @@ -73,10 +128,9 @@ relion: configure_with: cmake configure_args: - "-DTORCH_HOME_PATH=${PREFIX}/torch" - - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/${P}-${V}/bin/python" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/relion-5.0/bin/python" - "-DFORCE_OWN_FFTW=ON" - "-DFORCE_OWN_FLTK=ON" - - "-DFORCE_OWN_TBB=ON" - "-DCUDA=ON" - "-DCUDA_ARCH=80" # dep on the cuda arch of the oldest GPU #- "-DCudaTexture=ON" @@ -99,10 +153,9 @@ relion: configure_with: cmake configure_args: - "-DTORCH_HOME_PATH=${PREFIX}/torch" - - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/${P}-${V}/bin/python" + - "-DPYTHON_EXE_PATH=${PREFIX}/miniconda/envs/relion-5.0/bin/python" - "-DFORCE_OWN_FFTW=ON" - "-DFORCE_OWN_FLTK=ON" - - "-DFORCE_OWN_TBB=ON" - "-DCUDA=ON" - "-DCUDA_ARCH=61" # dep on the cuda arch of the oldest GPU - "-DCudaTexture=ON" diff --git a/EM/relion/modulefile b/EM/relion/modulefile index 1dac00d..53760e2 100644 --- a/EM/relion/modulefile +++ b/EM/relion/modulefile @@ -44,7 +44,7 @@ setenv RELION_QSUB_TEMPLATE /opt/psi/overlays/Alps/EM/relion/$V/scripts/multi_gp setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.6.4/bin/MotionCor2" -setenv RELION_TOPAZ_EXECUTABLE /opt/psi/overlays/Alps/EM/relion/$V/miniconda/envs/$P-$V/bin/topaz -setenv RELION_PYTHON_EXECUTABLE /opt/psi/overlays/Alps/EM/relion/$V/miniconda/envs/$P-$V/bin/python +setenv RELION_TOPAZ_EXECUTABLE /opt/psi/overlays/Alps/EM/relion/$V/miniconda/envs/relion-5.0/bin/topaz +setenv RELION_PYTHON_EXECUTABLE /opt/psi/overlays/Alps/EM/relion/$V/miniconda/envs/relion-5.0/bin/python setenv RELION_TORCH_HOME_PATH /opt/psi/overlays/Alps/EM/relion/$V/torch/ From dc2fab8546cf7945c7f4cf56127ef707dd0bb511 Mon Sep 17 00:00:00 2001 From: germann_e Date: Tue, 8 Apr 2025 10:41:40 +0200 Subject: [PATCH 129/158] ADD: first visit draft --- Tools/visit/build | 17 +++++++++++++++++ Tools/visit/files/config.yaml | 19 +++++++++++++++++++ Tools/visit/files/variants.rhel7 | 3 +++ Tools/visit/modulefile | 18 ++++++++++++++++++ 4 files changed, 57 insertions(+) create mode 100755 Tools/visit/build create mode 100644 Tools/visit/files/config.yaml create mode 100644 Tools/visit/files/variants.rhel7 create mode 100644 Tools/visit/modulefile diff --git a/Tools/visit/build b/Tools/visit/build new file mode 100755 index 0000000..a2669f7 --- /dev/null +++ b/Tools/visit/build @@ -0,0 +1,17 @@ +#!/usr/bin/env modbuild + +pbuild::prep() { + : +} + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + visit-install ${V} linux-$(uname -p) $PREFIX +} diff --git a/Tools/visit/files/config.yaml b/Tools/visit/files/config.yaml new file mode 100644 index 0000000..843d6e8 --- /dev/null +++ b/Tools/visit/files/config.yaml @@ -0,0 +1,19 @@ +--- +format: 1 +gnuplot: + defaults: + group: Tools + overlay: base + relstage: stable + systems: [sles15.5] + docfiles: [Copyright, NEWS, README] + urls: + - url: https://github.com/visit-dav/visit/releases/download/v${V_PKG}/visit-install${V_PKG//./_} + shasums: + visit-3.4.2: 65b5ad7facc0f7281026c78c2adeff07a31965136da150e3d9d00341907367da + versions: + 3.4.2: + config: + relstage: unstable + systems: [rhel*] + diff --git a/Tools/visit/files/variants.rhel7 b/Tools/visit/files/variants.rhel7 new file mode 100644 index 0000000..94dcdde --- /dev/null +++ b/Tools/visit/files/variants.rhel7 @@ -0,0 +1,3 @@ +gnuplot/5.4.3 stable +gnuplot/5.4.4 stable +gnuplot/5.4.5 stable diff --git a/Tools/visit/modulefile b/Tools/visit/modulefile new file mode 100644 index 0000000..8fba736 --- /dev/null +++ b/Tools/visit/modulefile @@ -0,0 +1,18 @@ +#%Pmodule + +module-whatis "portable command-line driven graphing utility" +module-url "http://www.gnuplot.info/" +module-license "See \$GNUPLOT_DIR/share/doc/gnuplot/Copyright" +module-maintainer "Achim Gsell " + +module-help " +Gnuplot is a portable command-line driven graphing utility for Linux, +OS/2, MS Windows, OSX, VMS, and many other platforms. The source code +is copyrighted but freely distributed (i.e., you don't have to pay for +it). It was originally created to allow scientists and students to +visualize mathematical functions and data interactively, but has grown +to support many non-interactive uses such as web scripting. It is also +used as a plotting engine by third-party applications like Octave. +Gnuplot has been supported and under active development since 1986. +" + From f3d8509830b589b4a02c986b980e4a4c24b6e7ba Mon Sep 17 00:00:00 2001 From: Germann Elsa Sylvia Date: Tue, 8 Apr 2025 15:35:36 +0200 Subject: [PATCH 130/158] ADD: final visit build script --- Tools/visit/build | 7 ++----- Tools/visit/files/config.yaml | 15 +++++++++------ 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/Tools/visit/build b/Tools/visit/build index a2669f7..d52c52d 100755 --- a/Tools/visit/build +++ b/Tools/visit/build @@ -1,9 +1,5 @@ #!/usr/bin/env modbuild -pbuild::prep() { - : -} - pbuild::configure() { : } @@ -13,5 +9,6 @@ pbuild::compile() { } pbuild::install() { - visit-install ${V} linux-$(uname -p) $PREFIX + cd "${PMODULES_DISTFILESDIR}" + bash "./visit-install-${V_PKG}" ${V} linux-$(uname -p) ${PREFIX} } diff --git a/Tools/visit/files/config.yaml b/Tools/visit/files/config.yaml index 843d6e8..6e8d785 100644 --- a/Tools/visit/files/config.yaml +++ b/Tools/visit/files/config.yaml @@ -1,19 +1,22 @@ --- format: 1 -gnuplot: +visit: defaults: group: Tools overlay: base relstage: stable systems: [sles15.5] docfiles: [Copyright, NEWS, README] - urls: - - url: https://github.com/visit-dav/visit/releases/download/v${V_PKG}/visit-install${V_PKG//./_} - shasums: - visit-3.4.2: 65b5ad7facc0f7281026c78c2adeff07a31965136da150e3d9d00341907367da versions: 3.4.2: config: + urls: + - url: https://github.com/visit-dav/visit/releases/download/v${V_PKG}/visit-install3_4_2 + name: visit-install-${V_PKG} + unpacker: none + - url: https://github.com/visit-dav/visit/releases/download/v${V_PKG}/visit3_4_2.linux-x86_64-rocky8.tar.gz + name: visit3_4_2.linux-x86_64.tar.gz + unpacker: none relstage: unstable - systems: [rhel*] + systems: [sles*] From 360bb13e4ecaeaa782aca564c54eb541c1df4ee8 Mon Sep 17 00:00:00 2001 From: Germann Elsa Sylvia Date: Tue, 8 Apr 2025 15:40:10 +0200 Subject: [PATCH 131/158] FIX: module descrition and rm old variant file --- Tools/visit/files/variants.rhel7 | 3 --- Tools/visit/modulefile | 16 +++++----------- 2 files changed, 5 insertions(+), 14 deletions(-) delete mode 100644 Tools/visit/files/variants.rhel7 diff --git a/Tools/visit/files/variants.rhel7 b/Tools/visit/files/variants.rhel7 deleted file mode 100644 index 94dcdde..0000000 --- a/Tools/visit/files/variants.rhel7 +++ /dev/null @@ -1,3 +0,0 @@ -gnuplot/5.4.3 stable -gnuplot/5.4.4 stable -gnuplot/5.4.5 stable diff --git a/Tools/visit/modulefile b/Tools/visit/modulefile index 8fba736..722eb8f 100644 --- a/Tools/visit/modulefile +++ b/Tools/visit/modulefile @@ -1,18 +1,12 @@ #%Pmodule -module-whatis "portable command-line driven graphing utility" -module-url "http://www.gnuplot.info/" -module-license "See \$GNUPLOT_DIR/share/doc/gnuplot/Copyright" +module-whatis "Open Source, interactive, scalable, visualization, animation and analysis tool" +module-url "https://visit-dav.github.io/visit-website/about/" +module-license "BSD 3-Clause License" module-maintainer "Achim Gsell " module-help " -Gnuplot is a portable command-line driven graphing utility for Linux, -OS/2, MS Windows, OSX, VMS, and many other platforms. The source code -is copyrighted but freely distributed (i.e., you don't have to pay for -it). It was originally created to allow scientists and students to -visualize mathematical functions and data interactively, but has grown -to support many non-interactive uses such as web scripting. It is also -used as a plotting engine by third-party applications like Octave. -Gnuplot has been supported and under active development since 1986. +VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. +From Unix, Windows or Mac workstations, users can interactively visualize and analyze data ranging in scale from small (<10 core) desktop-sized projects to large (>10,000 core) leadership-class computing facility simulation campaigns. " From 33d05777ad489a544ca06b0ceb598dfc15fd1b9f Mon Sep 17 00:00:00 2001 From: "Feichtinger Derek Heinrich (ADM)" Date: Thu, 24 Apr 2025 16:36:46 +0200 Subject: [PATCH 132/158] move anaconda_2024.08 to stable --- Programming/anaconda/files/config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Programming/anaconda/files/config.yaml b/Programming/anaconda/files/config.yaml index 8784b66..463c9c1 100644 --- a/Programming/anaconda/files/config.yaml +++ b/Programming/anaconda/files/config.yaml @@ -12,4 +12,4 @@ anaconda: - url: https://repo.anaconda.com/miniconda/Miniconda3-py39_24.5.0-0-Linux-x86_64.sh name: miniconda-2024.08.sh unpacker: none - relstage: unstable + relstage: stable From 5bcb149bb4bee355a5fe6e78d274404bb24f17ae Mon Sep 17 00:00:00 2001 From: Hans-Nikolai Viessmann Date: Thu, 15 May 2025 16:18:54 +0200 Subject: [PATCH 133/158] add version fpart 1.7.0 --- Tools/fpart/build | 6 ++++++ Tools/fpart/files/config.yaml | 18 ++++++++++++++++++ Tools/fpart/modulefile | 12 ++++++++++++ 3 files changed, 36 insertions(+) create mode 100755 Tools/fpart/build create mode 100644 Tools/fpart/files/config.yaml create mode 100644 Tools/fpart/modulefile diff --git a/Tools/fpart/build b/Tools/fpart/build new file mode 100755 index 0000000..916ff80 --- /dev/null +++ b/Tools/fpart/build @@ -0,0 +1,6 @@ +#!/usr/bin/env modbuild + +# we need to generate the configure file +pbuild::post_prep() { + autoreconf -i +} diff --git a/Tools/fpart/files/config.yaml b/Tools/fpart/files/config.yaml new file mode 100644 index 0000000..9b2535a --- /dev/null +++ b/Tools/fpart/files/config.yaml @@ -0,0 +1,18 @@ +--- +format: 1 +fpart: + defaults: + group: Tools + overlay: base + relstage: stable + configure_with: autotools + build_variants: first_match + target_cpus: [x86_64] + systems: [rhel8] + docfiles: [COPYING, README.md, Changelog.md] + urls: + - url: https://github.com/martymac/$P/archive/refs/tags/$P-${V_PKG}.tar.gz + shasums: + fpart-1.7.0.tar.gz: e5f82dd90001ed53200b2383bcfd520b1d8ee06d6a2a75b39d37d68daef20c88 + versions: + 1.7.0: diff --git a/Tools/fpart/modulefile b/Tools/fpart/modulefile new file mode 100644 index 0000000..41f99d5 --- /dev/null +++ b/Tools/fpart/modulefile @@ -0,0 +1,12 @@ +#%Module1.0 + +module-whatis "Fpart is a Filesystem partitioner" +module-url "https://www.fpart.org/" +module-license "BSD 2 Clause" +module-maintainer "Hans-Nikolai Viessmann Date: Mon, 19 May 2025 08:45:26 +0200 Subject: [PATCH 134/158] fix modulefiles whatis message (no quotes) --- Tools/fpart/modulefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Tools/fpart/modulefile b/Tools/fpart/modulefile index 41f99d5..0c23a00 100644 --- a/Tools/fpart/modulefile +++ b/Tools/fpart/modulefile @@ -6,7 +6,7 @@ module-license "BSD 2 Clause" module-maintainer "Hans-Nikolai Viessmann Date: Tue, 20 May 2025 11:07:55 +0200 Subject: [PATCH 135/158] VSCode build-block added --- Tools/VSCode/build | 12 ++++++++++++ Tools/VSCode/files/config.yaml | 20 ++++++++++++++++++++ Tools/VSCode/modulefile | 16 ++++++++++++++++ 3 files changed, 48 insertions(+) create mode 100755 Tools/VSCode/build create mode 100644 Tools/VSCode/files/config.yaml create mode 100644 Tools/VSCode/modulefile diff --git a/Tools/VSCode/build b/Tools/VSCode/build new file mode 100755 index 0000000..89c436d --- /dev/null +++ b/Tools/VSCode/build @@ -0,0 +1,12 @@ +#!/usr/bin/env modbuild + +pbuild::install() { + : + cd "${PREFIX}" + tar --strip-components=1 -xvf "${PMODULES_DISTFILESDIR}/VSCode-${V_PKG}.tar.gz" +} +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Tools/VSCode/files/config.yaml b/Tools/VSCode/files/config.yaml new file mode 100644 index 0000000..448938b --- /dev/null +++ b/Tools/VSCode/files/config.yaml @@ -0,0 +1,20 @@ +--- +format: 1 +VSCode: + defaults: + group: Tools + overlay: base + relstage: stable + systems: [.*] + build_functions: + configure: [] + compile: [] + urls: + - url: https://update.code.visualstudio.com/${V_PKG}/linux-x64/stable + name: VSCode-${V_PKG}.tar.gz + unpacker: none + shasums: + versions: + 1.100.2: + config: + relstage: unstable diff --git a/Tools/VSCode/modulefile b/Tools/VSCode/modulefile new file mode 100644 index 0000000..e3b9bf6 --- /dev/null +++ b/Tools/VSCode/modulefile @@ -0,0 +1,16 @@ +#%Module1.0 + +module-whatis "lightweight but powerful source code editor" +module-url "https://code.visualstudio.com/docs" +module-license "See: https://code.visualstudio.com/license" +module-maintainer "Achim Gsell " + +module-help " +Visual Studio Code is a lightweight but powerful source code editor +which runs on your desktop and is available for Windows, macOS and +Linux. It comes with built-in support for JavaScript, TypeScript +and Node.js and has a rich ecosystem of extensions for other languages +(such as C++, C#, Java, Python, PHP, Go) and runtimes (such as .NET +and Unity). Begin your journey with VS Code with these introductory +videos: https://code.visualstudio.com/docs/introvideos/overview +" From b3b65f88d95f1758ed228adc8efa7c757080a1cb Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 20 May 2025 15:30:04 +0200 Subject: [PATCH 136/158] SHA256 sum added --- Tools/VSCode/files/config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/Tools/VSCode/files/config.yaml b/Tools/VSCode/files/config.yaml index 448938b..9ffd6c7 100644 --- a/Tools/VSCode/files/config.yaml +++ b/Tools/VSCode/files/config.yaml @@ -14,6 +14,7 @@ VSCode: name: VSCode-${V_PKG}.tar.gz unpacker: none shasums: + VSCode-1.100.2.tar.gz: 5c2cbbeaa08b92340dce899a78d66be8d92c09b4d75313bfdfc46fb3bddca5c0 versions: 1.100.2: config: From 43d425a7c3ed05bc8f1800d48fe3f61d7a55caac Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 20 May 2025 15:38:56 +0200 Subject: [PATCH 137/158] old versions added to YAML config --- Tools/VSCode/files/config.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/Tools/VSCode/files/config.yaml b/Tools/VSCode/files/config.yaml index 9ffd6c7..aeaa30c 100644 --- a/Tools/VSCode/files/config.yaml +++ b/Tools/VSCode/files/config.yaml @@ -19,3 +19,9 @@ VSCode: 1.100.2: config: relstage: unstable + 1.87.0: + config: + relstage: stable + 1.38.1_rhel7;1.73.1: + config: + relstage: deprecated From ccef6c571af0f52a80563de723ec67fb4ba868f5 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Wed, 21 May 2025 15:34:12 +0200 Subject: [PATCH 138/158] gnuplot: legacy build script removed --- Tools/gnuplot/build | 11 ----------- Tools/gnuplot/build-yaml | 7 ------- Tools/gnuplot/files/config.yaml | 20 ++++++++++---------- 3 files changed, 10 insertions(+), 28 deletions(-) delete mode 100755 Tools/gnuplot/build-yaml diff --git a/Tools/gnuplot/build b/Tools/gnuplot/build index 02f5bfd..4d92699 100755 --- a/Tools/gnuplot/build +++ b/Tools/gnuplot/build @@ -1,16 +1,5 @@ #!/usr/bin/env modbuild -pbuild::set_download_url \ - "https://sourceforge.net/projects/gnuplot/files/$P/$V/$P-$V.tar.gz" -pbuild::set_sha256sum 'gnuplot-5.2.4.tar.gz:1515f000bd373aaa53b16183f274189d4f5e0ae47d22f434857933d16a4770cb' -pbuild::install_docfiles 'Copyright' 'NEWS' 'README' - -pbuild::add_to_group 'Tools' - -pbuild::pre_configure() { - pbuild::add_configure_args '--with-latex=no' - pbuild::add_configure_args '--with-qt=no' -} # Local Variables: # mode: sh # sh-basic-offset: 8 diff --git a/Tools/gnuplot/build-yaml b/Tools/gnuplot/build-yaml deleted file mode 100755 index 4d92699..0000000 --- a/Tools/gnuplot/build-yaml +++ /dev/null @@ -1,7 +0,0 @@ -#!/usr/bin/env modbuild - -# Local Variables: -# mode: sh -# sh-basic-offset: 8 -# tab-width: 8 -# End: diff --git a/Tools/gnuplot/files/config.yaml b/Tools/gnuplot/files/config.yaml index 9e709c2..00ac193 100644 --- a/Tools/gnuplot/files/config.yaml +++ b/Tools/gnuplot/files/config.yaml @@ -10,6 +10,8 @@ gnuplot: urls: - url: https://sourceforge.net/projects/gnuplot/files/$P/$V/$P-${V_PKG}.tar.gz shasums: + gnuplot-6.0.1.tar.gz: e85a660c1a2a1808ff24f7e69981ffcbac66a45c9dcf711b65610b26ea71379a + gnuplot-6.0.0.tar.gz: 635a28f0993f6ab0d1179e072ad39b8139d07f51237f841d93c6c2ff4b1758ec gnuplot-5.4.10.tar.gz: 975d8c1cc2c41c7cedc4e323aff035d977feb9a97f0296dd2a8a66d197a5b27c gnuplot-5.4.9.tar.gz: a328a021f53dc05459be6066020e9a71e8eab6255d3381e22696120d465c6a97 gnuplot-5.4.8.tar.gz: 931279c7caad1aff7d46cb4766f1ff41c26d9be9daf0bcf0c79deeee3d91f5cf @@ -26,18 +28,16 @@ gnuplot: gnuplot-5.0.0.tar.gz: 417d4bc5bc914a60409bb75cf18dd14f48b07f53c6ad3c4a4d3cd9a8d7370faf gnuplot-4.6.3.tar.gz: df5ffafa25fb32b3ecc0206a520f6bca8680e6dcc961efd30df34c0a1b7ea7f5 versions: - 5.4.{0,1,2,3,4,5,8,9};5.2.{0,4,6,7,8};5.0.0;4.6.3: - 5.4.10: + 6.0.1;6.0.0: config: relstage: stable - 6.0.0: - config: - relstage: unstable - systems: [rhel*] + systems: [rhel*, sles*] configure_args: ['--with-latex=no', '--with-qt=no'] - 6.0.1: + 5.4.{0,1,2,3,4,5,8,9,10}: config: - relstage: unstable - systems: [rhel*] - configure_args: ['--with-latex=no', '--with-qt=no'] + relstage: stable + systems: [rhel*, sles*] + 5.2.{0,4,6,7,8};5.0.0: + config: + relstage: deprecated From 113d296b5022c0af9a1763f6399ebd992138da8d Mon Sep 17 00:00:00 2001 From: gsell Date: Wed, 21 May 2025 16:23:34 +0200 Subject: [PATCH 139/158] gcc: use dedicated modulefile for Merlin7 --- Programming/gcc/files/config.yaml | 1 + Programming/gcc/modulefile-alps | 28 ++++++++++++++++++++++++++++ 2 files changed, 29 insertions(+) create mode 100644 Programming/gcc/modulefile-alps diff --git a/Programming/gcc/files/config.yaml b/Programming/gcc/files/config.yaml index a625fce..0d4e8db 100644 --- a/Programming/gcc/files/config.yaml +++ b/Programming/gcc/files/config.yaml @@ -86,6 +86,7 @@ gcc: systems: [rhel.*] - overlay: PSI systems: [login.*.merlin7.psi.ch, cn.*.merlin7.psi.ch, gpu.*.merlin7.psi.ch] + modulefile: modulefile-alps - overlay: base systems: [rhel.*] diff --git a/Programming/gcc/modulefile-alps b/Programming/gcc/modulefile-alps new file mode 100644 index 0000000..a1f7b84 --- /dev/null +++ b/Programming/gcc/modulefile-alps @@ -0,0 +1,28 @@ +#%Module1.0 + +module-whatis "GNU Compiler Collection" +module-url "http://gcc.gnu.org/" +module-license "GNU GPL v2/v3" +module-maintainer "Achim Gsell " + +module-help " +The GNU Compiler Collection includes front ends for C, C++, Objective-C, +Fortran, Java, Ada, and Go, as well as libraries for these languages +(libstdc++, libgcj,...). GCC was originally written as the compiler for +the GNU operating system. + +This module includes compilers for +- C/C++ +- Objective-C/Objective-C++ +- Fortran +" + +module-addgroup "Compiler" + +setenv CC $PREFIX/bin/gcc +setenv CXX $PREFIX/bin/g++ +setenv F77 $PREFIX/bin/gfortran +setenv F90 $PREFIX/bin/gfortran +setenv FC $PREFIX/bin/gfortran +setenv FORTRAN $PREFIX/bin/gfortran + From 75cf0f446a7b25aea2462e4c558822a6f0a1316c Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 13:29:05 +0200 Subject: [PATCH 140/158] curl: new module added --- Libraries/libpsl/build | 2 ++ Libraries/libpsl/files/config.yaml | 16 ++++++++++++++++ Libraries/libpsl/modulefile | 16 ++++++++++++++++ Tools/curl/build | 7 +++++++ Tools/curl/files/config.yaml | 21 +++++++++++++++++++++ Tools/curl/modulefile | 15 +++++++++++++++ 6 files changed, 77 insertions(+) create mode 100755 Libraries/libpsl/build create mode 100644 Libraries/libpsl/files/config.yaml create mode 100644 Libraries/libpsl/modulefile create mode 100755 Tools/curl/build create mode 100644 Tools/curl/files/config.yaml create mode 100644 Tools/curl/modulefile diff --git a/Libraries/libpsl/build b/Libraries/libpsl/build new file mode 100755 index 0000000..6e021f3 --- /dev/null +++ b/Libraries/libpsl/build @@ -0,0 +1,2 @@ +#!/usr/bin/env modbuild + diff --git a/Libraries/libpsl/files/config.yaml b/Libraries/libpsl/files/config.yaml new file mode 100644 index 0000000..30532b8 --- /dev/null +++ b/Libraries/libpsl/files/config.yaml @@ -0,0 +1,16 @@ +format: 1 +libpsl: + defaults: + group: Libraries + overlay: base + relstage: stable + docfiles: [] + urls: + - url: https://github.com/rockdaboot/$P/releases/download/${V_PKG}/$P-${V_PKG}.tar.gz + + shasums: + + versions: + 0.21.5: + config: + diff --git a/Libraries/libpsl/modulefile b/Libraries/libpsl/modulefile new file mode 100644 index 0000000..2bff60b --- /dev/null +++ b/Libraries/libpsl/modulefile @@ -0,0 +1,16 @@ +#%Module1.0 + +module-whatis "C library to handle the Public Suffix List" +module-url "https://github.com/rockdaboot/libpsl" +module-license "See https://github.com/rockdaboot/libpsl/blob/master/LICENSE" +module-maintainer "Achim Gsell " + +module-help " +A Public Suffix List is a collection of Top Level Domains (TLDs) suffixes. +TLDs include Global Top Level Domains (gTLDs) like .com and .net; Country +Top Level Domains (ccTLDs) like .de and .cn; and Brand Top Level Domains +like .apple and .google. Brand TLDs allows users to register their own +top level domain that exist at the same level as ICANN's gTLDs. Brand TLDs +are sometimes referred to as Vanity Domains. +" + diff --git a/Tools/curl/build b/Tools/curl/build new file mode 100755 index 0000000..4d92699 --- /dev/null +++ b/Tools/curl/build @@ -0,0 +1,7 @@ +#!/usr/bin/env modbuild + +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Tools/curl/files/config.yaml b/Tools/curl/files/config.yaml new file mode 100644 index 0000000..a31b6f7 --- /dev/null +++ b/Tools/curl/files/config.yaml @@ -0,0 +1,21 @@ +--- +format: 1 +curl: + defaults: + group: Tools + overlay: base + relstage: stable + configure_args: + - --with-openssl + docfiles: [] + urls: + - url: https://curl.se/download/$P-${V_PKG}.tar.gz + shasums: + + versions: + 8.13.0: + config: + build_requires: [libpsl/0.21.5, openssl/3.4.1] + 8.11.0: + config: + build_requires: [libpsl/0.21.5, openssl/1.1.1w] diff --git a/Tools/curl/modulefile b/Tools/curl/modulefile new file mode 100644 index 0000000..4dafa22 --- /dev/null +++ b/Tools/curl/modulefile @@ -0,0 +1,15 @@ +#%Pmodule + +module-whatis "command line tool and library for transferring data with URLs" +module-url "https://curl.se" +module-license "See \$PREFIX/share/doc/curl/curl.txt" +module-maintainer "Achim Gsell " + +module-help " +curl is used in command lines or scripts to transfer data. curl is also +libcurl, used in cars, television sets, routers, printers, audio equipment, +mobile phones, tablets, medical devices, settop boxes, computer games, +media players and is the Internet transfer engine for countless software +applications in over twenty billion installations. +" + From 36876af888b0f54c16a98bc05b8d583f424a138e Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 14:16:20 +0200 Subject: [PATCH 141/158] patchelf: release stage changed to stable --- System/patchelf/files/config.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/System/patchelf/files/config.yaml b/System/patchelf/files/config.yaml index 320cfd0..523990d 100644 --- a/System/patchelf/files/config.yaml +++ b/System/patchelf/files/config.yaml @@ -18,6 +18,5 @@ patchelf: 0.8.1;0.11;0.12;0.14.5: 0.18.0: config: - relstage: unstable build_requires: [gcc/12.3.0] From 1996b245c3e5808e0a27c1f5d84deb2ade63f121 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 14:28:51 +0200 Subject: [PATCH 142/158] Python: updated including dependencies --- Programming/Python/build | 20 ++------- .../Python/{build-xml => build-legacy} | 24 ++++++++--- Programming/Python/files/config.yaml | 8 ++-- Programming/TclTk/build | 34 +++++++++++++-- Programming/TclTk/{build_Tk => build-Tk} | 22 ++++++---- Programming/TclTk/build_Tcl | 35 --------------- Programming/TclTk/files/config.yaml | 32 ++++++++++++++ Programming/TclTk/files/variants.macos10.14 | 1 - Programming/TclTk/files/variants.rhel6 | 1 - Programming/perl/build | 5 --- Programming/perl/files/config.yaml | 13 ++++++ Tools/openssl/build | 21 +++------ Tools/openssl/files/config.yaml | 43 +++++++++++++++++++ Tools/xz/build | 26 +++-------- Tools/xz/files/config.yaml | 28 ++++++++++++ 15 files changed, 199 insertions(+), 114 deletions(-) rename Programming/Python/{build-xml => build-legacy} (68%) rename Programming/TclTk/{build_Tk => build-Tk} (73%) delete mode 100755 Programming/TclTk/build_Tcl create mode 100644 Programming/TclTk/files/config.yaml delete mode 100644 Programming/TclTk/files/variants.macos10.14 delete mode 100644 Programming/TclTk/files/variants.rhel6 create mode 100644 Programming/perl/files/config.yaml create mode 100644 Tools/openssl/files/config.yaml create mode 100644 Tools/xz/files/config.yaml diff --git a/Programming/Python/build b/Programming/Python/build index bace901..6940835 100755 --- a/Programming/Python/build +++ b/Programming/Python/build @@ -1,19 +1,5 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://www.python.org/ftp/python/${V_PKG}/$P-${V_PKG}.tgz" - -pbuild::set_sha256sum 'Python-3.7.3.tgz:d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff' -pbuild::set_sha256sum 'Python-2.7.12.tgz:3cb522d17463dfa69a155ab18cffa399b358c966c0363d6c8b5b3bf1384da4b6' -pbuild::set_sha256sum 'Python-2.7.14.tgz:304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8' -pbuild::set_sha256sum 'Python-2.7.16.tgz:01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5' -pbuild::set_sha256sum 'Python-3.6.3.tgz:ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91' -pbuild::set_sha256sum 'Python-3.7.3.tgz:d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff' -pbuild::set_sha256sum 'Python-3.7.4.tgz:d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3' - -pbuild::add_to_group 'Programming' - -pbuild::compile_in_sourcetree - pbuild::pre_configure() { local -a cflags=() local -a ldflags=() @@ -74,7 +60,7 @@ pbuild::post_install() { std::info "Building scipy\n" pip${V_MAJOR} install scipy - std::info "Building matplotlub\n" + std::info "Building matplotlib\n" pip${V_MAJOR} install matplotlib std::info "Building ipython\n" @@ -95,8 +81,8 @@ pbuild::post_install() { std::info "Building virtualenv\n" pip${V_MAJOR} install virtualenv - std::info "Building virtualenv\n" - pip${V_MAJOR} install ansible ansible-core==2.15.4 + #std::info "Building ansible\n" + #pip${V_MAJOR} install ansible ansible-core==2.15.4 } diff --git a/Programming/Python/build-xml b/Programming/Python/build-legacy similarity index 68% rename from Programming/Python/build-xml rename to Programming/Python/build-legacy index fcd556e..bace901 100755 --- a/Programming/Python/build-xml +++ b/Programming/Python/build-legacy @@ -1,5 +1,19 @@ #!/usr/bin/env modbuild +pbuild::set_download_url "https://www.python.org/ftp/python/${V_PKG}/$P-${V_PKG}.tgz" + +pbuild::set_sha256sum 'Python-3.7.3.tgz:d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff' +pbuild::set_sha256sum 'Python-2.7.12.tgz:3cb522d17463dfa69a155ab18cffa399b358c966c0363d6c8b5b3bf1384da4b6' +pbuild::set_sha256sum 'Python-2.7.14.tgz:304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8' +pbuild::set_sha256sum 'Python-2.7.16.tgz:01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5' +pbuild::set_sha256sum 'Python-3.6.3.tgz:ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91' +pbuild::set_sha256sum 'Python-3.7.3.tgz:d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff' +pbuild::set_sha256sum 'Python-3.7.4.tgz:d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3' + +pbuild::add_to_group 'Programming' + +pbuild::compile_in_sourcetree + pbuild::pre_configure() { local -a cflags=() local -a ldflags=() @@ -60,7 +74,7 @@ pbuild::post_install() { std::info "Building scipy\n" pip${V_MAJOR} install scipy - std::info "Building matplotlib\n" + std::info "Building matplotlub\n" pip${V_MAJOR} install matplotlib std::info "Building ipython\n" @@ -78,11 +92,11 @@ pbuild::post_install() { std::info "Building pandas\n" pip${V_MAJOR} install pandas - #std::info "Building virtualenv\n" - #pip${V_MAJOR} install virtualenv + std::info "Building virtualenv\n" + pip${V_MAJOR} install virtualenv - #std::info "Building ansible\n" - #pip${V_MAJOR} install ansible ansible-core==2.15.4 + std::info "Building virtualenv\n" + pip${V_MAJOR} install ansible ansible-core==2.15.4 } diff --git a/Programming/Python/files/config.yaml b/Programming/Python/files/config.yaml index 4041769..eba845b 100644 --- a/Programming/Python/files/config.yaml +++ b/Programming/Python/files/config.yaml @@ -25,14 +25,14 @@ Python: Python-3.9.17.tgz: 8ead58f669f7e19d777c3556b62fae29a81d7f06a7122ff9bc57f7dd82d7e014 Python-3.9.18.tgz: 504ce8cfd59addc04c22f590377c6be454ae7406cb1ebf6f5a350149225a9354 versions: - 3.9.18-1: + 3.13.2: config: relstage: unstable - build_requires: [openssl/1.1.1w, TclTk/8.6.9, xz/5.2.4] - 3.9.18: + build_requires: [openssl/3.4.1, TclTk/8.6.16, xz/5.8.0] + 3.9.18;3.9.21;3.10.16;3.11.11;3.12.9: config: relstage: unstable - build_requires: [openssl/1.1.1w, TclTk/8.6.9, xz/5.2.4] + runtime_deps: [openssl/3.4.1, TclTk/8.6.16, xz/5.8.0] 3.9.17: config: relstage: unstable diff --git a/Programming/TclTk/build b/Programming/TclTk/build index d7fb54a..4b8359e 100755 --- a/Programming/TclTk/build +++ b/Programming/TclTk/build @@ -1,4 +1,32 @@ -#!/bin/bash +#!/usr/bin/env modbuild -./build_Tcl "$@" ||exit $? -./build_Tk -f "$@" +#pbuild::install_docfiles 'license.terms' 'README' + +pbuild::configure_Darwin() { + export CXX=/usr/bin/clang++ + export CC=/usr/bin/clang + PATH+=":/opt/X11/bin" + export PKG_CONFIG_PATH="/opt/X11/share/pkgconfig:/opt/X11/lib/pkgconfig:$PKG_CONFIG_PATH" + "${SRC_DIR}/macosx/configure" \ + --prefix="${PREFIX}" \ + --enable-threads \ + --disable-symbols \ + || exit 1 +} + +pbuild::configure() { + "${SRC_DIR}/unix/configure" \ + --prefix="${PREFIX}" \ + || exit 1 +} + +pbuild::post_install() { + { cd "${PREFIX}"/bin && rm -f tclsh && ln -fs tclsh${V%.*} tclsh; }; +} + +pbuild::post_install_Darwin() { + local -r libtcl="libtcl${V_MAJOR}.${V_MINOR}.dylib" + install_name_tool \ + -id @executable_path/../lib/${libtcl} \ + "${PREFIX}/lib/${libtcl}" +} diff --git a/Programming/TclTk/build_Tk b/Programming/TclTk/build-Tk similarity index 73% rename from Programming/TclTk/build_Tk rename to Programming/TclTk/build-Tk index d85ff18..5d3d1c0 100755 --- a/Programming/TclTk/build_Tk +++ b/Programming/TclTk/build-Tk @@ -1,14 +1,20 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "ftp://ftp.tcl.tk/pub/tcl/tk${V_MAJOR}_${V_MINOR}/tk${V_PKG}-src.tar.gz" - -pbuild::add_to_group 'Programming' - export PATH="${PREFIX}/bin:$PATH" -export C_INCLUDE_PATH="${PREFIX}/include:${C_INCLUDE_PATH}" -export LIBRARY_PATH="${PREFIX}/lib:${LIBRARY_PATH}" +if [[ -v C_INCLUDE_PATH ]]; then + C_INCLUDE_PATH="${PREFIX}/include:${C_INCLUDE_PATH}" +else + C_INCLUDE_PATH="${PREFIX}/include" +fi +export C_INCLUDE_PATH +if [[ -v LIBRARY_PATH ]]; then + LIBRARY_PATH="${PREFIX}/lib:${LIBRARY_PATH}" +else + LIBRARY_PATH="${PREFIX}/lib" +fi +export LIBRARY_PATH -pbuild::configure_Darwin() { +pbuil:d:configure_Darwin() { PATH+=":/opt/X11/bin" export CXX=/usr/bin/clang++ export CC=/usr/bin/clang @@ -24,7 +30,7 @@ pbuild::configure_Darwin() { || exit 1 } -pbuild::configure_Linux() { +pbuild::configure() { "${SRC_DIR}/unix/configure" \ --prefix="${PREFIX}" \ --with-tcl="${PREFIX}/lib" \ diff --git a/Programming/TclTk/build_Tcl b/Programming/TclTk/build_Tcl deleted file mode 100755 index e2a8eda..0000000 --- a/Programming/TclTk/build_Tcl +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env modbuild - -pbuild::set_download_url "ftp://ftp.tcl.tk/pub/tcl/tcl8_6/tcl${V_PKG}-src.tar.gz" - -pbuild::add_to_group 'Programming' -pbuild::install_docfiles 'license.terms' 'README' - -pbuild::configure_Darwin() { - export CXX=/usr/bin/clang++ - export CC=/usr/bin/clang - PATH+=":/opt/X11/bin" - export PKG_CONFIG_PATH="/opt/X11/share/pkgconfig:/opt/X11/lib/pkgconfig:$PKG_CONFIG_PATH" - "${SRC_DIR}/macosx/configure" \ - --prefix="${PREFIX}" \ - --enable-threads \ - --disable-symbols \ - || exit 1 -} - -pbuild::configure_Linux() { - "${SRC_DIR}/unix/configure" \ - --prefix="${PREFIX}" \ - || exit 1 -} - -pbuild::post_install() { - { cd "${PREFIX}"/bin && rm -f tclsh && ln -fs tclsh${V%.*} tclsh; }; -} - -pbuild::post_install_Darwin() { - local -r libtcl="libtcl${V_MAJOR}.${V_MINOR}.dylib" - install_name_tool \ - -id @executable_path/../lib/${libtcl} \ - "${PREFIX}/lib/${libtcl}" -} diff --git a/Programming/TclTk/files/config.yaml b/Programming/TclTk/files/config.yaml new file mode 100644 index 0000000..5d192cb --- /dev/null +++ b/Programming/TclTk/files/config.yaml @@ -0,0 +1,32 @@ +format: 1 +TclTk: + defaults: + group: Programming + overlay: base + relstage: stable + urls: + - url: http://prdownloads.sourceforge.net/tcl/tcl${V_PKG}-src.tar.gz + shasums: + versions: + 8.6.16: + config: + sub_packages: + - name: Tk + version: 8.6.16 + build_args: + 8.6.9: + config: + sub_packages: + - name: Tk + version: 8.6.9 + build_args: + +Tk: + type: sub_package + defaults: + urls: + - url: http://prdownloads.sourceforge.net/tcl/tk${V_PKG}-src.tar.gz + versions: + 8.6.16: + 8.6.9: + diff --git a/Programming/TclTk/files/variants.macos10.14 b/Programming/TclTk/files/variants.macos10.14 deleted file mode 100644 index a4f9b5b..0000000 --- a/Programming/TclTk/files/variants.macos10.14 +++ /dev/null @@ -1 +0,0 @@ -TclTk/8.6.9 stable diff --git a/Programming/TclTk/files/variants.rhel6 b/Programming/TclTk/files/variants.rhel6 deleted file mode 100644 index a4f9b5b..0000000 --- a/Programming/TclTk/files/variants.rhel6 +++ /dev/null @@ -1 +0,0 @@ -TclTk/8.6.9 stable diff --git a/Programming/perl/build b/Programming/perl/build index 8a481af..140372a 100755 --- a/Programming/perl/build +++ b/Programming/perl/build @@ -1,10 +1,5 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "http://www.cpan.org/src/5.0/$P-$V.tar.gz" - -pbuild::compile_in_sourcetree -pbuild::add_to_group 'Programming' - pbuild::configure() { "${SRC_DIR}"/configure.gnu \ --prefix="${PREFIX}" \ diff --git a/Programming/perl/files/config.yaml b/Programming/perl/files/config.yaml new file mode 100644 index 0000000..606fa5f --- /dev/null +++ b/Programming/perl/files/config.yaml @@ -0,0 +1,13 @@ +format: 1 +perl: + defaults: + group: Programming + overlay: base + relstage: stable + compile_in_sourcetree: true + urls: + - url: http://www.cpan.org/src/5.0/$P-$V.tar.gz + + shasums: + versions: + 5.30.0;5.40.0;5.40.1: diff --git a/Tools/openssl/build b/Tools/openssl/build index 3d64adb..3f0ea3f 100755 --- a/Tools/openssl/build +++ b/Tools/openssl/build @@ -1,24 +1,13 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://www.openssl.org/source/$P-$V.tar.gz" - # use system gcc to compile -declare -rx CC=gcc +#declare -rx CC=gcc -pbuild::add_to_group 'Tools' -pbuild::compile_in_sourcetree - -pbuild::pre_configure_Darwin() { - pbuild::add_configure_args 'darwin64-x86_64-cc' -} - -pbuild::pre_configure_Linux() { - pbuild::add_configure_args 'linux-x86_64' -} - -pbuild::configure() { +pbuild::configure(){ export CFLAGS='-fPIC' - "${SRC_DIR}"/Configure shared --prefix="${PREFIX}" "${CONFIGURE_ARGS[@]}" \ + local -r os=$(uname -s) + local -r machine=$(uname -m) + "${SRC_DIR}"/Configure shared --prefix="${PREFIX}" "${os,,}-${machine}" \ || exit 1 } diff --git a/Tools/openssl/files/config.yaml b/Tools/openssl/files/config.yaml new file mode 100644 index 0000000..d85cbe4 --- /dev/null +++ b/Tools/openssl/files/config.yaml @@ -0,0 +1,43 @@ +--- +format: 1 +openssl: + defaults: + group: Tools + overlay: base + relstage: stable + compile_in_sourcetree: true + urls: + - url: https://www.openssl.org/source/$P-$V.tar.gz + shasums: + versions: + 3.4.1: + config: + docfiles: + - ACKNOWLEDGEMENTS.md + - AUTHORS.md + - CHANGES.md + - CODE-OF-CONDUCT.md + - CONTRIBUTING.md + - HACKING.md + - INSTALL.md + - LICENSE.txt + - NEWS.md + - NOTES-ANDROID.md + - NOTES-ANSI.md + - NOTES-DJGPP.md + - NOTES-NONSTOP.md + - NOTES-PERL.md + - NOTES-POSIX.md + - NOTES-UNIX.md + - NOTES-VALGRIND.md + - NOTES-VMS.md + - NOTES-WINDOWS.md + - README-ENGINES.md + - README-FIPS.md + - README-PROVIDERS.md + - README-QUIC.md + - README.md + - SUPPORT.md + build_requires: + - perl/5.40.1 + diff --git a/Tools/xz/build b/Tools/xz/build index 6501335..145bb9e 100755 --- a/Tools/xz/build +++ b/Tools/xz/build @@ -1,24 +1,12 @@ #!/usr/bin/env modbuild -pbuild::add_to_group 'Tools' - -pbuild::set_download_url \ - "https://sourceforge.net/projects/lzmautils/files/$P-${V_PKG}.tar.gz" - -pbuild::set_sha256sum 'xz-5.2.4.tar.gz:b512f3b726d3b37b6dc4c8570e137b9311e7552e8ccbab4d39d47ce5f4177145' -pbuild::install_docfiles \ - AUTHORS \ - COPYING \ - COPYING.GPLv2 \ - COPYING.GPLv3 \ - COPYING.LGPLv2.1 \ - ChangeLog \ - NEWS \ - PACKAGERS \ - README \ - THANKS \ - TODO - +pbuild::post_prep(){ + # autogen.sh exits with an error if po4a + # is not installed. For now we ignore this. + # :FIXME: + # build a po4a module + ./autogen.sh || : +} # Local Variables: # mode: sh # sh-basic-offset: 8 diff --git a/Tools/xz/files/config.yaml b/Tools/xz/files/config.yaml new file mode 100644 index 0000000..9f51112 --- /dev/null +++ b/Tools/xz/files/config.yaml @@ -0,0 +1,28 @@ +--- +format: 1 +xz: + defaults: + group: Tools + overlay: base + relstage: stable + docfiles: + - AUTHORS + - COPYING + - COPYING.GPLv2 + - COPYING.GPLv3 + - COPYING.LGPLv2.1 + - ChangeLog + - NEWS + - PACKAGERS + - README + - THANKS + - TODO + urls: + - url: https://sourceforge.net/projects/lzmautils/files/$P-${V_PKG}.tar.gz + shasums: + versions: + 5.8.0: + config: + relstage: unstable + + From 951cc09b0e2b9afec722d62d90f7ce0048f16d90 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 15:09:27 +0200 Subject: [PATCH 143/158] xz/5.8.0: release stage changed to stable --- Tools/xz/files/config.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/Tools/xz/files/config.yaml b/Tools/xz/files/config.yaml index 9f51112..088b846 100644 --- a/Tools/xz/files/config.yaml +++ b/Tools/xz/files/config.yaml @@ -23,6 +23,4 @@ xz: versions: 5.8.0: config: - relstage: unstable - From 1c82a7a7b9b6c8eea18a7f0b024f2e2b40360275 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 15:10:22 +0200 Subject: [PATCH 144/158] Python: release stages of new versions changed to stable --- Programming/Python/files/config.yaml | 39 +++++++++++++++------------- 1 file changed, 21 insertions(+), 18 deletions(-) diff --git a/Programming/Python/files/config.yaml b/Programming/Python/files/config.yaml index eba845b..37ec1dd 100644 --- a/Programming/Python/files/config.yaml +++ b/Programming/Python/files/config.yaml @@ -8,34 +8,37 @@ Python: - url: https://www.python.org/ftp/python/${V_PKG}/$P-${V_PKG}.tgz shasums: - Python-2.7.12.tgz: 3cb522d17463dfa69a155ab18cffa399b358c966c0363d6c8b5b3bf1384da4b6 - Python-2.7.14.tgz: 304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8 - Python-2.7.16.tgz: 01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5 - Python-2.7.17.tgz: f22059d09cdf9625e0a7284d24a13062044f5bf59d93a7f3382190dfa94cecde - Python-2.7.18.tgz: da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814 - Python-3.6.11.tgz: 96621902f89746fffc22f39749c07da7c2917b232e72352e6837d41850f7b90c - Python-3.6.3.tgz: ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91 - Python-3.7.3.tgz: d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff - Python-3.7.4.tgz: d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3 - Python-3.7.8.tgz: 0e25835614dc221e3ecea5831b38fa90788b5389b99b675a751414c858789ab0 - Python-3.8.12.tgz: 316aa33f3b7707d041e73f246efedb297a70898c4b91f127f66dc8d80c596f1a - Python-3.8.4.tgz: 32c4d9817ef11793da4d0d95b3191c4db81d2e45544614e8449255ca9ae3cc18 - Python-3.8.8.tgz: 76c0763f048e4f9b861d24da76b7dd5c7a3ba7ec086f40caedeea359263276f7 - Python-3.9.10.tgz: 1aa9c0702edbae8f6a2c95f70a49da8420aaa76b7889d3419c186bfc8c0e571e - Python-3.9.17.tgz: 8ead58f669f7e19d777c3556b62fae29a81d7f06a7122ff9bc57f7dd82d7e014 + Python-3.13.2.tgz: b8d79530e3b7c96a5cb2d40d431ddb512af4a563e863728d8713039aa50203f9 + Python-3.12.9.tgz: 45313e4c5f0e8acdec9580161d565cf5fea578e3eabf25df7cc6355bf4afa1ee + Python-3.11.11.tgz: f2e22ed965a93cfeb642378ed6e6cdbc127682664b24123679f3d013fafe9cd0 + Python-3.10.16.tgz: f2e22ed965a93cfeb642378ed6e6cdbc127682664b24123679f3d013fafe9cd0 + Python-3.9.21.tgz: 667c3ba2ca98d39ead1162f6548c3475768582e2ff89e0821d25eb956ac09944 Python-3.9.18.tgz: 504ce8cfd59addc04c22f590377c6be454ae7406cb1ebf6f5a350149225a9354 + Python-3.9.17.tgz: 8ead58f669f7e19d777c3556b62fae29a81d7f06a7122ff9bc57f7dd82d7e014 + Python-3.9.10.tgz: 1aa9c0702edbae8f6a2c95f70a49da8420aaa76b7889d3419c186bfc8c0e571e + Python-3.8.8.tgz: 76c0763f048e4f9b861d24da76b7dd5c7a3ba7ec086f40caedeea359263276f7 + Python-3.8.4.tgz: 32c4d9817ef11793da4d0d95b3191c4db81d2e45544614e8449255ca9ae3cc18 + Python-3.8.12.tgz: 316aa33f3b7707d041e73f246efedb297a70898c4b91f127f66dc8d80c596f1a + Python-3.7.8.tgz: 0e25835614dc221e3ecea5831b38fa90788b5389b99b675a751414c858789ab0 + Python-3.7.4.tgz: d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3 + Python-3.7.3.tgz: d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff + Python-3.6.3.tgz: ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91 + Python-3.6.11.tgz: 96621902f89746fffc22f39749c07da7c2917b232e72352e6837d41850f7b90c + Python-2.7.18.tgz: da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814 + Python-2.7.17.tgz: f22059d09cdf9625e0a7284d24a13062044f5bf59d93a7f3382190dfa94cecde + Python-2.7.16.tgz: 01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5 + Python-2.7.14.tgz: 304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8 + Python-2.7.12.tgz: 3cb522d17463dfa69a155ab18cffa399b358c966c0363d6c8b5b3bf1384da4b6 versions: 3.13.2: config: - relstage: unstable build_requires: [openssl/3.4.1, TclTk/8.6.16, xz/5.8.0] 3.9.18;3.9.21;3.10.16;3.11.11;3.12.9: config: - relstage: unstable runtime_deps: [openssl/3.4.1, TclTk/8.6.16, xz/5.8.0] 3.9.17: config: - relstage: unstable + relstage: deprecated build_requires: [openssl/1.1.1v, TclTk/8.6.9, xz/5.2.4] 3.9.10: 3.8.12: From d6f6c561d63cf04653d5c06d593563c80318732a Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 15:16:23 +0200 Subject: [PATCH 145/158] ruby and ruby-install added --- Programming/ruby/build | 5 +++++ Programming/ruby/files/config.yaml | 16 ++++++++++++++++ Programming/ruby/modulefile | 13 +++++++++++++ System/ruby-install/build | 19 +++++++++++++++++++ System/ruby-install/files/config.yaml | 17 +++++++++++++++++ System/ruby-install/modulefile | 11 +++++++++++ 6 files changed, 81 insertions(+) create mode 100755 Programming/ruby/build create mode 100644 Programming/ruby/files/config.yaml create mode 100644 Programming/ruby/modulefile create mode 100755 System/ruby-install/build create mode 100644 System/ruby-install/files/config.yaml create mode 100644 System/ruby-install/modulefile diff --git a/Programming/ruby/build b/Programming/ruby/build new file mode 100755 index 0000000..a3145ee --- /dev/null +++ b/Programming/ruby/build @@ -0,0 +1,5 @@ +#!/usr/bin/env modbuild + +pbuild::install(){ + ruby-install --prefix "${PREFIX}" ruby "${V_PKG}" +} diff --git a/Programming/ruby/files/config.yaml b/Programming/ruby/files/config.yaml new file mode 100644 index 0000000..fa819c2 --- /dev/null +++ b/Programming/ruby/files/config.yaml @@ -0,0 +1,16 @@ +--- +format: 1 +ruby: + defaults: + group: Programming + relstage: stable + docfiles: + configure_args: + build_functions: + prep: [] + configure: [] + compile: [] + versions: + 3.4.4: + config: + build_requires: [ruby-install/0.10.1] diff --git a/Programming/ruby/modulefile b/Programming/ruby/modulefile new file mode 100644 index 0000000..2de7128 --- /dev/null +++ b/Programming/ruby/modulefile @@ -0,0 +1,13 @@ +#%Module1.0 + +module-whatis "Ruby, open source programming language" +module-url "https://www.ruby-lang.org/" +module-license "https://www.ruby-lang.org/en/about/license.txt" +module-maintainer "Achim Gsell " + +module-help " +Ruby is a dynamic, open source programming language with a focus on +simplicity and productivity. It has an elegant syntax that is natural +to read and easy to write. +" + diff --git a/System/ruby-install/build b/System/ruby-install/build new file mode 100755 index 0000000..04d0972 --- /dev/null +++ b/System/ruby-install/build @@ -0,0 +1,19 @@ +#!/usr/bin/env modbuild + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + make -e install +} + +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/System/ruby-install/files/config.yaml b/System/ruby-install/files/config.yaml new file mode 100644 index 0000000..6de68c2 --- /dev/null +++ b/System/ruby-install/files/config.yaml @@ -0,0 +1,17 @@ +--- +format: 1 +ruby-install: + defaults: + group: System + overlay: base + relstage: stable + patch_files: [] + compile_in_sourcetree: true + urls: + - url: https://github.com/postmodern/$P/releases/download/v${V_PKG}/$P-${V_PKG}.tar.gz + shasums: + ruby-install-0.10.1.tar.gz: 7f563af2bae257c006a5dba0b1976e0885d3814332cc4391eeaa88d702753289 + versions: + 0.10.1: + config: + build_requires: [] diff --git a/System/ruby-install/modulefile b/System/ruby-install/modulefile new file mode 100644 index 0000000..d40eb1c --- /dev/null +++ b/System/ruby-install/modulefile @@ -0,0 +1,11 @@ +#%Module1.0 + +module-whatis "Ruby installer" +module-url "https://github.com/postmodern/ruby-install" +module-license "MIT" +module-maintainer "Achim Gsell " + +module-help " +Installs Ruby, JRuby, TruffleRuby (native / GraalVM), or mruby. +" + From b8f23dede3a09621ff12890be0effbce61282347 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 15:16:51 +0200 Subject: [PATCH 146/158] asciidoctor added --- Tools/asciidoctor/build | 6 ++++++ Tools/asciidoctor/files/config.yaml | 16 ++++++++++++++++ Tools/asciidoctor/modulefile | 11 +++++++++++ 3 files changed, 33 insertions(+) create mode 100755 Tools/asciidoctor/build create mode 100644 Tools/asciidoctor/files/config.yaml create mode 100644 Tools/asciidoctor/modulefile diff --git a/Tools/asciidoctor/build b/Tools/asciidoctor/build new file mode 100755 index 0000000..362fbec --- /dev/null +++ b/Tools/asciidoctor/build @@ -0,0 +1,6 @@ +#!/usr/bin/env modbuild + +pbuild::install(){ + /usr/bin/which gem + "${RUBY_DIR}/bin/gem" install --install-dir="${PREFIX}" asciidoctor -v "${V_PKG}" +} diff --git a/Tools/asciidoctor/files/config.yaml b/Tools/asciidoctor/files/config.yaml new file mode 100644 index 0000000..4fc02dd --- /dev/null +++ b/Tools/asciidoctor/files/config.yaml @@ -0,0 +1,16 @@ +--- +format: 1 +asciidoctor: + defaults: + group: Tools + relstage: stable + docfiles: + configure_args: + build_functions: + prep: [] + configure: [] + compile: [] + versions: + 2.0.23: + config: + build_requires: [ruby/3.4.4] diff --git a/Tools/asciidoctor/modulefile b/Tools/asciidoctor/modulefile new file mode 100644 index 0000000..8264463 --- /dev/null +++ b/Tools/asciidoctor/modulefile @@ -0,0 +1,11 @@ +#%Module1.0 + +module-whatis "Ruby-based text processor for parsing AsciiDoc" +module-url "https://asciidoctor.org" +module-license "MIT" +module-maintainer "Achim Gsell " + +module-help " +" + +prepend-path GEM_PATH $PREFIX From ca60ced542d378642813dc198d0085ed46e59319 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 15:19:09 +0200 Subject: [PATCH 147/158] perl: YAML config file added --- Programming/perl/files/config.yaml | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 Programming/perl/files/config.yaml diff --git a/Programming/perl/files/config.yaml b/Programming/perl/files/config.yaml new file mode 100644 index 0000000..30521e6 --- /dev/null +++ b/Programming/perl/files/config.yaml @@ -0,0 +1,30 @@ +format: 1 +perl: + defaults: + group: Programming + overlay: base + relstage: stable + compile_in_sourcetree: true + urls: + - url: http://www.cpan.org/src/5.0/$P-${V_PKG}.tar.gz + + shasums: + perl-5.30.1.tar.gz: f160169fd7b1bd13d1b78b3fa23a5af91709fe732d2d9504c0b40b445846aff5 + perl-5.30.0.tar.gz: 851213c754d98ccff042caa40ba7a796b2cee88c5325f121be5cbb61bbf975f2 + perl-5.28.1.tar.gz: 3ebf85fe65df2ee165b22596540b7d5d42f84d4b72d84834f74e2e0b8956c347 + perl-5.26.1.tar.gz: e763aa485e8dc1a70483dbe6d615986bbf32b977f38016480d68c99237e701dd + perl-5.10.1.tar.gz: cb7f26ea4b2b28d6644354d87a269d01cac1b635287dae64e88eeafa24b44f35 + perl-5.8.5.tar.gz: 3dd1cba53ce6348ed5119b5f7d1ef6cd4d165f89e4ecc7c21adf7932e0df2709 + perl-5.8.1.tar.gz: 90f5ef25b993cea2def2648d7bca9e351f2e417004cdc76fa02a9ec235ce4490 + + versions: + 5.40.2: + config: + + 5.30.0;5.28.1: + config: + relstage: stable + + 5.10.1;5.26.1: + config: + relstage: deprecated From c9f35ef17699c05104b34cb1a8c6fc0178576606 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 15:20:50 +0200 Subject: [PATCH 148/158] perl: build script updated --- Programming/perl/build | 5 ----- 1 file changed, 5 deletions(-) diff --git a/Programming/perl/build b/Programming/perl/build index 8a481af..140372a 100755 --- a/Programming/perl/build +++ b/Programming/perl/build @@ -1,10 +1,5 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "http://www.cpan.org/src/5.0/$P-$V.tar.gz" - -pbuild::compile_in_sourcetree -pbuild::add_to_group 'Programming' - pbuild::configure() { "${SRC_DIR}"/configure.gnu \ --prefix="${PREFIX}" \ From df6cc05a4aa6c068c57adbb5402a2d0920865899 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 15:21:28 +0200 Subject: [PATCH 149/158] git: new versions added --- Tools/git/build | 9 +++++---- Tools/git/build-git-lfs | 2 -- Tools/git/files/config.yaml | 29 ++++++----------------------- 3 files changed, 11 insertions(+), 29 deletions(-) diff --git a/Tools/git/build b/Tools/git/build index ebc480e..c05a15c 100755 --- a/Tools/git/build +++ b/Tools/git/build @@ -6,10 +6,11 @@ pbuild::pre_configure_Darwin() { pbuild::pre_configure() { #pbuild::add_configure_args "LIBS=-lintl" + #pbuild::add_configure_args "LDFLAGS=-lintl" pbuild::add_configure_args "--with-tcltk" pbuild::add_configure_args "--with-iconv=${GETTEXT_PREFIX}" pbuild::add_configure_args "--with-perl=${PERL_PREFIX}/bin/perl" - : + make configure } pbuild::post_compile() { @@ -17,9 +18,9 @@ pbuild::post_compile() { } pbuild::post_install() { - make install-doc V=1 XMLTO_EXTRA='--skip-validation' - make -C contrib/subtree prefix="${PREFIX}" install - make -C contrib/subtree prefix="${PREFIX}" install-doc XMLTO="xmlto --skip-validation" + make install-doc V=1 USE_ASCIIDOCTOR=1 XMLTO_EXTRA='--skip-validation' + make -C contrib/subtree prefix="${PREFIX}" install USE_ASCIIDOCTOR=1 + make -C contrib/subtree prefix="${PREFIX}" install-doc USE_ASCIIDOCTOR=1 XMLTO="xmlto --skip-validation" } # Local Variables: diff --git a/Tools/git/build-git-lfs b/Tools/git/build-git-lfs index ca4de42..0be7d65 100755 --- a/Tools/git/build-git-lfs +++ b/Tools/git/build-git-lfs @@ -1,7 +1,5 @@ #!/usr/bin/env modbuild -unset -f pbuild::configure -unset -f pbuild::compile pbuild::install(){ install -m 0755 git-lfs "${PREFIX}/bin" install -m 0755 -d "${PREFIX}/share/man/man{1,5,7}" diff --git a/Tools/git/files/config.yaml b/Tools/git/files/config.yaml index 1885092..3e849d5 100644 --- a/Tools/git/files/config.yaml +++ b/Tools/git/files/config.yaml @@ -20,12 +20,10 @@ git: git-2.8.1.tar.xz: e6626b43ba4bc63ad4918df4c275f50bd7f8af2ab54bde60496ad75e91e927fc git-2.3.3.tar.gz: c189e4a48d8805482f450db666330c79bcefae37e0d035c7717517126ddf4305 versions: - 2.45.2: + 2.49.0;2.46.4;2.45.3;2.43.6;2.42.4: config: - runtime_deps: [TclTk/8.6.9, openssl/1.1.1w] - build_requires: [gcc/10.4.0, perl/5.30.0, asciidoc/8.6.9-1, xmlto/0.0.28, gettext/0.19.8] - relstage: unstable - overlay: devel + runtime_deps: [TclTk/8.6.16, openssl/3.4.1] + build_requires: [gcc/10.4.0, curl/8.13.0, perl/5.40.2, asciidoctor/2.0.23, gettext/0.19.8, xmlto/0.0.28] docfiles: [COPYING, README.md] configure_args: - --with-tcltk @@ -35,24 +33,6 @@ git: - name: git-lfs version: 3.5.1 build_args: - 2.43.1: - config: - runtime_deps: [TclTk/8.6.9] - build_requires: [gcc/10.4.0, perl/5.30.0, asciidoc/8.6.9-1, xmlto/0.0.28, gettext/0.19.8, openssl/1.1.1w] - relstage: unstable - overlay: devel - docfiles: [COPYING, README.md] - configure_args: - - --with-tcltk - - --with-iconv=${GETTEXT_PREFIX} - - --with-perl=${PERL_PREFIX}/bin/perl - 2.42.0: - config: - runtime_deps: [TclTk/8.6.9] - build_requires: [gcc/10.4.0, perl/5.30.0, asciidoc/8.6.9-1, xmlto/0.0.28, gettext/0.19.8] - relstage: unstable - overlay: devel - docfiles: [COPYING, README.md] 2.39.1;2.37.2;2.37.0;2.33.1;2.30.0;2.22.0;2.21.0: config: runtime_deps: [TclTk/8.6.9] @@ -74,3 +54,6 @@ git-lfs: target_cpus: [x86_64] urls: - url: https://github.com/git-lfs/git-lfs/releases/download/v3.5.1/git-lfs-linux-amd64-v3.5.1.tar.gz + build_functions: + configure: [] + compile: [] From efff04518631f8644e57a24bb16a05cce54359f6 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 15:24:45 +0200 Subject: [PATCH 150/158] perl: version 5.40.1 added to config --- Programming/perl/files/config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Programming/perl/files/config.yaml b/Programming/perl/files/config.yaml index 30521e6..a3e0fdb 100644 --- a/Programming/perl/files/config.yaml +++ b/Programming/perl/files/config.yaml @@ -18,7 +18,7 @@ perl: perl-5.8.1.tar.gz: 90f5ef25b993cea2def2648d7bca9e351f2e417004cdc76fa02a9ec235ce4490 versions: - 5.40.2: + 5.40.2;5.40.1: config: 5.30.0;5.28.1: From e9b822868a5f311466f5e99ae39176c5c92bbd03 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 16:55:30 +0200 Subject: [PATCH 151/158] restic: new module --- Tools/restic/build | 11 +++++++++++ Tools/restic/files/config.yaml | 20 ++++++++++++++++++++ Tools/restic/modulefile | 13 +++++++++++++ 3 files changed, 44 insertions(+) create mode 100755 Tools/restic/build create mode 100644 Tools/restic/files/config.yaml create mode 100644 Tools/restic/modulefile diff --git a/Tools/restic/build b/Tools/restic/build new file mode 100755 index 0000000..fec0ffc --- /dev/null +++ b/Tools/restic/build @@ -0,0 +1,11 @@ +#!/usr/bin/env modbuild + +pbuild::install() { + install -m 0755 -d "${PREFIX}/bin" + install -m 0755 "${SRC_DIR}/restic_${V_PKG}_linux_amd64" "${PREFIX}/bin/restic" +} +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Tools/restic/files/config.yaml b/Tools/restic/files/config.yaml new file mode 100644 index 0000000..9bb8b72 --- /dev/null +++ b/Tools/restic/files/config.yaml @@ -0,0 +1,20 @@ +format: 1 +restic: + defaults: + group: Tools + overlay: base + relstage: stable + systems: [.*] + docfiles: [] + build_functions: + configure: [] + compile: [] + shasums: + restic_0.18.0_linux_amd64.bz2: 98f6dd8bf5b59058d04bfd8dab58e196cc2a680666ccee90275a3b722374438e + versions: + 0.18.0: + config: + target_cpus: [x86_64] + urls: + - url: https://github.com/restic/restic/releases/download/v${V_PKG}/restic_${V_PKG}_linux_amd64.bz2 + unpacker: 7z diff --git a/Tools/restic/modulefile b/Tools/restic/modulefile new file mode 100644 index 0000000..5eb56d9 --- /dev/null +++ b/Tools/restic/modulefile @@ -0,0 +1,13 @@ +#%Pmodule + +module-whatis "fast and secure backup program" +module-url "https://restic.readthedocs.io/en/stable/index.html" +module-license "BSD 2-Clause License" +module-maintainer "Achim Gsell " + +module-help " +Restic is a fast and secure backup program. In the following sections, we +will present typical workflows, starting with installing, preparing a new +repository, and making the first backup. +" + From cc2e188e56e61b96be62302494a959dbb3fb50da Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 19:11:05 +0200 Subject: [PATCH 152/158] neovim: new module added --- Tools/nvim/build | 14 ++++++++++++++ Tools/nvim/files/config.yaml | 20 ++++++++++++++++++++ Tools/nvim/modulefile | 11 +++++++++++ Tools/nvim/modulefiles/.release-0.8.2 | 1 + Tools/nvim/modulefiles/0.8.2 | 11 +++++++++++ 5 files changed, 57 insertions(+) create mode 100755 Tools/nvim/build create mode 100644 Tools/nvim/files/config.yaml create mode 100644 Tools/nvim/modulefile create mode 100644 Tools/nvim/modulefiles/.release-0.8.2 create mode 100644 Tools/nvim/modulefiles/0.8.2 diff --git a/Tools/nvim/build b/Tools/nvim/build new file mode 100755 index 0000000..2070f84 --- /dev/null +++ b/Tools/nvim/build @@ -0,0 +1,14 @@ +#!/usr/bin/env modbuild + +pbuild::install_linux_x86_64() { + cd "${PREFIX}" + tar --strip-components=1 -xvf "${PMODULES_DISTFILESDIR}/${P}-${V_PKG}-linux-x86_64.tar.gz" +} + +} + +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Tools/nvim/files/config.yaml b/Tools/nvim/files/config.yaml new file mode 100644 index 0000000..59fc2a7 --- /dev/null +++ b/Tools/nvim/files/config.yaml @@ -0,0 +1,20 @@ +--- +format: 1 +nvim: + defaults: + group: Tools + relstage: stable + shasums: + nvim-0.11.1-linux-x86_64.tar.gz: 92ecb2dbdfbd0c6d79b522e07c879f7743c5d395d0a4f13b0d4f668f8565527a + versions: + 0.11.1: + config: + target_cpus: [x86_64] + urls: + - url: https://github.com/neovim/neovim/releases/download/v${V_PKG}/${P}-linux-x86_64.tar.gz + name: ${P}-${V_PKG}-linux-x86_64.tar.gz + unpacker: none + build_functions: + configure: [] + compile: [] + install: [pbuild::install_linux_x86_64] diff --git a/Tools/nvim/modulefile b/Tools/nvim/modulefile new file mode 100644 index 0000000..85665e6 --- /dev/null +++ b/Tools/nvim/modulefile @@ -0,0 +1,11 @@ +#%Pmodule + +module-whatis "hyperextensible Vim-based text editor" +module-url "https://neovim.io" +module-license "iApache License Version 2.0" +module-maintainer "Achim Gsell " + +module-help " +hyperextensible Vim-based text editor +" + diff --git a/Tools/nvim/modulefiles/.release-0.8.2 b/Tools/nvim/modulefiles/.release-0.8.2 new file mode 100644 index 0000000..6842dbd --- /dev/null +++ b/Tools/nvim/modulefiles/.release-0.8.2 @@ -0,0 +1 @@ +unstable diff --git a/Tools/nvim/modulefiles/0.8.2 b/Tools/nvim/modulefiles/0.8.2 new file mode 100644 index 0000000..85665e6 --- /dev/null +++ b/Tools/nvim/modulefiles/0.8.2 @@ -0,0 +1,11 @@ +#%Pmodule + +module-whatis "hyperextensible Vim-based text editor" +module-url "https://neovim.io" +module-license "iApache License Version 2.0" +module-maintainer "Achim Gsell " + +module-help " +hyperextensible Vim-based text editor +" + From 2f6672d215b601b713fb87be1bf13baa925e8c2b Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 23 May 2025 19:12:33 +0200 Subject: [PATCH 153/158] neovim: unsued files removed --- Tools/nvim/modulefiles/.release-0.8.2 | 1 - Tools/nvim/modulefiles/0.8.2 | 11 ----------- 2 files changed, 12 deletions(-) delete mode 100644 Tools/nvim/modulefiles/.release-0.8.2 delete mode 100644 Tools/nvim/modulefiles/0.8.2 diff --git a/Tools/nvim/modulefiles/.release-0.8.2 b/Tools/nvim/modulefiles/.release-0.8.2 deleted file mode 100644 index 6842dbd..0000000 --- a/Tools/nvim/modulefiles/.release-0.8.2 +++ /dev/null @@ -1 +0,0 @@ -unstable diff --git a/Tools/nvim/modulefiles/0.8.2 b/Tools/nvim/modulefiles/0.8.2 deleted file mode 100644 index 85665e6..0000000 --- a/Tools/nvim/modulefiles/0.8.2 +++ /dev/null @@ -1,11 +0,0 @@ -#%Pmodule - -module-whatis "hyperextensible Vim-based text editor" -module-url "https://neovim.io" -module-license "iApache License Version 2.0" -module-maintainer "Achim Gsell " - -module-help " -hyperextensible Vim-based text editor -" - From 162a833ac4435d79949f13b78e923b087f29affc Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Mon, 26 May 2025 09:50:40 +0200 Subject: [PATCH 154/158] awscli: new version and YAM config --- Tools/awscli/files/config.yaml | 27 +++++++++++++++++++++++++++ Tools/awscli/files/variants | 1 - 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 Tools/awscli/files/config.yaml delete mode 100644 Tools/awscli/files/variants diff --git a/Tools/awscli/files/config.yaml b/Tools/awscli/files/config.yaml new file mode 100644 index 0000000..ff27567 --- /dev/null +++ b/Tools/awscli/files/config.yaml @@ -0,0 +1,27 @@ +--- +format: 1 +awscli: + defaults: + group: Tools + overlay: base + relstage: stable + systems: [.*] + build_functions: + configure: [] + compile: [] + shasums: + versions: + 2.27.22: + config: + relstage: unstable + urls: + - url: https://awscli.amazonaws.com/$P-exe-linux-x86_64-$V.zip + name: $P-${V_PKG}.zip + unpacker: none + 2.9.21: + config: + relstage: stable + urls: + - url: https://awscli.amazonaws.com/$P-exe-linux-x86_64-$V.zip + name: $P-${V_PKG}.zip + unpacker: none diff --git a/Tools/awscli/files/variants b/Tools/awscli/files/variants deleted file mode 100644 index a749239..0000000 --- a/Tools/awscli/files/variants +++ /dev/null @@ -1 +0,0 @@ -awscli/2.9.21 unstable From e0d44d07eac5fb16f7c50bc489fbacad834d8b73 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Mon, 26 May 2025 09:51:01 +0200 Subject: [PATCH 155/158] awscli: new version and YAM config --- Tools/awscli/build | 19 +++---------------- Tools/awscli/files/config.yaml | 4 ++-- 2 files changed, 5 insertions(+), 18 deletions(-) diff --git a/Tools/awscli/build b/Tools/awscli/build index ca3ba54..35c5125 100755 --- a/Tools/awscli/build +++ b/Tools/awscli/build @@ -1,23 +1,10 @@ #!/usr/bin/env modbuild -# download url actually not used, but the build script fails without it -pbuild::set_download_url "https://github.com/aws/aws-cli/archive/refs/tags/$V.tar.gz" -# pbuild::set_sha256sum 'gnuplot-5.2.4.tar.gz:1515f000bd373aaa53b16183f274189d4f5e0ae47d22f434857933d16a4770cb' -# pbuild::install_docfiles 'Copyright' 'NEWS' 'README' - -pbuild::add_to_group 'Tools' - -pbuild::configure() { - : -} -pbuild::compile() { - : -} pbuild::install() { - curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-$V.zip" -o "awscliv2.zip" - unzip awscliv2.zip - ./aws/install -i $PREFIX -b ${PREFIX}/bin --update + unzip "${PMODULES_DISTFILESDIR}/awscliv2.zip" + ./aws/install -i $PREFIX -b ${PREFIX}/bin --update } + # Local Variables: # mode: sh # sh-basic-offset: 8 diff --git a/Tools/awscli/files/config.yaml b/Tools/awscli/files/config.yaml index ff27567..2759c63 100644 --- a/Tools/awscli/files/config.yaml +++ b/Tools/awscli/files/config.yaml @@ -13,14 +13,14 @@ awscli: versions: 2.27.22: config: - relstage: unstable + relstage: stable urls: - url: https://awscli.amazonaws.com/$P-exe-linux-x86_64-$V.zip name: $P-${V_PKG}.zip unpacker: none 2.9.21: config: - relstage: stable + relstage: deprecated urls: - url: https://awscli.amazonaws.com/$P-exe-linux-x86_64-$V.zip name: $P-${V_PKG}.zip From 28641a2c41a9ad8ce7d318e0d66f1e6986a195f8 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Mon, 26 May 2025 10:11:20 +0200 Subject: [PATCH 156/158] visit: configure build functions in YAML config file --- Tools/visit/build | 8 -------- Tools/visit/files/config.yaml | 6 ++++-- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/Tools/visit/build b/Tools/visit/build index d52c52d..ba4f528 100755 --- a/Tools/visit/build +++ b/Tools/visit/build @@ -1,13 +1,5 @@ #!/usr/bin/env modbuild -pbuild::configure() { - : -} - -pbuild::compile() { - : -} - pbuild::install() { cd "${PMODULES_DISTFILESDIR}" bash "./visit-install-${V_PKG}" ${V} linux-$(uname -p) ${PREFIX} diff --git a/Tools/visit/files/config.yaml b/Tools/visit/files/config.yaml index 6e8d785..89a31b9 100644 --- a/Tools/visit/files/config.yaml +++ b/Tools/visit/files/config.yaml @@ -5,8 +5,11 @@ visit: group: Tools overlay: base relstage: stable - systems: [sles15.5] + systems: [sles.*, rhel.*] docfiles: [Copyright, NEWS, README] + build_functions: + configure: [] + compile: [] versions: 3.4.2: config: @@ -18,5 +21,4 @@ visit: name: visit3_4_2.linux-x86_64.tar.gz unpacker: none relstage: unstable - systems: [sles*] From 5898e6a738cb6ffde410913c5084bf2754d9139e Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Mon, 26 May 2025 10:14:23 +0200 Subject: [PATCH 157/158] visit: release stage changed to stable --- Tools/visit/files/config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Tools/visit/files/config.yaml b/Tools/visit/files/config.yaml index 89a31b9..74f630c 100644 --- a/Tools/visit/files/config.yaml +++ b/Tools/visit/files/config.yaml @@ -20,5 +20,5 @@ visit: - url: https://github.com/visit-dav/visit/releases/download/v${V_PKG}/visit3_4_2.linux-x86_64-rocky8.tar.gz name: visit3_4_2.linux-x86_64.tar.gz unpacker: none - relstage: unstable + relstage: stable From 310b15e779ec7c072d6397d1481788fdb0391f9c Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Mon, 26 May 2025 11:15:48 +0200 Subject: [PATCH 158/158] ncurses: module added --- Libraries/ncurses/build | 3 +++ Libraries/ncurses/files/config.yaml | 26 ++++++++++++++++++++++++++ Libraries/ncurses/modulefile | 12 ++++++++++++ 3 files changed, 41 insertions(+) create mode 100755 Libraries/ncurses/build create mode 100644 Libraries/ncurses/files/config.yaml create mode 100644 Libraries/ncurses/modulefile diff --git a/Libraries/ncurses/build b/Libraries/ncurses/build new file mode 100755 index 0000000..ca41f09 --- /dev/null +++ b/Libraries/ncurses/build @@ -0,0 +1,3 @@ +#!/usr/bin/env modbuild + +export LC_ALL=C diff --git a/Libraries/ncurses/files/config.yaml b/Libraries/ncurses/files/config.yaml new file mode 100644 index 0000000..7e6096b --- /dev/null +++ b/Libraries/ncurses/files/config.yaml @@ -0,0 +1,26 @@ +--- +format: 1 +ncurses: + defaults: + group: Libraries + overlay: base + relstage: stable + docfiles: [] + configure_args: + - --with-shared + - --disable-db-install + - --with-termlib + urls: + - url: https://invisible-island.net/archives/${P}/${P}-${V_PKG}.tar.gz + + shasums: + ncurses-6.5.tar.gz: 136d91bc269a9a5785e5f9e980bc76ab57428f604ce3e5a5a90cebc767971cc6 + ncurses-6.3.tar.gz: 97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059 + + versions: + 6.5: + config: + relstage: stable + 6.3: + config: + relstage: deprecated diff --git a/Libraries/ncurses/modulefile b/Libraries/ncurses/modulefile new file mode 100644 index 0000000..8095afb --- /dev/null +++ b/Libraries/ncurses/modulefile @@ -0,0 +1,12 @@ +#%Module1.0 + +module-whatis "GNU Mpc" +module-url "http://www.multiprecision.org" +module-license "GNU LGPL v3" +module-maintainer "Achim Gsell " + +module-help " +Gnu Mpc is a C library for the arithmetic of complex numbers with +arbitrarily high precision and correct rounding of the result. +" +