From 846c36ceeb3661cd2c4363d3fd6629088ab59238 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Tue, 9 Jun 2020 18:03:14 +0200 Subject: [PATCH 01/41] new GCC versions build --- Libraries/gmp/build | 2 -- Libraries/gmp/files/variants | 1 + Libraries/mpc/files/variants | 1 + Libraries/mpfr/files/variants | 1 + Programming/gcc/build | 1 - Programming/gcc/files/variants.rhel6 | 4 ++++ 6 files changed, 7 insertions(+), 3 deletions(-) diff --git a/Libraries/gmp/build b/Libraries/gmp/build index 4f302ba..5f4ffcc 100755 --- a/Libraries/gmp/build +++ b/Libraries/gmp/build @@ -10,5 +10,3 @@ declare -rx CPP=/usr/bin/cpp pbuild::add_configure_args "--disable-shared" pbuild::add_configure_args "--with-pic" -pbuild::make_all - diff --git a/Libraries/gmp/files/variants b/Libraries/gmp/files/variants index bbc09b3..e881a18 100644 --- a/Libraries/gmp/files/variants +++ b/Libraries/gmp/files/variants @@ -4,3 +4,4 @@ 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 diff --git a/Libraries/mpc/files/variants b/Libraries/mpc/files/variants index ed9d355..ffdd49b 100644 --- a/Libraries/mpc/files/variants +++ b/Libraries/mpc/files/variants @@ -6,3 +6,4 @@ 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 diff --git a/Libraries/mpfr/files/variants b/Libraries/mpfr/files/variants index 2bc2629..a728d5f 100644 --- a/Libraries/mpfr/files/variants +++ b/Libraries/mpfr/files/variants @@ -7,3 +7,4 @@ 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 diff --git a/Programming/gcc/build b/Programming/gcc/build index 274f9df..623b03f 100755 --- a/Programming/gcc/build +++ b/Programming/gcc/build @@ -36,7 +36,6 @@ pbuild::pre_configure() { 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-build-config=bootstrap-debug" pbuild::add_configure_args "--with-pkgversion='PSI Environment Module'" pbuild::add_configure_args "--with-build-config=bootstrap-debug" } diff --git a/Programming/gcc/files/variants.rhel6 b/Programming/gcc/files/variants.rhel6 index d7dc1a8..3ddf273 100644 --- a/Programming/gcc/files/variants.rhel6 +++ b/Programming/gcc/files/variants.rhel6 @@ -24,11 +24,15 @@ 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 From d3c3dc4171c0cad1a9940c68c1680186e14bbb21 Mon Sep 17 00:00:00 2001 From: gsell Date: Mon, 15 Jun 2020 14:54:31 +0200 Subject: [PATCH 02/41] Update README.md --- MPI/elegant/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index 8254c23..b4c2317 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -13,7 +13,7 @@ Instructions to build `Pelegant`: https://ops.aps.anl.gov/publish/Pelegant_manual/node2.html -## Get the software +## Getting the software and required configuration files **Main page** @@ -24,7 +24,7 @@ https://ops.aps.anl.gov/publish/Pelegant_manual/node2.html * http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.base.configure.tar.gz * http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.extensions.configure.tar.gz -**Configure files for elegant, spiffe, genesis, and shower** +**Configuration files for elegant, spiffe, genesis, and shower** * http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=oag.apps.configure.tar.gz From 4780f6a0d35ac56724321081cac8631e5383f98d Mon Sep 17 00:00:00 2001 From: gsell Date: Mon, 15 Jun 2020 15:23:06 +0200 Subject: [PATCH 03/41] Update README.md --- MPI/elegant/README.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index b4c2317..5b96e99 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -1,10 +1,7 @@ -# How to compile (P)elegant +# Building a module for (P)elegant ## Official build instructions -> -Go down for PSI build instructions! - Instructions to setup `epics/base`, `epics/extensions` compile `SDDS` and `elegant`. The instructions to build from source are almost at the end of the page: https://www.aps.anl.gov/Accelerator-Operations-Physics/Software/installationGuide_Linux From 285f9b0e519df1879a15c61b2d3a23d9ccd9f76a Mon Sep 17 00:00:00 2001 From: gsell Date: Mon, 15 Jun 2020 15:24:17 +0200 Subject: [PATCH 04/41] Update README.md --- MPI/elegant/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index 5b96e99..a73ee32 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -14,7 +14,7 @@ https://ops.aps.anl.gov/publish/Pelegant_manual/node2.html **Main page** -* https://www1.aps.anl.gov/Accelerator-Operations-Physics/Software +* https://www.aps.anl.gov/Accelerator-Operations-Physics/Software **Configuration files for EPICS build system (base and extensions)** From a15e931e78076783990aa3ff49618adb7b05d1e9 Mon Sep 17 00:00:00 2001 From: gsell Date: Mon, 15 Jun 2020 15:47:34 +0200 Subject: [PATCH 05/41] Update README.md --- MPI/elegant/README.md | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index a73ee32..62001f3 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -1,20 +1,22 @@ # Building a module for (P)elegant -## Official build instructions +## Home page and official build instructions -Instructions to setup `epics/base`, `epics/extensions` compile `SDDS` and `elegant`. The instructions to build from source are almost at the end of the page: +Elgant is a software packages produced by the [Accelerator Operations +and Physics Group](https://www.aps.anl.gov/Accelerator-Operations-Physics/Software). +It requires the EPICS build-system and SDDS. The EPICS build-system is completely +based on Makefiles. This makes it a bit harder to compile and more error prone. -https://www.aps.anl.gov/Accelerator-Operations-Physics/Software/installationGuide_Linux +Instructions to setup `epics/base`, `epics/extensions` and to compile `SDDS` as +well as `elegant` can be found +[here](https://www.aps.anl.gov/Accelerator-Operations-Physics/Software/installationGuide_Linux). +The instructions to build from source are almost at the end of the page. -Instructions to build `Pelegant`: - -https://ops.aps.anl.gov/publish/Pelegant_manual/node2.html +Instructions to build [`Pelegant`](https://ops.aps.anl.gov/publish/Pelegant_manual/node2.html) ## Getting the software and required configuration files -**Main page** -* https://www.aps.anl.gov/Accelerator-Operations-Physics/Software **Configuration files for EPICS build system (base and extensions)** From f02e5c63df9dd09a0c445b5e4086d36bd6b528f0 Mon Sep 17 00:00:00 2001 From: gsell Date: Mon, 15 Jun 2020 19:02:20 +0200 Subject: [PATCH 06/41] Update README.md --- MPI/elegant/README.md | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index 62001f3..34504d6 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -16,7 +16,9 @@ Instructions to build [`Pelegant`](https://ops.aps.anl.gov/publish/Pelegant_manu ## Getting the software and required configuration files +**file defining constants and some functions** +https://ops.aps.anl.gov/cgi-bin/oagLog4.cgi?name=defns.rpn **Configuration files for EPICS build system (base and extensions)** @@ -38,13 +40,17 @@ Instructions to build [`Pelegant`](https://ops.aps.anl.gov/publish/Pelegant_manu ## Required Modules ``` -module load gcc/7.3.0 gsl/2.4 OpenBLAS/0.2.20 mpich/3.2.1 +module load gcc/8.4.0 gsl/2.6 OpenBLAS/0.3.10 mpich/3.2.1 +``` +or +``` +module load gcc/8.4.0 gsl/2.6 OpenBLAS/0.3.10 openmpi/3.1.6 ``` ## Set used versions ``` -SDDS_VERSION=3.6.1 -ELEGANT_VERSION=34.2.0 +SDDS_VERSION=4.3 +ELEGANT_VERSION=2020.2.0 ``` ## Setup Environment @@ -100,8 +106,7 @@ sed -i "s/clean::/clean:/" RULES_PYTHON make -e "${ARGS[@]}" ``` -> -You have to fix the `clean::` target in `${PREFIX}/oag/apps/configure/PYTHON_RULES` +> You have to fix the `clean::` target in `${PREFIX}/oag/apps/configure/PYTHON_RULES` ## Build required tools and libraries from SDDS ``` From 0a5ffcfe30495a48c3352237674d8fb9b0e0657a Mon Sep 17 00:00:00 2001 From: gsell Date: Tue, 16 Jun 2020 17:03:08 +0200 Subject: [PATCH 07/41] Update README.md --- MPI/elegant/README.md | 58 +++++++++++++++++++++---------------------- 1 file changed, 28 insertions(+), 30 deletions(-) diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index 34504d6..33c5c6a 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -14,28 +14,17 @@ The instructions to build from source are almost at the end of the page. Instructions to build [`Pelegant`](https://ops.aps.anl.gov/publish/Pelegant_manual/node2.html) -## Getting the software and required configuration files +## Getting required configuration files -**file defining constants and some functions** +* [file defining constants and some functions](https://ops.aps.anl.gov/cgi-bin/oagLog4.cgi?name=defns.rpn) +* [EPICS base configuration](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.base.configure.tar.gz) +* [EPICS extensions configuration](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.extensions.configure.tar.gz) +* [Configuration files for elegant, spiffe, genesis, and shower](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=oag.apps.configure.tar.gz) -https://ops.aps.anl.gov/cgi-bin/oagLog4.cgi?name=defns.rpn +## SDDS and Elegant sources -**Configuration files for EPICS build system (base and extensions)** - -* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.base.configure.tar.gz -* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.extensions.configure.tar.gz - -**Configuration files for elegant, spiffe, genesis, and shower** - -* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=oag.apps.configure.tar.gz - -**SDDS source** - -* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=SDDS.3.6.1.tar.gz - -**elegant source** - -* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=elegant.34.2.0.tar.gz +* [SDDS 4.3.1 source](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=SDDS.4.3.0.tar.gz) +* [Elegant 2020.2.0 source](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=elegant.2020.2.0.tar.gz) ## Required Modules @@ -44,17 +33,14 @@ module load gcc/8.4.0 gsl/2.6 OpenBLAS/0.3.10 mpich/3.2.1 ``` or ``` -module load gcc/8.4.0 gsl/2.6 OpenBLAS/0.3.10 openmpi/3.1.6 +module load gcc/8.4.0 gsl/2.6 lapack/3.9.0 openmpi/3.1.6 ``` -## Set used versions -``` -SDDS_VERSION=4.3 -ELEGANT_VERSION=2020.2.0 -``` ## Setup Environment ``` +SDDS_VERSION=4.3 +ELEGANT_VERSION=2020.2.0 source "${PMODULES_ROOT}/config/modbuild.conf" DOWNLOAD_DIR="${PMODULES_DISTFILESDIR}/elegant" PREFIX="${PMODULES_ROOT}/MPI/elegant/${ELEGANT_VERSION}/${MPI}/${MPI_VERSION}/${COMPILER}/${COMPILER_VERSION}" @@ -64,15 +50,13 @@ export HOST_ARCH=linux-x86_64 export EPICS_HOST_ARCH=linux-x86_64 export RPN_DEFNS="${PREFIX}/RPN_DEFNS/defns.rpn" export PERLLIB="${PREFIX}/lib/perl" -``` -``` ARGS=() ARGS+=( "GNU_BIN=$GCC_DIR/bin" ) ARGS+=( "LD=/usr/bin/ld" ) ARGS+=( "AR=/usr/bin/ar -rc" ) ARGS+=( "RANLIB=/usr/bin/ranlib" ) -ARGS+=( "EPICS_BASE=${PREFIX}" ) +ARGS+=( "EPICS_BASE=${EPICS_BASE}" ) ARGS+=( "INSTALL_LOCATION=${PREFIX}" ) ARGS+=( "INSTALL_LIB=${PREFIX}/lib" ) ARGS+=( "INSTALL_SHRLIB=${PREFIX}/lib" ) @@ -113,17 +97,31 @@ make -e "${ARGS[@]}" cd "${PREFIX}" tar xvf "${DOWNLOAD_DIR}/SDDS.${SDDS_VERSION}.tar.gz" cd "${PREFIX}/epics/extensions/src/SDDS/" +sed -i -e "s/\( sddspseudoinverse_SYS_LIB.*\)/\1 gfortran/" SDDSaps/pseudoInverse/Makefile +sed -i -e "s/\( sddsmatrixop_SYS_LIBS.*\)/\1 gfortran/" SDDSaps/pseudoInverse/Makefile + +make -e "${ARGS[@]}" -C png && \ +make -e "${ARGS[@]}" +make -e "${ARGS[@]}" -C SDDSlib clean +make "${ARGS[@]}" MPI=1 -C SDDSlib + + +make -e "${ARGS[@]}" -C pgapack && \ + make -e "${ARGS[@]}" -C fftpack && \ make -e "${ARGS[@]}" -C lzma && \ make -e "${ARGS[@]}" -C matlib && \ make -e "${ARGS[@]}" -C mdbcommon && \ make -e "${ARGS[@]}" -C mdblib && \ make -e "${ARGS[@]}" -C mdbmth && \ +make -e "${ARGS[@]}" -C SDDSlib && \ +make -e "${ARGS[@]}" -C SDDSaps/pseudoInverse OP_SYS_LDLIBS=-lgfortran + make -e "${ARGS[@]}" -C meschach && \ make -e "${ARGS[@]}" -C namelist && \ -make -e "${ARGS[@]}" -C pgapack && \ make -e "${ARGS[@]}" -C rpns/code && \ -make -e "${ARGS[@]}" -C SDDSlib && \ + + make -e "${ARGS[@]}" -C SDDSlib clean make "${ARGS[@]}" MPI=1 -C SDDSlib ``` From 25a87799ec384d3be200fe68bf96a4fec17228a3 Mon Sep 17 00:00:00 2001 From: gsell Date: Tue, 16 Jun 2020 17:26:41 +0200 Subject: [PATCH 08/41] Update README.md --- MPI/elegant/README.md | 34 +++++++++++++++++++--------------- 1 file changed, 19 insertions(+), 15 deletions(-) diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index 33c5c6a..2050fd8 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -57,12 +57,14 @@ ARGS+=( "LD=/usr/bin/ld" ) ARGS+=( "AR=/usr/bin/ar -rc" ) ARGS+=( "RANLIB=/usr/bin/ranlib" ) ARGS+=( "EPICS_BASE=${EPICS_BASE}" ) -ARGS+=( "INSTALL_LOCATION=${PREFIX}" ) -ARGS+=( "INSTALL_LIB=${PREFIX}/lib" ) -ARGS+=( "INSTALL_SHRLIB=${PREFIX}/lib" ) -ARGS+=( "INSTALL_TCLLIB=${PREFIX}/lib" ) -ARGS+=( "INSTALL_BIN=${PREFIX}/bin" ) ARGS+=( "SYSGSL=1") + +#ARGS+=( "INSTALL_LOCATION=${PREFIX}" ) +#ARGS+=( "INSTALL_LIB=${PREFIX}/lib" ) +#ARGS+=( "INSTALL_SHRLIB=${PREFIX}/lib" ) +#ARGS+=( "INSTALL_TCLLIB=${PREFIX}/lib" ) +#ARGS+=( "INSTALL_BIN=${PREFIX}/bin" ) + ``` ## Prepare base build environment @@ -102,8 +104,6 @@ sed -i -e "s/\( sddsmatrixop_SYS_LIBS.*\)/\1 gfortran/" SDDSaps/pseudoInverse/M make -e "${ARGS[@]}" -C png && \ make -e "${ARGS[@]}" -make -e "${ARGS[@]}" -C SDDSlib clean -make "${ARGS[@]}" MPI=1 -C SDDSlib make -e "${ARGS[@]}" -C pgapack && \ @@ -126,16 +126,20 @@ make -e "${ARGS[@]}" -C SDDSlib clean make "${ARGS[@]}" MPI=1 -C SDDSlib ``` -## Compile (P)elegant +## Compile elegant -``` cd "${PREFIX}" tar xvf "${DOWNLOAD_DIR}/elegant.${ELEGANT_VERSION}.tar.gz" - -PATH+=":${PREFIX}/bin" - cd "${PREFIX}/oag/apps/src/elegant" -make -e "${ARGS[@]}" -make clean -make "${ARGS[@]}" Pelegant +make -e "${ARGS[@]}" STATIC_BUILD=NO + +## Compile Pelegant + +``` +cd "${PREFIX}/epics/extensions/src/SDDS/" +make -e "${ARGS[@]}" -C SDDSlib clean +make "${ARGS[@]}" MPI=1 -C SDDSlib +cd "${PREFIX}/oag/apps/src/elegant" +make clean +make "${ARGS[@]}" STATIC_BUILD=NO Pelegant ``` From 931bd68b3e1c337ba13ef4ae5c5ea4d685094bb3 Mon Sep 17 00:00:00 2001 From: gsell Date: Tue, 16 Jun 2020 18:40:23 +0200 Subject: [PATCH 09/41] Update README.md --- MPI/elegant/README.md | 44 ++++++++++--------------------------------- 1 file changed, 10 insertions(+), 34 deletions(-) diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index 2050fd8..785c766 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -58,13 +58,6 @@ ARGS+=( "AR=/usr/bin/ar -rc" ) ARGS+=( "RANLIB=/usr/bin/ranlib" ) ARGS+=( "EPICS_BASE=${EPICS_BASE}" ) ARGS+=( "SYSGSL=1") - -#ARGS+=( "INSTALL_LOCATION=${PREFIX}" ) -#ARGS+=( "INSTALL_LIB=${PREFIX}/lib" ) -#ARGS+=( "INSTALL_SHRLIB=${PREFIX}/lib" ) -#ARGS+=( "INSTALL_TCLLIB=${PREFIX}/lib" ) -#ARGS+=( "INSTALL_BIN=${PREFIX}/bin" ) - ``` ## Prepare base build environment @@ -83,7 +76,7 @@ make -e "${ARGS[@]}" ## Unpack EPICS extensions and OAG apps configuration ``` -ARGS+=( "TOOLS=${PREFIX}/bin") +#ARGS+=( "TOOLS=${PREFIX}/bin") cd "${PREFIX}" tar xvf "${DOWNLOAD_DIR}/epics.extensions.configure.tar.gz" tar xvf "${DOWNLOAD_DIR}/oag.apps.configure.tar.gz" @@ -92,10 +85,9 @@ sed -i "s/clean::/clean:/" RULES_PYTHON make -e "${ARGS[@]}" ``` -> You have to fix the `clean::` target in `${PREFIX}/oag/apps/configure/PYTHON_RULES` - ## Build required tools and libraries from SDDS ``` + cd "${PREFIX}" tar xvf "${DOWNLOAD_DIR}/SDDS.${SDDS_VERSION}.tar.gz" cd "${PREFIX}/epics/extensions/src/SDDS/" @@ -104,42 +96,26 @@ sed -i -e "s/\( sddsmatrixop_SYS_LIBS.*\)/\1 gfortran/" SDDSaps/pseudoInverse/M make -e "${ARGS[@]}" -C png && \ make -e "${ARGS[@]}" - - -make -e "${ARGS[@]}" -C pgapack && \ - -make -e "${ARGS[@]}" -C fftpack && \ -make -e "${ARGS[@]}" -C lzma && \ -make -e "${ARGS[@]}" -C matlib && \ -make -e "${ARGS[@]}" -C mdbcommon && \ -make -e "${ARGS[@]}" -C mdblib && \ -make -e "${ARGS[@]}" -C mdbmth && \ -make -e "${ARGS[@]}" -C SDDSlib && \ -make -e "${ARGS[@]}" -C SDDSaps/pseudoInverse OP_SYS_LDLIBS=-lgfortran - -make -e "${ARGS[@]}" -C meschach && \ -make -e "${ARGS[@]}" -C namelist && \ -make -e "${ARGS[@]}" -C rpns/code && \ - - -make -e "${ARGS[@]}" -C SDDSlib clean -make "${ARGS[@]}" MPI=1 -C SDDSlib ``` ## Compile elegant +``` +PATH+=":$PREFIX/epics/extensions/bin/linux-x86_64" cd "${PREFIX}" tar xvf "${DOWNLOAD_DIR}/elegant.${ELEGANT_VERSION}.tar.gz" cd "${PREFIX}/oag/apps/src/elegant" -make -e "${ARGS[@]}" STATIC_BUILD=NO +make "${ARGS[@]}" STATIC_BUILD=NO +``` ## Compile Pelegant ``` cd "${PREFIX}/epics/extensions/src/SDDS/" -make -e "${ARGS[@]}" -C SDDSlib clean -make "${ARGS[@]}" MPI=1 -C SDDSlib +make "${ARGS[@]}" -C pgapack +make "${ARGS[@]}" -C SDDSlib clean +make "${ARGS[@]}" MPI=1 -C SDDSlib cd "${PREFIX}/oag/apps/src/elegant" make clean -make "${ARGS[@]}" STATIC_BUILD=NO Pelegant +make SYSGSL=1 Pelegant ``` From 60f98fa57a91663b339d2c0ba3fa2a5d684c3950 Mon Sep 17 00:00:00 2001 From: gsell Date: Wed, 17 Jun 2020 10:19:11 +0200 Subject: [PATCH 10/41] Update README.md --- MPI/elegant/README.md | 47 +++++++++++++++++++------------------------ 1 file changed, 21 insertions(+), 26 deletions(-) diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index 785c766..e6d6c38 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -51,59 +51,58 @@ export EPICS_HOST_ARCH=linux-x86_64 export RPN_DEFNS="${PREFIX}/RPN_DEFNS/defns.rpn" export PERLLIB="${PREFIX}/lib/perl" +PATH+=":$PREFIX/epics/extensions/bin/${EPICS_HOST_ARCH}" + ARGS=() ARGS+=( "GNU_BIN=$GCC_DIR/bin" ) ARGS+=( "LD=/usr/bin/ld" ) ARGS+=( "AR=/usr/bin/ar -rc" ) ARGS+=( "RANLIB=/usr/bin/ranlib" ) -ARGS+=( "EPICS_BASE=${EPICS_BASE}" ) ARGS+=( "SYSGSL=1") ``` -## Prepare base build environment +## Prepare everything -EPICS base configuration ``` mkdir -p "${PREFIX}" mkdir -p "${RPN_DEFNS%/*}" cp "${DOWNLOAD_DIR}/defns.rpn" "${RPN_DEFNS}" cd "${PREFIX}" tar xvf "${DOWNLOAD_DIR}/epics.base.configure.tar.gz" -cd epics/base -make -e "${ARGS[@]}" -``` - -## Unpack EPICS extensions and OAG apps configuration - -``` -#ARGS+=( "TOOLS=${PREFIX}/bin") -cd "${PREFIX}" tar xvf "${DOWNLOAD_DIR}/epics.extensions.configure.tar.gz" tar xvf "${DOWNLOAD_DIR}/oag.apps.configure.tar.gz" +tar xvf "${DOWNLOAD_DIR}/SDDS.${SDDS_VERSION}.tar.gz" +tar xvf "${DOWNLOAD_DIR}/elegant.${ELEGANT_VERSION}.tar.gz" +``` + +## Configure EPICS base and OAG applications + +``` +cd epics/base +make "${ARGS[@]}" cd "${PREFIX}/oag/apps/configure" sed -i "s/clean::/clean:/" RULES_PYTHON -make -e "${ARGS[@]}" +make "${ARGS[@]}" ``` -## Build required tools and libraries from SDDS -``` +## Compile SDDS -cd "${PREFIX}" -tar xvf "${DOWNLOAD_DIR}/SDDS.${SDDS_VERSION}.tar.gz" +``` cd "${PREFIX}/epics/extensions/src/SDDS/" sed -i -e "s/\( sddspseudoinverse_SYS_LIB.*\)/\1 gfortran/" SDDSaps/pseudoInverse/Makefile sed -i -e "s/\( sddsmatrixop_SYS_LIBS.*\)/\1 gfortran/" SDDSaps/pseudoInverse/Makefile -make -e "${ARGS[@]}" -C png && \ -make -e "${ARGS[@]}" +make "${ARGS[@]}" -C png && \ +make "${ARGS[@]}" + +make "${ARGS[@]}" -C pgapack +make "${ARGS[@]}" -C SDDSlib clean +make "${ARGS[@]}" MPI=1 -C SDDSlib ``` ## Compile elegant ``` -PATH+=":$PREFIX/epics/extensions/bin/linux-x86_64" -cd "${PREFIX}" -tar xvf "${DOWNLOAD_DIR}/elegant.${ELEGANT_VERSION}.tar.gz" cd "${PREFIX}/oag/apps/src/elegant" make "${ARGS[@]}" STATIC_BUILD=NO ``` @@ -111,10 +110,6 @@ make "${ARGS[@]}" STATIC_BUILD=NO ## Compile Pelegant ``` -cd "${PREFIX}/epics/extensions/src/SDDS/" -make "${ARGS[@]}" -C pgapack -make "${ARGS[@]}" -C SDDSlib clean -make "${ARGS[@]}" MPI=1 -C SDDSlib cd "${PREFIX}/oag/apps/src/elegant" make clean make SYSGSL=1 Pelegant From 308fd1c890a67108c2b2fdab0f1bf527fb157a14 Mon Sep 17 00:00:00 2001 From: bliven_s Date: Wed, 15 Jul 2020 16:57:12 +0200 Subject: [PATCH 11/41] CrYOLO/1.6.1 modules There are _cpu and _gpu flags available, which are selected based on fancy modulefile code (Thanks Achim) --- EM/crYOLO/files/variants | 2 ++ EM/crYOLO/modulefile | 15 ++++++++--- .../2019.07/conda-env-defs/cryolo/README.md | 3 ++- .../cryolo/{cryolo.yml => cryolo-cpu.yml} | 4 +-- .../conda-env-defs/cryolo/cryolo-gpu.yml | 14 ++++++++++ .../anaconda/files/admintools/conda_setup.sh | 14 ++++++++++ .../files/admintools/kernelwrapper.sh | 27 +++++++++++++++++++ Programming/anaconda/modulefile | 3 ++- 8 files changed, 75 insertions(+), 7 deletions(-) rename Programming/anaconda/2019.07/conda-env-defs/cryolo/{cryolo.yml => cryolo-cpu.yml} (77%) create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-gpu.yml create mode 100644 Programming/anaconda/files/admintools/conda_setup.sh create mode 100755 Programming/anaconda/files/admintools/kernelwrapper.sh diff --git a/EM/crYOLO/files/variants b/EM/crYOLO/files/variants index 7dc6e35..92b226c 100644 --- a/EM/crYOLO/files/variants +++ b/EM/crYOLO/files/variants @@ -1,3 +1,5 @@ crYOLO/1.2.3 unstable cuda/9.0.176 crYOLO/1.5.6_gpu unstable anaconda/2019.07 +crYOLO/1.6.1_gpu unstable anaconda/2019.07 +crYOLO/1.6.1_cpu unstable anaconda/2019.07 diff --git a/EM/crYOLO/modulefile b/EM/crYOLO/modulefile index 596f793..41cf27a 100644 --- a/EM/crYOLO/modulefile +++ b/EM/crYOLO/modulefile @@ -26,19 +26,28 @@ convolutional neural networks and utilizes the popular You Only Look Once set shelltype [module-info shelltype] switch -- $shelltype { "sh" { + puts stdout "source \"\${ANACONDA_PREFIX}\"/admintools/conda_setup.sh;\n" } default { puts stderr "Shells of type '$shelltype' are NOT supported!" } } -#set useflag [string map {{:} {}} $USEFLAGS] -#puts stderr "conda activate cryolo-${V_PKG}-${USEFLAGS%\n" +# 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 cryolo-1.5.6-gpu;\n" + puts stdout "conda activate $env_to_activate;\n" } "unload" - "remove" { diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md b/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md index 46e620a..18c111c 100644 --- a/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md +++ b/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md @@ -2,7 +2,8 @@ IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. pmod6) - export TMPDIR=/opt/tmp/bliven_s + export TMPDIR=/opt/tmp/$USER + export XDG_CACHE_HOME=/opt/tmp/$USER/.cache CONDA_COPY_ALWAYS=1 conda env create --file cryolo.yml conda activate cryolo diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-cpu.yml similarity index 77% rename from Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml rename to Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-cpu.yml index 42b1fe6..284af71 100644 --- a/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml +++ b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-cpu.yml @@ -1,4 +1,4 @@ -name: cryolo-1.5.6-gpu +name: cryolo-1.6.1-cpu channels: - defaults dependencies: @@ -11,4 +11,4 @@ dependencies: - intel-openmp==2019.4 - pip - pip: - - cryolo[gpu]==1.5.6 + - cryolo[cpu]==1.6.1 diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-gpu.yml b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-gpu.yml new file mode 100644 index 0000000..ec523e2 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-gpu.yml @@ -0,0 +1,14 @@ +name: cryolo-1.6.1-gpu +channels: + - defaults +dependencies: + - python=3.6 + - pyqt=5 + - cudnn=7.1.2 + - numpy==1.14.5 + - cython + - wxPython==4.0.4 + - intel-openmp==2019.4 + - pip + - pip: + - cryolo[gpu]==1.6.1 diff --git a/Programming/anaconda/files/admintools/conda_setup.sh b/Programming/anaconda/files/admintools/conda_setup.sh new file mode 100644 index 0000000..6ff904f --- /dev/null +++ b/Programming/anaconda/files/admintools/conda_setup.sh @@ -0,0 +1,14 @@ +# simulate `conda init` type hook +# Expects CONDA_EXE and CONDA_PREFIX to be set +__conda_setup="$("${CONDA_EXE:-conda}" 'shell.bash' 'hook' 2> /dev/null)" +if [ $? -eq 0 ]; then + eval "$__conda_setup" +else + if [ -f "${CONDA_PREFIX:?CONDA_PREFIX not set}/etc/profile.d/conda.sh" ]; then + . "${CONDA_PREFIX}/etc/profile.d/conda.sh" + else + export PATH="${CONDA_PREFIX}/bin:$PATH" + fi +fi +unset __conda_setup + diff --git a/Programming/anaconda/files/admintools/kernelwrapper.sh b/Programming/anaconda/files/admintools/kernelwrapper.sh new file mode 100755 index 0000000..24268dd --- /dev/null +++ b/Programming/anaconda/files/admintools/kernelwrapper.sh @@ -0,0 +1,27 @@ +#!/bin/bash +dbgecho() { + DBGLOG=/tmp/kernelwrapper-${USER}.log + if [[ $DEBUG_JUPYTER_WRAPPER == 1 ]]; then + echo "$1" >> $DBGLOG + fi +} + +DATE=$(date +%Y-%m-%dT%H:%M) +dbgecho "$DATE: $@" + +# ensure that module commands are available +dbgecho "sourcing profile.bash" +source /opt/psi/config/profile.bash + +dbgecho "sourcing conda.sh" +source /opt/psi/Programming/anaconda/2019.07/conda/etc/profile.d/conda.sh &>> $DBGLOG + +dbgecho "Running activate" +conda activate $1 + +# undefine module command since it causes error in the notebook when using +# shell escapes +unset -f module +shift +exec "$@" + diff --git a/Programming/anaconda/modulefile b/Programming/anaconda/modulefile index 899b652..3afbc1c 100644 --- a/Programming/anaconda/modulefile +++ b/Programming/anaconda/modulefile @@ -57,7 +57,8 @@ switch [module-info mode] { # but we need to prevent conflicts with a conda from a different source. # puts stderr "DEBUG: Using conda from $P/$V\n" - puts stdout "source \"$PREFIX/conda/etc/profile.d/conda.sh\";\n" + #puts stdout "source \"$PREFIX/conda/etc/profile.d/conda.sh\";\n" + puts stdout "source $PREFIX/admintools/conda_setup.sh;\n" # Activate base? No: anaconda should just provide the conda tool #puts stdout "conda activate;\n" From ac7fb7ebc2cc5d172a5baf88a6ecf6c23d273672 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 10:21:50 +0200 Subject: [PATCH 12/41] vtk 8.2.0 build, old version deprecated --- Compiler/vtk/5/variants.Linux | 10 ---------- Compiler/vtk/6/variants.Linux | 1 - Compiler/vtk/7/variants.Linux | 1 - Compiler/vtk/8/variants.Linux | 1 - Compiler/vtk/files/variants.rhel6 | 11 +++++++++++ 5 files changed, 11 insertions(+), 13 deletions(-) delete mode 100644 Compiler/vtk/5/variants.Linux delete mode 100644 Compiler/vtk/6/variants.Linux delete mode 100644 Compiler/vtk/7/variants.Linux delete mode 100644 Compiler/vtk/8/variants.Linux create mode 100644 Compiler/vtk/files/variants.rhel6 diff --git a/Compiler/vtk/5/variants.Linux b/Compiler/vtk/5/variants.Linux deleted file mode 100644 index ea19eb6..0000000 --- a/Compiler/vtk/5/variants.Linux +++ /dev/null @@ -1,10 +0,0 @@ -vtk/5.10.1 stable b:cmake/2.8.12.2 gcc/4.7.4 -vtk/5.10.1 stable b:cmake/2.8.12.2 gcc/4.8.3 -vtk/5.10.1 stable b:cmake/3.1.3 gcc/4.8.4 -vtk/5.10.1 stable b:cmake/3.4.1 gcc/4.8.5 -vtk/5.10.1 stable b:cmake/3.1.3 gcc/4.9.2 -vtk/5.10.1 stable b:cmake/3.6.3 gcc/4.9.4 -vtk/5.10.1 stable b:cmake/3.6.3 gcc/5.3.0 -vtk/5.10.1 stable b:cmake/3.6.3 gcc/6.2.0 - -vtk/5.10.1 unstable b:cmake/3.1.3 intel/15.3 diff --git a/Compiler/vtk/6/variants.Linux b/Compiler/vtk/6/variants.Linux deleted file mode 100644 index 6f70840..0000000 --- a/Compiler/vtk/6/variants.Linux +++ /dev/null @@ -1 +0,0 @@ -vtk/6.3.0 unstable b:cmake/3.6.3 gcc/6.2.0 diff --git a/Compiler/vtk/7/variants.Linux b/Compiler/vtk/7/variants.Linux deleted file mode 100644 index f4c4034..0000000 --- a/Compiler/vtk/7/variants.Linux +++ /dev/null @@ -1 +0,0 @@ -vtk/7.0.0 unstable b:cmake/3.6.3 gcc/6.2.0 diff --git a/Compiler/vtk/8/variants.Linux b/Compiler/vtk/8/variants.Linux deleted file mode 100644 index 580fb68..0000000 --- a/Compiler/vtk/8/variants.Linux +++ /dev/null @@ -1 +0,0 @@ -vtk/8.0.0 unstable b:cmake/3.6.3 gcc/5.4.0 diff --git a/Compiler/vtk/files/variants.rhel6 b/Compiler/vtk/files/variants.rhel6 new file mode 100644 index 0000000..fe1b334 --- /dev/null +++ b/Compiler/vtk/files/variants.rhel6 @@ -0,0 +1,11 @@ +vtk/5.10.1 deprecated b:cmake/2.8.12.2 gcc/{4.7.4,4.8.3} +vtk/5.10.1 deprecated b:cmake/3.1.3 gcc/{4.8.4,4.9.2} +vtk/5.10.1 deprecated b:cmake/3.1.3 intel/15.3 + +vtk/5.10.1 deprecated b:cmake/3.6.3 gcc/{4.8.5,4.9.4,5.3.0} + +vtk/7.0.0 deprecated b:cmake/3.6.3 gcc/6.2.0 +vtk/8.0.0 deprecated b:cmake/3.6.3 gcc/5.4.0 + +vtk/8.2.0 unstable b:cmake/3.15.5 gcc/{7.5.0,8.4.0,9.3.0} + From 3d31179ed7f644b41d255ec07c05fea731b4c0b8 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 10:42:20 +0200 Subject: [PATCH 13/41] OpenBLAS 0.3.9 and 0.3.10 build --- Compiler/OpenBLAS/files/variants.rhel6 | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Compiler/OpenBLAS/files/variants.rhel6 b/Compiler/OpenBLAS/files/variants.rhel6 index 5e8c3cc..d56d4e6 100644 --- a/Compiler/OpenBLAS/files/variants.rhel6 +++ b/Compiler/OpenBLAS/files/variants.rhel6 @@ -6,3 +6,6 @@ OpenBLAS/0.2.20_omp stable gcc/7.3.0 OpenBLAS/0.2.20 stable intel/17.4 OpenBLAS/0.3.7 stable gcc/{7.4.0,8.3.0,9.2.0} + +OpenBLAS/0.3.9 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} +OpenBLAS/0.3.10 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} From 0eff95b244acc154ebc031e84b21411270b93772 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 11:42:57 +0200 Subject: [PATCH 14/41] boost/1.73 build, without Python --- Compiler/boost/build | 60 ++++++++++++++--------------- Compiler/boost/files/variants | 39 ------------------- Compiler/boost/files/variants.rhel6 | 25 ++++++++++++ 3 files changed, 55 insertions(+), 69 deletions(-) delete mode 100644 Compiler/boost/files/variants create mode 100644 Compiler/boost/files/variants.rhel6 diff --git a/Compiler/boost/build b/Compiler/boost/build index e836e3d..5b2d34b 100755 --- a/Compiler/boost/build +++ b/Compiler/boost/build @@ -1,44 +1,44 @@ #!/usr/bin/env modbuild +pbuild::set_download_url "https://netcologne.dl.sourceforge.net/project/${P}/${P}/$V/${P}_${V_PKG//./_}.tar.gz" +#pbuild::set_download_url "https://dl.bintray.com/boostorg/release/${V_PKG}/source/${P}_${V_PKG//./_}.tar.gz" -#pbuild::set_download_url "https://netcologne.dl.sourceforge.net/project/$P/$P/$V/$P_${V_MAJOR}_${V_MINOR}_${V_PATCHLVL}.tar.gz" -pbuild::set_download_url "https://dl.bintray.com/boostorg/release/${V_PKG}/source/${P}_${V_PKG//./_}.tar.gz" pbuild::add_to_group 'Compiler' BOOST_BUILD_PATH="${BUILD_DIR}" -pbuild::configure() { - cd "${SRC_DIR}" - "${SRC_DIR}"/bootstrap.sh \ - --prefix="${PREFIX}" \ - --with-libraries=all \ - --with-python-root="${PYTHON_PREFIX}" \ - || exit 1 +TOOLSET='' + +pbuild::pre_configure() { + case "${COMPILER}" in + gcc ) + TOOLSET=gcc + ;; + * ) + std::die 1 "Unsupported compiler!" + ;; + esac } pbuild::compile() { - cd "${SRC_DIR}" - ./b2 \ - --build-type=minimal \ - --build-dir="${BUILD_DIR}" \ - --layout=system \ + cd "${SRC_DIR}" + ./bootstrap.sh \ + --prefix="${PREFIX}" \ + --with-toolset=${TOOLSET} \ + --without-libraries=python \ + || exit 1 + ./b2 \ + --build-dir="${BUILD_DIR}" \ + --layout=system \ + --without-python \ --without-mpi \ - variant=release \ - link=shared,static \ - threading=multi \ - stage + toolset=${TOOLSET} \ + variant=release \ + link=shared,static \ + threading=multi \ + install -j 3 \ + || exit 1 } pbuild::install() { - cd "${SRC_DIR}" - ./b2 \ - --build-type=minimal \ - --build-dir="${BUILD_DIR}" \ - --layout=system \ - --without-mpi \ - variant=release \ - link=shared,static \ - threading=multi \ - install + : } - - diff --git a/Compiler/boost/files/variants b/Compiler/boost/files/variants deleted file mode 100644 index d20237b..0000000 --- a/Compiler/boost/files/variants +++ /dev/null @@ -1,39 +0,0 @@ -boost/1.55.0 stable gcc/4.7.4 b:Python/3.4.0 -boost/1.55.0 stable gcc/4.8.3 b:Python/3.4.0 -boost/1.55.0 stable gcc/4.8.4 b:Python/3.4.0 -boost/1.55.0 stable gcc/4.8.5 b:Python/2.7.11 -boost/1.55.0 stable gcc/4.9.2 b:Python/3.4.0 - -boost/1.57.0 stable gcc/4.8.2 b:Python/3.4.0 - -boost/1.58.0 stable gcc/4.8.4 b:Python/3.4.0 -boost/1.58.0 stable gcc/4.8.5 b:Python/2.7.11 -boost/1.58.0 stable gcc/4.9.3 b:Python/2.7.11 -boost/1.58.0 stable gcc/6.3.0 b:Python/2.7.12 - -boost/1.61.0 stable gcc/4.8.5 b:Python/2.7.11 -boost/1.61.0 stable gcc/6.2.0 b:Python/2.7.11 - -boost/1.62.0 stable gcc/4.8.5 Python/2.7.12 -boost/1.62.0 stable gcc/4.9.4 Python/2.7.12 -boost/1.62.0 stable gcc/5.4.0 Python/2.7.12 -boost/1.62.0 stable gcc/6.2.0 Python/2.7.12 -boost/1.62.0 stable gcc/6.3.0 Python/2.7.12 -boost/1.62.0 stable gcc/7.1.0 Python/2.7.12 -boost/1.63.0 stable gcc/6.3.0 Python/2.7.12 -boost/1.64.0 stable gcc/5.4.0 Python/2.7.12 - -boost/1.66.0 stable gcc/5.5.0 b:Python/2.7.12 -boost/1.66.0 stable gcc/6.4.0 b:Python/2.7.12 -boost/1.66.0 stable gcc/7.3.0 b:Python/2.7.12 -boost/1.66.0 stable clang-macos/9.0.0 b:Python/2.7.12 -boost/1.66.0 stable intel/17.4 b:Python/2.7.12 - -boost/1.67.0 stable gcc/5.5.0 b:Python/2.7.14 -boost/1.67.0 stable gcc/6.4.0 b:Python/2.7.14 -boost/1.67.0 stable gcc/7.3.0 b:Python/2.7.14 -boost/1.67.0 stable clang-macos/9.0.0 b:Python/2.7.14 -boost/1.67.0 stable intel/17.4 b:Python/2.7.14 - -boost/1.68.0 stable gcc/7.3.0 b:Python/2.7.14 -boost/1.68.0 stable gcc/8.2.0 b:Python/2.7.14 diff --git a/Compiler/boost/files/variants.rhel6 b/Compiler/boost/files/variants.rhel6 new file mode 100644 index 0000000..51cd332 --- /dev/null +++ b/Compiler/boost/files/variants.rhel6 @@ -0,0 +1,25 @@ +boost/1.55.0 deprecated gcc/{4.7.4,4.8.3,4.8.4,4.9.2} b:Python/3.4.0 +boost/1.55.0 deprecated gcc/4.8.5 b:Python/2.7.11 + +boost/1.57.0 deprecated gcc/4.8.2 b:Python/3.4.0 + +boost/1.58.0 deprecated gcc/4.8.4 b:Python/3.4.0 +boost/1.58.0 deprecated gcc/{4.8.5,4.9.3} b:Python/2.7.11 + +boost/1.61.0 deprecated gcc/{4.8.5,6.2.0} b:Python/2.7.11 + +boost/1.62.0 deprecated gcc/{4.8.5,4.9.4,5.4.0,6.2.0,6.3.0,7.1.0} Python/2.7.12 + +boost/1.63.0 deprecated gcc/6.3.0 Python/2.7.12 + +boost/1.64.0 deprecated gcc/5.4.0 Python/2.7.12 + +boost/1.66.0 stable gcc/{5.5.0,6.4.0,7.3.0} b:Python/2.7.14 +boost/1.66.0 stable intel/17.4 b:Python/2.7.12 + +boost/1.67.0 stable gcc/{5.5.0,6.4.0,7.3.0} b:Python/2.7.14 +boost/1.67.0 stable intel/17.4 b:Python/2.7.14 + +boost/1.68.0 stable gcc/{7.3.0,8.2.0} b:Python/2.7.14 + +boost/1.73.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} b:zlib/1.2.11 From c63771f61a381f2d0deb0b63850fe422f61b4592 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 11:49:28 +0200 Subject: [PATCH 15/41] gsl/2.6 build with current GCCs --- Compiler/gsl/files/variants.rhel6 | 1 + 1 file changed, 1 insertion(+) diff --git a/Compiler/gsl/files/variants.rhel6 b/Compiler/gsl/files/variants.rhel6 index c4ea7a2..236f69e 100644 --- a/Compiler/gsl/files/variants.rhel6 +++ b/Compiler/gsl/files/variants.rhel6 @@ -13,3 +13,4 @@ gsl/2.5 stable gcc/{6.3.0,7.3.0,7.4.0,8.3.0,9.1.0} gsl/2.5 stable intel/19.4 gsl/2.6 stable gcc/{7.4.0,8.3.0,9.1.0,9.2.0} +gsl/2.6 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} From 44035be349c8cc9a8b36907b7357bff7b58e2ae1 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 13:45:54 +0200 Subject: [PATCH 16/41] gtest/1.10.0 build --- Compiler/gtest/files/variants.rhel6 | 1 + 1 file changed, 1 insertion(+) diff --git a/Compiler/gtest/files/variants.rhel6 b/Compiler/gtest/files/variants.rhel6 index 639fb93..becc451 100644 --- a/Compiler/gtest/files/variants.rhel6 +++ b/Compiler/gtest/files/variants.rhel6 @@ -1,2 +1,3 @@ gtest/1.7.0 stable gcc/{5.4.0,6.4.0,7.3.0,7.4.0} b:cmake/3.10.3 gtest/1.8.1 stable gcc/{5.5.0,6.4.0,7.4.0,8.3.0,9.2.0} b:cmake/3.10.3 +gtest/1.10.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} b:cmake/3.15.5 From c6d83ce4f632accfa2803aad4cd4ab19dbff5fcb Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 14:02:30 +0200 Subject: [PATCH 17/41] template for 'New variant' reviewed --- .gitlab/issue_templates/New variant.md | 24 +++++++----------------- 1 file changed, 7 insertions(+), 17 deletions(-) diff --git a/.gitlab/issue_templates/New variant.md b/.gitlab/issue_templates/New variant.md index 1c048f7..4d13e50 100644 --- a/.gitlab/issue_templates/New variant.md +++ b/.gitlab/issue_templates/New variant.md @@ -1,21 +1,11 @@ # New module variant -[//]: # (open an issue for each version and System) +* **Name:** +* **Version:** +* **Group:** +* **with:** +* **System:** +* **Overlay** - -| **Name** | **Version** | **Group** | **with** | **System** | **Overlay** | -|----------|-------------|-----------|------------|------------|-------------| -| | | | | | default | - - -[//]: # (if you do not have hierarchival dependencies use the check-list below -- [ ] build -- [ ] tested -- [ ] released - -[//]: # (otherwise use check-lists like the one below for each variant) -- [ ] version X.Y.Z with WITH1 - - [ ] build - - [ ] tested - - [ ] released +~"New variant" From 3f56eb1bcc6babdb3a1b8c8797aba020b11f968d Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 14:07:45 +0200 Subject: [PATCH 18/41] mpich/3.3.2 build, cleanup variant files --- Compiler/mpich/files/variants | 12 ------------ Compiler/mpich/files/variants.rhel6 | 8 ++++++++ 2 files changed, 8 insertions(+), 12 deletions(-) delete mode 100644 Compiler/mpich/files/variants create mode 100644 Compiler/mpich/files/variants.rhel6 diff --git a/Compiler/mpich/files/variants b/Compiler/mpich/files/variants deleted file mode 100644 index 8ebff5e..0000000 --- a/Compiler/mpich/files/variants +++ /dev/null @@ -1,12 +0,0 @@ -mpich/3.2.1 stable gcc/4.8.5 -mpich/3.2.1 stable gcc/5.5.0 -mpich/3.2.1 stable gcc/6.4.0 -mpich/3.2.1 stable gcc/7.3.0 -mpich/3.2.1 stable gcc/8.2.0 -mpich/3.2.1_merlin unstable gcc/6.4.0 b:binutils/2.29 b:mxm/3.6.3104 -mpich/3.2.1_merlin unstable gcc/7.3.0 b:binutils/2.29 b:mxm/3.6.3104 -mpich/3.2.1 stable intel/17.4 - -mpich/3.3 stable gcc/7.3.0 -mpich/3.3 stable gcc/7.4.0 -mpich/3.3 stable gcc/8.3.0 diff --git a/Compiler/mpich/files/variants.rhel6 b/Compiler/mpich/files/variants.rhel6 new file mode 100644 index 0000000..ca89e5f --- /dev/null +++ b/Compiler/mpich/files/variants.rhel6 @@ -0,0 +1,8 @@ +mpich/3.1.4 deprecated gcc/{4.7.4,4.8.4,4.9.2,5.1.0} +mpich/3.1.4 deprecated intel/15.2 + +mpich/3.2.1 stable gcc/{4.8.5,5.5.0,6.4.0,7.3.0,8.2.0} +mpich/3.2.1 stable intel/17.4 + +mpich/3.3 stable gcc/{7.3.0,7.4.0,8.3.0} +mpich/3.3.2 unstable gcc/{7.5.0,8.4.0,9.3.0} From a47ccfe69b9ad8395d42dad587b403a5a199e970 Mon Sep 17 00:00:00 2001 From: gsell Date: Thu, 16 Jul 2020 14:09:34 +0200 Subject: [PATCH 19/41] Update New variant.md --- .gitlab/issue_templates/New variant.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.gitlab/issue_templates/New variant.md b/.gitlab/issue_templates/New variant.md index 4d13e50..d884fa4 100644 --- a/.gitlab/issue_templates/New variant.md +++ b/.gitlab/issue_templates/New variant.md @@ -1,11 +1,10 @@ # New module variant * **Name:** -* **Version:** * **Group:** * **with:** * **System:** * **Overlay** -~"New variant" +/label ~"New variant" From 32e818391ad49cccce278511721addad7dfab802 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 14:40:48 +0200 Subject: [PATCH 20/41] mpich: variants.merlin added --- Compiler/mpich/files/variants.merlin | 1 + 1 file changed, 1 insertion(+) create mode 100644 Compiler/mpich/files/variants.merlin diff --git a/Compiler/mpich/files/variants.merlin b/Compiler/mpich/files/variants.merlin new file mode 100644 index 0000000..30ac8ad --- /dev/null +++ b/Compiler/mpich/files/variants.merlin @@ -0,0 +1 @@ +mpich/3.2.1_merlin unstable gcc/{6.4.0,7.3.0} b:binutils/2.29 b:mxm/3.6.3104 From ff54c6df40738c00cd8d155f81a47543a0ae01ad Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 14:45:32 +0200 Subject: [PATCH 21/41] openmpi: fix handling of fallback libraries in modulefile --- Compiler/openmpi/modulefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Compiler/openmpi/modulefile b/Compiler/openmpi/modulefile index 68458ac..52e5c50 100644 --- a/Compiler/openmpi/modulefile +++ b/Compiler/openmpi/modulefile @@ -28,7 +28,7 @@ setenv MPIRUN $PREFIX/bin/mpirun set libibverbs [glob -nocomplain /usr/lib{64,}/libibverbs.so.1*] set libnuma [glob -nocomplain /usr/lib{64,}/libnuma.so.1*] set librdmacm [glob -nocomplain /usr/lib{64,}/librdmacm.so.1*] -set libucx [glob -nocomplain /usr/lib{64,}/libuc[mpst].so.0*] +set libucx [glob -nocomplain /usr/lib{64,}/libuc\[mpst\].so.0*] if { $libibverbs eq "" || $libnuma eq "" || $librdmacm eq "" || $libucx eq "" } { if { [file isdirectory $PREFIX/lib/fallback] } { From 01ed7c9387f4a36a3c28d9deeb9e7901300ad234 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 14:45:55 +0200 Subject: [PATCH 22/41] openmpi/3.1.6 build --- Compiler/openmpi/files/variants.rhel6 | 1 + 1 file changed, 1 insertion(+) diff --git a/Compiler/openmpi/files/variants.rhel6 b/Compiler/openmpi/files/variants.rhel6 index 646a5db..0f78053 100644 --- a/Compiler/openmpi/files/variants.rhel6 +++ b/Compiler/openmpi/files/variants.rhel6 @@ -38,6 +38,7 @@ openmpi/3.1.2 stable gcc/{7.3.0,8.2.0} openmpi/3.1.2 stable intel/18.4 openmpi/3.1.3 stable gcc/{4.8.5,5.5.0,6.4.0,6.5.0,7.3.0,8.2.0,8.3.0} openmpi/3.1.4 stable gcc/{7.4.0,8.3.0,9.1.0,9.2.0} +openmpi/3.1.6 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/4.0.0 stable gcc/{5.5,6.4,6.5,7.3,7.4,8.2,8.3}.0 From ec15d8cf55b11a52b9f95e44e512f415eec9d936 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 15:00:39 +0200 Subject: [PATCH 23/41] H5hut cleanup build-scripts and variants --- HDF5/H5hut/1.99/variants | 25 ----------------- HDF5/H5hut/build | 27 ++++++++----------- HDF5/H5hut/{2 => files}/variants.Edison | 0 HDF5/H5hut/{2 => files}/variants.macos1014 | 0 .../{2/variants => files/variants.rhel6} | 2 ++ 5 files changed, 13 insertions(+), 41 deletions(-) delete mode 100644 HDF5/H5hut/1.99/variants rename HDF5/H5hut/{2 => files}/variants.Edison (100%) rename HDF5/H5hut/{2 => files}/variants.macos1014 (100%) rename HDF5/H5hut/{2/variants => files/variants.rhel6} (95%) diff --git a/HDF5/H5hut/1.99/variants b/HDF5/H5hut/1.99/variants deleted file mode 100644 index 89a54ed..0000000 --- a/HDF5/H5hut/1.99/variants +++ /dev/null @@ -1,25 +0,0 @@ -H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.6.5 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.6.5 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.8.2 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.8.2 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.8.4 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.8.4 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.6.5 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.6.5 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.8.2 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.8.2 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.8.4 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.8.4 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.6.5 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.6.5 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.8.2 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.8.2 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.8.4 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.8.4 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.8.5 openmpi/1.8.8 hdf5/1.8.12 b:libtool b:autoconf b:automake -H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.6.5 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.6.5 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.8.2 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.8.2 hdf5/1.8.14 -H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.8.4 hdf5/1.8.12 -H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.8.4 hdf5/1.8.14 diff --git a/HDF5/H5hut/build b/HDF5/H5hut/build index d167828..75790b4 100755 --- a/HDF5/H5hut/build +++ b/HDF5/H5hut/build @@ -1,6 +1,6 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "http://amas.web.psi.ch/Downloads/$P/$P-$V.tar.gz" +pbuild::set_download_url "http://amas.web.psi.ch/Downloads/$P/$P-${V_PKG}.tar.gz" pbuild::add_to_group 'HDF5' pbuild::install_docfiles 'AUTHORS' 'COPYING' @@ -8,32 +8,27 @@ if [[ ${V_MAJOR} == 1 ]]; then pbuild::compile_in_sourcetree fi -pbuild::pre_configure() { - : ./autogen.sh +pbuild::post_prep() { + ./autogen.sh } -pbuild::configure() { +pbuild::pre_configure() { + pbuild::add_configure_args "--enable-parallel" + pbuild::add_configure_args "--enable-debug" + pbuild::add_configure_args "--enable-shared" + pbuild::add_configure_args "--with-hdf5=$HDF5_PREFIX" + pbuild::add_configure_args "--with-pic" if (( V_MAJOR >= 2 )); then - : config_args+=" --enable-python" + : pbuild::add_configure_args "--enable-python" fi case "${COMPILER}" in "clang-macos" ) : ;; * ) - config_args+='--enable-fortran' + pbuild::add_configure_args '--enable-fortran' ;; esac - - "${SRC_DIR}"/configure \ - --prefix="${PREFIX}" \ - --enable-parallel \ - --enable-debug \ - --enable-shared \ - --with-hdf5=$HDF5_PREFIX \ - --with-pic \ - ${config_args} \ - || exit 1 } pbuild::compile() { diff --git a/HDF5/H5hut/2/variants.Edison b/HDF5/H5hut/files/variants.Edison similarity index 100% rename from HDF5/H5hut/2/variants.Edison rename to HDF5/H5hut/files/variants.Edison diff --git a/HDF5/H5hut/2/variants.macos1014 b/HDF5/H5hut/files/variants.macos1014 similarity index 100% rename from HDF5/H5hut/2/variants.macos1014 rename to HDF5/H5hut/files/variants.macos1014 diff --git a/HDF5/H5hut/2/variants b/HDF5/H5hut/files/variants.rhel6 similarity index 95% rename from HDF5/H5hut/2/variants rename to HDF5/H5hut/files/variants.rhel6 index ea3b5f2..bdad738 100644 --- a/HDF5/H5hut/2/variants +++ b/HDF5/H5hut/files/variants.rhel6 @@ -1,3 +1,5 @@ +H5hut/1.99.13 deprecated gcc/{4.7.4,4.8.3,4.8.4,4.9.2} openmpi/{1.6.5,1.8.2,1.8.4} hdf5/{1.8.12,1.8.14} + H5hut/2.0.0rc2 deprecated gcc/4.8.5 openmpi/1.10.2 hdf5/1.8.17 b:automake/1.14 b:autoconf/2.69 b:libtool/2.4.2 b:Python/2.7.12 b:parmetis/4.0.3 H5hut/2.0.0rc3 deprecated gcc/5.4.0 openmpi/1.10.4 hdf5/1.8.17 b:automake/1.14 b:autoconf/2.69 b:libtool/2.4.2 b:Python/2.7.12 b:parmetis/4.0.3 From 1bb62ff14a26ea2c50ee4def890e5783f76eeea8 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 15:08:50 +0200 Subject: [PATCH 24/41] =?UTF-8?q?H5hut/2.0.0rc6=20build=20with=20current?= =?UTF-8?q?=20de=C3pendencies?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- HDF5/H5hut/files/variants.merlin6 | 2 ++ HDF5/H5hut/files/variants.rhel6 | 1 + 2 files changed, 3 insertions(+) create mode 100644 HDF5/H5hut/files/variants.merlin6 diff --git a/HDF5/H5hut/files/variants.merlin6 b/HDF5/H5hut/files/variants.merlin6 new file mode 100644 index 0000000..7fdfd46 --- /dev/null +++ b/HDF5/H5hut/files/variants.merlin6 @@ -0,0 +1,2 @@ +H5hut/2.0.0rc6_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm hdf5/1.10.6_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 + diff --git a/HDF5/H5hut/files/variants.rhel6 b/HDF5/H5hut/files/variants.rhel6 index bdad738..3838b03 100644 --- a/HDF5/H5hut/files/variants.rhel6 +++ b/HDF5/H5hut/files/variants.rhel6 @@ -21,4 +21,5 @@ H5hut/2.0.0rc5 stable gcc/7.3.0 openmpi/3.1.3 hdf5/1.10.4 b:automake/1.16.1 b: H5hut/2.0.0rc6 stable gcc/7.3.0 openmpi/3.1.3 hdf5/1.10.4 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/7.4.0 openmpi/3.1.4 hdf5/1.10.5 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 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 hdf5/1.10.6 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 From 909a9d48d7d5d039311e3824ea0165a9a0dffbb3 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 15:14:18 +0200 Subject: [PATCH 25/41] trilinos/12.18.1: module build, cleanup variants --- HDF5/trilinos/12/variants | 20 ------------------- HDF5/trilinos/build | 2 +- HDF5/trilinos/{12 => files}/variants.Darwin | 0 HDF5/trilinos/files/variants.merlin6 | 1 + HDF5/trilinos/files/variants.rhel6 | 22 +++++++++++++++++++++ 5 files changed, 24 insertions(+), 21 deletions(-) delete mode 100644 HDF5/trilinos/12/variants rename HDF5/trilinos/{12 => files}/variants.Darwin (100%) create mode 100644 HDF5/trilinos/files/variants.merlin6 create mode 100644 HDF5/trilinos/files/variants.rhel6 diff --git a/HDF5/trilinos/12/variants b/HDF5/trilinos/12/variants deleted file mode 100644 index 83b689f..0000000 --- a/HDF5/trilinos/12/variants +++ /dev/null @@ -1,20 +0,0 @@ -trilinos/12.2.1 unstable gcc/4.8.2 openmpi/1.6.5 hdf5/1.8.12 b:cmake/3.6.3 b:OpenBLAS/0.2.9 b:parmetis/4.0.3 - -trilinos/12.8.1 stable gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3 -trilinos/12.10.1 stable gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3 - -trilinos/12.10.1-1 stable gcc/{5.4.0,6.2.0} openmpi/1.10.4 hdf5/1.8.18 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3 -trilinos/12.10.1-2 stable gcc/5.4.0 openmpi/1.10.4 hdf5/1.8.18 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3 - - -trilinos/12.12.1 stable gcc/7.3.0 openmpi/1.10.7 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 -trilinos/12.12.1 stable gcc/7.3.0 openmpi/2.1.2 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 -trilinos/12.12.1 stable gcc/7.3.0 openmpi/3.0.0 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 -trilinos/12.12.1 stable gcc/7.3.0 openmpi/3.1.2 hdf5/1.10.3 b:cmake/3.9.6 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 -trilinos/12.12.1 stable gcc/7.3.0 openmpi/3.1.3 hdf5/1.10.4 b:cmake/3.9.6 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 -trilinos/12.12.1 stable gcc/7.4.0 openmpi/3.1.4 hdf5/1.10.5 b:cmake/3.10.3 b:OpenBLAS/0.3.7 b:parmetis/4.0.3 -trilinos/12.12.1 stable gcc/7.3.0 mpich/3.3 hdf5/1.10.4 b:cmake/3.9.6 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 - -trilinos/12.12.1 stable intel/17.4 openmpi/1.10.7 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 -trilinos/12.12.1 stable intel/17.4 openmpi/2.1.2 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 -trilinos/12.12.1 stable intel/17.4 openmpi/3.0.0 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 diff --git a/HDF5/trilinos/build b/HDF5/trilinos/build index 3047df6..162f654 100755 --- a/HDF5/trilinos/build +++ b/HDF5/trilinos/build @@ -2,7 +2,7 @@ pbuild::set_download_url \ "https://github.com/$P/$P/tarball/$P-release-${V//./-}" \ - "$P-$V.tar.gz" + "$P-${V_PKG}.tar.gz" pbuild::set_sha256sum \ "trilinos-12.12.1.tar.gz:c8f2029fa36230b9f384c56139aaa33111227bcf653e73f7daf3c9efdecc1d2d" diff --git a/HDF5/trilinos/12/variants.Darwin b/HDF5/trilinos/files/variants.Darwin similarity index 100% rename from HDF5/trilinos/12/variants.Darwin rename to HDF5/trilinos/files/variants.Darwin diff --git a/HDF5/trilinos/files/variants.merlin6 b/HDF5/trilinos/files/variants.merlin6 new file mode 100644 index 0000000..aa8ebf1 --- /dev/null +++ b/HDF5/trilinos/files/variants.merlin6 @@ -0,0 +1 @@ +trilinos/12.18.1_slurm unstable 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 diff --git a/HDF5/trilinos/files/variants.rhel6 b/HDF5/trilinos/files/variants.rhel6 new file mode 100644 index 0000000..00b8695 --- /dev/null +++ b/HDF5/trilinos/files/variants.rhel6 @@ -0,0 +1,22 @@ +#trilinos/11.10.2 deprecated b:cmake/2.8.12.2 gcc/{4.7.4,4.8.3,4.8.4,9.2.0} openmpi/{1.6.5,1.8.2,1.8.4} OpenBLAS/0.2.9 parmetis/3.2.0 +#trilinos/11.12.1 deprecated b:cmake/2.8.12.2 gcc/{4.7.4,4.8.3,4.8.4,9.2.0} openmpi/{1.6.5,1.8.2,1.8.4} OpenBLAS/0.2.9 parmetis/3.2.0 +#trilinos/11.14.1 deprecated b:cmake/3.1.3 gcc/{4.7.4,4.8.3,4.8.4,9.2.0} openmpi/{1.6.5,1.8.2,1.8.4} OpenBLAS/0.2.9 parmetis/3.2.0 +#trilinos/11.14.3 deprecated b:cmake/3.4.1 gcc/4.8.5 openmpi/1.10.2 b:OpenBLAS/0.2.9 b:parmetis/3.2.0 +#trilinos/11.14.3 deprecated b:cmake/3.4.1 gcc/6.2.0 openmpi/{1.10.2,1.10.4,2.0.1} b:OpenBLAS/0.2.9 b:parmetis/3.2.0 + +trilinos/12.2.1 deprecated gcc/4.8.2 openmpi/1.6.5 hdf5/1.8.12 b:cmake/3.6.3 b:OpenBLAS/0.2.9 b:parmetis/4.0.3 + +trilinos/12.8.1 stable gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3 +trilinos/12.10.1 stable gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3 + +trilinos/12.10.1-1 stable gcc/{5.4.0,6.2.0} openmpi/1.10.4 hdf5/1.8.18 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3 +trilinos/12.10.1-2 stable gcc/5.4.0 openmpi/1.10.4 hdf5/1.8.18 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3 + +trilinos/12.12.1 stable gcc/7.3.0 openmpi/{1.10.7,2.1.2,3.0.0,3.1.2,3.1.3} hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 + +trilinos/12.12.1 stable gcc/7.4.0 openmpi/3.1.4 hdf5/1.10.5 b:cmake/3.10.3 b:OpenBLAS/0.3.7 b:parmetis/4.0.3 +trilinos/12.12.1 stable gcc/7.3.0 mpich/3.3 hdf5/1.10.4 b:cmake/3.9.6 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 + +trilinos/12.12.1 stable intel/17.4 openmpi/{1.10.7,2.1.2,3.0.0} hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3 + +trilinos/12.18.1 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 hdf5/1.10.6 b:cmake/3.15.5 b:OpenBLAS/0.3.10 b:parmetis/4.0.3 From f89bd777c9e3aef5b53d7b8f64bb7ec310f04e6c Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 15:29:33 +0200 Subject: [PATCH 26/41] lapack/3.9.0: new build-block added --- Compiler/lapack/build | 17 +++++++++++++ Compiler/lapack/files/variants.rhel6 | 1 + Compiler/lapack/modulefile | 21 ++++++++++++++++ MPI/parmetis/3/variants | 24 ------------------- MPI/parmetis/{4 => files}/variants.Edison | 0 .../{4/variants => files/variants.rhel6} | 0 6 files changed, 39 insertions(+), 24 deletions(-) create mode 100755 Compiler/lapack/build create mode 100644 Compiler/lapack/files/variants.rhel6 create mode 100644 Compiler/lapack/modulefile delete mode 100644 MPI/parmetis/3/variants rename MPI/parmetis/{4 => files}/variants.Edison (100%) rename MPI/parmetis/{4/variants => files/variants.rhel6} (100%) diff --git a/Compiler/lapack/build b/Compiler/lapack/build new file mode 100755 index 0000000..0665726 --- /dev/null +++ b/Compiler/lapack/build @@ -0,0 +1,17 @@ +#!/usr/bin/env modbuild + +pbuild::set_download_url "https://github.com/Reference-LAPACK/$P/archive/v${V_PKG}.tar.gz" + +pbuild::add_configure_args '-DCBLAS=ON' +pbuild::add_configure_args '-DLAPACKE=ON' + +pbuild::add_to_group 'Compiler' +pbuild::install_docfiles \ + 'README.md' \ + 'LICENSE' + +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/Compiler/lapack/files/variants.rhel6 b/Compiler/lapack/files/variants.rhel6 new file mode 100644 index 0000000..71d6728 --- /dev/null +++ b/Compiler/lapack/files/variants.rhel6 @@ -0,0 +1 @@ +lapack/3.9.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} b:cmake/3.15.5 diff --git a/Compiler/lapack/modulefile b/Compiler/lapack/modulefile new file mode 100644 index 0000000..771cee5 --- /dev/null +++ b/Compiler/lapack/modulefile @@ -0,0 +1,21 @@ +#%Module1.0 + +module-whatis "Linear Algebra PACKage" +module-url "http://www.netlib.org/lapack/" +module-license "See $PREFIX/share/doc/openmpi/LICENSE" +module-maintainer "Achim Gsell " +module-help " +LAPACK is written in Fortran 90 and provides routines for solving +systems of simultaneous linear equations, least-squares solutions +of linear systems of equations, eigenvalue problems, and singular +value problems. The associated matrix factorizations (LU, Cholesky,i +QR, SVD, Schur, generalized Schur) are also provided, as are related +computations such as reordering of the Schur factorizations and +estimating condition numbers. Dense and banded matrices are handled, +but not general sparse matrices. In all areas, similar functionality +is provided for real and complex matrices, in both single and double +precision. + +This modules also includes the C-bindings in the library liblapack.a +and the BLAS library libcblas.a. +" diff --git a/MPI/parmetis/3/variants b/MPI/parmetis/3/variants deleted file mode 100644 index 20cccdc..0000000 --- a/MPI/parmetis/3/variants +++ /dev/null @@ -1,24 +0,0 @@ -parmetis/3.2.0 stable gcc/4.7.4 openmpi/1.6.5 -parmetis/3.2.0 stable gcc/4.7.4 openmpi/1.8.2 -parmetis/3.2.0 stable gcc/4.7.4 openmpi/1.8.4 -parmetis/3.2.0 stable gcc/4.7.4 openmpi/1.8.8 -parmetis/3.2.0 stable gcc/4.8.3 openmpi/1.6.5 -parmetis/3.2.0 stable gcc/4.8.3 openmpi/1.8.2 -parmetis/3.2.0 stable gcc/4.8.3 openmpi/1.8.4 -parmetis/3.2.0 stable gcc/4.8.4 openmpi/1.6.5 -parmetis/3.2.0 stable gcc/4.8.4 openmpi/1.8.2 -parmetis/3.2.0 stable gcc/4.8.4 openmpi/1.8.4 -parmetis/3.2.0 stable gcc/4.8.5 openmpi/1.8.8 -parmetis/3.2.0 stable gcc/4.8.5 openmpi/1.10.2 -parmetis/3.2.0 stable gcc/4.9.2 openmpi/1.6.5 -parmetis/3.2.0 stable gcc/4.9.2 openmpi/1.8.2 -parmetis/3.2.0 stable gcc/4.9.2 openmpi/1.8.4 -parmetis/3.2.0 stable gcc/4.9.3 openmpi/1.8.8 -parmetis/3.2.0 unstable gcc/5.3.0 openmpi/1.8.8 -parmetis/3.2.0 unstable gcc/5.3.0 openmpi/1.10.2 -parmetis/3.2.0 unstable gcc/6.1.0 openmpi/1.8.8 -parmetis/3.2.0 unstable gcc/6.1.0 openmpi/1.10.2 -parmetis/3.2.0 unstable gcc/6.2.0 openmpi/1.10.2 -parmetis/3.2.0 unstable gcc/6.2.0 openmpi/1.10.4 -parmetis/3.2.0 unstable gcc/6.2.0 openmpi/2.0.1 -parmetis/3.2.0 unstable gcc/7.3.0 openmpi/3.0.1 diff --git a/MPI/parmetis/4/variants.Edison b/MPI/parmetis/files/variants.Edison similarity index 100% rename from MPI/parmetis/4/variants.Edison rename to MPI/parmetis/files/variants.Edison diff --git a/MPI/parmetis/4/variants b/MPI/parmetis/files/variants.rhel6 similarity index 100% rename from MPI/parmetis/4/variants rename to MPI/parmetis/files/variants.rhel6 From d1af65426b0cd75e9aa933d6144e91d3a85176e9 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 15:42:26 +0200 Subject: [PATCH 27/41] amrex/18.07_3d: build with current GCCs and openmpi for rhel6 and merlin6 --- MPI/amrex/files/variants | 29 ----------------------------- MPI/amrex/files/variants.merlin6 | 2 ++ MPI/amrex/files/variants.rhel6 | 15 +++++++++++++++ 3 files changed, 17 insertions(+), 29 deletions(-) delete mode 100644 MPI/amrex/files/variants create mode 100644 MPI/amrex/files/variants.merlin6 create mode 100644 MPI/amrex/files/variants.rhel6 diff --git a/MPI/amrex/files/variants b/MPI/amrex/files/variants deleted file mode 100644 index 6975014..0000000 --- a/MPI/amrex/files/variants +++ /dev/null @@ -1,29 +0,0 @@ -amrex/18.07_2d stable gcc/7.3.0 openmpi/1.10.7 b:cmake/3.9.6 -amrex/18.07_2d stable gcc/7.3.0 openmpi/2.1.5 b:cmake/3.9.6 -amrex/18.07_2d stable gcc/7.3.0 openmpi/3.0.0 b:cmake/3.9.6 -amrex/18.07_2d stable gcc/7.3.0 openmpi/3.1.2 b:cmake/3.9.6 -amrex/18.07_2d stable gcc/7.3.0 openmpi/3.1.3 b:cmake/3.9.6 -amrex/18.07_2d stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.10.3 - -amrex/18.07_2d stable gcc/8.2.0 openmpi/1.10.7 b:cmake/3.9.6 -amrex/18.07_2d stable gcc/8.2.0 openmpi/2.1.5 b:cmake/3.9.6 -amrex/18.07_2d stable gcc/8.2.0 openmpi/3.1.3 b:cmake/3.9.6 - -amrex/18.07_2d stable gcc/7.3.0 mpich/3.2.1 b:cmake/3.9.6 -amrex/18.07_2d stable gcc/8.2.0 mpich/3.2.1 b:cmake/3.9.6 - - -amrex/18.07_3d stable gcc/7.3.0 openmpi/1.10.7 b:cmake/3.9.6 -amrex/18.07_3d stable gcc/7.3.0 openmpi/2.1.5 b:cmake/3.9.6 -amrex/18.07_3d stable gcc/7.3.0 openmpi/3.0.0 b:cmake/3.9.6 -amrex/18.07_3d stable gcc/7.3.0 openmpi/3.1.2 b:cmake/3.9.6 -amrex/18.07_3d stable gcc/7.3.0 openmpi/3.1.3 b:cmake/3.9.6 -amrex/18.07_3d stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.10.3 - -amrex/18.07_3d stable gcc/8.2.0 openmpi/1.10.7 b:cmake/3.9.6 -amrex/18.07_3d stable gcc/8.2.0 openmpi/2.1.5 b:cmake/3.9.6 -amrex/18.07_3d stable gcc/8.2.0 openmpi/3.1.3 b:cmake/3.9.6 - -amrex/18.07_3d stable gcc/7.3.0 mpich/3.2.1 b:cmake/3.9.6 -amrex/18.07_3d stable gcc/8.2.0 mpich/3.2.1 b:cmake/3.9.6 - diff --git a/MPI/amrex/files/variants.merlin6 b/MPI/amrex/files/variants.merlin6 new file mode 100644 index 0000000..ddd3bae --- /dev/null +++ b/MPI/amrex/files/variants.merlin6 @@ -0,0 +1,2 @@ +amrex/18.07_3d_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:cmake/3.15.5 + diff --git a/MPI/amrex/files/variants.rhel6 b/MPI/amrex/files/variants.rhel6 new file mode 100644 index 0000000..e72a265 --- /dev/null +++ b/MPI/amrex/files/variants.rhel6 @@ -0,0 +1,15 @@ +amrex/18.07_2d stable gcc/7.3.0 openmpi/{1.10.7,2.1.5,3.0.0,3.1.2,3.1.3} b:cmake/3.9.6 + +amrex/18.07_2d stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.10.3 + +amrex/18.07_2d stable gcc/8.2.0 openmpi/{1.10.7,2.1.5,3.1.3} b:cmake/3.9.6 + +amrex/18.07_2d stable gcc/{7.3.0,8.2.0} mpich/3.2.1 b:cmake/3.9.6 + +amrex/18.07_3d stable gcc/7.3.0 openmpi/{1.10.7,2.1.5,3.0.0,3.1.2,3.1.3} b:cmake/3.9.6 +amrex/18.07_3d stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.10.3 +amrex/18.07_3d stable gcc/8.2.0 openmpi/{1.10.7,2.1.5,3.1.3} b:cmake/3.9.6 +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 unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6 b:cmake/3.15.5 + From f87d02aef66fe225e595b1ded733c9d85261f67f Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 15:49:34 +0200 Subject: [PATCH 28/41] boost/1.~7[03].0: build with current GCCs and openmpi --- MPI/boost/files/variants.merlin6 | 3 +++ MPI/boost/files/variants.rhel6 | 3 +++ 2 files changed, 6 insertions(+) create mode 100644 MPI/boost/files/variants.merlin6 diff --git a/MPI/boost/files/variants.merlin6 b/MPI/boost/files/variants.merlin6 new file mode 100644 index 0000000..15aaa7c --- /dev/null +++ b/MPI/boost/files/variants.merlin6 @@ -0,0 +1,3 @@ +boost/1.70.0_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:zlib/1.2.11 +boost/1.73.0_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:zlib/1.2.11 + diff --git a/MPI/boost/files/variants.rhel6 b/MPI/boost/files/variants.rhel6 index afea691..a71432e 100644 --- a/MPI/boost/files/variants.rhel6 +++ b/MPI/boost/files/variants.rhel6 @@ -16,3 +16,6 @@ boost/1.68.0-1 stable gcc/7.3.0 mpich/3.3 b:zlib/1.2.11 boost/1.70.0 stable gcc/7.3.0 openmpi/3.1.3 b:zlib/1.2.11 boost/1.70.0 stable gcc/7.4.0 openmpi/3.1.4 b:zlib/1.2.11 + +boost/1.70.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:zlib/1.2.11 +boost/1.73.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:zlib/1.2.11 From 7e8ed1b74070fe029c714cb25a56b46ea8f93e8a Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 16:13:18 +0200 Subject: [PATCH 29/41] elegant/2020.2.0: module build --- MPI/elegant/build | 22 ++++++++++++++++++++++ MPI/elegant/files/variants.merlin6 | 1 + MPI/elegant/files/variants.rhel6 | 4 ++++ MPI/elegant/modulefile | 14 +++++++++++--- 4 files changed, 38 insertions(+), 3 deletions(-) create mode 100755 MPI/elegant/build create mode 100644 MPI/elegant/files/variants.merlin6 create mode 100644 MPI/elegant/files/variants.rhel6 diff --git a/MPI/elegant/build b/MPI/elegant/build new file mode 100755 index 0000000..6cb8745 --- /dev/null +++ b/MPI/elegant/build @@ -0,0 +1,22 @@ +#!/usr/bin/env modbuild + +pbuild::add_to_group 'MPI' + +pbuild::prep() { + : +} +pbuild::configure() { + : +} +pbuild::compile() { + : +} +pbuild::install() { + : +} + +# Local Variables: +# mode: sh +# sh-basic-offset: 8 +# tab-width: 8 +# End: diff --git a/MPI/elegant/files/variants.merlin6 b/MPI/elegant/files/variants.merlin6 new file mode 100644 index 0000000..f1ac524 --- /dev/null +++ b/MPI/elegant/files/variants.merlin6 @@ -0,0 +1 @@ +elegant/2020.2.0_merlin6 unstable gcc/8.4.0 openmpi/3.1.6_slurm gsl/2.6 diff --git a/MPI/elegant/files/variants.rhel6 b/MPI/elegant/files/variants.rhel6 new file mode 100644 index 0000000..1f30d1c --- /dev/null +++ b/MPI/elegant/files/variants.rhel6 @@ -0,0 +1,4 @@ +elegant/2020.2.0 unstable gcc/8.4.0 openmpi/3.1.6 gsl/2.6 +elegant/32.0.0 deprecated gcc/5.4.0 openmpi/1.10.4 +elegant/33.1.2 deprecated gcc/5.4.0 openmpi/1.10.4 +elegant/34.2.0 deprecated gcc/7.3.0 mpich/3.2.1 diff --git a/MPI/elegant/modulefile b/MPI/elegant/modulefile index 8d5c272..040d321 100644 --- a/MPI/elegant/modulefile +++ b/MPI/elegant/modulefile @@ -18,6 +18,14 @@ and ramping machines. The code provides simulation of various collective effects, such as wakes and coherent synchrotron radiation. " -setenv RPN_DEFNS $PREFIX/RPN-DEFNS -setenv HOST_ARCH linux-x86_64 -setenv EPICS_HOST_ARCH linux-x86_64 +setenv RPN_DEFNS $PREFIX/RPN_DEFNS +setenv HOST_ARCH linux-x86_64 +setenv EPICS_HOST_ARCH linux-x86_64 + +append-path PATH $PREFIX/epics/extensions/bin/linux-x86_64 +append-path PATH $PREFIX/oag/apps/bin/linux-x86_64 + +append-path LIBRARY_PATH $PREFIX/epics/extensions/lib/linux-x86_64 +append-path C_INCLUDE_PATH $PREFIX/epics/extensions/include +append-path CPLUS_INCLUDE_PATH $PREFIX/epics/extensions/include +append-path PKG_CONFIG_PATH $PREFIX/epics/base/lib From 075f98cd20901a32fbabe5da343fb9dde7e86894 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Thu, 16 Jul 2020 16:13:21 +0200 Subject: [PATCH 30/41] Add relion 3.1.0 --- EM/relion/README.md | 7 ++++--- EM/relion/files/variants | 3 ++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/EM/relion/README.md b/EM/relion/README.md index f63b42b..33c92ee 100644 --- a/EM/relion/README.md +++ b/EM/relion/README.md @@ -3,8 +3,9 @@ ## Installation Relion is installed from git. The ./build script should work for both stable -(tags) and unstable (branches) versions. +(tags) and unstable (branches) versions. It should be run on Merlin6 from an +admin account. -Currently only gcc/7.4.0 is used. Better performance is reported with -intel icc and MKL, but this would require additional openmpi variants. +Currently only gcc/7.4.0 is used. Better performance is reported with intel icc +and MKL, but this would require additional openmpi variants. diff --git a/EM/relion/files/variants b/EM/relion/files/variants index 34ef8b8..08cb86b 100644 --- a/EM/relion/files/variants +++ b/EM/relion/files/variants @@ -1,5 +1,6 @@ relion/2.1.b1 stable gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44 relion/3.0_beta stable gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44 -relion/3.0.8 unstable 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 stable 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-beta unstable 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 unstable 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 From e06914aa36638ae48701c057f11df3c7a5db63b1 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 16:44:19 +0200 Subject: [PATCH 31/41] hdf5/1.10.6 module build for rhel6 and merlin6 --- MPI/hdf5/build | 2 +- MPI/hdf5/files/variants.merlin6 | 2 ++ MPI/hdf5/files/variants.rhel6 | 1 + 3 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 MPI/hdf5/files/variants.merlin6 diff --git a/MPI/hdf5/build b/MPI/hdf5/build index c3d4dd4..b82cc29 100755 --- a/MPI/hdf5/build +++ b/MPI/hdf5/build @@ -1,6 +1,6 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://support.hdfgroup.org/ftp/HDF5/releases/$P-${V_MAJOR}.${V_MINOR}/$P-$V/src/hdf5-$V.tar.bz2" +pbuild::set_download_url "https://support.hdfgroup.org/ftp/HDF5/releases/$P-${V_MAJOR}.${V_MINOR}/$P-$V/src/hdf5-${V_PKG}.tar.bz2" pbuild::add_to_group 'MPI' pbuild::install_docfiles ACKNOWLEDGMENTS diff --git a/MPI/hdf5/files/variants.merlin6 b/MPI/hdf5/files/variants.merlin6 new file mode 100644 index 0000000..f0a10c9 --- /dev/null +++ b/MPI/hdf5/files/variants.merlin6 @@ -0,0 +1,2 @@ +hdf5/1.10.6_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm + diff --git a/MPI/hdf5/files/variants.rhel6 b/MPI/hdf5/files/variants.rhel6 index 3c471fa..8b2a001 100644 --- a/MPI/hdf5/files/variants.rhel6 +++ b/MPI/hdf5/files/variants.rhel6 @@ -37,3 +37,4 @@ hdf5/1.10.4 stable gcc/{5.5.0,6.4.0,7.3.0,8.2.0} openmpi/3.1.3 hdf5/1.10.4 stable gcc/7.3.0 mpich/3.3 hdf5/1.10.5 stable gcc/{7.4.0,8.3.0} openmpi/3.1.4 +hdf5/1.10.6 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 From 899dfdfcb07ce54e6db9615e0cd4f22d5fb6c009 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 16:48:17 +0200 Subject: [PATCH 32/41] parmetis/4.0.3 module build for rhel6 and merlin6 with current GCCs and opemmpi --- MPI/parmetis/files/variants.merlin6 | 2 ++ MPI/parmetis/files/variants.rhel6 | 40 ++++++++++++----------------- 2 files changed, 19 insertions(+), 23 deletions(-) create mode 100644 MPI/parmetis/files/variants.merlin6 diff --git a/MPI/parmetis/files/variants.merlin6 b/MPI/parmetis/files/variants.merlin6 new file mode 100644 index 0000000..a060ecc --- /dev/null +++ b/MPI/parmetis/files/variants.merlin6 @@ -0,0 +1,2 @@ +parmetis/4.0.3_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:cmake/3.15.5 + diff --git a/MPI/parmetis/files/variants.rhel6 b/MPI/parmetis/files/variants.rhel6 index e1893ac..a370896 100644 --- a/MPI/parmetis/files/variants.rhel6 +++ b/MPI/parmetis/files/variants.rhel6 @@ -1,31 +1,25 @@ +parmetis/3.2.0 stable 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 stable gcc/{4.7.4,4.8.5,4.9.3,5.3.0,6.1.0} openmpi/1.8.8 + +parmetis/3.2.0 stable gcc/{4.8.5,5.3.0,6.1.0,6.2.0} openmpi/1.10.2 + +parmetis/3.2.0 stable gcc/6.2.0 openmpi/{1.10.4,2.0.1} + +parmetis/3.2.0 stable gcc/7.3.0 openmpi/3.0.1 + parmetis/4.0.3 stable gcc/4.8.2 openmpi/1.6.5 b:cmake/3.4.1 -parmetis/4.0.3 stable gcc/4.8.5 openmpi/1.10.2 b:cmake/3.4.1 -parmetis/4.0.3 stable gcc/4.9.4 openmpi/1.10.2 b:cmake/3.4.1 -parmetis/4.0.3 stable gcc/5.3.0 openmpi/1.10.2 b:cmake/3.4.1 -parmetis/4.0.3 stable gcc/5.4.0 openmpi/1.10.2 b:cmake/3.4.1 -parmetis/4.0.3 stable gcc/6.1.0 openmpi/1.10.2 b:cmake/3.4.1 -parmetis/4.0.3 stable gcc/6.2.0 openmpi/1.10.2 b:cmake/3.4.1 +parmetis/4.0.3 stable 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 unstable gcc/4.8.5 openmpi/1.10.4 b:cmake/3.6.3 -parmetis/4.0.3 unstable gcc/4.9.4 openmpi/1.10.4 b:cmake/3.6.3 -parmetis/4.0.3 unstable gcc/5.4.0 openmpi/1.10.4 b:cmake/3.6.3 -parmetis/4.0.3 unstable gcc/6.2.0 openmpi/1.10.4 b:cmake/3.6.3 +parmetis/4.0.3 stable 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 unstable gcc/6.2.0 openmpi/2.0.1 b:cmake/3.6.3 +parmetis/4.0.3 stable gcc/6.2.0 openmpi/2.0.1 b:cmake/3.6.3 -parmetis/4.0.3 stable gcc/7.3.0 openmpi/1.10.7 b:cmake/3.6.3 -parmetis/4.0.3 stable gcc/7.3.0 openmpi/2.1.2 b:cmake/3.6.3 -parmetis/4.0.3 stable gcc/7.3.0 openmpi/3.0.0 b:cmake/3.6.3 -parmetis/4.0.3 stable gcc/7.3.0 openmpi/3.0.1 b:cmake/3.9.6 -parmetis/4.0.3 stable gcc/7.3.0 openmpi/3.1.2 b:cmake/3.9.6 -parmetis/4.0.3 stable gcc/7.3.0 openmpi/3.1.3 b:cmake/3.9.6 +parmetis/4.0.3 stable 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 stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.9.6 -parmetis/4.0.3 stable clang-macos/9.0.0 openmpi/1.10.7 b:cmake/3.6.3 -parmetis/4.0.3 stable clang-macos/9.0.0 openmpi/2.1.2 b:cmake/3.6.3 -parmetis/4.0.3 stable clang-macos/9.0.0 openmpi/3.0.0 b:cmake/3.6.3 -parmetis/4.0.3 stable intel/17.4 openmpi/1.10.7 b:cmake/3.6.3 -parmetis/4.0.3 stable intel/17.4 openmpi/2.1.2 b:cmake/3.6.3 -parmetis/4.0.3 stable intel/17.4 openmpi/3.0.0 b:cmake/3.6.3 +parmetis/4.0.3 stable 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 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:cmake/3.9.6 From 40a24127d00ee70148133f9fa8cb594537a92627 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Thu, 16 Jul 2020 17:19:52 +0200 Subject: [PATCH 33/41] openssl/1.1.1g module build --- Tools/openssl/files/variants | 4 ---- Tools/openssl/files/variants.rhel6 | 5 +++++ 2 files changed, 5 insertions(+), 4 deletions(-) delete mode 100644 Tools/openssl/files/variants create mode 100644 Tools/openssl/files/variants.rhel6 diff --git a/Tools/openssl/files/variants b/Tools/openssl/files/variants deleted file mode 100644 index 3891bf4..0000000 --- a/Tools/openssl/files/variants +++ /dev/null @@ -1,4 +0,0 @@ -openssl/1.0.2h deprecated -openssl/1.0.2j stable -openssl/1.0.2o stable -openssl/1.0.2r stable diff --git a/Tools/openssl/files/variants.rhel6 b/Tools/openssl/files/variants.rhel6 new file mode 100644 index 0000000..ceb6c27 --- /dev/null +++ b/Tools/openssl/files/variants.rhel6 @@ -0,0 +1,5 @@ +openssl/1.0.2h deprecated +openssl/1.0.2j deprecated +openssl/1.0.2o deprecated +openssl/1.0.2r stable +openssl/1.1.1g unstable From 45f7cd318910d0a5809fb55293bc01e3230929dc Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Jul 2020 10:03:24 +0200 Subject: [PATCH 34/41] Python: newer version of include pip - no need to run get-pip.py --- Programming/Python/build | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/Programming/Python/build b/Programming/Python/build index eb53bfa..871aeba 100755 --- a/Programming/Python/build +++ b/Programming/Python/build @@ -56,8 +56,11 @@ pbuild::post_install() { ln -fs "${PREFIX}/include/python${V%.*}m" "${PREFIX}/include/python" ln -fs "${PREFIX}/include/python${V%.*}m" "${PREFIX}/include/python${V%.*}" PATH+=":${PREFIX}/bin" - cd "${BUILDBLOCK_DIR}" - "${PREFIX}/bin/python" 'get-pip.py' + + if (( V_MAJOR == 2 || (V_MAJOR == 3 && V_MINOR <= 7) )); then + cd "${BUILDBLOCK_DIR}" + "${PREFIX}/bin/python" 'get-pip.py' + fi std::info "Building numpy\n" pip${V_MAJOR} install numpy From b5e65bc1256170c0effffb68dee0c32aa8aac885 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Jul 2020 11:33:45 +0200 Subject: [PATCH 35/41] Python: fixes in build script - prepend to PATH and LD_LIBRARY_PATH not append - set CFLAFS too (same as CPPFLAFS) --- Programming/Python/build | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Programming/Python/build b/Programming/Python/build index 871aeba..ad0be5b 100755 --- a/Programming/Python/build +++ b/Programming/Python/build @@ -48,14 +48,14 @@ pbuild::post_install_Linux() { } pbuild::post_install() { - export LD_LIBRARY_PATH+=":${PREFIX}/lib" - export LDFLAGS="-L${OPENSSL_LIBRARY_DIR}" + 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 LD_LIBRARY_PATH+=":${PREFIX}/lib" + export LDFLAGS="-L${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%.*}" - PATH+=":${PREFIX}/bin" if (( V_MAJOR == 2 || (V_MAJOR == 3 && V_MINOR <= 7) )); then cd "${BUILDBLOCK_DIR}" From ba6f2334bbf44b3908740d2eb2c46f8ade372ab3 Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Jul 2020 11:40:54 +0200 Subject: [PATCH 36/41] Python/{3.7.8,3.8.4}: modules build --- Programming/Python/files/variants.rhel6 | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/Programming/Python/files/variants.rhel6 b/Programming/Python/files/variants.rhel6 index cf1b0bb..3380dbc 100644 --- a/Programming/Python/files/variants.rhel6 +++ b/Programming/Python/files/variants.rhel6 @@ -2,8 +2,15 @@ Python/2.7.11 stable openssl/1.0.2j Tcl/8.6.4 Tk/8.6.4 Python/2.7.12 stable openssl/1.0.2j Tcl/8.6.4 Tk/8.6.4 Python/2.7.14 stable openssl/1.0.2o Tcl/8.6.4 Tk/8.6.4 Python/2.7.16 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 +Python/2.7.17 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 +# commented, problems to build ssl module +#Python/2.7.18 unstable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 Python/3.4.0 deprecated openssl/1.0.2m Tcl/8.6.4 Tk/8.6.4 Python/3.4.3 stable openssl/1.0.2m Tcl/8.6.4 Tk/8.6.4 Python/3.6.3 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 +# commented, problems to build ssl module +#Python/3.6.11 unstable b:openssl/1.1.1g b:TclTk/8.6.9 b:xz/5.2.4 Python/3.7.3 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 Python/3.7.4 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 +Python/3.7.8 unstable b:openssl/1.1.1g b:TclTk/8.6.9 b:xz/5.2.4 +Python/3.8.4 unstable b:openssl/1.1.1g b:TclTk/8.6.9 b:xz/5.2.4 From 174cda266c6ce76e6647c3ee2da8b8153743705d Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Jul 2020 11:43:54 +0200 Subject: [PATCH 37/41] emacs: fix in build-script - pbuild::make_all must not be called --- Tools/emacs/build | 1 - 1 file changed, 1 deletion(-) diff --git a/Tools/emacs/build b/Tools/emacs/build index 7261baa..cba9fe2 100755 --- a/Tools/emacs/build +++ b/Tools/emacs/build @@ -35,5 +35,4 @@ pbuild::post_install_Darwin() { } pbuild::add_to_group 'Tools' -pbuild::make_all From e749e9f6330c2adfe70e888f5d88f7e5eb1d598e Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Jul 2020 11:47:53 +0200 Subject: [PATCH 38/41] emacs/26.3: build module --- Tools/emacs/files/variants | 1 + 1 file changed, 1 insertion(+) diff --git a/Tools/emacs/files/variants b/Tools/emacs/files/variants index 75f456e..d084e9d 100644 --- a/Tools/emacs/files/variants +++ b/Tools/emacs/files/variants @@ -1,3 +1,4 @@ emacs/25.1 stable b:libungif/4.1.4 b:tiff/4.0.3 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 From 0eb1f32f3cc559379feacfbba9072236a291b4ad Mon Sep 17 00:00:00 2001 From: Achim Gsell Date: Fri, 17 Jul 2020 11:51:11 +0200 Subject: [PATCH 39/41] gnuplot/5.2.8: build module --- Tools/gnuplot/files/variants | 1 + 1 file changed, 1 insertion(+) diff --git a/Tools/gnuplot/files/variants b/Tools/gnuplot/files/variants index 6f27cb7..7a89952 100644 --- a/Tools/gnuplot/files/variants +++ b/Tools/gnuplot/files/variants @@ -4,3 +4,4 @@ gnuplot/5.2.0 stable gnuplot/5.2.4 stable gnuplot/5.2.6 stable gnuplot/5.2.7 stable +gnuplot/5.2.8 stable From b987afe19599a77263251f1d8c04a9067d790be0 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Fri, 7 Aug 2020 13:09:56 +0200 Subject: [PATCH 40/41] Add some python dev tools to hpce-tools --- .../2019.07/conda-env-defs/hpce-tools/hpce-tools.yml | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) 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 19d540e..ebab9ed 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 @@ -6,5 +6,15 @@ channels: dependencies: - python=3.6 - ldapuserdir - - cython # for pyslurm + # python development - conda-build + - cython # for pyslurm + - black + - flake8 + - mypy + - mypy_extensions + - typing_extensions + - tox + - tox-conda + - pytest + - bpython From 0b438a9d2e91a8815d3190ebd145e48e52d244c6 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Fri, 7 Aug 2020 23:07:30 +0200 Subject: [PATCH 41/41] Add scicat_client to the datacatalog module. The script is based off the scicat_client-0.1.0 anaconda environment. Conda does not need to be activated to run, so the pmodule simple symlinks the entrypoint to the module bin. --- .../conda-env-defs/scicat_client/README.md | 20 ++++++++++++++++++ .../scicat_client/scicat_client.yml | 18 ++++++++++++++++ Tools/datacatalog/README.md | 20 ++++++++++++++++++ Tools/datacatalog/README.md_template | 21 ------------------- Tools/datacatalog/build | 3 +++ 5 files changed, 61 insertions(+), 21 deletions(-) create mode 100644 Programming/anaconda/2019.07/conda-env-defs/scicat_client/README.md create mode 100644 Programming/anaconda/2019.07/conda-env-defs/scicat_client/scicat_client.yml create mode 100644 Tools/datacatalog/README.md delete mode 100644 Tools/datacatalog/README.md_template diff --git a/Programming/anaconda/2019.07/conda-env-defs/scicat_client/README.md b/Programming/anaconda/2019.07/conda-env-defs/scicat_client/README.md new file mode 100644 index 0000000..fa4e98a --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/scicat_client/README.md @@ -0,0 +1,20 @@ +# scicat-client + +The scicat-client environment is used in the datacatalog module. Contact +Spencer Bliven, Stephan Egli, or Leo Sala for more info. + +## Installing + +First, create the conda environment + + conda env create -f scicat_client.yml + +Next, install scicat_client. Eventually this should be done automatically +through conda, but for now it needs to be installed from source. + + git clone git@github.com:paulscherrerinstitute/scicat_client.git + cd scicat_client + conda activate scicat_client-0.1.0 + python setup.py install + + diff --git a/Programming/anaconda/2019.07/conda-env-defs/scicat_client/scicat_client.yml b/Programming/anaconda/2019.07/conda-env-defs/scicat_client/scicat_client.yml new file mode 100644 index 0000000..b50b0f5 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/scicat_client/scicat_client.yml @@ -0,0 +1,18 @@ +# Clean environment based on pure conda-forge packages +name: scicat_client-0.1.0 +channels: + - conda-forge + - http://conda-pkg.intranet.psi.ch +dependencies: + - python=3.8 + - requests + # development tools + - conda-build + - black + - flake8 + - mypy + - mypy_extensions + - typing_extensions + - tox + - tox-conda + - pytest diff --git a/Tools/datacatalog/README.md b/Tools/datacatalog/README.md new file mode 100644 index 0000000..7d08119 --- /dev/null +++ b/Tools/datacatalog/README.md @@ -0,0 +1,20 @@ +# Datacatalog + +## Overview + +This module provides tools to interface with the Data Catalog (discovery.psi.ch). + +## Installation + +Run `./build ` to install the latest version. This downloads the +latest versions of the datasetIngestor, datasetRetriever, and datasetArchiver +tools. Note that the downloads are not versioned, so make sure that the current +variant matches the installed binaries. + +The `scicat_client` script is also installed. This is maintained as an anaconda +environment, then symlinked into the datacatalog pmodule. Anaconda hard-codes +the correct python interpreter, so all dependencies should resolve even though +the conda module is not activated. See +Programming/anaconda/2019.07/conda-env-defs/scicat_client for environment +installation details. + diff --git a/Tools/datacatalog/README.md_template b/Tools/datacatalog/README.md_template deleted file mode 100644 index 77355fb..0000000 --- a/Tools/datacatalog/README.md_template +++ /dev/null @@ -1,21 +0,0 @@ -# The Mellanox MXM communication library - -## Overview - -The Mellanox MXM communication library provides support for the Mellanox MXM interface for InfiniBand. - -## Installation - -For the module we use a RPM distributed by HP. - -1. Create new directory `/opt/psi/System/mxm/VERSION_merlin` -1. Download RPM from https://downloads.linux.hpe.com/sdr/repo/mlnx_ofed/RedHatEnterpriseServer/ -1. Unpack RPM with `rpm2cpio RPM | cpio -i --make-dirs` somewhere -1. copy all files from `opt/mellanox/mxm` to the module directory -1. adapt directories in `lib/pkg-config/mxm.pc` -1. add new variant to `files/variants` -1. run the build-script to install the modulefile and to set the release - - -> **Note:** The shared library `libmxm.so`provided by the RPMs for RHEL 6 cannot be used to compile other software. -They requiry GLIBC >= 2.14, but on RHEL 6 only 2.12 is installed! \ No newline at end of file diff --git a/Tools/datacatalog/build b/Tools/datacatalog/build index 0492450..77e2ff3 100755 --- a/Tools/datacatalog/build +++ b/Tools/datacatalog/build @@ -25,5 +25,8 @@ pbuild::install() { /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" }