Merge branch 'master' into 267-toolchain-for-ippl-opal-with-gcc-12-3-0

2023-11-14 16:22:50 +01:00
parent 8ed7191881 0360c5bed3
commit 2f71af1609
20 changed files with 164 additions and 26 deletions
--- a/EM/IMOD/build
+++ b/EM/IMOD/build
@@ -1,4 +1,5 @@
 #!/usr/bin/env modbuild
+set -e

 pbuild::add_to_group 'EM'

@@ -7,6 +8,11 @@ pbuild::prep() {
    : ${CUDA_VERSION:?No CUDA_VERSION set}
    local cuda="${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
    local dst="$PMODULES_DISTFILESDIR/${filename}"
    if [ -f "$dst" ]; then
        echo "Found cached $dst" >&2
@@ -15,7 +21,7 @@ pbuild::prep() {
            --location \
            --fail \
            --output "$dst" \
-            "https://bio3d.colorado.edu/imod/AMD64-RHEL5/$filename"
+            "$url"
    fi
    }

--- a/EM/IMOD/files/variants
+++ b/EM/IMOD/files/variants
@@ -1,2 +1,4 @@
 IMOD/4.9.5	stable	
-IMOD/4.11.20	unstable	cuda/10.1.105
+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
--- a/EM/PEET/files/variants
+++ b/EM/PEET/files/variants
@@ -1,2 +1,2 @@
 PEET/1.15.1a	stable	gcc/9.5.0 matlab/2020b
-PEET/1.16.0	unstable	gcc/9.5.0 matlab/2021b
+PEET/1.16.0	stable	gcc/9.5.0 matlab/2021b
--- a/EM/dynamo/1.1.538/config
+++ 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
+
--- 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 `$V/config`.
 3. Run `build <version>`
 4. module load dynamo/$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 $DYNAMO_ROOT/cuda
    make clean
--- a/EM/dynamo/build
+++ b/EM/dynamo/build
@@ -51,6 +51,8 @@ pbuild::prep() {
    download_dynamo "$DYNAMO_ID" "$TAR_FILE"
    mkdir -p "$PREFIX"
    unpack "$TAR_FILE" "$PREFIX/bin"
+
+    cp -n "$BUILDBLOCK_DIR/dynamo_activate_MCR.sh" "$PREFIX/bin/"
 }

 pbuild::configure() {
--- a/EM/dynamo/dynamo_activate_MCR.sh
+++ 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
--- 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
--- 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
--- a/Programming/Julia/build
+++ b/Programming/Julia/build
@@ -0,0 +1,17 @@
+#!/usr/bin/env modbuild
+
+pbuild::set_download_url "https://julialang-s3.julialang.org/bin/linux/x64/${V_MAJOR}.${V_MINOR}/julia-${V_PKG}-linux-x86_64.tar.gz"
+
+pbuild::add_to_group 'Programming'
+pbuild::install_docfiles 'LICENSE.md' 
+
+pbuild::compile_in_sourcetree
+
+pbuild::compile() {
+  :
+}
+
+pbuild::install() {
+  rsync -av . "${PREFIX}"
+}
+
--- a/Programming/Julia/files/variants.rhel7
+++ b/Programming/Julia/files/variants.rhel7
@@ -0,0 +1 @@
+Julia/1.9.2    stable
--- a/Programming/Julia/modulefile
+++ b/Programming/Julia/modulefile
@@ -0,0 +1,12 @@
+#%Module1.0
+
+module-whatis		"Julia"
+module-url		"https://julialang.org/"
+module-license		"https://github.com/JuliaLang/julia/blob/master/LICENSE.md"
+module-maintainer       "Marc Caubet Serrabou <marc.caubet@psi.ch>"
+module-help	"
+Julia is a high-level, high-performance dynamic language for technical
+computing. 
+"
+
+module-addgroup	Programming
--- 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]
--- a/Programming/clang/build
+++ b/Programming/clang/build
@@ -1,24 +1,29 @@
 #!/usr/bin/env modbuild

-pbuild::set_download_url \
-	"https://github.com/llvm/llvm-project/releases/download/llvmorg-${V_PKG}/llvm-project-${V_PKG}.src.tar.xz"
-
 pbuild::add_to_group 'Programming'
+
+pbuild::set_download_url \
+    "https://github.com/llvm/llvm-project/releases/download/llvmorg-${V_PKG}/llvm-project-${V_PKG}.src.tar.xz"
+
 #pbuild::install_docfiles 'AUTHORS' 'LICENSE' 'NEWS' 'README'

-
 pbuild::configure() {
-	cmake \
-		-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-		-DCMAKE_BUILD_TYPE=Release \
-		-DLLVM_ENABLE_PROJECTS="clang;clang-tools-extra;libunwind;lldb;lld;openmp" \
-		-DGCC_INSTALL_PREFIX="${GCC_DIR}" \
-		-G "Unix Makefiles" \
-		"${SRC_DIR}/llvm" \
-		|| exit 1
+    # To expose the correct GCC libstd++ to build system, we need to both set
+    # the correct CC/CXX *and* force the build linker to use the pmodule GCC
+    # library.
+    GCC_CXXLIBDIR="${GCC_DIR}/lib64"
+    CC="${GCC_DIR}/bin/gcc"
+    CXX="${GCC_DIR}/bin/g++"
+    cmake \
+        -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_CXX_LINK_FLAGS="-Wl,-R,${GCC_CXXLIBDIR} -L${GCC_CXXLIBDIR}" \
+        -DLLVM_ENABLE_PROJECTS="clang;clang-tools-extra;lldb;lld;openmp" \
+        -DLLVM_ENABLE_RUNTIMES="libunwind" \
+        "${CONFIGURE_ARGS[@]}" \
+        -G "Unix Makefiles" \
+        "${SRC_DIR}/llvm" \
+    || exit 1
 }

-pbuild::post_install() {
-	# :FIXME: copy libstdc++ and libgcc from used gcc to $PREFIX/lib64
-	:
-}
+# vim: ts=4 sw=4 et 
--- a/Programming/clang/files/variants.rhel7
+++ b/Programming/clang/files/variants.rhel7
@@ -1 +1,2 @@
 clang/12.0.0_rhel7	stable	b:cmake/3.15.5 b:gcc/9.3.0 b:Python/3.8.4 b:xz/5.2.4 b:binutils/2.29
+clang/15.0.6_rhel7	unstable	b:cmake/3.23.2 b:gcc/12.1.0 b:Python/3.9.10 b:xz/5.2.4 b:binutils/2.37
--- 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
--- 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
@@ -50,5 +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
--- a/Tools/redis/build
+++ b/Tools/redis/build
@@ -0,0 +1,31 @@
+#!/usr/bin/env modbuild
+
+pbuild::add_to_group 'Tools'
+
+pbuild::set_download_url \
+	"https://github.com/redis/redis/archive/${V_PKG}.tar.gz"
+
+pbuild::compile_in_sourcetree
+pbuild::install_docfiles \
+	00-RELEASENOTES \
+	BUGS \
+	CODE_OF_CONDUCT.md \
+	CONTRIBUTING.md \
+	COPYING \
+	INSTALL \
+	MANIFESTO \
+	README.md \
+	SECURITY.md \
+	TLS.md
+
+pbuild::configure() { :; }
+
+pbuild::install() {
+	make PREFIX="${PREFIX}" install
+}
+
+# Local Variables:
+# mode: sh
+# sh-basic-offset: 8
+# tab-width: 8
+# End:
--- a/Tools/redis/files/variants
+++ b/Tools/redis/files/variants
@@ -0,0 +1,2 @@
+redis/7.0.12	stable
+
--- a/Tools/redis/modulefile
+++ b/Tools/redis/modulefile
@@ -0,0 +1,16 @@
+#%Pmodule
+
+module-whatis		"open source, in-memory data store"
+module-url		"https://redis.io"
+module-license		"GNUPLOT_DIR/share/doc/redis/COPYING"
+module-maintainer	"Achim Gsell <achim.gsell@psi.ch>"
+
+module-help		"
+Redis is an open source (BSD licensed), in-memory data structure store used
+as a database, cache, message broker, and streaming engine. Redis provides
+data structures such as strings, hashes, lists, sets, sorted sets with range
+queries, bitmaps, hyperloglogs, geospatial indexes, and streams. Redis has
+built-in replication, Lua scripting, LRU eviction, transactions, and different
+levels of on-disk persistence, and provides high availability via Redis
+Sentinel and automatic partitioning with Redis Cluster.
+"