Merge branch 'EESSI:2023.06-software.eessi.io' into siesta

Author: ocaisa

.github/workflows/tests_link_nvidia_host_libraries.yml

@@ -120,6 +120,8 @@ jobs:
         # List dir with libraries
         echo "Showing content of /tmp/nvidia_libs"
         echo "$(ls -l /tmp/nvidia_libs)"
+        echo "Showing content of /tmp/nvidia_libs_duplicate"
+        echo "$(ls -l /tmp/nvidia_libs_duplicate)"
         echo "Showing content of /opt/eessi/nvidia/x86_64/host"
         echo "$(ls -l /opt/eessi/nvidia/x86_64/host)"
 
@@ -152,9 +154,9 @@ jobs:
             exit 1
           fi
           
-          # Verify it points to our mock library in /tmp/nvidia_libs
-          if [[ "$target" != "/tmp/nvidia_libs/$lib"* && "$target" != *"/tmp/nvidia_libs/"* ]]; then
-            echo "Error: Symlink $lib_path points to $target, which is not in our mock directory"
+          # Verify it points to our mock library in /tmp/nvidia_libs or /tmp/nvidia_libs_duplicate
+          if [[ "$target" != "/tmp/nvidia_libs/$lib"* && "$target" != "/tmp/nvidia_libs_duplicate/$lib"* ]]; then
+            echo "Error: Symlink $lib_path points to $target, which is not in our mock directories"
             exit 1
           fi
           
@@ -194,3 +196,4 @@ jobs:
         echo "$output" | grep "have already been linked" || { echo "Missing 'already linked' message"; exit 1; }
         
         echo "Second normal run test passed"
+        

EESSI-install-software.sh

@@ -271,6 +271,7 @@ fi
 
 # Install NVIDIA drivers in host_injections (if they exist)
 if command_exists "nvidia-smi"; then
+    export LD_LIBRARY_PATH="/.singularity.d/libs:${LD_LIBRARY_PATH}"
     nvidia-smi --version
     ec=$?
     if [ ${ec} -eq 0 ]; then 

bot/build.sh

@@ -184,6 +184,15 @@ if [[ "${REPOSITORY_NAME}" == "dev.eessi.io" ]]; then
     COMMON_ARGS+=("--repository" "software.eessi.io,access=ro")
 fi
 
+# add $software_layer_dir and /dev as extra bind paths
+#  - $software_layer_dir is needed because it is used as prefix for running scripts
+#  - /dev is needed to access /dev/fuse
+COMMON_ARGS+=("--extra-bind-paths" "${software_layer_dir},/dev")
+
+# pass through '--contain' to avoid leaking in scripts into the container session
+# note, --pass-through can be used multiple times if needed
+COMMON_ARGS+=("--pass-through" "--contain")
+
 # make sure to use the same parent dir for storing tarballs of tmp
 PREVIOUS_TMP_DIR=${PWD}/previous_tmp
 

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.4-2023a.yml

@@ -54,3 +54,8 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22610
         from-commit: 10e47e2fdd4f23fd5a52ae167771f8e9c78da411
+  - lit-18.1.2-GCCcore-12.3.0.eb
+      # needed due to changed/new dependencies for R-bundle-CRAN-2023.12-foss-2023a.eb
+      # without any from-commit this will use a version from April 6, 2024
+      # https://github.com/easybuilders/easybuild-easyconfigs/blob/88f6f9c7439c535e62461e6e71b1961c7be118b8/easybuild/easyconfigs/l/lit/lit-18.1.2-GCCcore-12.3.0.eb
+      # EB 5.0.0 has a few changes to that

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.4-2023b.yml

@@ -36,4 +36,12 @@ easyconfigs:
   - EveryBeam-0.6.1-foss-2023b.eb:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21765
-        from-commit: c7e4bfe1a57cf9781ce346ba8ae9081644408c23 
+        from-commit: c7e4bfe1a57cf9781ce346ba8ae9081644408c23
+  - lit-18.1.7-GCCcore-13.2.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20902
+        from-commit: 79f4cf21490f7f5b187af889be5426c1332a497d
+  - astropy-7.0.0-gfbf-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22469
+        from-commit: fc22841fef99cbb2a221c18029b15e692e78c27c

easystacks/software.eessi.io/2023.06/grace/accel/nvidia/eessi-2023.06-eb-4.9.4-2023b-CUDA.yml

@@ -0,0 +1,17 @@
+easyconfigs:
+  - CUDA-12.4.0.eb:
+      options:
+        accept-eula-for: CUDA
+        # see https://github.com/easybuilders/easybuild-easyblocks/pull/3516
+        include-easyblocks-from-commit: 3469151ce7e4f85415c877dee555aeea7691c757
+  - UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.4.0.eb
+  - UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21565
+        from-commit: 46141a3f40e699433fac03af2d3ed81bd5a62da7
+  - OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21926
+        # from-commit: de79ec74eb076e1aceda5e21235a73c05ed6764c
+        # use merge commit
+        from-commit: f3bd10b19f7caf4de3302bc7a73749341db9c7d8

easystacks/software.eessi.io/2023.06/grace/eessi-2023.06-eb-4.9.4-001-system.yml

@@ -0,0 +1,20 @@
+easyconfigs:
+  - EasyBuild-4.8.2.eb
+  - EasyBuild-4.9.0.eb
+  - EasyBuild-4.9.1.eb
+  - EasyBuild-4.9.2.eb
+  - EasyBuild-4.9.3.eb
+  - EasyBuild-4.9.4.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21465
+        from-commit: 39cdebd7bd2cb4a9c170ee22439401316b2e7a25
+  - Nextflow-23.10.0.eb
+  - ReFrame-4.3.3.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22183
+        from-commit: 2b2fe53c885799cbf13b77ddfa9532c48b296e9d  
+  - ReFrame-4.6.2.eb
+  - Pandoc-3.6.2.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22493
+        from-commit: da8ed20bad0dd1c6533c568f6c4fbb7c3d15342e

easystacks/software.eessi.io/2023.06/grace/eessi-2023.06-eb-4.9.4-2023a.yml

@@ -0,0 +1,92 @@
+easyconfigs:
+  - GCCcore-12.3.0.eb
+  - OpenBLAS-0.3.23-GCC-12.3.0.eb
+  - Rust-1.70.0-GCCcore-12.3.0.eb
+  - OpenMPI-4.1.5-GCC-12.3.0
+  - foss-2023a.eb
+  - pybind11-2.11.1-GCCcore-12.3.0.eb
+  - SciPy-bundle-2023.07-gfbf-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21693
+        from-commit: 7c5144d2c1a061cd9f08b5901970b7f6ec5eb5c0  
+  - TensorFlow-2.13.0-foss-2023a.eb
+  - X11-20230603-GCCcore-12.3.0.eb
+  - HarfBuzz-5.3.1-GCCcore-12.3.0.eb
+  - Qt5-5.15.10-GCCcore-12.3.0.eb
+  - OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb
+  - LHAPDF-6.5.4-GCC-12.3.0.eb
+  - LoopTools-2.15-GCC-12.3.0.eb
+  - R-4.3.2-gfbf-2023a.eb
+  - Boost-1.82.0-GCC-12.3.0.eb:
+      options:
+        # source URLs for Boost have changed, corresponding PR is
+        # https://github.com/easybuilders/easybuild-easyconfigs/pull/22157
+        from-commit: 5bebccf792ccf35a8ee3250bc8fed86dff5d5df9
+  - netCDF-4.9.2-gompi-2023a.eb
+  - FFmpeg-6.0-GCCcore-12.3.0.eb
+  - ALL-0.9.2-foss-2023a.eb
+  - CDO-2.2.2-gompi-2023a.eb
+  - BWA-0.7.17-20220923-GCCcore-12.3.0.eb
+  - METIS-5.1.0-GCCcore-12.3.0.eb
+  - SCOTCH-7.0.3-gompi-2023a.eb
+  - CGAL-5.6-GCCcore-12.3.0.eb
+  - ParaView-5.11.2-foss-2023a.eb
+  - gnuplot-5.4.8-GCCcore-12.3.0.eb
+  - Boost.MPI-1.82.0-gompi-2023a.eb: 
+      options:
+        # source URLs for Boost.MPI have changed, corresponding PR is
+        # https://github.com/easybuilders/easybuild-easyconfigs/pull/22240
+        # Boost.MPI is a dependency of ESPResSo
+        from-commit: e610fe1ac5393d1de668a466fdaaea74c580ee03
+  - ESPResSo-4.2.1-foss-2023a.eb
+  - Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb
+  - Pillow-10.0.0-GCCcore-12.3.0.eb
+  - sympy-1.12-gfbf-2023a.eb
+  - networkx-3.1-gfbf-2023a.eb
+  - expecttest-0.1.5-GCCcore-12.3.0.eb
+  - PyYAML-6.0-GCCcore-12.3.0.eb
+  - pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb
+  - pytest-rerunfailures-12.0-GCCcore-12.3.0.eb
+  - pytest-shard-0.1.2-GCCcore-12.3.0.eb
+  - scikit-learn-1.3.1-gfbf-2023a.eb
+  - MUMPS-5.6.1-foss-2023a-metis.eb:
+      options:
+        # source URLs for MUMPS have changed, corresponding PR is
+        # https://github.com/easybuilders/easybuild-easyconfigs/pull/22582
+        # MUMPS is a dependency of snakemake
+        from-commit: 0437ff1ad34283398f55d4a6e01e6540b1ae9688
+  - snakemake-8.4.2-foss-2023a.eb
+  - LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb
+  - PyTorch-2.1.2-foss-2023a.eb
+  - matplotlib-3.7.2-gfbf-2023a.eb
+  - PyQt5-5.15.10-GCCcore-12.3.0.eb
+  - Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb
+  - dask-2023.9.2-foss-2023a.eb
+  - JupyterNotebook-7.0.2-GCCcore-12.3.0.eb
+  - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
+  - Z3-4.12.2-GCCcore-12.3.0.eb
+  - PyOpenGL-3.1.7-GCCcore-12.3.0.eb
+  - OpenJPEG-2.5.0-GCCcore-12.3.0.eb
+  - Highway-1.0.4-GCCcore-12.3.0.eb
+  - ELPA-2023.05.001-foss-2023a.eb
+  - libxc-6.2.2-GCC-12.3.0.eb:
+      options:
+        # possible change in gitlabs tarball packaging, affected by .gitattributes
+        # https://github.com/easybuilders/easybuild-easyconfigs/pull/22580
+        from-commit: 456d64bbeacf465e8f7e7ff378864e26352d045d
+  - ParMETIS-4.0.3-gompi-2023a.eb: 
+      options:
+        # source URLs for ParMETIS-4.0.3 have changed, corresponding PR is
+        # https://github.com/easybuilders/easybuild-easyconfigs/pull/22579
+        # ParMETIS-4.0.3 is a dependency of SuperLU_DIST-8.1.2
+        from-commit: 977e5208a720f23ace41b83b84da8b717d0aeada
+  - SuperLU_DIST-8.1.2-foss-2023a.eb
+  - PETSc-3.20.3-foss-2023a.eb
+  - MODFLOW-6.4.4-foss-2023a.eb
+  - NLopt-2.7.1-GCCcore-12.3.0.eb
+  - nettle-3.9.1-GCCcore-12.3.0.eb
+  - Xvfb-21.1.8-GCCcore-12.3.0.eb
+  - libsndfile-1.2.2-GCCcore-12.3.0.eb
+  - PostgreSQL-16.1-GCCcore-12.3.0.eb
+  - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
+  - GDAL-3.7.1-foss-2023a.eb