Merge pull request #989 from trz42/2023.06-grace-2023b-eb492-apps

{2023.06}[2023b,grace] apps originally built with EB 4.9.2 + changes to bot/build.sh and eessi_container.sh

Author: TopRichard

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/grace/eessi-2023.06-eb-4.9.4-2023b.yml

@@ -105,3 +105,47 @@ easyconfigs:
 #      options:
 #        from-pr: 20792
   - Valgrind-3.23.0-gompi-2023b.eb
+# from here on easyconfigs were originally built with EB 4.9.2
+  - IPython-8.17.2-GCCcore-13.2.0.eb
+  - dlb-3.4-gompi-2023b.eb
+# originally built with EB 4.9.2, PR 20889 was included since EB 4.9.3
+#  - pystencils-1.3.4-gfbf-2023b.eb:
+#      options:
+#        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
+#        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7
+  - pystencils-1.3.4-gfbf-2023b.eb
+# originally built with EB 4.9.2, PR 21017 was included since EB 4.9.3, PR 3393
+#   was included since EB 4.9.3
+#  - Extrae-4.2.0-gompi-2023b.eb:
+#      options:
+#        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21017
+#        from-commit: 120f4d56efebd2bc61382db4c84a664a339c66cf
+#        # see https://github.com/easybuilders/easybuild-easyblocks/pull/3393
+#        include-easyblocks-from-commit: c4951c78d62fa5cf8e9f6fe0ead212d2a4d7cb9c
+  - Extrae-4.2.0-gompi-2023b.eb
+  - Boost.MPI-1.83.0-gompi-2023b.eb:
+      options:
+        # source URLs for Boost.* have changed, corresponding PR is
+        # https://github.com/easybuilders/easybuild-easyconfigs/pull/22240
+        # Boost.MPI is a dependency of pyMBE
+        from-commit: e610fe1ac5393d1de668a466fdaaea74c580ee03
+# originally built with EB 4.9.2, PR 21034 was included since EB 4.9.3
+#  - pyMBE-0.8.0-foss-2023b.eb:
+#      options:
+#        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21034
+#        from-commit: 76e7fc6657bab64bfbec826540a3a8f0040258f2
+  - pyMBE-0.8.0-foss-2023b.eb
+# originally built with EB 4.9.2, PR 21200 was included since EB 4.9.3
+#  - STAR-2.7.11b-GCC-13.2.0.eb:
+#      options:
+#        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21200
+#        from-commit: 765ba900daf5953e306c4dad896febe52fdd6c00
+  - STAR-2.7.11b-GCC-13.2.0.eb
+  - HPL-2.3-foss-2023b.eb
+# originally built with EB 4.9.2, PR 21366 was included since EB 4.9.3
+#  - R-bundle-CRAN-2024.06-foss-2023b.eb:
+#      options:
+#        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21366
+#        # we use a commit from the Brunsli PR here to get rid of the Highway dependency
+#        from-commit: 1736a123b1685836452587a5c51793257570bb2d
+  - R-bundle-CRAN-2024.06-foss-2023b.eb

eessi_container.sh

@@ -89,6 +89,8 @@ display_help() {
   echo "  -n | --nvidia MODE      - configure the container to work with NVIDIA GPUs,"
   echo "                            MODE==install for a CUDA installation, MODE==run to"
   echo "                            attach a GPU, MODE==all for both [default: false]"
+  echo "  -p | --pass-through ARG - argument to pass through to the launch of the"
+  echo "                            container; can be given multiple times [default: not set]"
   echo "  -r | --repository CFG   - configuration file or identifier defining the"
   echo "                            repository to use; can be given multiple times;"
   echo "                            CFG may include a suffix ',access={ro,rw}' to"
@@ -126,6 +128,7 @@ VERBOSE=0
 STORAGE=
 LIST_REPOS=0
 MODE="shell"
+PASS_THROUGH=()
 SETUP_NVIDIA=0
 REPOSITORIES=()
 RESUME=
@@ -182,6 +185,10 @@ while [[ $# -gt 0 ]]; do
       NVIDIA_MODE="$2"
       shift 2
       ;;
+    -p|--pass-through)
+      PASS_THROUGH+=("$2")
+      shift 2
+      ;;
     -r|--repository)
       REPOSITORIES+=("$2")
       shift 2
@@ -842,6 +849,11 @@ if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
     export APPTAINERENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
+# add pass through arguments
+for arg in "${PASS_THROUGH[@]}"; do
+    ADDITIONAL_CONTAINER_OPTIONS+=(${arg})
+done
+
 echo "Launching container with command (next line):"
 echo "singularity ${RUN_QUIET} ${MODE} ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} $@"
 singularity ${RUN_QUIET} ${MODE} "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER} "$@"