Merge branch 'nessi.no-2023.06' of github.com:NorESSI/software-layer …

…into nessi-2023.06-Valgrind/3.21.0-gompi/2023b
NorESSI · Jun 17, 2024 · 6794648 · 6794648
2 parents eeade02 + b5cf785
commit 6794648
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diff --git a/bot/test.sh b/bot/test.sh
@@ -204,6 +204,9 @@ if [[ -z ${RESUME_DIR} ]]; then
 else
   TEST_STEP_ARGS+=("--resume" "${RESUME_DIR}")
 fi
+# Bind mount /sys/fs/cgroup so that we can determine the amount of memory available in our cgroup for
+# Reframe configuration
+TEST_STEP_ARGS+=("--extra-bind-paths" "/sys/fs/cgroup:/hostsys/fs/cgroup:ro")
 
 # prepare arguments to test_suite.sh (specific to test step)
 declare -a TEST_SUITE_ARGS=()

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -13,3 +13,4 @@ easyconfigs:
         from-pr: 20379
   - ParaView-5.11.1-foss-2022b.eb
   - SEPP-4.5.1-foss-2022b.eb
+  - Valgrind-3.21.0-gompi-2022b.eb
diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -55,6 +55,9 @@ easyconfigs:
   - PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb:
       options:
         cuda-compute-capabilities: 6.0,6.1,7.0,7.5,8.0,8.6,8.9,9.0
+  - BLAST+-2.14.1-gompi-2023a.eb:
+      options:     
+        from-pr: 20751
   # PyTorch-bundle-CUDA's dependencies without CUDA
   - librosa-0.10.1-foss-2023a.eb
   - NLTK-3.8.1-foss-2023a.eb
@@ -76,3 +79,6 @@ easyconfigs:
   - tensorboard-2.15.1-gfbf-2023a.eb
   - tqdm-4.66.1-GCCcore-12.3.0.eb
   - bx-python-0.10.0-foss-2023a.eb
+  - BLAST+-2.14.1-gompi-2023a.eb:
+      options:     
+        from-pr: 20784
diff --git a/eessi_container.sh b/eessi_container.sh
@@ -70,46 +70,48 @@ export EESSI_REPOS_CFG_FILE="${EESSI_REPOS_CFG_DIR}/repos.cfg"
 display_help() {
   echo "usage: $0 [OPTIONS] [[--] SCRIPT or COMMAND]"
   echo " OPTIONS:"
-  echo "  -a | --access {ro,rw}  - ro (read-only), rw (read & write) [default: ro]"
-  echo "  -c | --container IMG   - image file or URL defining the container to use"
-  echo "                           [default: docker://ghcr.io/eessi/build-node:debian11]"
-  echo "  -f | --fakeroot        - run the container with --fakeroot [default: false]"
-  echo "                           Note, currently this option is ignored."
-  echo "  -g | --storage DIR     - directory space on host machine (used for"
-  echo "                           temporary data) [default: 1. TMPDIR, 2. /tmp]"
-  echo "  -h | --help            - display this usage information [default: false]"
-  echo "  -i | --host-injections - directory to link to for host_injections "
-  echo "                           [default: /..storage../opt-eessi]"
-  echo "  -l | --list-repos      - list available repository identifiers [default: false]"
-  echo "  -m | --mode MODE       - with MODE==shell (launch interactive shell) or"
-  echo "                           MODE==run (run a script or command) [default: shell]"
-  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 "  -o | --lower-dirs DIRS - list of ':' separated directories that are used"
-  echo "                           in front of the default lower dir (CVMFS repo);"
-  echo "                           fuse-overlayfs will merge all lower directories;"
-  echo "                           the option can be used to make certain directories"
-  echo "                           in the CVMFS repo writable [default: none]"
-  echo "  -r | --repository CFG  - configuration file or identifier defining the"
-  echo "                           repository to use [default: EESSI via"
-  echo "                           default container, see --container]"
-  echo "  -u | --resume DIR/TGZ  - resume a previous run from a directory or tarball,"
-  echo "                           where DIR points to a previously used tmp directory"
-  echo "                           (check for output 'Using DIR as tmp ...' of a previous"
-  echo "                           run) and TGZ is the path to a tarball which is"
-  echo "                           unpacked the tmp dir stored on the local storage space"
-  echo "                           (see option --storage above) [default: not set]"
-  echo "  -s | --save DIR/TGZ    - save contents of tmp directory to a tarball in"
-  echo "                           directory DIR or provided with the fixed full path TGZ"
-  echo "                           when a directory is provided, the format of the"
-  echo "                           tarball's name will be {REPO_ID}-{TIMESTAMP}.tgz"
-  echo "                           [default: not set]"
-  echo "  -v | --verbose         - display more information [default: false]"
-  echo "  -x | --http-proxy URL  - provides URL for the env variable http_proxy"
-  echo "                           [default: not set]; uses env var \$http_proxy if set"
-  echo "  -y | --https-proxy URL - provides URL for the env variable https_proxy"
-  echo "                           [default: not set]; uses env var \$https_proxy if set"
+  echo "  -a | --access {ro,rw}   - ro (read-only), rw (read & write) [default: ro]"
+  echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
+  echo "                            To specify multiple bind paths, separate by comma."
+  echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
+  echo "  -c | --container IMG    - image file or URL defining the container to use"
+  echo "                            [default: docker://ghcr.io/eessi/build-node:debian11]"
+  echo "  -f | --fakeroot         - run the container with --fakeroot [default: false]"
+  echo "  -g | --storage DIR      - directory space on host machine (used for"
+  echo "                            temporary data) [default: 1. TMPDIR, 2. /tmp]"
+  echo "  -h | --help             - display this usage information [default: false]"
+  echo "  -i | --host-injections  - directory to link to for host_injections "
+  echo "                            [default: /..storage../opt-eessi]"
+  echo "  -l | --list-repos       - list available repository identifiers [default: false]"
+  echo "  -m | --mode MODE        - with MODE==shell (launch interactive shell) or"
+  echo "                            MODE==run (run a script or command) [default: shell]"
+  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 "  -o | --lower-dirs DIRS  - list of ':' separated directories that are used"
+  echo "                            in front of the default lower dir (CVMFS repo);"
+  echo "                            fuse-overlayfs will merge all lower directories;"
+  echo "                            the option can be used to make certain directories"
+  echo "                            in the CVMFS repo writable [default: none]"
+  echo "  -r | --repository CFG   - configuration file or identifier defining the"
+  echo "                            repository to use [default: EESSI via"
+  echo "                            default container, see --container]"
+  echo "  -u | --resume DIR/TGZ   - resume a previous run from a directory or tarball,"
+  echo "                            where DIR points to a previously used tmp directory"
+  echo "                            (check for output 'Using DIR as tmp ...' of a previous"
+  echo "                            run) and TGZ is the path to a tarball which is"
+  echo "                            unpacked the tmp dir stored on the local storage space"
+  echo "                            (see option --storage above) [default: not set]"
+  echo "  -s | --save DIR/TGZ     - save contents of tmp directory to a tarball in"
+  echo "                            directory DIR or provided with the fixed full path TGZ"
+  echo "                            when a directory is provided, the format of the"
+  echo "                            tarball's name will be {REPO_ID}-{TIMESTAMP}.tgz"
+  echo "                            [default: not set]"
+  echo "  -v | --verbose          - display more information [default: false]"
+  echo "  -x | --http-proxy URL   - provides URL for the env variable http_proxy"
+  echo "                            [default: not set]; uses env var \$http_proxy if set"
+  echo "  -y | --https-proxy URL  - provides URL for the env variable https_proxy"
+  echo "                            [default: not set]; uses env var \$https_proxy if set"
   echo
   echo " If value for --mode is 'run', the SCRIPT/COMMAND provided is executed. If"
   echo " arguments to the script/command start with '-' or '--', use the flag terminator"
@@ -141,6 +143,10 @@ while [[ $# -gt 0 ]]; do
       ACCESS="$2"
       shift 2
       ;;
+    -b|--extra-bind-paths)
+      EXTRA_BIND_PATHS="$2"
+      shift 2
+      ;;
     -c|--container)
       CONTAINER="$2"
       shift 2
@@ -453,6 +459,9 @@ fi
 BIND_PATHS="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
 # provide a '/tmp' inside the container
 BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
+if [[ ! -z ${EXTRA_BIND_PATHS} ]]; then
+    BIND_PATHS="${BIND_PATHS},${EXTRA_BIND_PATHS}"
+fi
 
 [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
 

diff --git a/reframe_config_bot.py.tmpl b/reframe_config_bot.py.tmpl
@@ -34,6 +34,11 @@ site_configuration = {
                             'options': ['--mem={size}'],
                         }
                     ],
+                    'extras': {
+                        # Make sure to round down, otherwise a job might ask for more mem than is available
+                        # per node
+                        'mem_per_node': __MEM_PER_NODE__,
+                    },
                     'max_jobs': 1
                     }
                 ]

diff --git a/test_suite.sh b/test_suite.sh
@@ -135,7 +135,7 @@ export RFM_PREFIX=$PWD/reframe_runs
 echo "Configured reframe with the following environment variables:"
 env | grep "RFM_"
 
-# Inject correct CPU properties into the ReFrame config file
+# Inject correct CPU/memory properties into the ReFrame config file
 cpuinfo=$(lscpu)
 if [[ "${cpuinfo}" =~ CPU\(s\):[^0-9]*([0-9]+) ]]; then
     cpu_count=${BASH_REMATCH[1]}
@@ -165,11 +165,20 @@ if [[ "${cpuinfo}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
 else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
 fi
+cgroup_mem_bytes=$(cat /hostsys/fs/cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOB_ID}/memory.limit_in_bytes)
+if [[ $? -eq 0 ]]; then
+    # Convert to MiB
+    cgroup_mem_mib=$((cgroup_mem_bytes/(1024*1024)))
+else
+    fatal_error "Failed to get the memory limit in bytes from the current cgroup"
+fi
 cp ${RFM_CONFIG_FILE_TEMPLATE} ${RFM_CONFIG_FILES}
 sed -i "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILES
+# on local systems the change below is not the case, it works on AWS
+# sed -i "s/__MEM_PER_NODE__/${cgroup_mem_mib}/g" $RFM_CONFIG_FILES
 
 # Workaround for https://github.com/EESSI/software-layer/pull/467#issuecomment-1973341966
 export PSM3_DEVICES='self,shm'  # this is enough, since we only run single node for now