use singularity/vcell-3.10.0 and /local in slurm scripts

.github/workflows/CI-full.yml

@@ -12,7 +12,7 @@ jobs:
   build:
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Get the VCell version from tags
       id: version
       run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10})
@@ -23,7 +23,7 @@ jobs:
         echo "VCELL_DEPLOY_REMOTE_DIR=/share/apps/vcell3/deployed_github" >> $GITHUB_ENV
         echo "VCELL_MANAGER_NODE=vcellapi-beta.cam.uchc.edu" >> $GITHUB_ENV
     - name: setup ssh-agent
-      uses: webfactory/ssh-agent@v0.5.3
+      uses: webfactory/ssh-agent@v0.8.0
       with:
         ssh-private-key: ${{ secrets.VC_KEY }}
     - name: get installer secrets

.github/workflows/NightlyBMDB_CLI.yml

@@ -163,7 +163,7 @@ jobs:
           fi
 
       - name: Upload failures
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: set_${{ matrix.sets }}.report
           path: ${{ github.workspace }}/errors.report
@@ -241,7 +241,7 @@ jobs:
           fi
 
       - name: Upload failures
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: set_${{ matrix.sets }}.report
           path: ${{ github.workspace }}/errors.report

.github/workflows/ci_cd.yml

@@ -160,7 +160,7 @@ jobs:
     if: ${{ github.event_name == 'release' }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
         uses: actions/setup-python@v4

.github/workflows/codeql-analysis.yml

@@ -38,7 +38,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: setup java 17 with maven cache
       uses: actions/setup-java@v3

.github/workflows/create_bs_singularity.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           ref: ${{ github.event.inputs.commit_sha }}
 

.github/workflows/debug.yml

@@ -11,7 +11,7 @@ jobs:
   build:
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: insert version
       run: |
         set -ux

.github/workflows/objective-c-xcode-debug.yml

@@ -14,7 +14,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set Default Scheme
         run: |
           scheme_list=$(xcodebuild -list -json | tr -d "\n")

.github/workflows/site_deploy.yml

@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
     - name: checkout tag
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: ${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }}
     - name: setup global environment variables
@@ -50,7 +50,7 @@ jobs:
         	echo "VCELL_INSTALLER_REMOTE_DIR="/share/apps/vcell3/apache_webroot/htdocs/webstart/Test"" >> $GITHUB_ENV;\
         else echo "Unknown site name ${{ github.event.inputs.vcell_site }}"; exit 1; fi; fi; fi
     - name: setup ssh-agent
-      uses: webfactory/ssh-agent@v0.5.3
+      uses: webfactory/ssh-agent@v0.8.0
       with:
         ssh-private-key: ${{ secrets.VC_KEY }}
     - name: get installer secrets
@@ -77,7 +77,7 @@ jobs:
         scp docker/swarm/$VCELL_CONFIG_FILE_NAME ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}
         scp docker/swarm/variables ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}/variables_$VCELL_TAG
     - name: upload variables
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: variables
         path: docker/swarm/variables
@@ -91,7 +91,7 @@ jobs:
         ./generate_installers.sh ./${VCELL_CONFIG_FILE_NAME}
     - name: upload generated installers
       if: ${{ github.event.inputs.server_only != 'true' }}
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: installers
         path: docker/swarm/generated_installers
@@ -142,7 +142,7 @@ jobs:
         fi
     - name: update generated installers
       if: ${{ github.event.inputs.server_only != 'true' }}
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: installers
         path: installers
@@ -157,7 +157,7 @@ jobs:
     needs: notarize
     steps:
     - name: checkout tag
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: ${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }}
     - name: retrieve installers and variables
@@ -172,7 +172,7 @@ jobs:
         mkdir ../docker/swarm/generated_installers
         mv * ../docker/swarm/generated_installers
     - name: setup ssh-agent
-      uses: webfactory/ssh-agent@v0.5.3
+      uses: webfactory/ssh-agent@v0.8.0
       with:
         ssh-private-key: ${{ secrets.VC_KEY }}
     - name: retrieve config file

docker/build/Dockerfile-submit-dev

@@ -73,6 +73,7 @@ ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
     slurm_tmpdir="slurm-tmpdir-not-set" \
     slurm_local_singularity_dir="slurm_local_singularity_dir-not-set" \
     slurm_central_singularity_dir="slurm_central_singularity_dir-not-set" \
+    slurm_singularity_module_name="slurm_singularity_module_name-not-set" \
     jmsblob_minsize=100000 \
     vcell_ssh_cmd_cmdtimeout="cmdSrvcSshCmdTimeoutMS-not-set" \
     vcell_ssh_cmd_restoretimeout="cmdSrvcSshCmdRestoreTimeoutFactor-not-set" \
@@ -124,6 +125,7 @@ ENTRYPOINT java \
 	-Dvcell.slurm.tmpdir="${slurm_tmpdir}" \
 	-Dvcell.slurm.local.singularity.dir="${slurm_local_singularity_dir}" \
 	-Dvcell.slurm.central.singularity.dir="${slurm_central_singularity_dir}" \
+	-Dvcell.slurm.singularity.module.name="${slurm_singularity_module_name}" \
 	-Dvcell.batch.singularity.image="${batch_singularity_imagefile}" \
 	-Dvcell.opt.singularity.image="${opt_singularity_imagefile}" \
 	-Dvcell.batch.docker.name="${docker_name}" \

docker/swarm/docker-compose.yml

@@ -174,6 +174,7 @@ services:
       - slurm_tmpdir=${VCELL_SLURM_TMPDIR}
       - slurm_local_singularity_dir=${VCELL_SLURM_LOCAL_SINGULARITY_DIR}
       - slurm_central_singularity_dir=${VCELL_SLURM_CENTRAL_SINGULARITY_DIR}
+      - slurm_singularity_module_name=${VCELL_SLURM_SINGULARITY_MODULE_NAME}
       - simdatadir_archive_internal=${VCELL_SIMDATADIR_ARCHIVE_INTERNAL}
       - simdatadir_archive_external=${VCELL_SIMDATADIR_ARCHIVE_EXTERNAL}
 

docker/swarm/localconfig_realslurm_oracle.sh

@@ -97,6 +97,7 @@ VCELL_SLURM_QOS_PU=$vcell_slurm_qos_pu
 VCELL_SLURM_TMPDIR=/scratch/vcell
 VCELL_SLURM_LOCAL_SINGULARITY_DIR=/state/partition1/singularityImages
 VCELL_SLURM_CENTRAL_SINGULARITY_DIR=/share/apps/vcell3/singularityImages
+VCELL_SLURM_SINGULARITY_MODULE_NAME=singularity/vcell-3.10.0
 
 #
 # VCELL_API_PORT_EXTERNAL uses 443 for Beta and Rel (but on different machines/swarm clusters)
@@ -112,10 +113,10 @@ VCELL_S3PROXY_PORT_EXTERNAL=$((8086 + _site_port_offset))
 VCELL_HTC_NODELIST=
 VCELL_BATCH_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-batch:${VCELL_TAG}"
 VCELL_BATCH_SINGULARITY_FILENAME="${VCELL_BATCH_DOCKER_IMAGE//[\/:]/_}.img"
-VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL="/state/partition1/singularityImages/${VCELL_BATCH_SINGULARITY_FILENAME}"
+VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_BATCH_SINGULARITY_FILENAME}"
 VCELL_OPT_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-opt:${VCELL_TAG}"
 VCELL_OPT_SINGULARITY_FILENAME="${VCELL_OPT_DOCKER_IMAGE//[\/:]/_}.img"
-VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL="/state/partition1/singularityImages/${VCELL_OPT_SINGULARITY_FILENAME}"
+VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_OPT_SINGULARITY_FILENAME}"
 VCELL_SMTP_HOSTNAME=vdsmtp.cam.uchc.edu
 VCELL_SMTP_PORT=25
 [email protected]
@@ -156,6 +157,7 @@ VCELL_DEBUG_PORT_VCELL_SUBMIT=$((VCELL_DEBUG_PORT_BASE+5))
 VCELL_DEBUG_PORT_VCELL_WEB=$((VCELL_DEBUG_PORT_BASE+6))
 VCELL_DEPLOY_SECRETS_DIR=${HOME}/vcellkeys_oracle
 VCELL_EXPORT_BASEURL=$VCELL_EXPORT_BASEURL
+VCELL_S3_EXPORT_BASEURL=VCELL_S3_EXPORT_BASEURL_not_set
 VCELL_EXPORTDIR_HOST=$VCELL_EXPORTDIR_HOST
 VCELL_HTC_NODELIST=$VCELL_HTC_NODELIST
 VCELL_HTCLOGS_EXTERNAL=/share/apps/vcell3/dev_htclogs
@@ -181,17 +183,18 @@ VCELL_SIMDATADIR_ARCHIVE_INTERNAL=/share/apps/vcell12/users
 VCELL_SIMDATADIR_ARCHIVE_HOST=/Volumes/vcell-1/users
 VCELL_SIMDATADIR_EXTERNAL=/share/apps/vcell3/users
 VCELL_SIMDATADIR_HOST=/Volumes/vcell/users
-VCELL_SIMDATADIR_SECONDARY_EXTERNAL=/share/apps/vcell3/users
+VCELL_SIMDATADIR_SECONDARY_EXTERNAL=/share/apps/vcell7/users
 VCELL_SIMDATADIR_SECONDARY_HOST=/Volumes/vcell/users
 VCELL_SIMDATADIR_PARALLEL_EXTERNAL=/share/apps/vcell3parallel
 VCELL_SITE_CAMEL=${_site_camel}
 VCELL_SITE=$VCELL_SITE
-VCELL_SLURM_CENTRAL_SINGULARITY_DIR=${VCELL_SLURM_CENTRAL_SINGULARITY_DIR}
 VCELL_SLURM_CMD_SACCT=$VCELL_SLURM_CMD_SACCT
 VCELL_SLURM_CMD_SBATCH=$VCELL_SLURM_CMD_SBATCH
 VCELL_SLURM_CMD_SCANCEL=$VCELL_SLURM_CMD_SCANCEL
 VCELL_SLURM_CMD_SQUEUE=$VCELL_SLURM_CMD_SQUEUE
 VCELL_SLURM_LOCAL_SINGULARITY_DIR=${VCELL_SLURM_LOCAL_SINGULARITY_DIR}
+VCELL_SLURM_CENTRAL_SINGULARITY_DIR=${VCELL_SLURM_CENTRAL_SINGULARITY_DIR}
+VCELL_SLURM_SINGULARITY_MODULE_NAME=${VCELL_SLURM_SINGULARITY_MODULE_NAME}
 VCELL_SLURM_PARTITION_PU=$VCELL_SLURM_PARTITION_PU
 VCELL_SLURM_PARTITION=$VCELL_SLURM_PARTITION
 VCELL_SLURM_QOS_PU=$VCELL_SLURM_QOS_PU

docker/swarm/localconfig_realslurm_oracle_zeke.sh

@@ -99,6 +99,7 @@ VCELL_SLURM_QOS_PU=$vcell_slurm_qos_pu
 VCELL_SLURM_TMPDIR=/scratch/vcell
 VCELL_SLURM_LOCAL_SINGULARITY_DIR=/state/partition1/singularityImages
 VCELL_SLURM_CENTRAL_SINGULARITY_DIR=/share/apps/vcell3/singularityImages
+VCELL_SLURM_SINGULARITY_MODULE_NAME=singularity/vcell-3.10.0
 
 #
 # VCELL_API_PORT_EXTERNAL uses 443 for Beta and Rel (but on different machines/swarm clusters)
@@ -114,10 +115,10 @@ VCELL_S3PROXY_PORT_EXTERNAL=$((8086 + _site_port_offset))
 VCELL_HTC_NODELIST=
 VCELL_BATCH_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-batch:${VCELL_TAG}"
 VCELL_BATCH_SINGULARITY_FILENAME="${VCELL_BATCH_DOCKER_IMAGE//[\/:]/_}.img"
-VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL="/state/partition1/singularityImages/${VCELL_BATCH_SINGULARITY_FILENAME}"
+VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_BATCH_SINGULARITY_FILENAME}"
 VCELL_OPT_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-opt:${VCELL_TAG}"
 VCELL_OPT_SINGULARITY_FILENAME="${VCELL_OPT_DOCKER_IMAGE//[\/:]/_}.img"
-VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL="/state/partition1/singularityImages/${VCELL_OPT_SINGULARITY_FILENAME}"
+VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_OPT_SINGULARITY_FILENAME}"
 VCELL_SMTP_HOSTNAME=vdsmtp.cam.uchc.edu
 VCELL_SMTP_PORT=25
 [email protected]
@@ -164,6 +165,7 @@ VCELL_DEBUG_PORT_VCELL_WEB=$((VCELL_DEBUG_PORT_BASE+6))
 
 VCELL_DEPLOY_SECRETS_DIR=/media/zeke/DiskDrive/Home/Work/CCAM/VCellDummyFiles
 VCELL_EXPORT_BASEURL=$VCELL_EXPORT_BASEURL
+VCELL_S3_EXPORT_BASEURL=VCELL_S3_EXPORT_BASEURL_not_set
 VCELL_EXPORTDIR_HOST=$VCELL_EXPORTDIR_HOST
 VCELL_HTC_NODELIST=$VCELL_HTC_NODELIST
 VCELL_HTCLOGS_EXTERNAL=/share/apps/vcell3/dev_htclogs
@@ -203,12 +205,13 @@ VCELL_SIMDATADIR_PARALLEL_EXTERNAL=/share/apps/vcell3parallel
 VCELL_SITE_CAMEL=${_site_camel}
 VCELL_SITE=$VCELL_SITE
 
-VCELL_SLURM_CENTRAL_SINGULARITY_DIR=${VCELL_SLURM_CENTRAL_SINGULARITY_DIR}
 VCELL_SLURM_CMD_SACCT=$VCELL_SLURM_CMD_SACCT
 VCELL_SLURM_CMD_SBATCH=$VCELL_SLURM_CMD_SBATCH
 VCELL_SLURM_CMD_SCANCEL=$VCELL_SLURM_CMD_SCANCEL
 VCELL_SLURM_CMD_SQUEUE=$VCELL_SLURM_CMD_SQUEUE
 VCELL_SLURM_LOCAL_SINGULARITY_DIR=${VCELL_SLURM_LOCAL_SINGULARITY_DIR}
+VCELL_SLURM_CENTRAL_SINGULARITY_DIR=${VCELL_SLURM_CENTRAL_SINGULARITY_DIR}
+VCELL_SLURM_SINGULARITY_MODULE_NAME=${VCELL_SLURM_SINGULARITY_MODULE_NAME}
 VCELL_SLURM_PARTITION_PU=$VCELL_SLURM_PARTITION_PU
 VCELL_SLURM_PARTITION=$VCELL_SLURM_PARTITION
 VCELL_SLURM_QOS_PU=$VCELL_SLURM_QOS_PU

docker/swarm/localconfig_realslurm_postgres.sh

@@ -97,6 +97,7 @@ VCELL_SLURM_QOS_PU=$vcell_slurm_qos_pu
 VCELL_SLURM_TMPDIR=/scratch/vcell
 VCELL_SLURM_LOCAL_SINGULARITY_DIR=/state/partition1/singularityImages
 VCELL_SLURM_CENTRAL_SINGULARITY_DIR=/share/apps/vcell3/singularityImages
+VCELL_SLURM_SINGULARITY_MODULE_NAME=singularity/vcell-3.10.0
 
 #
 # VCELL_API_PORT_EXTERNAL uses 443 for Beta and Rel (but on different machines/swarm clusters)
@@ -112,10 +113,10 @@ VCELL_S3PROXY_PORT_EXTERNAL=$((8086 + _site_port_offset))
 VCELL_HTC_NODELIST=
 VCELL_BATCH_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-batch:${VCELL_TAG}"
 VCELL_BATCH_SINGULARITY_FILENAME="${VCELL_BATCH_DOCKER_IMAGE//[\/:]/_}.img"
-VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL="/state/partition1/singularityImages/${VCELL_BATCH_SINGULARITY_FILENAME}"
+VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_BATCH_SINGULARITY_FILENAME}"
 VCELL_OPT_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-opt:${VCELL_TAG}"
 VCELL_OPT_SINGULARITY_FILENAME="${VCELL_OPT_DOCKER_IMAGE//[\/:]/_}.img"
-VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL="/state/partition1/singularityImages/${VCELL_OPT_SINGULARITY_FILENAME}"
+VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_OPT_SINGULARITY_FILENAME}"
 VCELL_SMTP_HOSTNAME=vdsmtp.cam.uchc.edu
 VCELL_SMTP_PORT=25
 [email protected]
@@ -156,6 +157,7 @@ VCELL_DEBUG_PORT_VCELL_SUBMIT=$((VCELL_DEBUG_PORT_BASE+5))
 VCELL_DEBUG_PORT_VCELL_WEB=$((VCELL_DEBUG_PORT_BASE+6))
 VCELL_DEPLOY_SECRETS_DIR=${HOME}/vcellkeys_postgres
 VCELL_EXPORT_BASEURL=$VCELL_EXPORT_BASEURL
+VCELL_S3_EXPORT_BASEURL=VCELL_S3_EXPORT_BASEURL_not_set
 VCELL_EXPORTDIR_HOST=$VCELL_EXPORTDIR_HOST
 VCELL_HTC_NODELIST=$VCELL_HTC_NODELIST
 VCELL_HTCLOGS_EXTERNAL=/share/apps/vcell3/dev_htclogs
@@ -181,17 +183,18 @@ VCELL_SIMDATADIR_ARCHIVE_INTERNAL=/share/apps/vcell12/users
 VCELL_SIMDATADIR_ARCHIVE_HOST=/Volumes/vcell-1/users
 VCELL_SIMDATADIR_EXTERNAL=/share/apps/vcell3/users
 VCELL_SIMDATADIR_HOST=/Volumes/vcell/users
-VCELL_SIMDATADIR_SECONDARY_EXTERNAL=/share/apps/vcell3/users
+VCELL_SIMDATADIR_SECONDARY_EXTERNAL=/share/apps/vcell7/users
 VCELL_SIMDATADIR_SECONDARY_HOST=/Volumes/vcell/users
 VCELL_SIMDATADIR_PARALLEL_EXTERNAL=/share/apps/vcell3parallel
 VCELL_SITE_CAMEL=${_site_camel}
 VCELL_SITE=$VCELL_SITE
-VCELL_SLURM_CENTRAL_SINGULARITY_DIR=${VCELL_SLURM_CENTRAL_SINGULARITY_DIR}
 VCELL_SLURM_CMD_SACCT=$VCELL_SLURM_CMD_SACCT
 VCELL_SLURM_CMD_SBATCH=$VCELL_SLURM_CMD_SBATCH
 VCELL_SLURM_CMD_SCANCEL=$VCELL_SLURM_CMD_SCANCEL
 VCELL_SLURM_CMD_SQUEUE=$VCELL_SLURM_CMD_SQUEUE
 VCELL_SLURM_LOCAL_SINGULARITY_DIR=${VCELL_SLURM_LOCAL_SINGULARITY_DIR}
+VCELL_SLURM_CENTRAL_SINGULARITY_DIR=${VCELL_SLURM_CENTRAL_SINGULARITY_DIR}
+VCELL_SLURM_SINGULARITY_MODULE_NAME=${VCELL_SLURM_SINGULARITY_MODULE_NAME}
 VCELL_SLURM_PARTITION_PU=$VCELL_SLURM_PARTITION_PU
 VCELL_SLURM_PARTITION=$VCELL_SLURM_PARTITION
 VCELL_SLURM_QOS_PU=$VCELL_SLURM_QOS_PU

docker/swarm/serverconfig-uch.sh

@@ -46,7 +46,7 @@ case $VCELL_SITE in
 		;;
 	BETA)
 		_site_port_offset=1
-		VCELL_API_HOST_EXTERNAL=vcellapi.cam.uchc.edu
+		VCELL_API_HOST_EXTERNAL=http://vcellapi.cam.uchc.edu
 		VCELL_API_PORT_EXTERNAL=443
 		VCELL_DEBUG_PORT_BASE=5010
 		_applicationId="1471-8022-1038-5552"
@@ -62,7 +62,7 @@ case $VCELL_SITE in
 	TEST)
 		_site_port_offset=3
 		# VCELL_API_PORT_EXTERNAL=8081
-		VCELL_API_HOST_EXTERNAL=vcellapi-test.cam.uchc.edu
+		VCELL_API_HOST_EXTERNAL=http://vcellapi-test.cam.uchc.edu
 		VCELL_API_PORT_EXTERNAL=443
 		VCELL_DEBUG_PORT_BASE=5030
 		_applicationId="1471-8022-1038-5555"
@@ -119,8 +119,9 @@ VCELL_SLURM_PARTITION_PU=$vcell_slurm_partition_pu
 VCELL_SLURM_RESERVATION_PU=$vcell_slurm_reservation_pu
 VCELL_SLURM_QOS_PU=$vcell_slurm_qos_pu
 VCELL_SLURM_TMPDIR=/scratch/vcell
-VCELL_SLURM_LOCAL_SINGULARITY_DIR=/state/partition1/singularityImages
+VCELL_SLURM_LOCAL_SINGULARITY_DIR=/local/singularityImages
 VCELL_SLURM_CENTRAL_SINGULARITY_DIR=/share/apps/vcell3/singularityImages
+VCELL_SLURM_SINGULARITY_MODULE_NAME=singularity/vcell-3.10.0
 
 #
 # VCELL_API_PORT_EXTERNAL uses 443 for Beta and Rel (but on different machines/swarm clusters)
@@ -136,10 +137,10 @@ VCELL_S3PROXY_PORT_EXTERNAL=$((8086 + _site_port_offset))
 VCELL_HTC_NODELIST=
 VCELL_BATCH_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-batch:${VCELL_TAG}"
 VCELL_BATCH_SINGULARITY_FILENAME="${VCELL_BATCH_DOCKER_IMAGE//[\/:]/_}.img"
-VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL="/state/partition1/singularityImages/${VCELL_BATCH_SINGULARITY_FILENAME}"
+VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_BATCH_SINGULARITY_FILENAME}"
 VCELL_OPT_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-opt:${VCELL_TAG}"
 VCELL_OPT_SINGULARITY_FILENAME="${VCELL_OPT_DOCKER_IMAGE//[\/:]/_}.img"
-VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL="/state/partition1/singularityImages/${VCELL_OPT_SINGULARITY_FILENAME}"
+VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_OPT_SINGULARITY_FILENAME}"
 VCELL_SMTP_HOSTNAME=vdsmtp.cam.uchc.edu
 VCELL_SMTP_PORT=25
 [email protected]
@@ -211,12 +212,13 @@ VCELL_SIMDATADIR_SECONDARY_HOST=/share/apps/vcell7/users
 VCELL_SIMDATADIR_PARALLEL_EXTERNAL=/share/apps/vcell3parallel
 VCELL_SITE_CAMEL=${_site_camel}
 VCELL_SITE=$VCELL_SITE
-VCELL_SLURM_CENTRAL_SINGULARITY_DIR=${VCELL_SLURM_CENTRAL_SINGULARITY_DIR}
 VCELL_SLURM_CMD_SACCT=$VCELL_SLURM_CMD_SACCT
 VCELL_SLURM_CMD_SBATCH=$VCELL_SLURM_CMD_SBATCH
 VCELL_SLURM_CMD_SCANCEL=$VCELL_SLURM_CMD_SCANCEL
 VCELL_SLURM_CMD_SQUEUE=$VCELL_SLURM_CMD_SQUEUE
 VCELL_SLURM_LOCAL_SINGULARITY_DIR=${VCELL_SLURM_LOCAL_SINGULARITY_DIR}
+VCELL_SLURM_CENTRAL_SINGULARITY_DIR=${VCELL_SLURM_CENTRAL_SINGULARITY_DIR}
+VCELL_SLURM_SINGULARITY_MODULE_NAME=${VCELL_SLURM_SINGULARITY_MODULE_NAME}
 VCELL_SLURM_PARTITION_PU=$VCELL_SLURM_PARTITION_PU
 VCELL_SLURM_PARTITION=$VCELL_SLURM_PARTITION
 VCELL_SLURM_QOS_PU=$VCELL_SLURM_QOS_PU

vcell-core/src/main/java/cbit/vcell/resource/PropertyLoader.java

@@ -96,6 +96,7 @@ public static void setConfigProvider(VCellConfigProvider configProvider) {
 	public static final String slurm_tmpdir					= record("vcell.slurm.tmpdir",ValueType.GEN);
 	public static final String slurm_local_singularity_dir	= record("vcell.slurm.local.singularity.dir",ValueType.GEN);
 	public static final String slurm_central_singularity_dir= record("vcell.slurm.central.singularity.dir",ValueType.GEN);
+	public static final String slurm_singularity_module_name= record("vcell.slurm.singularity.module.name",ValueType.GEN);
 	public static final String sgeModulePath				= record("vcell.htc.sge.module",ValueType.GEN);
 	public static final String pbsModulePath				= record("vcell.htc.pbs.module",ValueType.GEN);
 	public static final String MPI_HOME_INTERNAL		        = record("vcell.htc.mpi.home",ValueType.DIR);

vcell-server/src/main/java/cbit/vcell/message/server/batch/sim/HtcSimulationWorker.java

@@ -671,6 +671,7 @@ public static void main(String[] args) throws IOException {
 		PropertyLoader.vcellbatch_docker_name,
 		PropertyLoader.slurm_local_singularity_dir,
 		PropertyLoader.slurm_central_singularity_dir,
+		PropertyLoader.slurm_singularity_module_name,
 		PropertyLoader.slurm_reservation,
 		PropertyLoader.slurm_qos,
 		PropertyLoader.slurm_partition_pu,