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Docker N5
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Add N5 dir to docker build file
AvocadoMoon committed Nov 14, 2023

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1 parent 3a8b669 commit ebe8829
Showing 2 changed files with 30 additions and 18 deletions.
1 change: 1 addition & 0 deletions docker/build/Dockerfile-data-dev
Original file line number Diff line number Diff line change
@@ -89,6 +89,7 @@ ENTRYPOINT java \
-Dvcell.python.executable=/usr/local/bin/python \
-Dvcell.primarySimdatadir.internal=/simdata \
-Dvcell.secondarySimdatadir.internal=/simdata_secondary \
-Dvcell.n5DataDir.internal=/n5DataDir \
-Dvcell.primarySimdatadir.external="${simdatadir_external}" \
-Dvcell.simdataCacheSize="${simdataCacheSize}" \
-Dvcell.export.baseDir.internal=/exportdir/ \
47 changes: 29 additions & 18 deletions docker/swarm/localconfig_realslurm_oracle_zeke.sh
Original file line number Diff line number Diff line change
@@ -120,7 +120,7 @@ VCELL_SMTP_HOSTNAME=vdsmtp.cam.uchc.edu
VCELL_SMTP_PORT=25
[email protected]
VCELL_EXPORT_BASEURL=http://vcell.org/export/
VCELL_EXPORTDIR_HOST=/Volumes/vcell/export/
VCELL_EXPORTDIR_HOST=/media/zeke/DiskDrive/Home/Work/CCAM/TempStorage/export
VCELL_MAX_JOBS_PER_SCAN=100
VCELL_MAX_ODE_JOBS_PER_USER=100
VCELL_MAX_PDE_JOBS_PER_USER=40
@@ -136,65 +136,70 @@ VCELL_SSH_CMD_RESTORE_TIMEOUT=5
cat <<EOF >"$_outputfile"
VCELL_API_HOST_EXTERNAL=$VCELL_API_HOST_EXTERNAL
VCELL_API_PORT_EXTERNAL=$VCELL_API_PORT_EXTERNAL
VCELL_BATCH_DOCKER_IMAGE=$VCELL_BATCH_DOCKER_IMAGE
VCELL_BATCH_HOST=$VCELL_BATCH_HOST
VCELL_BATCH_SINGULARITY_FILENAME=$VCELL_BATCH_SINGULARITY_FILENAME
VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL=$VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL
VCELL_BATCH_USER=vcell
VCELL_BIOFORMATS_JAR_FILE=vcell-bioformats-0.0.9-jar-with-dependencies.jar
VCELL_BIOFORMATS_JAR_URL=http://vcell.org/webstart/vcell-bioformats-0.0.9-jar-with-dependencies.jar
VCELL_BUILD_NUMBER=$VCELL_BUILD_NUMBER
VCELL_CLIENT_APPID=${_applicationId}
VCELL_DB_DRIVER=$VCELL_DB_DRIVER
VCELL_DB_URL=$VCELL_DB_URL
VCELL_DB_USER=$VCELL_DB_USER
VCELL_DEBUG_PORT_VCELL_API=$((VCELL_DEBUG_PORT_BASE+1))
VCELL_DEBUG_PORT_VCELL_DATA=$((VCELL_DEBUG_PORT_BASE+2))
VCELL_DEBUG_PORT_VCELL_DB=$((VCELL_DEBUG_PORT_BASE+3))
VCELL_DEBUG_PORT_VCELL_SCHED=$((VCELL_DEBUG_PORT_BASE+4))
VCELL_DEBUG_PORT_VCELL_SUBMIT=$((VCELL_DEBUG_PORT_BASE+5))
VCELL_DEBUG_PORT_VCELL_WEB=$((VCELL_DEBUG_PORT_BASE+6))
VCELL_DEPLOY_SECRETS_DIR=${HOME}/vcellkeys_oracle
VCELL_DEPLOY_SECRETS_DIR=/media/zeke/DiskDrive/Home/Work/CCAM/VCellDummyFiles
VCELL_EXPORT_BASEURL=$VCELL_EXPORT_BASEURL
VCELL_EXPORTDIR_HOST=$VCELL_EXPORTDIR_HOST
VCELL_HTC_NODELIST=$VCELL_HTC_NODELIST
VCELL_HTCLOGS_EXTERNAL=/share/apps/vcell3/dev_htclogs
VCELL_HTCLOGS_HOST=/Volumes/vcell/dev_htclogs
VCELL_INSTALLER_JRE_LINUX32=linux-x86-1.8.0_66
VCELL_INSTALLER_JRE_LINUX64=linux-amd64-1.8.0_66
VCELL_INSTALLER_JRE_MAC=macosx-amd64-1.8.0_141
VCELL_INSTALLER_JRE_WIN32=windows-x86-1.8.0_141
VCELL_INSTALLER_JRE_WIN64=windows-amd64-1.8.0_141
VCELL_INSTALLER_JREDIR=${HOME}/.install4j6/jres
VCELL_HTCLOGS_HOST=/media/zeke/DiskDrive/Home/Work/CCAM/TempStorage/dev_htclogs
VCELL_JMS_SIM_HOST_EXTERNAL=$VCELL_JMS_SIM_HOST_EXTERNAL
VCELL_JMS_SIM_PORT_EXTERNAL=$VCELL_JMS_SIM_PORT_EXTERNAL
VCELL_JMS_SIM_RESTPORT_EXTERNAL=$VCELL_JMS_SIM_RESTPORT_EXTERNAL
VCELL_MAX_JOBS_PER_SCAN=$VCELL_MAX_JOBS_PER_SCAN
VCELL_MAX_ODE_JOBS_PER_USER=$VCELL_MAX_ODE_JOBS_PER_USER
VCELL_MAX_PDE_JOBS_PER_USER=$VCELL_MAX_PDE_JOBS_PER_USER
VCELL_MONGO_HOST_EXTERNAL=$VCELL_MONGO_HOST_EXTERNAL
VCELL_MONGO_PORT_EXTERNAL=$VCELL_MONGO_PORT_EXTERNAL
VCELL_NATIVESOLVERDIR_EXTERNAL=/share/apps/vcell3/nativesolvers
VCELL_OPT_DOCKER_IMAGE=$VCELL_OPT_DOCKER_IMAGE
VCELL_OPT_SINGULARITY_FILENAME=$VCELL_OPT_SINGULARITY_FILENAME
VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL=$VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL
VCELL_REPO_NAMESPACE=$VCELL_REPO_NAMESPACE
VCELL_SECRETS_DIR=${HOME}/vcellkeys_oracle
VCELL_N5_DATADIR_HOST=/share/apps/vcell3/n5
VCELL_SECRETS_DIR=/media/zeke/DiskDrive/Home/Work/CCAM/VCellDummyFiles
VCELL_N5_DATADIR_HOST=/media/zeke/DiskDrive/Home/Work/CCAM/TempStorage/N5Dir
VCELL_S3PROXY_PORT_EXTERNAL=$VCELL_S3PROXY_PORT_EXTERNAL
VCELL_SIMDATADIR_ARCHIVE_EXTERNAL=/share/apps/vcell12/users
VCELL_SIMDATADIR_ARCHIVE_INTERNAL=/share/apps/vcell12/users
VCELL_SIMDATADIR_ARCHIVE_HOST=/Volumes/vcell-1/users
VCELL_SIMDATADIR_ARCHIVE_HOST_ORIG=/Volumes/vcell-2/users
VCELL_SIMDATADIR_ARCHIVE_HOST=/media/zeke/DiskDrive/Home/Work/CCAM/TempStorage/users
VCELL_SIMDATADIR_EXTERNAL=/share/apps/vcell3/users
VCELL_SIMDATADIR_HOST=/Volumes/vcell/users
VCELL_SIMDATADIR_HOST=/media/zeke/DiskDrive/Home/Work/CCAM/TempStorage/users
VCELL_SIMDATADIR_SECONDARY_EXTERNAL=/share/apps/vcell3/users
VCELL_SIMDATADIR_SECONDARY_HOST=/Volumes/vcell/users
VCELL_SIMDATADIR_SECONDARY_EXTERNAL_ORIG=/share/apps/vcell7/users
VCELL_SIMDATADIR_SECONDARY_HOST_ORIG=/Volumes/vcell-1/users
VCELL_SIMDATADIR_SECONDARY_HOST=~/Mnts/RemoteVolumes/VCell05/users
VCELL_SIMDATADIR_PARALLEL_EXTERNAL=/share/apps/vcell3parallel
VCELL_SITE_CAMEL=${_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
@@ -208,17 +213,23 @@ VCELL_SLURM_QOS=$VCELL_SLURM_QOS
VCELL_SLURM_RESERVATION_PU=$VCELL_SLURM_RESERVATION_PU
VCELL_SLURM_RESERVATION=$VCELL_SLURM_RESERVATION
VCELL_SLURM_TMPDIR=$VCELL_SLURM_TMPDIR
VCELL_SMTP_EMAILADDRESS=${VCELL_SMTP_EMAILADDRESS}
VCELL_SMTP_HOSTNAME=${VCELL_SMTP_HOSTNAME}
VCELL_SMTP_PORT=${VCELL_SMTP_PORT}
VCELL_SSH_CMD_RESTORE_TIMEOUT=$VCELL_SSH_CMD_RESTORE_TIMEOUT
VCELL_SSH_CMD_TIMEOUT=$VCELL_SSH_CMD_TIMEOUT
VCELL_SSL_IGNORE_CERT_PROBLEMS=true
VCELL_SSL_IGNORE_HOST_MISMATCH=true
VCELL_SUBMIT_SERVICE_HOST=submit
VCELL_TAG=$VCELL_TAG
VCELL_UPDATE_SITE=http://vcell.org/webstart/${_site_camel}
VCELL_VERSION_NUMBER=$VCELL_VERSION_NUMBER
VCELL_VERS
ION_NUMBER=$VCELL_VERSION_NUMBER
VCELL_VERSION=${_site_camel}_Version_${VCELL_VERSION_NUMBER}_build_${VCELL_BUILD_NUMBER}
VCELL_WEB_DATA_PORT=$VCELL_WEB_DATA_PORT
EOF

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