data/docker/swarm/serverconfig-uch.sh

#!/usr/bin/env bash

shopt -s -o nounset

if [ "$#" -ne 6 ]; then
    echo "usage: config.sh SITE (REPO/NAMESPACE | NAMESPACE) TAG VCELL_VERSION_NUMBER VCELL_BUILD_NUMBER OUTPUTFILE"
    exit 1
fi

_site=$1
_repo=$2
_tag=$3
_version_number=$4
_build_number=$5
_outputfile=$6

echo "args: | $1 | $2 | $3 | $4 | $5 | $6 |"

_site_lower=$(echo "$_site" | tr '[:upper:]' '[:lower:]')
_site_upper=$(echo "$_site" | tr '[:lower:]' '[:upper:]')
_site_camel="${_site_upper:0:1}${_site_lower:1:100}"


VCELL_SITE="${_site_upper}"
VCELL_REPO_NAMESPACE=$_repo
VCELL_TAG=$_tag
VCELL_VERSION_NUMBER=$_version_number
VCELL_BUILD_NUMBER=$_build_number
#SLURM parameter values
vcell_slurm_partition=vcell
vcell_slurm_reservation=
vcell_slurm_qos=vcell
vcell_slurm_partition_pu=vcellpu
vcell_slurm_reservation_pu=vcellpu
vcell_slurm_qos_pu=vcellpu


case $VCELL_SITE in
	REL)
		_site_port_offset=0
		VCELL_API_HOST_EXTERNAL=vcell.cam.uchc.edu
		VCELL_S3_EXPORT_BASEURL=https://vcell.cam.uchc.edu
		VCELL_API_PORT_EXTERNAL=443
		VCELL_API_PREFIX_V0="/api/v0"
		VCELL_API_PREFIX_V1="/api/v1"
		_applicationId="1471-8022-1038-5553"
		;;
	ALPHA)
		_site_port_offset=2
		VCELL_API_HOST_EXTERNAL=vcell-dev.cam.uchc.edu
		VCELL_S3_EXPORT_BASEURL=https://vcell-dev.cam.uchc.edu
		VCELL_API_PORT_EXTERNAL=443
		VCELL_API_PREFIX_V0="/api/v0"
		VCELL_API_PREFIX_V1="/api/v1"
		_applicationId="1471-8022-1038-5554"
		;;
	TEST)
		_site_port_offset=3
		# VCELL_API_PORT_EXTERNAL=8081
		VCELL_API_HOST_EXTERNAL=vcell-stage.cam.uchc.edu
		VCELL_S3_EXPORT_BASEURL=https://vcell-stage.cam.uchc.edu
		VCELL_API_PORT_EXTERNAL=443
		VCELL_API_PREFIX_V0="/api/v0"
		VCELL_API_PREFIX_V1="/api/v1"
		_applicationId="1471-8022-1038-5555"
		;;
	*)
		printf 'ERROR: Unknown site: %s\n' "$1" >&2
		;;
esac

VCELL_DB_URL="jdbc:oracle:thin:@vcell-oracle.cam.uchc.edu:1521/ORCLPDB1"
VCELL_DB_DRIVER="oracle.jdbc.driver.OracleDriver"
VCELL_DB_USER="vcell"
VCELL_DEBUG_PORT_BASE=5000
VCELL_JMS_SIM_HOST_EXTERNAL=$VCELL_API_HOST_EXTERNAL
VCELL_MONGO_HOST_EXTERNAL=$VCELL_API_HOST_EXTERNAL
VCELL_BATCH_HOST="hpc-ext-1.cam.uchc.edu,hpc-ext-2.cam.uchc.edu,hpc-ext-3.cam.uchc.edu,hpc-ext-4.cam.uchc.edu"
#VCELL_BATCH_HOST=vcell-service.cam.uchc.edu
VCELL_SLURM_CMD_SBATCH=sbatch
VCELL_SLURM_CMD_SACCT=sacct
VCELL_SLURM_CMD_SQUEUE=squeue
VCELL_SLURM_CMD_SCANCEL=scancel
VCELL_SLURM_PARTITION=$vcell_slurm_partition
VCELL_SLURM_RESERVATION=$vcell_slurm_reservation
VCELL_SLURM_QOS=$vcell_slurm_qos
VCELL_SLURM_PARTITION_PU=$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=/local/singularityImages
VCELL_SLURM_CENTRAL_SINGULARITY_DIR=/share/apps/vcell3/singularityImages
VCELL_SLURM_SINGULARITY_MODULE_NAME=singularity/vcell-3.10.0

VCELL_JMS_SIM_PORT_EXTERNAL=$((61616 + _site_port_offset))
VCELL_JMS_SIM_RESTPORT_EXTERNAL=$((8161 + _site_port_offset))
VCELL_MONGO_PORT_EXTERNAL=$((27017 + _site_port_offset))
VCELL_HTC_NODELIST=
VCELL_BATCH_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-batch:${VCELL_TAG}"
VCELL_BATCH_SINGULARITY_FILENAME="${VCELL_BATCH_DOCKER_IMAGE//[\/:]/_}.img"
VCELL_BATCH_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_BATCH_SINGULARITY_FILENAME}"
VCELL_OPT_DOCKER_IMAGE="${VCELL_REPO_NAMESPACE}/vcell-opt:${VCELL_TAG}"
VCELL_OPT_SINGULARITY_FILENAME="${VCELL_OPT_DOCKER_IMAGE//[\/:]/_}.img"
VCELL_OPT_SINGULARITY_IMAGE_EXTERNAL="${VCELL_SLURM_LOCAL_SINGULARITY_DIR}/${VCELL_OPT_SINGULARITY_FILENAME}"
VCELL_SMTP_HOSTNAME=vdsmtp.cam.uchc.edu
VCELL_SMTP_PORT=25
VCELL_SMTP_EMAILADDRESS=VCell_Support@uchc.edu
VCELL_EXPORT_BASEURL=http://vcell.org/export/
VCELL_EXPORTDIR_HOST=/opt/vcelldata/export/
VCELL_MAX_JOBS_PER_SCAN=100
VCELL_MAX_ODE_JOBS_PER_USER=100
VCELL_MAX_PDE_JOBS_PER_USER=40
VCELL_SSH_CMD_TIMEOUT=10000
VCELL_SSH_CMD_RESTORE_TIMEOUT=5

#
# write out the environment file to be for:
# 1. deployment actions (e.g. deploy-installers.sh)
# 2. runtime environment for the docker stack run command (kubernetes uses ConfigMaps in vcell-fluxcd repo), what about VCell Installers?
#
cat <<EOF >"$_outputfile"
VCELL_API_HOST_EXTERNAL=$VCELL_API_HOST_EXTERNAL
VCELL_API_PORT_EXTERNAL=$VCELL_API_PORT_EXTERNAL
VCELL_API_PREFIX_V0=$VCELL_API_PREFIX_V0
VCELL_API_PREFIX_V1=$VCELL_API_PREFIX_V1
VCELL_BATCH_DOCKER_IMAGE=$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=/usr/local/deploy
VCELL_EXPORT_BASEURL=$VCELL_EXPORT_BASEURL
VCELL_S3_EXPORT_BASEURL=$VCELL_S3_EXPORT_BASEURL
VCELL_EXPORTDIR_HOST=$VCELL_EXPORTDIR_HOST
VCELL_HTC_NODELIST=$VCELL_HTC_NODELIST
VCELL_HTCLOGS_EXTERNAL=/share/apps/vcell3/htclogs
VCELL_HTCLOGS_HOST=/opt/vcelldata/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=/usr/local/deploy
VCELL_N5_DATADIR_HOST=/share/apps/vcell3/n5
VCELL_SIMDATADIR_ARCHIVE_EXTERNAL=/share/apps/vcell12/users
VCELL_SIMDATADIR_ARCHIVE_INTERNAL=/share/apps/vcell12/users
VCELL_SIMDATADIR_ARCHIVE_HOST=/share/apps/vcell12/users
VCELL_SIMDATADIR_EXTERNAL=/share/apps/vcell3/users
VCELL_SIMDATADIR_HOST=/opt/vcelldata/users
VCELL_SIMDATADIR_SECONDARY_EXTERNAL=/share/apps/vcell7/users
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_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_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=$VCELL_SSH_CMD_TIMEOUT
VCELL_SSL_IGNORE_CERT_PROBLEMS=false
VCELL_SSL_IGNORE_HOST_MISMATCH=true
VCELL_SUBMIT_SERVICE_HOST=submit
VCELL_TAG=$VCELL_TAG
VCELL_UPDATE_SITE=http://vcell.org/webstart/${_site_camel}
VCELL_VERSION_NUMBER=$VCELL_VERSION_NUMBER
VCELL_VERSION=${_site_camel}_Version_${VCELL_VERSION_NUMBER}_build_${VCELL_BUILD_NUMBER}
EOF