Parabricks Quickstart: Earlier Versions

ssh wustlkey@compute1-client-1.ris.wustl.edu

# Use scratch file system for temp space
export SCRATCH1=/scratch1/fs1/${COMPUTE_ALLOCATION}

# Use Active storage for input and output data
export STORAGE1=/storage1/fs1/${STORAGE_ALLOCATION}/Active

# Mapping for the Parabricks license(s) is required
export LSF_DOCKER_VOLUMES="/scratch1/fs1/ris/application/parabricks-license:/opt/parabricks $SCRATCH1:$SCRATCH1 $STORAGE1:$STORAGE1 $HOME:$HOME"
export PATH="/opt/miniconda/bin:$PATH"

# Use host level communications for the GPUs
export LSF_DOCKER_NETWORK=host

# Use debug flag when trying to figure out why your job failed to launch on the cluster
#export LSF_DOCKER_RUN_LOGLEVEL=DEBUG

# Use entry point because the parabricks container has other entrypoints but our cluster, by default, requires /bin/sh
export LSF_DOCKER_ENTRYPOINT=/bin/sh

# Create tmp dir
export TMP_DIR=${STORAGE1}"/parabricks-tmp"
[ ! -d $TMP_DIR ] && mkdir $TMP_DIR