job_template_common.txt

#!/bin/bash
#SBATCH --mail-user=${job_email}
#SBATCH --mail-type=${job_email_options}
#SBATCH --nodes=1
#SBATCH --ntasks=${job_ppn}
#SBATCH --time=${job_walltime}
#SBATCH --mem=${job_memory}mb
#SBATCH -o ${job_output_file}

smemwatch -k 90 -d 50 $$$$ &
# List info
uname -a

# Make sure tmp directory is made
mkdir -p $TMPDIR

XNATHOST=${XNAT_HOST}
XNATUSER=${XNAT_USER}
SESSLIMIT=40
SLEEPMAX=300
SLEEPSHORT=120

# Check number of open sessions on host before we download
echo "Checking that we can download"
SLEEPSECS=$[ ( $RANDOM % $SLEEPSHORT ) ]s && echo "$SLEEPSECS" && sleep $SLEEPSECS
while true;do
    SESSID=`curl -s -n "$XNATHOST/data/JSESSION"`
    #echo "JSESSIONID=$SESSID"
    SESSCOUNT=`curl -s -b "JSESSIONID=$SESSID" "$XNATHOST/data/user/$XNATUSER/sessions" | cut -s -f2 -d ":" | cut -f1 -d "}"`
    echo "$SESSCOUNT"
    echo "$SESSLIMIT"
    if (( "$SESSCOUNT" > "$SESSLIMIT" )); then
        echo -n "Cannot download yet, too many open sessions, sleeping "
        curl -s -b "JSESSIONID=$SESSID" -X DELETE "$XNATHOST/data/JSESSION"
	SLEEPSECS=$[ ( $RANDOM % $SLEEPMAX ) ]s && echo "$SLEEPSECS" && sleep $SLEEPSECS
    else
        echo "Looks good, ready to download" 
	curl -s -b "JSESSIONID=$SESSID" -X DELETE "$XNATHOST/data/JSESSION"
        break
    fi
done
#echo "DONE! JSESSIONID=$SESSID"


# Run mega docker
singularity exec --cleanenv --contain --bind /home/$USER/.dax_settings.ini:/home/$USER/.dax_settings.ini --bind /home/$USER/.daxnetrc:/home/$USER/.daxnetrc --bind /nobackup/$USER:/nobackup/$USER --bind /tmp:/tmp --bind /data/mcr/centos7/dax_local/ldax_credentials:/data/mcr/centos7/dax_local/ldax_credentials --bind /data/mcr/centos7/dax_local/bashrc_ldax_megadocker:${HOME}/.bashrc /data/mcr/singularity/mega_docker/vuiiscci_mega_docker_4.2.0-2020-07-13.img scl enable python27 'bash -c "
source ${HOME}/.bashrc && \
export PYTHONNOUSERSITE=TRUE && \
export OPENBLAS_NUM_THREADS=1 && \
export LM_LICENSE_FILE=9327@vm-infr-license.vampire && \
export PYTHONPATH=/data/mcr/masimatlab/trunk/xnatspiders/python/:/data/mcr/masimatlab/trunk/xnatspiders/SpiderUtils/ && \
export PATH=\"$PATH\":/usr/local/matlab/2013a/bin:/data/mcr/fsl5/bin/:/data/mcr/camino/bin/:/data/mcr/masimatlab/trunk/xnatspiders/python/justinlib_v1_1_0/xnatlib:/data/mcr/masimatlab/trunk/xnatspiders/python/justinlib_v1_1_0/pythonlib && \
export FSLDIR=/data/mcr/fsl5 && \
source /data/mcr/fsl5/etc/fslconf/fsl.sh && \
export CAMINO_HEAP_SIZE=30000 && \
export FREESURFER_HOME=/data/mcr/freesurfer && \
export FREESURFER_PBS_TEMPLATE=/data/mcr/masimatlab/trunk/xnatspiders/pbs_templates/FreesurferReconAllWithQC_PBS_template.txt && \
source /data/mcr/freesurfer/SetUpFreeSurfer.sh && \
xvfb-run -a --server-num=$((65536+$$$$)) --server-args=\"-screen 0 1920x1280x24 -ac\" \
${job_cmds}\
"'