robocord.job

#!/bin/bash
#
# This script should be run:
#   sbatch --array=0-3999 robocord.job
# Where the total number of jobs (3999 in the example above) can be
# any number.
#
#SBATCH --job-name=RoboCORD
#SBATCH --output=robocord-output/log-output-%a.txt
#SBATCH --error=robocord-output/log-error-%a.txt
#SBATCH --cpus-per-task 16
#SBATCH --mem=50000
#SBATCH --time=4:00:00
#SBATCH --mail-user=gaurav@renci.org

set -e # Exit immediately if a pipeline fails.

export JAVA_OPTS="-Xmx50G"
export MY_SCIGRAPH=omnicorp-scigraph-$SLURM_ARRAY_TASK_ID

export METADATA_SIZE=$(wc -l < robocord-data/metadata.csv)
export CHUNK_SIZE=$(($METADATA_SIZE/$SLURM_ARRAY_TASK_MAX))
export FROM_ROW=$(($SLURM_ARRAY_TASK_ID * $CHUNK_SIZE))
export UNTIL_ROW=$(($FROM_ROW + $CHUNK_SIZE))
export OUTPUT_FILENAME=robocord-output/result_from_${FROM_ROW}_until_${UNTIL_ROW}.tsv

if [ -f $OUTPUT_FILENAME ]; then
    echo Output filename $OUTPUT_FILENAME already exists, skipping.
else
    echo "Duplicating omnicorp-scigraph so we can use it on multiple clusters"
    cp -R omnicorp-scigraph "scigraphs/$MY_SCIGRAPH"

    echo "Starting RoboCORD from row $FROM_ROW until $UNTIL_ROW."
    sbt "runMain org.renci.robocord.RoboCORD --metadata robocord-data/metadata.csv --from-row $FROM_ROW --until-row $UNTIL_ROW --output-prefix robocord-output/result --neo4j-location scigraphs/$MY_SCIGRAPH robocord-data"

    rm -rf "scigraphs/$MY_SCIGRAPH"
    echo "Deleted duplicated omnicorp-scigraph"
fi