Jobscript

Example job script used to test application installation:

#!/bin/bash
#SBATCH --job-name=structure_threader_1.3.10_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=2gb
#SBATCH --time=24:00:00
#SBATCH --output=structure_threader_1.3.10_test.log

echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/structure_threader/1.3.10
TEST_DATADIR=${TEST_PWD}/example_data
TEST_WORKDIR=${TEST_PWD}/test_output

cd ${TEST_PWD}

module load structure/2.3.4
module load structure_threader/1.3.10

# Remove any previous test results and re-create a working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir ${TEST_WORKDIR}
cd ${TEST_WORKDIR}


echo "Starting test run at $(date) on $(hostname)..."

###################################
structure_threader \
    run \
    -K 4 \
    -i ${TEST_DATADIR}/TestData/SmallTestData.structure \
    -o ${TEST_WORKDIR}/output \
    -t ${SLURM_CPUS_ON_NODE:-4} \
    -st ${HPC_STRUCTURE_BIN}/structure
###################################

# There should be some files in the work directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR}/output -type f ! -empty -ls

echo "Test complete at $(date)."