Benchmark / test report

Container name: Singularity.Exonerate-2.4.0-foss-2021b.localimage.sif

test script

#!/bin/bash

#SBATCH -J plcr-exonerate-cpu-test
#SBATCH -N 1
#SBATCH --ntasks-per-node=48
#SBATCH -A plgcyfsoftware2022-cpu
#SBATCH -t 05:00:00

PLCR="/net/ascratch/people/plgklimas/Exonerate"
CONT="Singularity.Exonerate-2.4.0-foss-2021b.localimage.sif"

#PLCR2="/net/pr2/plcr"
#PLCR='/net/pr2/scratch/people/plgklimas/bowtie'

echo "PLCR test: $SLURM_JOB_NAME"
echo "PLCR jobid: $SLURM_JOBID"
echo "PLCR path: $PLCR"

echo "Test performed on: "`date`
echo "Testing container: $CONT"
SHA=`dd bs=1M if=$PLCR/images/$CONT 2>/dev/null | sha256sum | cut -d' ' -f1`
echo "Container checksum: $SHA"

cd $TMPDIR

wget 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz' 
gzip -dk hg38.fa.gz
mv $TMPDIR/hg38.fa $TMPDIR/hg38.fasta

singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT prefetch ERR2356727
singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT fastq-dump ERR2356727/ERR2356727.sra 
sed -n '1~4s/^@/>/p;2~4p' ERR2356727.fastq > ERR2356727.fasta
time singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT exonerate ERR2356727.fasta hg38.fasta --cores 48
RC=$?
echo  "Test completed, rc=$RC, "

test results

PLCR test: plcr-exonerat# Benchmark / test report

Container name: Singularity.PSI4-1.3.2-foss-2021b-Python-3.9.6.localimage.sif


## test script

```bash
#!/bin/bash

#SBATCH -J plcr-psi4-cpu-test-2
#SBATCH -N 1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=38
#SBATCH --exclusive

PLCR=${PLCR:-/net/pr2/plcr}
CONT=${1:-Singularity.PSI4-1.3.2-foss-2021b-Python-3.9.6.localimage.sif}

echo "PLCR test: $SLURM_JOB_NAME"
echo "PLCR jobid: $SLURM_JOBID"
echo "PLCR path: $PLCR"

echo "Test performed on: "`date`
echo "Testing container: $CONT"
SHA=`dd bs=1M if=$PLCR/images/$CONT 2>/dev/null | sha256sum | cut -d' ' -f1`
echo "Container checksum: $SHA"

cd $TMPDIR
cat > input << EOF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EOF
cat input | base64 -d | gzip -d > input.dat
export OMP_PROC_BIND=close
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
export NUM_THREADS=$SLURM_CPUS_PER_TASK
export PSI_SCRATCH="$TMPDIR/"
time srun --cpu-bind=cores singularity -s run -B $PWD:/host_pwd -B "$TMPDIR/" --pwd /host_pwd $PLCR/images/$CONT psi4 -i input.dat -o output.dat -n $SLURM_CPUS_PER_TASK -s "$TMPDIR/" #NTASKS
RC=$?
grep 'Wall Time:' timer.dat | tail -1 | awk '{print $3" s"}'  > result
echo  "Test completed, rc=$RC, " $(cat result)

test results

2022-10-24T13:37:05 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2022-10-24T13:37:06 prefetch.3.0.0: 1) Downloading 'ERR2356727'...
2022-10-24T13:37:06 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2022-10-24T13:37:06 prefetch.3.0.0:  Downloading via HTTPS...
2022-10-24T13:37:13 prefetch.3.0.0:  HTTPS download succeed
2022-10-24T13:37:13 prefetch.3.0.0:  'ERR2356727' is valid
2022-10-24T13:37:13 prefetch.3.0.0: 1) 'ERR2356727' was downloaded successfully
2022-10-24T13:37:13 prefetch.3.0.0: 'ERR2356727' has 0 unresolved dependencies
Read 1222704 spots for ERR2356727/ERR2356727.sra
Written 1222704 spots for ERR2356727/ERR2356727.sra
Test completed, rc=0,