Benchmark / test report

Container name: Singularity.SAMtools-1.13-GCC-10.3.0.localimage.sif

test script

#!/bin/bash

#SBATCH -J plcr-samtools-cpu-test
#SBATCH -N 1
#SBATCH --ntasks-per-node=1

PLCR=${PLCR:-/net/pr2/plcr}
CONT=${1:-Singularity.SAMtools-1.13-GCC-10.3.0.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
wget -q 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshS3AlnRep1.bam'
mv wgEncodeUwRepliSeqSknshS3AlnRep1.bam eg.bam

time singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT samtools sort -n eg.bam -o egs.bam
RC=$?

echo  "Test completed, rc=$RC, "

test results

PLCR test: plcr-samtools-cpu-test
PLCR jobid: 400254
PLCR path: /net/pr2/plcr
Test performed on: pią, 20 maj 2022, 14:38:28 CEST
Testing container: Singularity.SAMtools-1.13-GCC-10.3.0.localimage.sif
Container checksum: 5a363de7d5778ffb08d1cf65941e2f863a42dd2e0d3f3e313d028a787387f01a

[bam_sort_core] merging from 4 files and 1 in-memory blocks...

real    4m3,532s
user    3m58,497s
sys 0m2,581s
Test completed, rc=0,