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johandahlberg/performance_test.sh

Created February 11, 2016 14:04
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Quick and dirty performance test of proot at Uppmax
Raw
performance_test.sh
echo "Time in container"
for i in $(seq 1 5)
do
/usr/bin/time -f "time: %e" proot -S debian-sid --bind=/proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-13-3/03-BAM/ samtools mpileup -r 22:1-23096112 /proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-13-3/03-BAM/CEP-13-3.clean.dedup.recal.bam 2>&1 > test.pileup | grep time
done
echo "Time outside container"
for i in $(seq 1 5)
do
/usr/bin/time -f "time: %e" samtools mpileup -r 22:1-23096112 /proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-13-3/03-BAM/CEP-13-3.clean.dedup.recal.bam 2>&1 > test.pileup | grep time
done
Raw
results.txt
Time in container
time: 36.84
time: 38.17
time: 38.46
time: 38.46
time: 40.20
Time outside container
time: 31.57
time: 32.23
time: 31.08
time: 30.54
time: 29.56
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