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mr-c/Linux khmer speed test

Created December 15, 2014 17:07
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khmer speed tests
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Linux khmer speed test
for threads in {1..12}
do echo Threads: ${threads}
sudo su -c "echo 3 > /proc/sys/vm/drop_caches"
/usr/bin/time load-into-counting.py --threads ${threads} --report-total-kmers null data/25k-casava1_8.fq.bz2
done |& tee load-log2-readparser
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mr-c commented Dec 15, 2014

OS X / Seqan+spinlocks

ged-iworker:speed-test mcrusoe$ grep 'user\|Total' load-log-osx-seqan-spin2 
Total number of unique k-mers: 244751
        3.57 real         0.59 user         0.14 sys
Total number of unique k-mers: 244749
        4.16 real         0.79 user         0.14 sys
Total number of unique k-mers: 244746
        4.48 real         1.06 user         0.13 sys
Total number of unique k-mers: 244745
        4.64 real         1.29 user         0.12 sys

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