khmer speed tests

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

OS X / ReadParser

ged-iworker:speed-test mcrusoe$ grep 'user\|Total' load-log-osx-readparser 
Total number of unique k-mers: 244751
        2.48 real         0.44 user         0.04 sys
Total number of unique k-mers: 244736
        1.26 real         0.69 user         0.04 sys
Total number of unique k-mers: 244766
        2.17 real         1.07 user         0.04 sys
Total number of unique k-mers: 244756
        1.96 real         1.23 user         0.04 sys

OS X / Seqan+Mutex

ged-iworker:speed-test mcrusoe$ grep 'user\|Total' load-log-osx-seqanmutex 
Total number of unique k-mers: 244751
        5.34 real         0.58 user         0.13 sys
Total number of unique k-mers: 244751
        3.37 real         0.67 user         0.21 sys
Total number of unique k-mers: 244750
        4.80 real         0.69 user         0.25 sys
Total number of unique k-mers: 244751
        6.45 real         0.69 user         0.24 sys

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