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

Linux / Seqan+spinlocks

(env)mcrusoe@athyra:~/khmer/gl-master$ grep 'user\|Total' load-log2-spinlocks1                                                                                                                                                                                                          
Total number of unique k-mers: 244751
0.68user 0.06system 0:03.40elapsed 21%CPU (0avgtext+0avgdata 19600maxresident)k
Total number of unique k-mers: 244750
1.26user 0.06system 0:02.40elapsed 55%CPU (0avgtext+0avgdata 19616maxresident)k
Total number of unique k-mers: 244750
1.21user 0.03system 0:01.78elapsed 69%CPU (0avgtext+0avgdata 19720maxresident)k
Total number of unique k-mers: 244747
1.56user 0.04system 0:01.77elapsed 90%CPU (0avgtext+0avgdata 21648maxresident)k
Total number of unique k-mers: 244745
1.71user 0.02system 0:01.61elapsed 107%CPU (0avgtext+0avgdata 19748maxresident)k
Total number of unique k-mers: 244741
2.25user 0.05system 0:01.71elapsed 134%CPU (0avgtext+0avgdata 21568maxresident)k
Total number of unique k-mers: 244740
2.55user 0.05system 0:01.79elapsed 144%CPU (0avgtext+0avgdata 21792maxresident)k
Total number of unique k-mers: 244746
3.34user 0.03system 0:01.83elapsed 184%CPU (0avgtext+0avgdata 19784maxresident)k
Total number of unique k-mers: 244745
4.25user 0.03system 0:02.27elapsed 188%CPU (0avgtext+0avgdata 21752maxresident)k
Total number of unique k-mers: 244745
5.23user 0.04system 0:02.23elapsed 236%CPU (0avgtext+0avgdata 21760maxresident)k
Total number of unique k-mers: 244744
6.46user 0.04system 0:01.82elapsed 357%CPU (0avgtext+0avgdata 23936maxresident)k
Total number of unique k-mers: 244747
8.00user 0.05system 0:02.16elapsed 371%CPU (0avgtext+0avgdata 21740maxresident)k

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