Page StellarTuning

export CPUPROFILE=stellar.prof
LD_PRELOAD="/usr/lib/libprofiler.so.0" ./stellar -d hs_ref_chr10.fa -q contig_0000aa.fa.2000 -l 30 -k 16 -e 0.03
google-pprof ./stellar stellar.prof

Total: 284 samples
     197  69.4%  69.4%      205  72.2% seqan::_swiftMultiProcessQGram
      16   5.6%  75.0%       24   8.5% void _align_banded_nw_best_ends
       8   2.8%  77.8%       19   6.7% seqan::value (inline)
       6   2.1%  79.9%        6   2.1% _int_malloc
       6   2.1%  82.0%       18   6.3% seqan::_alignBandedSmithWaterman
       5   1.8%  83.8%       11   3.9% seqan::begin (inline)
       4   1.4%  85.2%       13   4.6% seqan::_extendSeedGappedXDropOneDirection
       4   1.4%  86.6%        8   2.8% seqan::host (inline)
       4   1.4%  88.0%       13   4.6% seqan::score (inline)
       3   1.1%  89.1%        9   3.2% seqan::length (inline)
       3   1.1%  90.1%        3   1.1% seqan::move (inline)
       3   1.1%  91.2%        3   1.1% seqan::nextPosition (inline)
       2   0.7%  91.9%        2   0.7% 0x00007fffff6e47e6
       2   0.7%  92.6%        2   0.7% _int_free
       2   0.7%  93.3%        5   1.8% seqan::deallocate
       2   0.7%  94.0%        2   0.7% seqan::end (inline)
       1   0.4%  94.4%        1   0.4% 00007f577cae7040
       1   0.4%  94.7%        4   1.4% 00007f577cae707a
       1   0.4%  95.1%        1   0.4% 0x00007fffff6e4814
       1   0.4%  95.4%        1   0.4% __memmove_ssse3_back
       1   0.4%  95.8%        1   0.4% bool _negativeMerge
       1   0.4%  96.1%        9   3.2% seqan::Segment::operator[] (inline)
       1   0.4%  96.5%        9   3.2% seqan::String::operator[] (inline)
       1   0.4%  96.8%        1   0.4% seqan::_alignBandedSmithWatermanDeclump
       1   0.4%  97.2%        8   2.8% seqan::_allocateStorage (inline)
       1   0.4%  97.5%        1   0.4% seqan::_dataValue (inline)
       1   0.4%  97.9%        1   0.4% seqan::_max (inline)
       1   0.4%  98.2%        1   0.4% seqan::_validStringSetLimits (inline)
       1   0.4%  98.6%        2   0.7% seqan::empty (inline)
       1   0.4%  98.9%        1   0.4% seqan::scoreGapExtend (inline)
       1   0.4%  99.3%        1   0.4% seqan::toSourcePosition (inline)

# Overhead      Command                 Shared Object  Symbol
# ….....  …........  ….........................  …...
#
    12.95%      stellar  ./stellar                     [.] void _align_banded_nw_best_ends, seqan::Alloc >, ExtensionEndPosition, seqan::S
    11.66%      stellar  ./stellar                     [.] int seqan::_extendSeedGappedXDropOneDirection, seqan::Alloc, seqan::Alloc >, seqan::InfixSegment>, seqa
    10.76%      stellar  /lib/libc-2.11.3.so           [.] _int_malloc
     6.83%      stellar  [kernel]                      [.] 0xffffffffff600100
     4.33%      stellar  ./stellar                     [.] int seqan::_localAlignmentNext, seqan::Alloc >, seqan::InfixSegm
     3.82%      stellar  [vdso]                        [.] 0x007fffd8fd4706
     2.99%      stellar  /lib/libc-2.11.3.so           [.] _int_free
     2.47%      stellar  ./stellar                     [.] void _splitAtXDrops, seqan::Alloc >, seqan::InfixSegment
     1.72%      stellar  ./stellar                     [.] T.5958
     1.66%      stellar  ./stellar                     [.] T.5975
     1.64%      stellar  /lib/libc-2.11.3.so           [.] __GI___libc_malloc
     1.36%      stellar  ./stellar                     [.] bool seqan::_swiftMultiProcessQGram, seqan::Alloc >, seqan::Swift, seqan::Alloc >, seqan::ArrayGaps, seqan::Segment, seqan::Pair, void> seqan::_alignBandedSmithWatermanTrace, seqan::Alloc >, seqan::InfixSegment>,
     1.09%      stellar  ./stellar                     [.] bool _extendAndExtract >, seqan::String, seqan::Alloc >, int, d
     0.97%      stellar  /lib/libc-2.11.3.so           [.] __GI___libc_free
     0.88%      stellar  /lib/libc-2.11.3.so           [.] malloc_consolidate
     0.88%      stellar  /usr/lib/libstdc++.so.6.0.13  [.] operator delete(void*)
     0.86%      stellar  ./stellar                     [.] _profileSignalDumpTest(double)
     0.80%      stellar  /lib/libc-2.11.3.so           [.] _wordcopy_fwd_aligned
     0.70%      stellar  ./stellar                     [.] bool _bestExtension, seqan::Alloc >, seqan::InfixSegment>, seqan::Seed::TMatrixPosition seqan::_getNextBestEndPosition(seqan::LocalAlignmentFinder&, int)
     0.51%      stellar  /usr/lib/libstdc++.so.6.0.13  [.] operator new(unsigned long)
     0.45%      stellar  ./stellar                     [.] seqan::Size > >::Type seqan::_clearSpace, unsigned long, seqan::TagGenerous_>(seqan:
     0.43%      stellar  [kernel]                      [k] select_task_rq_fair
     0.39%      stellar  [kernel]                      [k] resched_task
     0.39%      stellar  ./stellar                     [.] void seqan::assign, seqan::String >, seqan::TagGenerous_>(seqan::String, seqan::Alloc
     0.36%      stellar  ./stellar                     [.] void verifySwiftHit, seqan::Alloc >, seqan::InfixSegment>, double, int, unsigned int
     0.33%      stellar  ./stellar                     [.] void seqan::assign, seqan::Alloc >, seqan::InfixSegment>,
     0.33%      stellar  ./stellar                     [.] seqan::Iterator, seqan::Alloc >, seqan::InfixSegment>, se
     0.32%      stellar  [kernel]                      [k] task_rq_lock
     0.27%      stellar  ./stellar                     [.] clock_gettime@plt
     0.27%      stellar  ./stellar                     [.] void seqan::appendValue, unsigned long, seqan::TagGenerous_>(seqan::String >&, unsigned long const
     0.25%      stellar  ./stellar                     [.] void seqan::_finishAlign, seqan::Alloc >, seqan::InfixSegment>, seqan
     0.25%      stellar  [kernel]                      [k] try_to_wake_up
     0.24%      stellar  ./stellar                     [.] seqan::Size, seqan::Alloc > >::Type seqan::_Resize_String const>::resize_ > >::Type seqan::reserve, unsigned long, seqan::TagGenerous_>(seqan::Str
     0.20%      stellar  ./stellar                     [.] seqan::Size > >::Type seqan::reserve, unsigned long, seqan::TagGenerous_>(seqan::String