[Bioperl-l] SeqIO profiling
Ewan Birney
birney@ebi.ac.uk
Thu, 19 Sep 2002 11:24:43 +0100 (BST)
On Tue, 17 Sep 2002, Aaron J Mackey wrote:
>
> With my just-committed patches to Root and RootI (BEGIN->INIT and some
> small optimizations to _rearrange), things are marginally better
> (previously this took around 30 seconds, and _rearrange took more than 7
> seconds of the time):
>
> Total Elapsed Time = 23.99110 Seconds
> User Time = 26.62 Seconds
> Exclusive Times
> %Time ExclSec CumulS #Calls sec/call Csec/c Name
> 16.0 4.270 4.270 119910 0.0000 0.0000 Bio::Root::RootI::_rearrange
> 10.2 2.740 4.700 119910 0.0000 0.0000 Bio::Root::RootI::new
> 8.08 2.150 10.480 47962 0.0000 0.0002 Bio::PrimarySeq::new
> 7.59 2.020 25.150 23982 0.0001 0.0010 Bio::SeqIO::fasta::next_seq
> 6.12 1.630 17.210 23990 0.0001 0.0007 Bio::Seq::BEGIN
> 4.92 1.310 1.310 143892 0.0000 0.0000 Bio::Root::Root::verbose
> 4.43 1.180 3.580 47962 0.0000 0.0001 Bio::PrimarySeq::seq
> 3.08 0.820 0.820 95924 0.0000 0.0000 Bio::PrimarySeq::alphabet
> 2.97 0.790 0.790 119910 0.0000 0.0000 Bio::Root::Root::_create_object
> 2.89 0.770 3.630 23981 0.0000 0.0002 Bio::Annotation::Collection::new
> 2.89 0.770 1.830 23981 0.0000 0.0001 Bio::Annotation::TypeManager::new
> 2.85 0.760 1.490 23981 0.0000 0.0001 Bio::PrimarySeq::_guess_alphabet
> 2.48 0.660 3.510 47962 0.0000 0.0001 Bio::SeqIO::alphabet
> 2.37 0.630 18.190 23981 0.0000 0.0008 Bio::Seq::SeqFactory::create
> 2.22 0.590 0.750 23982 0.0000 0.0000 Bio::Root::IO::_readline
>
> I still don't understand why we're getting 6 times as many
> Bio::Root::RootI::new() calls (and 2 times as many PrimarySeq::new()
> calls) as we are next_seq() calls ... ?!?!
>
Very weird. Of course we build a Bio::Seq and that makes an
annotatiocollection I notice. Perhaps we should build an annotation
collection on demand in here
The clearest optimisation is to have some "special" constructors which
SeqIO knows about which by passes the _rerrange stuff.
> So that folks can play along at home, I've attached the testing script,
> and you can download my test protein database (~5 Mb, compressed) at:
> http://www.people.virginia.edu/~ajm6q/sp_protein.lseg.gz
>
> % perl -d:DProf testSeqIO.pl sp_protein.lseg
> % dprofpp -u
>
> [ ... etc ... ]
>
> -Aaron
>
> On Tue, 17 Sep 2002, Tim Bunce wrote:
>
> > Aaron,
> >
> > Can you send me the script and anything else I'd need to be able
> > to reproduce this data? Inclusing the data file. I'd like to take
> > a look at it (performance tuning is a particular interest of mine).
> >
> > What version of bioperl were you using? 1.0.2, or from the repository?
> >
> > Tim.
> >
> > On Thu, Sep 12, 2002 at 03:40:38PM -0400, Aaron J Mackey wrote:
> > >
> > > here's some more fuel for the fire; this is a profiling run from a
> > > super-simple script that invokes a SeqIO::fasta on a 24K sequence protein
> > > database, and does nothing else but call next_seq ... 24K calls to
> > > next_seq, but 120K calls to _rearrange and BEGIN!!
> > >
> > > Total Elapsed Time = 30.84184 Seconds
> > > User Time = 30.51116 Seconds
> > > Exclusive Times
> > > %Time ExclSec CumulS #Calls sec/call Csec/c Name
> > > 23.0 7.040 6.980 119910 0.0001 0.0001 Bio::Root::RootI::_rearrange
> > > 11.6 3.539 5.530 119914 0.0000 0.0000 Bio::Root::RootI::BEGIN
> > > 9.96 3.039 30.811 23982 0.0001 0.0013 Bio::SeqIO::fasta::next_seq
> > > 8.81 2.689 12.976 47969 0.0001 0.0003 Bio::PrimarySeq::BEGIN
> > > 5.67 1.730 1.658 143892 0.0000 0.0000 Bio::Root::Root::verbose
> > > 5.21 1.589 20.041 23981 0.0001 0.0008 Bio::Seq::new
> > > 3.77 1.150 3.434 47962 0.0000 0.0001 Bio::PrimarySeq::seq
> > > 3.02 0.920 5.134 47962 0.0000 0.0001 Bio::SeqIO::alphabet
> > > 2.92 0.890 2.454 23981 0.0000 0.0001 Bio::Annotation::TypeManager::new
> > > 2.88 0.880 4.514 23981 0.0000 0.0002 Bio::Annotation::Collection::new
> > > 2.75 0.840 0.792 95924 0.0000 0.0000 Bio::PrimarySeq::alphabet
> > > 2.72 0.830 0.850 119917 0.0000 0.0000 Bio::Root::Root::BEGIN
> > > 2.65 0.810 21.299 23981 0.0000 0.0009 Bio::Seq::SeqFactory::create
> > > 2.52 0.770 0.734 71943 0.0000 0.0000 Bio::Annotation::TypeManager::_add
> > > _type_map
> > > 2.43 0.740 1.336 23981 0.0000 0.0001 Bio::PrimarySeq::_guess_alphabet
> > >
> > > here's what the call trace looks like, for each $io->next_seq call:
> > >
> > > Bio::SeqIO::fasta::next_seq
> > > Bio::Root::IO::_readline
> > > File::Temp::BEGIN
> > > Bio::SeqIO::alphabet
> > > Bio::SeqIO::sequence_factory
> > > Bio::Seq::SeqFactory::create
> > > Bio::Seq::SeqFactory::type
> > > Bio::Root::Root::verbose
> > > Bio::Seq::new
> > > Bio::Root::RootI::new
> > > Bio::Root::Root::BEGIN
> > > Bio::Root::Root::verbose
> > > Bio::PrimarySeq::BEGIN
> > > Bio::Root::RootI::new
> > > Bio::Root::Root::BEGIN
> > > Bio::Root::Root::verbose
> > > Bio::Root::RootI::_rearrange
> > > Bio::PrimarySeq::seq
> > > Bio::Root::RootI::_rearrange
> > > Bio::PrimarySeq::validate_seq
> > > Bio::PrimarySeq::alphabet
> > > Bio::PrimarySeq::_guess_alphabet
> > > Bio::PrimarySeq::seq
> > > Bio::Root::RootI::_rearrange
> > > Bio::PrimarySeq::alphabet
> > > Bio::PrimarySeq::display_id
> > > Bio::PrimarySeq::primary_id
> > > Bio::PrimarySeq::desc
> > > Bio::Root::RootI::_rearrange
> > > Bio::Seq::primary_id
> > > Bio::Annotation::Collection::new
> > > Bio::Root::RootI::new
> > > Bio::Root::Root::BEGIN
> > > Bio::Root::Root::verbose
> > > Bio::Annotation::TypeManager::new
> > > Bio::Root::RootI::new
> > > Bio::Root::Root::BEGIN
> > > Bio::Root::Root::verbose
> > > Bio::Annotation::TypeManager::_add_type_map
> > > Bio::Annotation::TypeManager::_add_type_map
> > > Bio::Annotation::TypeManager::_add_type_map
> > > Bio::Annotation::Collection::_typemap
> > > Bio::Seq::annotation
> > > Bio::Seq::primary_seq
> > > UNIVERSAL::isa
> > > Bio::Seq::top_SeqFeatures
> > > Bio::Seq::alphabet
> > > Bio::Seq::primary_seq
> > > Bio::PrimarySeq::alphabet
> > > Bio::SeqIO::alphabet
> > > Bio::PrimarySeq::BEGIN
> > > Bio::Root::RootI::new
> > > Bio::Root::Root::BEGIN
> > > Bio::Root::Root::verbose
> > > Bio::Root::RootI::_rearrange
> > > Bio::PrimarySeq::alphabet
> > > Bio::Root::RootI::DESTROY
> > > Bio::Root::Root::_cleanup_methods
> > > Bio::Seq::DESTROY
> > > Bio::Root::RootI::DESTROY
> > > Bio::Root::Root::_cleanup_methods
> > > Bio::Root::RootI::DESTROY
> > > Bio::Root::Root::_cleanup_methods
> > > Bio::Root::RootI::DESTROY
> > > Bio::Root::Root::_cleanup_methods
> > >
> > >
> > > There's a fair amount of handling in Bio::Root::Root BEGIN that
> > > involves setting up Error usage; a $DONT_USE_ERROR in my test script
> > > improves things a little (down to 25 seconds instead of 30), but doesn't
> > > change much of the profile percentages.
> > >
> > > -Aaron
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
> --
> Aaron J Mackey
> Pearson Laboratory
> University of Virginia
> (434) 924-2821
> amackey@virginia.edu
>
>
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>.
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