[Bioperl-l] [StandAloneBLAST] Use more than one CPU + avoidBLAST reload

Kevin Brown Kevin.M.Brown at asu.edu
Mon Dec 10 18:23:01 UTC 2007


I use the -a option with blast all the time and it works, even on
multicore systems. 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Torsten Seemann
> Sent: Thursday, December 06, 2007 4:58 PM
> To: Sven Boekhoff
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] [StandAloneBLAST] Use more than one 
> CPU + avoidBLAST reload
> 
> Sven,
> 
> > I just started working with Perl and BioPerl. I'm quite 
> impressed what
> > can be easily done with this module. Today I found that my 
> second CPU
> > ist not used, but the first one run's at 100%. I tried to 
> include the
> > "-a"-parameter, but I was not successful:
> 
> My experience agrees with you, in that "-a" does not seem to work with
> the pre-compiled BLAST binaries you get from NCBI on a multi-core
> system.
> 
> I'm not sure why, as "ldd blastall" shows it links against
> "/lib64/tls/libpthread.so.0".
> 
> Any others have any ideas?
> 
> -- 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Monash University
> --Tel +61 3 9905 9010
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