[Bioclusters] BioPerl 1.2.3 and memory handling

Wed, 10 Nov 2004 13:25:59 -0500

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Hi everybody.

We're new to the Inquiry Xserve scientific cluster and trying to iron 
out a few things.

One thing is we seem to be coming up against is an out of memory 
error when getting large sequence analysis results (5,000 seq - at 
least- and above) back from BTblastall. The problem seems to be with 
BioPerl.

Might anyone here know if BioPerl is knows enough not to try and 
access more than 4gb of RAM in a single process (an OS X limit)? I'm 
told Blastall and BTblastall are and will chunk problems accordingly, 
but we're not certain if BioPerl is when called to merge large Blast 
results back together. It's the default version 1.2.3 that's supplied 
btw, and OS X 10.3.5 with all current updates just short of the 
latest 10.3.6 update.

- Al Tucker
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<div>Hi everybody.</div>
<div><br></div>
<div>We're new to the Inquiry Xserve scientific cluster and trying to
iron out a few things.</div>
<div><br></div>
<div>One thing is we seem to be coming up against is an out of memory
error when getting large sequence analysis results (5,000 seq - at
least- and above) back from BTblastall. The problem seems to be with
BioPerl.</div>
<div><br></div>
<div>Might anyone here know if BioPerl is knows enough not to try and
access more than 4gb of RAM in a single process (an OS X limit)? I'm
told Blastall and BTblastall are and will chunk problems accordingly,
but we're not certain if BioPerl is when called to merge large Blast
results back together. It's the default version 1.2.3 that's supplied
btw, and OS X 10.3.5 with all current updates just short of the latest
10.3.6 update.</div>
<div><br></div>
<div>- Al Tucker</div>
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