--============_-1112011335==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" 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 --============_-1112011335==_ma============ Content-Type: text/html; charset="us-ascii" <!doctype html public "-//W3C//DTD W3 HTML//EN"> <html><head><style type="text/css"><!-- blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 } --></style><title>BioPerl 1.2.3 and memory handling</title></head><body> <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> </body> </html> --============_-1112011335==_ma============--