On Wed, 23 Jun 2004 10:56:58 -0400, Susan Chacko wrote > I'm seeing exactly this same problem on our systems. It does not Hi Susan and Justin: Ok. Which binary are you using? Did you build it yourself? Is it one of the precompiled ones (including the Scalable Informatics LLC version)? Would you mind sharing it? > appear to be related to hardware, as I see it on all of the following: > - 2.8 GHz Xeon, 2 Gb RAM - 2.8 GHz Xeon, 4 Gb RAM - 1.8 GHz Athlon, 2 > Gb RAM - 1.4 GHz Athlon, 2 Gb RAM - 866 MHz Pentium III, 1 Gb RAM This strongly suggests software, either application or OS. > > They're all running RH 7.1 with updated kernels. I'm using the NCBI > blastall and the NCBI nt db. There aren't any missing libraries, > according to ldd. > > Our databases sit on a Netapp 960 Filer, and at first I thought that > was the problem, but I still see the failures when I copy the db to > local scratch on the nodes. Ok. What happens if you boot one of the units with a "mem=1024M" option, which forces Linux to use only 1 GB ram? There are some oddities that happen at the 4 GB region (really 3.8 GB or so depending upon which kernel you are using). > The problem appears _only_ with the combination of the nt database and > the '-a 2' flag on Blast. It is random, in that I get somewhere > between 5 and 20 failures out of 20 Blast runs with the same db+query. > I get no failures with other dbs (e.g. est) or if I don't use the -a flag. Ok, worth a test on my systems as well. If I build a static binary of blastall, would you be willing to give it a try? RH7.1 means probably i686 optimizations at best. It also means that the 2.96 GCC was probably used. This compiler had some problems generating good (and in some instances, correct) code. > I've also run Blast with the same db+query on an SGI Origin 3400 with > no failures, using -a 2, -a 3, -a 4. I presume this is with the native MIPSpro compilers (very good compilers BTW) and not gcc? > > I've emailed NCBI about this and am waiting for a response. Ok, please let me know if you would like help. Thanks. > > Susan. > > On Jun 16, 2004, at 11:21 AM, Justin Powell wrote: > > > I'm experiencing trouble with blastall 2.2.9 running blastn on a linux > > cluster against a recently downloaded version of the 'nt' database from > > ncbi. Intermittently I get a segmentation fault partway through the > > search. > > > > This happens both with precompiled blast and blast I compile myself. It > > happens on a two dual xeon systems running redhat9.0 and a dual athlon > > system running redhat7.1. Both systems have 4GB ram. It happens with > > several different query sequences, but never with the est nucleotide > > database. It also happens if I use fastacmd to dump the ncbi nt > > database > > into fasta format and then formatdb it myself. Blastdbs are kept > > locally > > so its not a networking issue. > > > > Strangely this also happens with blastall2.2.6 on the athlon system, > > I've > > not tested it on the xeon systems (or other releases). > > > > So I would guess, given the variety of systems, that its a bug which nt > > provokes specifically - but then I assume huge numbers of people must > > use > > blast to search nt on linux boxes and would have noticed already if > > this > > were the case. Anyone have any ideas what might be going on? > > > > > > Justin > > jacp1@mole.bio.cam.ac.uk > > > > _______________________________________________ > > Bioclusters maillist - Bioclusters@bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bioclusters > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman@scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615