I'm using precompliled 2.2.9 from the NCBI and same for my 2.2.6. I also have compiled 2.2.9 myself on both systems, with the same result. justin On Wed, 23 Jun 2004, Joe Landman wrote: > 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 > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters >