[ssml] BLAST fastacmd failed to fetch sequence from database stored on PVFS2 filesystem
jarod at nlbmol.ibp.ac.cn
Wed Dec 5 11:41:40 EST 2007
The architectures are same: same CPU, same MEM.
In the past, every node has a local scratch pool to store BLASTDB, at that
time, BLAST runnings are identical indeed. Recently I turn the local pool
into a PVFS pool, but it complains ...
And I have used BLAST 2.2.15 and the latest 2.2.17, both of the two versions
gave the warnings.
On Wednesday 05 December 2007 23:33, you wrote:
> I think perhaps (maybe) you are crossing architectures by using
> different FS... It doesn't seem like it because both are mounted on
> the same arch, where you run blast / fastacmd / etc. However, I think
> the files prepared on the different underlying file systems need to
> match the arch of the machine that they are hosted on... I think...
> Seems like you have a complex config, however, try running formatdb
> and fastacmd separately on each different disk and try again.
> Sorry for the confused reply, but first try running formatdb on each
> disk and check if the results are identical. If they are identical
> after re-running formatdb the question becomes whether you need to
> recompile formatdb on each different file server.
> Also you could try asking this kind of question on
> bioclusters at bioinformatics.org
> > There is a paper on 2002 (J.D Grant, et al, Bioinformatics 2002, 18(5):
> > 765-766) said they had developed a distributed BLAST and PSI-BLAST on a
> > cluster and the database was really stored on PVFS.
> > Is PVFS2 suitable for storage?
> > --
> > Yun He Ph.D.
> > National Laboratory of Biomacromolecules
> > Institute of Biophysics, Chinese Academy of Sciences
> > 15 Datun Road, Chaoyang District
> > Beijing 100101
> > China
> > Tel: +86 010 6488 8487
> > E-mail: jarod at nlbmol.ibp.ac.cn
> > or jarod at spg.biosci.tsinghua.edu.cn
> > _______________________________________________
> > ssml-general mailing list
> > ssml-general at bioinformatics.org
> > http://www.bioinformatics.org/mailman/listinfo/ssml-general
Yun He Ph.D.
National Laboratory of Biomacromolecules
Institute of Biophysics, Chinese Academy of Sciences
15 Datun Road, Chaoyang District
Tel: +86 010 6488 8487
E-mail: jarod at nlbmol.ibp.ac.cn
or jarod at spg.biosci.tsinghua.edu.cn
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