Hi,
I installed MPIBlast 1.4.0 on SGE clusters using SCore as the MPI lib
and everything seems fine.
I also manage to format the database, but however when I submit the job
using command 'mpisub' as below
mpisub 4x2 /usr/local/mpiblast_tool/bin/mpiblast -p blastp -d swissprot
-i swiss.input -o swiss.out
It gives me the following errors
SCOUT: Spawning done.
<0:0> SCORE: 8 nodes (4x2) ready.
Error opening Error opening Error opening /tmp/swissprot.mbf
open: Permission denied
Error/tmp/swissprot.mbf
open: Permission denied
/tmp/swissprot.mbf
open: Permission denied
opening /tmp/swissprot.mbf
open: Permission denied
Fatal Error:
Unable to access fragment list file
[3] MPI Abort by user Aborting program !
[3] Aborting program!
SCOUT: Session done.
In this case, no output is returned. One thing I notice is that the
headnode is trying to access the db segments from its own /tmp (which
doesn't exist but in compute nodes' /tmp).
However when I change the 'Local' variable in .ncbirc from '/tmp' to
some other directory which appear unique to both head node and backend
nodes, it works fine. Or else, I need to use '--removedb' option when
submiting the job to be able to get the output after the job run, this
is peculiar. Also, I notice even with '--removedb' used, the database is
not removed at all. Can someone point out anything I miss? The .ncbirc
looks like below
[NCBI]
Data=/software/man2/ncbi/data
[BLAST]
BLASTDB=/software/man2/mpiblast_data
BLASTMAT=/software/man2/ncbi/data
[mpiBLAST]
Shared=/home/ann/scratch/mpiblast/data/shared
Local=/tmp
Thanks for the help!
--
=============================================================
Ms Ann Jee Lee (Research Associate)
Manchester Computing (The North West Grid)
The University of Manchester,Oxford Road, Manchester, M13 9PL
Tel: +44 161 2757033 Mobile: 079 7658 6374
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