Hi
I am having problems getting mpiBLAST running, I have formatted the database
using the following command:
/export/home/software/mpiblast/bin/mpiformatdb --nfrags=4
--config-file=/export/home/other/ol8/TraceDB/human/mpiblast/mpiblast.conf
--debug -i tracedb -o T -p F
Then submit the job the the sun grid engine:
mpisub 4x4 /export/home/software/mpiblast/bin/mpiblast -np 4 -p blastp -d
tracedb -i test.fasta -o test.out --debug=debug
--config-file=/export/home/other/ol8/.mpiblastrc
It seems to start the jobs okay and shows one job running on the master node
and 4 on slave nodes. However I left it running and it still hadn't
completed many hours later. This is only a small test database too.
Looking at the error output from mpiblast.sh.e38334 there is an error saying
it can't find the index files (see below) even though this database
definitely exists in the correct location. Below are the error logs, the
database .nal index file and also output from the debug mode of mpiblast.
Also my .ncbirc file - the Shared and Local directories are definitely
present and can be accessed by all nodes on the cluster so it's confusing as
to why it isn't finding the database indexes. I've even tried adding
the "--config-file"
switch when starting mpiblast to point it directly to the config file but
still get the same error.
If anyone has any clue as to what the problem is it would be much
appreciated! If any more information is needed to sort this out let me know.
Hope someone can help...
-----------------------------------------
job error log:
SCOUT: Spawning done.
<0:0> SCORE: 16 nodes (4x4) ready.
logging to debug.3
logging to debug.12logging to logging to debug.logging to logging to
debulogging tologging to debu
logging to logging to debug.2
logging to debug.0
logging to lllogging to debug.1
l10
debug.13
g.6
debug.8
g.4
debug.9
debug.5
debug.14
ogging to debug.7
ogging to debug.15
ogging to debug.11
[blastall] WARNING: testseq: Could not find index files for database
/export/home/other/ol8/TraceDB/human/mpiblast/tracedb
[blastall] WARNING: testseq: Could not find index files for database
/export/home/other/ol8/TraceDB/human/mpiblast/tracedb
[blastall] FATAL ERROR: testseq: Database
/export/home/other/ol8/TraceDB/human/mpiblast/tracedb was not found or does
not exist
----------------------------------
tracedb.nal index file:
#
# Alias file created Thu Dec 21 12:01:41 2006
#
#
TITLE /export/home/other/ol8/TraceDB/human/mpiblast/tracedb
#
DBLIST /export/home/other/ol8/TraceDB/human/mpiblast/tracedb.000
/export/home/other/ol8/TraceDB/human/mpiblast/tracedb.001
/export/home/other/ol8/TraceDB/human/mpiblast/tracedb.002
/export/home/other/ol8/TraceDB/human/mpiblast/tracedb.003
#
#GILIST
#
#OIDLIST
#
-----------------------------------
.ncbirc file:
[NCBI]
Data=/export/home/software/ncbi/data/
[BLAST]
BLASTDB=/export/home/other/ol8/TraceDB/human/mpiblast/
BLASTMAT=/export/home/software/ncbi/data/
[mpiBLAST]
Shared=/export/home/other/ol8/TraceDB/human/mpiblast/
Local=/export/home/other/ol8/TraceDB/human/mpiblast/
------------------------------------------------
OUTPUT for debug files:
newton human/mpiblast> more debug.0
[0] 0.00608611 Locking fragment list
[0] 0.00616407 Locked fragment list
[0] 0.00790095 broadcasting file size of 5010
[0] 0.0298522 file size broadcasted
[0] 0.0302792 broadcasting file
[0] 0.0337241 file broadcasted
[0] 0.0337451 initializing ncbi ...blastall -n -p 4 -p blastp -i
test.fasta -o test.out -d
/export/home/other/ol8/TraceDB/human/mpiblast/tracedb
[0] 0.033802
(0) done initializing ncbi.
[0] 0.041579 Init blast error code 0
---------------------------------
newton human/mpiblast> more debug.1
[1] 0.00703812 Temp name base:
/export/home/other/ol8/TraceDB/human/mpiblast/test.fastaXXXXXX
[1] 0.011822 Got temp name:
/export/home/other/ol8/TraceDB/human/mpiblast/test.fastaY7B4Lm
[1] 0.0118461 waiting for file size broadcast
[1] 0.0299661 received file size broadcast of 5010
[1] 0.0299971 opening receive file
/export/home/other/ol8/TraceDB/human/mpiblast/test.fastaY7B4Lm
[1] 0.0333071 receiving file to
/export/home/other/ol8/TraceDB/human/mpiblast/test.fastaY7B4Lm
[1] 0.0337682 received file broadcast
[1] 0.240331 Query file received as
/export/home/other/ol8/TraceDB/human/mpiblast/test.fasta
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