Stephen Ficklin wrote:
Hi Joe,
Here's an example of one of the commands I've used:
/usr/local/mpi/bin/mpirun -np 32 -nolocal -machinefile machines
/usr/local/mpiblast/bin/mpiblast -p blastn -i PT_7G4_00005_fil.fas -d
tigr -m 7 -v 3 -b 3 -a 2
Ok, what is in your machines file?
Generally I'll submit this to SGE but I seem to get the same response
whether I run it through SGE or straight on the command line
Ok. For SGE, you want to use $TMPDIR/machines as the machines file, and
submit it with
qsub -pe mpich 32 ... rest of your command line with the -machinefile
$TMPDIR/machines ...
Also, don't use -a 2. This sets the numbe of threads to 2, and this
could be problematic for mpiblast. I am not sure if Aaron and Lucas
have used the -a NCPU switch, or what will happen. There may be some
odd interactions with the mpi libraries. Many mpi's are not thread safe
unless built with the threading options.
Start by taking of the -a 2 (just omit the -a switch entirely). Also
let us know what is in your machine file.
Joe
The tigr database is 4GB divided up using mpiformatdb into 32 pieces. >
Thanks,
Stephen
On Tue, 2006-01-10 at 10:17, Joe Landman wrote:
Stephen Ficklin wrote:
I may be wrong on my assessment, but it appears that when I try to run an
mpiblast that the master node (chosen by the algorithm) does all the work. I'll
get a constant load average of 1 on that node while the program is running. On
the other nodes I barely register any activity. For small database searches I
will get results, but for larger ones it takes too long and patience gives out
or it finishes with errors. The last large job I ran ended with this message
after giving a few results:
NULL_Caption] FATAL ERROR: CoreLib [002.005] 000049_0498_0531: File write
error 0 34645.5 Bailing out with signal -1
[0] MPI Abort by user Aborting program !
[0] Aborting program!
In any case it always seems to overload the master node but the workers seem to
be doing nothing. I've compiled MPIBlast for OSX, Linux and Solaris and I get
the samre response on all three platforms. Before I try an debugging I just
wanted to check to see if anyone had experienced something similar.
Hi Stephen:
Could you tell us how you are launching the job?
Joe
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