[torqueusers] Any one have experience of testing mpiBLAST through PBS

Hong, Xin xinhong at indiana.edu
Wed Apr 16 12:49:55 MDT 2008


Hello All,

I compile mpiBLAST on our linux-rhel4-x86_64 cluster. The test on interactive nodes runs well. However, I get error message with no debug file that were generated. I have no clue but guess it has something to do with PBS. I appreciate any hint on it.

Best,
Xin

xinhong at Quarry: /N/gpfsbr/xinhong/mpiblast/test> more testPBS.e282564
logging to pio.debug.0
logging to logging to pio.debug.1
logging to pio.debug.2
**io No such file or directoryError opening "quarry.fasta"
Fatal Error:
mpiblast_util.cpp(MpiBlast::broadcastFile): Unable to open file
[0] MPI Abort by user Aborting program !
[0] Aborting program!
    p4_error: latest msg from perror: No such file or directory
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.


xinhong at Quarry: /N/gpfsbr/xinhong/mpiblast/test> more testPBS.o282564
mpirun mpiblast exit code ( 0 is normal):
p0_19748:  p4_error: : -1
1
Done!

xinhong at Quarry: /N/gpfsbr/xinhong/mpiblast/test> more testPBS
#PBS -l nodes=2:ppn=2,walltime=1:00:00
#PBS -m ae
#PBS -N testPBS
echo "mpirun mpiblast exit code ( 0 is normal):"
mpirun -np 4 -machinefile $PBS_NODEFILE /N/soft/linux-rhel4-x86_64/mpiblast-1.5.0-pio/bin/mpiblast -p blastn -d mito.nt -i quarry.fasta  -o noninter
active4.out --use-parallel-write --debug=pio.debug
echo $?
echo "Done!"


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