Hi James:
[EMAIL PROTECTED] wrote:
Hi,
I am having some problems getting mpiblast to run correctly, I have
verified that blastall works against the input files, however when I try
to run mpiblast with them it behaves as follows:
ok ...
I run the following command: /opt/mpi/bin/mpirun -machinefile
machines -np 34 -nolocal
/usr/local/mpiblast-1.4/bin/mpiblast
--config-file=/users01/jlowey/mpiblast/mpiblast.conf --debug -p blastn
-d other_genomic -i /users01/jlowey/mpiblast/len100_320000.fa -o
mpioutput_32.txt
Could you use a "-v" on the mpirun command line as well? Might help to
see some of the messages from mpi.
I starts running, and in debug mode it copies the fragments to the
worker nodes, then the only process doing any work is on the fist node
in the list, it runs for several hours then dies. Nothing is in the
output file.
Does it stop working after a particular size? That is, if you divide
your input file in half, does it work? By a 1/10?
While it is running for several hours, are you sure the other nodes are
not doing anything? Have you run top on them? On the node with the
process running, what do top and vmstat 1 report for memory usage?
You might try running without the -nolocal switch (just don't start the
job on the head node).
Here is a snippet of the input file being used:
1 of 600000 Length 100 P1: 0.2500 0.2500 0.2500 0.2500 rand Fri Feb 03 14:03:38
2006
CACGTAAGCGTGCACGAAATATAAACATAGGTGCTAGCTTACCGGGTCATGCAAAACTGGTTGCAACAGTCTCCTAGCGTACTGTTAATAGCTTGCGCGG
2
TCAGCCGGCGCCTCCTCCATCTACAGAAGGTGAAGACCAGGCACGAACCCCGTAGACCAGAGCAGAATAACTTAAGGGGTAGTGCAAAACGTAATGGATT
3
GCGCAGTAAACCAGCCTCTATGCCATGGAACAGCACGGCCTCGGCGCCTAAAATTGAGAGCAACCAGCGGTTCTTTTACTGTCCATCGAGGACACTAGTC
.
.
.
319998
TCTATCATGAAAAACGTTCTTGGGGGCTCGACCTCGGACAGTATGGGCTCATAATTAATGGATTATCAAGTATAATTCTCTCGGTAAGAGAAGACCTCGA
319999
GTAGGAACGCTATATAGATCATTACTTTCGCTTGAGAACTAAATCAACGGTTGTAAGGTACGCGATGGTCCAGACGCAGACTTCCATCGGTGTTTGCTTT
320000
TTACGCCTTGATCAGGAACTAAGGAAACTTCTGTAGCACCATCCTTTAGAGGTTGACGGACGAGTCCGCAATTTCACTTTAAAGATGTATTCCAGACGTA
mpiblast works fine using another input file, I have verified this. Any ideas
what is going on??
Thanks,
James
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