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:
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
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.
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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