[Bioclusters] new on using clusters: problem running mpiblast (2)
Zhiliang Hu
hu at animalgenome.org
Fri Aug 31 15:55:42 EDT 2007
I did more trials on fixing possible problems with "mpiblast"
installations.
Now I have compiled
mpiblast-1.4.0 along with ncbi tool kit (June 2005), with
mpicc --version
gcc (GCC) 4.1.1 20070105 (Red Hat 4.1.1-52)
and run it with
mpirun (Open MPI) 1.2.3,
as following, and have errors:
> /opt/openmpi.gcc/bin/mpirun -np 14 -machinefile /home/zhu/tests/new/machines /home/local/bin/mpiblast -p blastp -i
./bait.fasta -d ecoli.aa > blastoutput.txt
1 0.087774 Bailing out with signal 11
[node001:13274] MPI_ABORT invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 0
0 0.0933368 Bailing out with signal 15
[node001:13273] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 0
13 0.13855 Bailing out with signal 15
[node001:13286] MPI_ABORT invoked on rank 13 in communicator
MPI_COMM_WORLD with errorcode 0
2 0.0967469 Bailing out with signal 15
[node001:13275] MPI_ABORT invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 0
3 0.1011 Bailing out with signal 15
[node001:13276] MPI_ABORT invoked on rank 3 in communicator MPI_COMM_WORLD
with errorcode 0
4 0.105819 Bailing out with signal 15
[node001:13277] MPI_ABORT invoked on rank 4 in communicator MPI_COMM_WORLD
with errorcode 0
5 0.109716 Bailing out with signal 15
[node001:13278] MPI_ABORT invoked on rank 5 in communicator MPI_COMM_WORLD
with errorcode 0
6 0.113549 Bailing out with signal 15
[node001:13279] MPI_ABORT invoked on rank 6 in communicator MPI_COMM_WORLD
with errorcode 0
7 0.117464 Bailing out with signal 15
[node001:13280] MPI_ABORT invoked on rank 7 in communicator MPI_COMM_WORLD
with errorcode 0
8 0.120678 Bailing out with signal 15
[node001:13281] MPI_ABORT invoked on rank 8 in communicator MPI_COMM_WORLD
with errorcode 0
9 0.124318 Bailing out with signal 15
[node001:13282] MPI_ABORT invoked on rank 9 in communicator MPI_COMM_WORLD
with errorcode 0
10 0.127826 Bailing out with signal 15
[node001:13283] MPI_ABORT invoked on rank 10 in communicator
MPI_COMM_WORLD with errorcode 0
11 0.131605 Bailing out with signal 15
[node001:13284] MPI_ABORT invoked on rank 11 in communicator
MPI_COMM_WORLD with errorcode 0
12 0.135169 Bailing out with signal 15
[node001:13285] MPI_ABORT invoked on rank 12 in communicator
MPI_COMM_WORLD with errorcode 0
Does anyone has clues what this is and possibly point me to the right
direction for a fix?
Thanks!
Zhiliang
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