I'm afraid I don't know much/anything about mpiblast -- it looks like
it could be a file system issue. For example, do you have permissions
to read/write /usr/local/aaa.fa, and/or does it already exist on all
the nodes where you're running? (I'm *guessing* that "-i foo" is the
input file)
On Aug 29, 2008, at 10:27 PM, Lee Amy wrote:
Hello,
I use Open MPI 1.2.5 to compile MPIBLAST 1.5, it runs well. When I
run job by this following command:
mpirun -np 21 -mca pls_rsh_agent rsh mpiblast -p blastn -d test.fa -
i /usr/local/aaa.fa -o output
It shows these error messages:
ADIOI_GEN_DELETE (line 22): **io No such file or directoryFatal Error:
mpiblast.cppError reading database mbf file
[gnode1:26957] MPI_ABORT invoked on rank 0 in communicator
MPI_COMM_WORLD with errorcode -1
4 0.010139 Bailing out with signal 15
[gnode2:11975] MPI_ABORT invoked on rank 4 in communicator
MPI_COMM_WORLD with errorcode 0
20 0.01599 Bailing out with signal 15
[gnode1:26961] MPI_ABORT invoked on rank 20 in communicator
MPI_COMM_WORLD with errorcode 0
16 0.00986695 Bailing out with signal 15
[gnode5:10829] MPI_ABORT invoked on rank 16 in communicator
MPI_COMM_WORLD with errorcode 0
5 0.0122449 Bailing out with signal 15
[gnode2:11976] MPI_ABORT invoked on rank 5 in communicator
MPI_COMM_WORLD with errorcode 0
1 0.0102971 Bailing out with signal 15
[gnode1:26958] MPI_ABORT invoked on rank 1 in communicator
MPI_COMM_WORLD with errorcode 0
17 0.012876 Bailing out with signal 15
[gnode5:10830] MPI_ABORT invoked on rank 17 in communicator
MPI_COMM_WORLD with errorcode 0
6 0.014256 Bailing out with signal 15
[gnode2:11977] MPI_ABORT invoked on rank 6 in communicator
MPI_COMM_WORLD with errorcode 0
2 0.0124009 Bailing out with signal 15
[gnode1:26959] MPI_ABORT invoked on rank 2 in communicator
MPI_COMM_WORLD with errorcode 0
18 0.0144899 Bailing out with signal 15
[gnode5:10831] MPI_ABORT invoked on rank 18 in communicator
MPI_COMM_WORLD with errorcode 0
7 0.016083 Bailing out with signal 15
[gnode2:11978] MPI_ABORT invoked on rank 7 in communicator
MPI_COMM_WORLD with errorcode 0
3 0.011174 Bailing out with signal 15
[gnode1:26960] MPI_ABORT invoked on rank 3 in communicator
MPI_COMM_WORLD with errorcode 0
19 0.0175061 Bailing out with signal 15
[gnode5:10832] MPI_ABORT invoked on rank 19 in communicator
MPI_COMM_WORLD with errorcode 0
12 0.00988579 Bailing out with signal 15
[gnode4:13462] MPI_ABORT invoked on rank 12 in communicator
MPI_COMM_WORLD with errorcode 0
13 0.012902 Bailing out with signal 15
[gnode4:13463] MPI_ABORT invoked on rank 13 in communicator
MPI_COMM_WORLD with errorcode 0
14 0.0149741 Bailing out with signal 15
[gnode4:13464] MPI_ABORT invoked on rank 14 in communicator
MPI_COMM_WORLD with errorcode 0
15 0.016958 Bailing out with signal 15
[gnode4:13465] MPI_ABORT invoked on rank 15 in communicator
MPI_COMM_WORLD with errorcode 0
8 0.0100341 Bailing out with signal 15
[gnode3:13459] MPI_ABORT invoked on rank 8 in communicator
MPI_COMM_WORLD with errorcode 0
9 0.0302022 Bailing out with signal 15
[gnode3:13460] MPI_ABORT invoked on rank 9 in communicator
MPI_COMM_WORLD with errorcode 0
10 0.032104 Bailing out with signal 15
[gnode3:13461] MPI_ABORT invoked on rank 10 in communicator
MPI_COMM_WORLD with errorcode 0
11 0.0338449 Bailing out with signal 15
[gnode3:13462] MPI_ABORT invoked on rank 11 in communicator
MPI_COMM_WORLD with errorcode 0
And the job stop. However, I don't know why this problem happened.
Could you tell me how to fix that?
Huge thanks to you.
Best Regards,
Amy Lee
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Jeff Squyres
Cisco Systems
