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Subject: Re: [OMPI users] Help: MPIBLAST Crash
From: Brock Palen (brockp_at_[hidden])
Date: 2008-09-02 09:09:28


Check out the first error:
> ADIOI_GEN_DELETE (line 22): **io No such file or directoryFatal Error:
> mpiblast.cppError reading database mbf file

Check to make sure all your files are in place.
Also many times you need to set you .ncbirc

Brock Palen
www.umich.edu/~brockp
Center for Advanced Computing
brockp_at_[hidden]
(734)936-1985

On Aug 30, 2008, at 1:27 AM, 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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