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Subject: Re: [OMPI users] mpiblast + openmpi + gridengine job faila to run
From: Sangamesh B (forum.san_at_[hidden])
Date: 2008-12-24 01:55:48


Thanks Reuti. That sorted out the problem.

Now mpiblast is able to run, but only on single node. i.e. mpiformatdb
-> 4 fragments, mpiblast - 4 processes. Since each node is having 4
cores, the job will run on a single node and works fine. With 8
processes, the job fails with following error message:

$ cat err.108.OMPI-Blast-Job
[0,1,7][btl_openib_component.c:1371:btl_openib_component_progress]
from compute-0-5.local to: compute-0-11.local error polling HP CQ with
status LOCAL LENGTH ERROR status number 1 for wr_id 12002616 opcode 42
[compute-0-11.local:09692] [0,0,0]-[0,1,2] mca_oob_tcp_msg_recv: readv
failed: Connection reset by peer (104)
[compute-0-11.local:09692] [0,0,0]-[0,1,4] mca_oob_tcp_msg_recv: readv
failed: Connection reset by peer (104)
4 0.674234 Bailing out with signal 15
[compute-0-5.local:10032] MPI_ABORT invoked on rank 4 in communicator
MPI_COMM_WORLD with errorcode 0
5 1.324 Bailing out with signal 15
[compute-0-5.local:10033] MPI_ABORT invoked on rank 5 in communicator
MPI_COMM_WORLD with errorcode 0
6 1.32842 Bailing out with signal 15
[compute-0-5.local:10034] MPI_ABORT invoked on rank 6 in communicator
MPI_COMM_WORLD with errorcode 0
[compute-0-11.local:09692] [0,0,0]-[0,1,3] mca_oob_tcp_msg_recv: readv
failed: Connection reset by peer (104)
0 0.674561 Bailing out with signal 15
[compute-0-11.local:09782] MPI_ABORT invoked on rank 0 in communicator
MPI_COMM_WORLD with errorcode 0
1 0.808846 Bailing out with signal 15
[compute-0-11.local:09783] MPI_ABORT invoked on rank 1 in communicator
MPI_COMM_WORLD with errorcode 0
2 0.81484 Bailing out with signal 15
[compute-0-11.local:09784] MPI_ABORT invoked on rank 2 in communicator
MPI_COMM_WORLD with errorcode 0
3 1.32249 Bailing out with signal 15
[compute-0-11.local:09785] MPI_ABORT invoked on rank 3 in communicator
MPI_COMM_WORLD with errorcode 0

I think its problem with OpenMPI. Its not able to communicate with
processes on another node.
Please help me to get it working on multiple nodes.

Thanks,
Sangamesh

On Tue, Dec 23, 2008 at 4:45 PM, Reuti <reuti_at_[hidden]> wrote:
> Hi,
>
> Am 23.12.2008 um 12:03 schrieb Sangamesh B:
>
>> Hello,
>>
>> I've compiled MPIBLAST-1.5.0-pio app on Rocks 4.3,Voltaire
>> infiniband based Linux cluster using Open MPI-1.2.8 + intel 10
>> compilers.
>>
>> The job is not running. Let me explain the configs:
>>
>> SGE job script:
>>
>> $ cat sge_submit.sh
>> #!/bin/bash
>>
>> #$ -N OMPI-Blast-Job
>>
>> #$ -S /bin/bash
>>
>> #$ -cwd
>>
>> #$ -e err.$JOB_ID.$JOB_NAME
>>
>> #$ -o out.$JOB_ID.$JOB_NAME
>>
>> #$ -pe orte 4
>>
>> /opt/openmpi_intel/1.2.8/bin/mpirun -np $NSLOTS
>> /opt/apps/mpiblast-150-pio_OMPI/bin/mpiblast -p blastp -d
>> Mtub_CDC1551_.faa -i 586_seq.fasta -o test.out
>>
>> The PE orte is:
>>
>> $ qconf -sp orte
>> pe_name orte
>> slots 999
>> user_lists NONE
>> xuser_lists NONE
>> start_proc_args /bin/true
>> stop_proc_args /bin/true
>> allocation_rule $fill_up
>> control_slaves FALSE
>> job_is_first_task TRUE
>
> you will need here:
>
> control_slaves TRUE
> job_is_first_task FALSE
>
> -- Reuti
>
>
>> urgency_slots min
>>
>> # /opt/openmpi_intel/1.2.8/bin/ompi_info | grep gridengine
>> MCA ras: gridengine (MCA v1.0, API v1.3, Component v1.2.8)
>> MCA pls: gridengine (MCA v1.0, API v1.3, Component v1.2.8)
>>
>> The SGE error and output files for the job are as follows:
>>
>> $ cat err.88.OMPI-Blast-Job
>> error: executing task of job 88 failed:
>> [compute-0-1.local:06151] ERROR: A daemon on node compute-0-1.local
>> failed to start as expected.
>> [compute-0-1.local:06151] ERROR: There may be more information available
>> from
>> [compute-0-1.local:06151] ERROR: the 'qstat -t' command on the Grid
>> Engine tasks.
>> [compute-0-1.local:06151] ERROR: If the problem persists, please restart
>> the
>> [compute-0-1.local:06151] ERROR: Grid Engine PE job
>> [compute-0-1.local:06151] ERROR: The daemon exited unexpectedly with
>> status 1.
>>
>> $ cat out.88.OMPI-Blast-Job
>>
>> There is nothing in output file.
>>
>> The qstat shows that job is running at some node. But on that node,
>> there is no mpiblast processes running as seen by top command.
>>
>> The ps command:
>>
>> # ps -ef | grep mpiblast
>> locuz 4018 4017 0 16:25 ? 00:00:00
>> /opt/openmpi_intel/1.2.8/bin/mpirun -np 4
>> /opt/apps/mpiblast-150-pio_OMPI/bin/mpiblast -p blastp -d
>> Mtub_CDC1551_.faa -i 586_seq.fasta -o test.out
>> root 4120 4022 0 16:27 pts/0 00:00:00 grep mpiblast
>>
>> shows this.
>>
>> The ibv_rc_pingpong tests work fine. The output of lsmod:
>>
>> # lsmod | grep ib
>> ib_sdp 57788 0
>> rdma_cm 38292 3 rdma_ucm,rds,ib_sdp
>> ib_addr 11400 1 rdma_cm
>> ib_local_sa 14864 1 rdma_cm
>> ib_mthca 157396 2
>> ib_ipoib 83928 0
>> ib_umad 20656 0
>> ib_ucm 21256 0
>> ib_uverbs 46896 8 rdma_ucm,ib_ucm
>> ib_cm 42536 3 rdma_cm,ib_ipoib,ib_ucm
>> ib_sa 28512 4 rdma_cm,ib_local_sa,ib_ipoib,ib_cm
>> ib_mad 43432 5 ib_local_sa,ib_mthca,ib_umad,ib_cm,ib_sa
>> ib_core 70544 14
>>
>> rdma_ucm,rds,ib_sdp,rdma_cm,iw_cm,ib_local_sa,ib_mthca,ib_ipoib,ib_umad,ib_ucm,ib_uverbs,ib_cm,ib_sa,ib_mad
>> ipv6 285089 23 ib_ipoib
>> libata 124585 1 ata_piix
>> scsi_mod 144529 2 libata,sd_mod
>>
>> What might be the problem?
>> We've used Voltaire OFA Roll from rocks - Gridstack.
>>
>> Thanks,
>> Sangamesh
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
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