[GE users] SGE 6.1u3 + OpenMPI 1.2.8 - what am I missing?

Chansup Byun chansup.byun at sun.com
Wed Dec 17 13:52:07 GMT 2008


I'm not sure if you checked the following FAQ:

http://www.open-mpi.org/faq/?category=running#run-n1ge-or-sge

- Chansup

On 12/16/08 17:59, Gerald Ragghianti wrote:
> OpenMPI can detect that you are running within SGE, and shouldn't 
> require many of the options to mpirun that you are providing.  I 
> recommend the following submit file:
>
> #$ -V
> #$ -pe OpenMPI 4
> /gpfs/fs0/share/bin/mpirun a.out
>
> Submit the job as follows:
>
> qsub submitfile.txt
>
> Also, make sure that mpirun is the one provided by openmpi 1.2.8.
>
> - Gerald
>
> Alex Chekholko wrote:
>   
>> Hi,
>>
>> I'm running SGE 6.1u3 on x86_64 and I just installed OpenMPI 1.2.8 and I'm trying to get it working.
>>
>> I can run mpirun commands on the headnode, so that works.
>>
>> I can qsub a non-parallel job that runs mpirun, so that works as well, so all my env vars are OK, I think.
>>
>> I'm trying to run a parallel job now, after creating the PE and adding the PE to my queue.
>>
>> # qconf -sp OpenMPI
>> pe_name           OpenMPI
>> slots             256
>> user_lists        NONE
>> xuser_lists       NONE
>> start_proc_args   /bin/true
>> stop_proc_args    /bin/true
>> allocation_rule   $round_robin
>> control_slaves    TRUE
>> job_is_first_task FALSE
>> urgency_slots     min
>>
>> Trying to run a job like this:
>> $ cat mpi/test_mpi.sh 
>> #!/bin/bash
>> /gpfs/fs0/share/bin/mpirun --mca pls_gridengine_verbose 1 --mca plm_rsh_agent ssh -np 4 a.out
>>
>> Where a.out is this code:
>> http://en.wikipedia.org/wiki/Message_Passing_Interface#Example_program
>>
>> via a command like this:
>> qsub -V -pe OpenMPI 4 mpi/test_mpi.sh
>>
>> Get an error output like this:
>> $ cat  test_mpi.sh.e1176114
>> local configuration node-r1-u32-c5-p11-o22.local not defined - using global configuration
>> local configuration node-r1-u32-c5-p11-o22.local not defined - using global configuration
>> Starting server daemon at host "node-r1-u32-c5-p11-o22.local"
>> local configuration node-r1-u32-c5-p11-o22.local not defined - using global configuration
>> Starting server daemon at host "node-r1-u30-c7-p11-o21.local"
>> Starting server daemon at host "node-r4-u15-c24-p16-o16.local"
>> local configuration node-r1-u32-c5-p11-o22.local not defined - using global configuration
>> Starting server daemon at host "node-r2-u34-c3-p14-o18.local"
>> Server daemon successfully started with task id "1.node-r1-u32-c5-p11-o22"
>> Establishing /usr/bin/ssh -o StrictHostChecking=no session to host node-r1-u32-c5-p11-o22.local ...
>> /usr/bin/ssh -o StrictHostChecking=no exited on signal 13 (PIPE)
>> reading exit code from shepherd ... Server daemon successfully started with task id "1.node-r4-u15-c24-p16-o16"
>> Server daemon successfully started with task id "1.node-r1-u30-c7-p11-o21"
>> Establishing /usr/bin/ssh -o StrictHostChecking=no session to host node-r1-u30-c7-p11-o21.local ...
>> /usr/bin/ssh -o StrictHostChecking=no exited on signal 13 (PIPE)
>> reading exit code from shepherd ... Establishing /usr/bin/ssh -o StrictHostChecking=no session to host node-r4-u15-c24-p16-o16.local ...
>> /usr/bin/ssh -o StrictHostChecking=no exited on signal 13 (PIPE)
>> reading exit code from shepherd ... Server daemon successfully started with task id "1.node-r2-u34-c3-p14-o18"
>> Establishing /usr/bin/ssh -o StrictHostChecking=no session to host node-r2-u34-c3-p14-o18.local ...
>> /usr/bin/ssh -o StrictHostChecking=no exited on signal 13 (PIPE)
>> reading exit code from shepherd ... timeout (60 s) expired while waiting on socket fd 5
>>
>> How do I diagnose this "signal 13 (PIPE)" message?  My qlogin/qrsh/qsh are configured per
>> http://gridengine.sunsource.net/howto/qrsh_qlogin_ssh.html
>> except I also added the "-o StrictHostChecking=no"
>>
>> Also, I'm using LDAP for user accounts, does that matter?  One thread I found said I _must_ use local accounts?
>> http://www.open-mpi.org/community/lists/users/2007/03/2826.php
>>
>> What am I missing?
>>
>> Thanks,
>>   
>>     
>
>
>

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