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Subject: Re: [OMPI users] Running openMPI job with torque
From: Govind Songara (govind.songara_at_[hidden])
Date: 2010-06-09 16:08:58


Hi Gus,

OpenMPI was not built with tm support.

The submission/execution hosts does not have any of the
PBS environment variable set
PBS_O_WORKDIR, $PBS_NODEFILE.
How i can make set it

regards
Govind

On 9 June 2010 18:45, Gus Correa <gus_at_[hidden]> wrote:

> Hi Govind
>
> Besides what Ralph said, make sure your OpenMPI was
> built with Torque ("tm") support.
>
> Suggestion:
> Do:
>
> ompi_info --all | grep tm
>
> It should show lines like these:
>
> MCA ras: tm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA plm: tm (MCA v2.0, API v2.0, Component v1.4.2)
> ...
>
> ***
>
> If your OpenMPI doesn't have torque support,
> you may need to add the nodes list to your mpirun command.
>
> Suggestion:
>
> /usr/lib64/openmpi/1.4-gcc/bin/mpirun -hostfile $PBS_NODEFILE -np 4 ./hello
>
> ***
>
> Also, assuming your OpenMPI has torque support:
>
> Did you request 4 nodes from torque?
>
> If you don't request the nodes and processors,
> torque will give you the default values
> (which may be one processor and one node).
>
> Suggestion:
>
> A script like this (adjusted to your site), tcsh style here,
> say, called run_my_pbs_job.tcsh:
>
> *********
>
> #! /bin/tcsh
> #PBS -l nodes=4:ppn=1
> #PBS -q default_at_your.torque.server
> #PBS -N myjob
> cd $PBS_O_WORKDIR
> /usr/lib64/openmpi/1.4-gcc/bin/mpirun -np 4 ./hello
>
> *********
>
> Then do:
> qsub run_my_pbs_job.tcsh
>
> **
>
> You can get more information about the PBS syntax using "man qsub".
>
> **
>
> I hope this helps,
> Gus Correa
> ---------------------------------------------------------------------
> Gustavo Correa
> Lamont-Doherty Earth Observatory - Columbia University
> Palisades, NY, 10964-8000 - USA
> ---------------------------------------------------------------------
>
> Ralph Castain wrote:
>
>>
>> On Jun 9, 2010, at 10:00 AM, Govind Songara wrote:
>>
>> Thanks Ralph after giving full path of hello it runs.
>>> But it run only on one rank
>>> Hello World! from process 0 out of 1 on node56.beowulf.cluster
>>>
>>
>> Just to check things out, I would do:
>>
>> mpirun --display-allocation --display-map -np 4 ....
>>
>> That should show you the allocation and where OMPI is putting the procs.
>>
>> there also a error
>>> >cat my-script.sh.e43
>>> stty: standard input: Invalid argument
>>>
>>
>> Not really sure here - must be an error in the script itself.
>>
>>
>>>
>>>
>>> On 9 June 2010 16:46, Ralph Castain <rhc_at_[hidden] <mailto:
>>> rhc_at_[hidden]>> wrote:
>>>
>>> You need to include the path to "hello" unless it sits in your
>>> PATH environment!
>>>
>>> On Jun 9, 2010, at 9:37 AM, Govind wrote:
>>>
>>>
>>>> #!/bin/sh
>>>> /usr/lib64/openmpi/1.4-gcc/bin/mpirun hello
>>>>
>>>>
>>>> On 9 June 2010 16:21, David Zhang <solarbikedz_at_[hidden]
>>>> <mailto:solarbikedz_at_[hidden]>> wrote:
>>>>
>>>> what does your my-script.sh looks like?
>>>>
>>>> On Wed, Jun 9, 2010 at 8:17 AM, Govind <govind.rhul_at_[hidden]
>>>> <mailto:govind.rhul_at_[hidden]>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I have installed following openMPI packge on worker node
>>>> from repo
>>>> openmpi-libs-1.4-4.el5.x86_64
>>>> openmpi-1.4-4.el5.x86_64
>>>> mpitests-openmpi-3.0-2.el5.x86_64
>>>> mpi-selector-1.0.2-1.el5.noarch
>>>>
>>>> torque-client-2.3.6-2cri.el5.x86_64
>>>> torque-2.3.6-2cri.el5.x86_64
>>>> torque-mom-2.3.6-2cri.el5.x86_64
>>>>
>>>>
>>>> Having some problem on running MPI jobs with torque
>>>> qsub -q long -l nodes=4 my-script.sh
>>>> 42.pbs1 <http://42.pbs1.pp.rhul.ac.uk/>
>>>>
>>>>
>>>> cat my-script.sh.e41
>>>> stty: standard input: Invalid argument
>>>>
>>>> --------------------------------------------------------------------------
>>>> mpirun was unable to launch the specified application as
>>>> it could not find an executable:
>>>>
>>>> Executable: hello
>>>> Node: node56.beowulf.cluster
>>>>
>>>> while attempting to start process rank 0.
>>>> ==================================
>>>>
>>>> I could run the binary directly on the node without any
>>>> problem.
>>>> mpiexec -n 4 hello
>>>> Hello World! from process 2 out of 4 on
>>>> node56.beowulf.cluster
>>>> Hello World! from process 0 out of 4 on
>>>> node56.beowulf.cluster
>>>> Hello World! from process 3 out of 4 on
>>>> node56.beowulf.cluster
>>>> Hello World! from process 1 out of 4 on
>>>> node56.beowulf.cluster
>>>>
>>>> Could you please advise, if I missing anything here.
>>>>
>>>>
>>>> Regards
>>>> Govind
>>>>
>>>> _______________________________________________
>>>> users mailing list
>>>> users_at_[hidden] <mailto:users_at_[hidden]>
>>>>
>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>
>>>>
>>>>
>>>>
>>>> -- David Zhang
>>>> University of California, San Diego
>>>>
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>>>>
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>>>
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>>
>>
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