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Subject: Re: [OMPI users] OpenMPI job initializing problem
From: Gus Correa (gus_at_[hidden])
Date: 2014-03-03 19:11:55


Hi

If I remember right, there were issues in the past with setting TMPDIR
on an NFS share. Maybe the same problem happens on Lustre?

http://arc.liv.ac.uk/pipermail/gridengine-users/2009-November/027767.html

FWIW, we leave it to the default local /tmp, and it works.

Gus Correa

On 03/03/2014 06:57 PM, Jeff Squyres (jsquyres) wrote:
> How about setting TMPDIR to a local filesystem?
>
>
> On Mar 3, 2014, at 3:43 PM, Beichuan Yan<beichuan.yan_at_[hidden]> wrote:
>
>> I agree there are two cases for pure-MPI mode: 1. Job fails with no apparent reason; 2 job complains shared-memory file on network file system, which can be resolved by " export TMPDIR=/home/yanb/tmp", /home/yanb/tmp is my local directory. The default TMPDIR points to a Lustre directory.
>>
>> There is no any other output. I checked my job with "qstat -n" and found that processes were actually not started on compute nodes even though PBS Pro has "started" my job.
>>
>> Beichuan
>>
>>> 3. Then I test pure-MPI mode: OPENMP is turned off, and each compute node runs 16 processes (clearly shared-memory of MPI is used). Four combinations of "TMPDIR" and "TCP" are tested:
>>> case 1:
>>> #export TMPDIR=/home/yanb/tmp
>>> TCP="--mca btl_tcp_if_include 10.148.0.0/16"
>>> mpirun $TCP -np 64 -npernode 16 -hostfile $PBS_NODEFILE ./paraEllip3d
>>> input.txt
>>> output:
>>> Start Prologue v2.5 Mon Mar 3 15:47:16 EST 2014 End Prologue v2.5 Mon
>>> Mar 3 15:47:16 EST 2014
>>> -bash: line 1: 448597 Terminated /var/spool/PBS/mom_priv/jobs/602244.service12.SC
>>> Start Epilogue v2.5 Mon Mar 3 15:50:51 EST 2014 Statistics
>>> cpupercent=0,cput=00:00:00,mem=7028kb,ncpus=128,vmem=495768kb,walltime
>>> =00:03:24 End Epilogue v2.5 Mon Mar 3 15:50:52 EST 2014
>>
>> It looks like you have two general cases:
>>
>> 1. The job fails for no apparent reason (like above), or 2. The job complains that your TMPDIR is on a shared filesystem
>>
>> Right?
>>
>> I think the real issue, then, is to figure out why your jobs are failing with no output.
>>
>> Is there anything in the stderr output?
>>
>> --
>> Jeff Squyres
>> jsquyres_at_[hidden]
>> For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
>>
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