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Subject: Re: [OMPI users] OpenMPI job initializing problem
From: Jeff Squyres (jsquyres) (jsquyres_at_[hidden])
Date: 2014-03-03 17:51:24


On Mar 3, 2014, at 1:48 PM, Beichuan Yan <beichuan.yan_at_[hidden]> wrote:

> 1. After sysadmin installed libibverbs-devel package, I build Open MPI 1.7.4 successfully with the command:
> ./configure --prefix=/work4/projects/openmpi/openmpi-1.7.4-gcc-compilers-4.7.3 --with-tm=/opt/pbs/default --with-verbs=/hafs_x86_64/devel/usr --with-verbs-libdir=/hafs_x86_64/devel/usr/lib64
>
> 2. Then I rebuild and run my job in hybrid MPI/OPENMP mode: each compute node only runs 1 process (this 1 process runs 16 OPENMP threads), it can get initialized and run well each time with $TCP setting as follows, this is great:
> TCP="--mca btl_tcp_if_include 10.148.0.0/16"
> mpirun $TCP -np 16 -hostfile $PBS_NODEFILE ./paraEllip3d input.txt

If you're using the native verbs API, you don't need that TCP clause.

Also, if you're running in a PBS job, you don't need the -hostfile clause. And if you're running one process per core in the allocated PBS job, you can skip the -np clause, too. You should be able to run with:

    mpirun ./paraEllip3d input.txt

If you want one process per server, then

    mpirun -np <num_servers> --map-by node ./paraEliip3d input.txt

> 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]
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