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Subject: Re: [OMPI users] Open MPI program cannot complete
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2010-10-25 13:39:30


Can you use the interactive mode of PBS to get 5 cores on 1 node? IIRC, "qsub -I ..." ?

Then you get a shell prompt with your allocated cores and can run stuff interactively. I don't know if your site allows this, but interactive debugging here might be *significantly* easier than try to automate some debugging.

On Oct 25, 2010, at 1:35 PM, Jack Bryan wrote:

> thanks
>
> I have to use #PBS to submit any jobs in my cluster.
> I cannot use command line to hang a job on my cluster.
>
> this is my script:
> --------------------------------------
> #!/bin/bash
> #PBS -N jobname
> #PBS -l walltime=00:08:00,nodes=1
> #PBS -q queuename
> COMMAND=/mypath/myprog
> NCORES=5
>
> cd $PBS_O_WORKDIR
> NODES=`cat $PBS_NODEFILE | wc -l`
> NPROC=$(( $NCORES * $NODES ))
>
> mpirun -np $NPROC --mca btl self,sm,openib $COMMAND
>
> -------------------------------------------
>
> Where should I put the (gdb --batch -ex 'bt full' -ex 'info reg' -pid ZOMBIE_PID) in the script ?
> And how to get ZOMBIE_PID from the script ?
>
> Any help is appreciated.
>
> thanks
>
> Oct. 25 2010
>
> Date: Mon, 25 Oct 2010 19:24:35 +0200
> From: jed_at_[hidden]
> To: users_at_[hidden]
> Subject: Re: [OMPI users] Open MPI program cannot complete
>
> On Mon, Oct 25, 2010 at 19:07, Jack Bryan <dtustudy68_at_[hidden]> wrote:
> I need to use #PBS parallel job script to submit a job on MPI cluster.
>
> Is it not possible to reproduce locally? Most clusters have a way to submit an interactive job (which would let you start this thing and then inspect individual processes). Ashley's Padb suggestion will certainly be better in a non-interactive environment.
>
> Where should I put the (gdb --batch -ex 'bt full' -ex 'info reg' -pid ZOMBIE_PID) in the script ?
>
> Is control returning to your script after rank 0 has exited? In that case, you can just put this on the next line.
>
> How to get the ZOMBIE_PID ?
>
> "ps" from the command line, or getpid() from C code.
>
> Jed
>
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-- 
Jeff Squyres
jsquyres_at_[hidden]
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