Provide better diagnostic when 'mpirun' cannot be found.
Also: Does it even make sense to have a default for 'command'?
--Leif
-------- Original Message --------
Subject: Re: [CIG-SHORT] Problem attempting to run on mutiple processors
Date: Mon, 18 Jun 2007 12:09:44 -0700
From: Leif Strand <leif@geodynamics.org>
To: Oliver Boyd <olboyd@usgs.gov>
CC: cig-short@geodynamics.org
References: <006d01c7af9d$96c8b250$c45a16f0$@gov>
<46731FA2.40207@geodynamics.org> <00e701c7b1be$ca3d8340$5eb889c0$@gov>
Oliver,
I apologize for that rather cryptic error message. It usually means it
can't find 'mpirun'.
Naturally, you could alter your PATH so that it can find 'mpirun' in the
context of the job. However, there is a good chance that 'mpirun' isn't
even the right command to use on your cluster.
So, I recommend creating the file ~/.pyre/pylith3d/pylith3d.cfg and
inserting something similar to the following:
[pylith3d.launcher]
command = /full/path/to/mpirun -np ${nodes}
Using a full pathname for 'mpirun' avoids the PATH environment problem.
But more importantly, you will have to edit 'command' so that it
produces the right command for your cluster. For example, if you are
using MPICH2, you would replace 'mpirun' with 'mpiexec'. On many
clusters, there is a special script to use (on our it's "mpirun.lsf")
and "-np ${nodes}" is omitted:
[pylith3d.launcher]
/opt/lsfhpc/6.2/linux2.6-glibc2.3-x86_64/bin/mpirun.lsf
To debug the "launcher" command, run PyLith as follows:
pylith3dapp.py pylith3d.cfg --launcher.dry
This will simply print the launcher command to the console, instead of
actually running it.
--Leif
Oliver Boyd wrote:
>
> Hi Leif,
>
> It looks like when I reinstalled a few of the compute nodes, I
> neglected to update gcc. I’ve now done this, and it appears to work
> fine. Thanks for the hint.
>
> As an aside, could you tell me how I can use the SGE batch system? I
> am not exactly sure why it doesn’t work. I use a program called qsub
> to submit the job. I give it an argument which is a script containing
> the command and a few options, e.g.
>
> > qsub pylith-1.sh
>
> where pylith-1.sh looks like
>
> #!/bin/bash
>
> #$ -cwd
>
> #$ -j y
>
> #$ -S /bin/bash
>
> pylith3dapp.py pylith3d.cfg
>
> The result of this attempt produces
>
> --pyre-start: mpirun: exit 127
>
> /usr/local/bin/pylith3dapp.py:
> /data/Software/Store/pylith3d-0.8.2/pylith3d/pypylith3d: exit 1
>
> Oliver
>
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