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Subject: Re: [OMPI users] OpenMPI fails to run with -np larger than 10
From: Seyyed Mohtadin Hashemi (haadah_at_[hidden])
Date: 2012-04-13 07:09:30


Hi,

Sorry that it took so long to answer, I didn't get any return mails and had
to check the digest for reply.

Anyway, when i compiled from scratch then i did use the tarballs from
open-mpi.org. GROMACS is not the problem (or at least i don't think so), i
just used it as a check to see if i could run parallel jobs - i am now
using OSU benchmarks because i can't be sure that the problem is not with
GROMACS.

On the new installation i have not installed (nor compiled) OMPI from the
official tarballs but rather installed the "openmpi-bin, openmpi-common,
libopenmpi1.3, openmpi-checkpoint, and libopenmpi-dev" packages using
apt-get.

As for the simple examples (i.e. ring_c, hello_c, and connectivity_c
extracted from the 1.4.2 official tarball) i get the exact same behavior as
with GROMACS/OSU bench.

I suspect you'll have to ask someone familiar with GROMACS about that
> specific package. As for testing OMPI, can you run the codes in the
> examples directory - e.g., "hello" and "ring"? I assume you are downloading
> and installing OMPI from our tarballs?
>

> On Apr 12, 2012, at 7:04 AM, Seyyed Mohtadin Hashemi wrote:
>

> > Hello,
>
>
>
> I have a very peculiar problem: I have a micro cluster with three nodes
> (18 cores total); the nodes are clones of each other and connected to a
> frontend via Ethernet and Debian squeeze as the OS for all nodes. When I
> run parallel jobs I can used up ?-np 10? if I go further the job crashes, I
> have primarily done tests with GROMACS (because that is what I will be
> running) but have also used OSU Micro-Benchmarks 3.5.2.
>
>
>
> For a simple parallel job I use: ?path/mpirun ?hostfile path/hostfile ?np
> XX ?d ?display-map path/mdrun_mpi ?s path/topol.tpr ?o path/output.trr?
>
>
>
> (path is global) For ?np XX being smaller than or 10 it works, however as
> soon as I make use of 11 or larger the whole thing crashes. The terminal
> dump is attached to this mail: when_working.txt is for ??np 10?,
> when_crash.txt is for ??np 12?, and OpenMPI_info.txt is output from
> ?path/mpirun --bynode --hostfile path/hostfile --tag-output ompi_info -v
> ompi full ?parsable?
>
>
>
> I have tried OpenMPI v.1.4.2 all the way up to beta v1.5.5, and all yield
> the same result.
>
>
>
> The output files are from a new install I did today: I formatted all
> nodes and started from a fresh minimal install of Squeeze and used "apt-get
> install gromacs gromacs-openmpi" and installed all dependencies. Then I ran
> two jobs using the parameters described above, I also did one with OSU
> bench (data is not included) it also crashed with ?-np? larger than 10.
>
>
>
> I hope somebody can help figure out what is wrong and how I can fix it.
>
>
>
> Best regards,
>
> Mohtadin
>
>
>
>
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