Afraid I have no idea how those packages were built, what release they correspond to, etc. I would suggest sticking with the tarballs.

Your output indicates a problem with shared memory when you completely fill the machine. Could be a couple of things, like running out of memory - but for now, try adding -mca btl ^sm to your cmd line. Should work.


On Apr 13, 2012, at 5:09 AM, Seyyed Mohtadin Hashemi wrote:

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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