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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