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 > > ***************************************************************************** > ** ** > ** WARNING: This email contains an attachment of a very suspicious type. ** > ** You are urged NOT to open this attachment unless you are absolutely ** > ** sure it is legitimate. Opening this attachment may cause irreparable ** > ** damage to your computer and your files. If you have any questions ** > ** about the validity of this message, PLEASE SEEK HELP BEFORE OPENING IT. ** > ** ** > ** This warning was added by the IU Computer Science Dept. mail scanner. ** > ***************************************************************************** > > <Archive.zip>_______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
