On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung <adeyo...@andrew.cmu.edu>wrote:
> Hi, > > Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you > know, automatic threading is awesome because it allows me to start parallel > runs without calling mpirun. So on version 4.5.5, I can start a job on > eight > CPUs using simply the command: > > mdrun -s topol.tpr -nt 8 > > However, now I am using a different node on my department's cluster, and > this node instead has Gromacs 4.5.4 (compiled without automatic threading). > So, I must use mpirun to start parallel runs. I have tried this command: > > mpirun -machinefile mymachines -np 8 mdrun -s topol.tpr > > I suppose this mdrun executable is not mpi-enabled. Have you compiled mdrun with "--enable-mpi" option? -Anirban > where mymachines is an (extensionless) file containing only the text "c60 > slots=8". (c60 is the name of the node that I am using.) > > I get this error message: > > "Missing: program name. Program mdrun either does not exist, is not > executable, or is an erroneous argument to mpirun." > > This is strange, because mdrun is, I think, in my path. For example, if I > type "mdrun -h", I get the manual page for mdrun (version 4.5.4). > > Then I tried the command "which mdrun", and it gave me this output: > > /usr/local/gromacs/bin/mdrun > > So, next I tried to call mdrun via mpirun using the specific path for > mdrun: > > mpirun -machinefile mymachines -np 8 /usr/local/gromacs/bin/mdrun -s > topol.tpr > > This starts running my simulation, but when I look in "top", the simulation > is only running on a single CPU; there is only one entry for mdrun in > "top", > and it has only %CPU=100 (not eight different entries for mdrun, nor one > entry with %CPU=800). Also, the simulation is going at the speed I would > expect for running on a single CPU -- it is very slow, so I am convinced > that, as "top" suggests, mdrun is running on only one CPU. > > Strangely, my colleagues are able to run jobs in parallel using the exact > commands that I described above. So apparently something is wrong with my > user ID, although there are no error messages (except the error message > about "Missing: program name" that I described). > > If you have time, do you have any suggestions for other things that I can > try? Do you think that something could be wrong with my bashrc file? > > Thanks for your time! > > Andrew DeYoung > Carnegie Mellon University > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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