On 30/04/2012 3:38 PM, Anirban Ghosh wrote:
On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung <adeyo...@andrew.cmu.edu <mailto: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.tprI 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?
Get a simple MPI test program and prove how you can run it in parallel. Then worry about GROMACS.
Mark
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