[gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun
Mark.Abraham at anu.edu.au
Mon Apr 30 07:42:47 CEST 2012
On 30/04/2012 3:38 PM, Anirban Ghosh wrote:
> On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung
> <adeyoung at andrew.cmu.edu <mailto:adeyoung at andrew.cmu.edu>> wrote:
> Typically, I use Gromacs 4.5.5 compiled with automatic threading.
> As you
> know, automatic threading is awesome because it allows me to start
> 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
> So, I must use mpirun to start parallel runs. I have tried this
> 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?
> 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:
> 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
> This starts running my simulation, but when I look in "top", the
> 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
> expect for running on a single CPU -- it is very slow, so I am
> 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
> 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.
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