[gmx-users] GROMACS on a cluster

Mark Abraham mark.j.abraham at gmail.com
Wed Oct 25 00:38:40 CEST 2017


This is a general issue with using MPI programs, not one specific to
GROMACS. Please read and follow the instructions for your cluster. The MPI
system needs to know how to find gmx_mpi on each rank on each node, but how
you should do this depends whether there's modules in use, or you have to
set the PATH, or you need to specify a full path to gmx_mpi.


On Tue, Oct 24, 2017 at 11:46 PM Ali Ahmed <aa5635737 at gmail.com> wrote:

> Dear GROMACS users
> I need to work on a cluster which has 30 nodes, each has 8 processors
> I need to work on 8 nodes (64 processors). For mdrun I used this command:
>  mpirun -np 64 gmx_mpi mdrun ......
> but the simulation failed to start and here is the error
> --------------------------------------------------------------------------
> mpirun was unable to find the specified executable file, and therefore
> did not launch the job.  This error was first reported for process
> rank 0; it may have occurred for other processes as well.
> NOTE: A common cause for this error is misspelling a mpirun command
>       line parameter option (remember that mpirun interprets the first
>       unrecognized command line token as the executable).
> Node:       login-1
> Executable: gmx_mpi
> --------------------------------------------------------------------------
> 16 total processes failed to start
> I could not figur this error.
> Any suggestions will be appreciated
> Thanks in advance
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