[gmx-users] MPI GPU job failed

[Albert]

Hi, I used your suggested command line, but it failed with the following 
messages:


-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.3
Source code file: 
/home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/gmxlib/gmx_detect_hardware.cpp, 
line: 458

Fatal error:
Incorrect launch configuration: mismatching number of PP MPI processes 
and GPUs per node.
gmx_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Halting program gmx mdrun
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Using 1 MPI process
Using 20 OpenMP threads

2 GPUs user-selected for this run.
Mapping of GPU IDs to the 1 PP rank in this node: 0,1


-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.3
Source code file: 
/home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/gmxlib/gmx_detect_hardware.cpp, 
line: 458

Fatal error:
Incorrect launch configuration: mismatching number of PP MPI processes 
and GPUs per node.
gmx_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------




On 08/11/2016 01:18 PM, jkrieger at mrc-lmb.cam.ac.uk wrote:
> The problem is you compiled gromacs with mpi (hence the default _mpi in
> your command). You therefore need to set the number of mpi processes
> rather than threads. The appropriate command would instead be the
> following:
>
> mpirun -np 2 gmx_mpi mdrun -v -s 62.tpr -gpu_id 01
>
> Alternatively you could compile a different gromacs version without mpi.
> This should have thread-mpi and openmp by default if you leave out
> DGMX_MPI=ON from the cmake command.
>
> Best wishes
> James