[gmx-users] multiple GPU on multiple nodes

cyberjhon cyberjhon at hotmail.com
Tue Feb 4 01:52:02 CET 2014

Dear Szilárd 

Thanks for your answer.

To submit the job I do;

qsub -l nodes=2:ppn=16,walltime=12:00:00 

Then, to run gromacs I can do:
aprun -n 1 mdrun_mpi -deffnm protein

And, I get the message that you mention, which is good
"1 GPU detected on host nid00900:" does not mean that only one GPU was

But If I do:
aprun -n 2 mdrun_mpi -deffnm protein

I get the error mentioned before
Program mdrun_mpi, VERSION 4.6.2
Source code file:
/N/soft/cle4/gromacs/gromacs-4.6.2/src/gmxlib/gmx_detect_hardware.c, line:

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

Even if I use -gpu_id 0 or -gpu_id 00, they do not work

I also tried what you told me before about CRAY_CUDA_MPS  and
export CRAY_CUDA_MPS= 1 
export CRAY_CUDA_PROXY=1   

I executed these commands before the aprun, and they did not work

So, can you tell me what is the command that you use on BW to use the GPU
located in each node?


John Michael

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