[gmx-users] GPU problem

pratibha kapoor kapoorpratibha7 at gmail.com
Wed Mar 12 14:49:40 CET 2014

Hi users,

I would like to run my job on gpu. I have compiled gromacs version 4.6.1
with cuda 5 in parallel, have changed cutoff scheme to verlet and generated
new *.tpr and finally running:
mdrun -v -deffnm md
I can see following lines in my output:

changing nstlist from 5 to 40, rlist from 1 to 1.084
using 1 MPI process
using 16 OpenMP threads
2 GPUs detected on host
1 GPU auto-selected for this run
Mapping of GPU to the 1PP rank in this node:#0

Note:potentially sub-optimal launch configuration, mdrun_mpi started with
less PP MPI process per node than GPUs available. Each PP MPI process can
use 1 GPU, 1GPU per node will be used.

This means GPU is being utilised. But I can't see any performance
enhancement (not even of 1ns) with this compared to case without GPU.

Is there something wrong in the steps I followed?  Any help is highly

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