[gmx-users] testing Gromacs 4.6 (git version) on GPUs

Susan Chacko susanc at helix.nih.gov
Wed Oct 31 15:37:33 CET 2012

Hi all,

I wanted to test the built-in support in Gromacs 4.6 (non-OpenMM) for GPUs.
I downloaded the latest git version and it built successfully, appears
to link the right CUDA libraries etc. 

I tried testing it with the Gromacs GPU benchmark suite 

The output md.log file reports:
NOTE: GPU(s) found, but the current simulation can not use GPUs
     To use a GPU, set the mdp option: cutoff-scheme = Verlet
     (for quick performance testing you can use the -testverlet option)

So I tried 'mdrun -s topol.tpr -testverlet' and got:
Program mdrun, VERSION 4.6-dev
Source code file: /usr/local/src/gromacs/gromacs/src/kernel/runner.c, line: 700

Fatal error:
Can only convert old tpr files to the Verlet cut-off scheme with 3D pbc
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Does anyone have a test set that I can use to check the performance of
Gromacs 4.6 on GPUs? I'm more of a sysadmin than a computational chemist, 
so I'm sort of reliant on the provided benchmark suites. 

Any suggestions welcomed and appreciated,

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