[gmx-users] gromacs on GPU

James Starlight jmsstarlight at gmail.com
Mon Jan 7 08:05:53 CET 2013

Today I've tried to test gpu performance on the benchmark system (
explicit solvent with pme )

grompp-gpu -f md_sd.mdp -c conf -p topol.top -o md_test
mdrun-gpu -device
"OpenMM:platform=Cuda,DeviceID=1,Memtest=15,force-device=no" -v
-deffnm md_test

that produce the error

Program mdrun-gpu, VERSION 4.5.5
Source code file: /home/own/gromacs_gpu/src/kernel/openmm_wrapper.cpp,
line: 1365

Fatal error:
OpenMM exception caught while initializating: cudaMemcpyToSymbol:
SetSim copy to cSim failed invalid device symbol
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

In the mailing list archive I've found the same error with the same
card posted some time ago

>From that topic I've understood that 670 graphic card is not supported
yet in Gromacs (4.55). I've checked the manual for the 4.6 beta
version and does not found anything about supporting of that card in
the lattest gromacs realeses as well. IS there any ways to solve that
problem ? Could that error be linked with some others ?  E.g I've
installed nvidia drivers + cuda first and openMM 4.01 than. During
gromacs compilation I've not forced with any errors.

Thanks for help

 2013/1/6 Justin Lemkul <jalemkul at vt.edu>:
> On 1/6/13 1:53 PM, James Starlight wrote:
>> OK!
>> I've compilated gromacs-gpu from the source using that tutorial for
>> the Debian OS
>> http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html
>> The only thing that it lack is the installation mdrun_d-gpu  but i'm
>> not sure that double precission can be used with gpu.
>> Could someone provide me with some tutorial which would show me basic
>> mdrun options with the calculation on my gpu as well as some testing
>> system?
> Everything you need to know (including benchmark systems) is posted at
> http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs.
> The invocation of mdrun-gpu is like any other mdrun, with GPU-specific
> information available by reading mdrun-gpu -h.
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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