[gmx-users] gromacs gpu code

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 7 10:49:21 CEST 2015


The CUDA support within the GROMACS CMake setup is not designed with such a
use in mind - only mdrun supports GPU acceleration now, and I have heard
very few suggestions of analysis tasks that are sufficiently
computationally demanding vs IO intensive to warrant even CPU-based
parallelism. Nonetheless, such a thing can likely be done. I would suggest
you get some experience building/reviewing the CMake support of a CUDA tool
that is simpler than mdrun. Our setup is complex because we try to do all
manner of auto-detection to make it easier for inexperienced users to build
GROMACS, so having some general CMake+CUDA experience will make
understanding what we do easier.


On Tue, Jul 7, 2015 at 10:30 AM Wayne Liang <chungwen.liang at gmail.com>

> Dear developers,
> I would like to write a new gromacs tool which can make use of GPU. I
> have some experience for implementing new analysis tools since gmx3.3
> (but only for cpu). I plan to write a cuda kernel that can be called
> from standard c code (g_xxx.c).
> I was trying to dig into nbnxn_cuda folder to find some hints of compiling
> cuda and c codes together. However, the CMakeList.txt makes me a bit
> confused.
> I would like to know is there any templates (CMakeList) I can refer
> to? or any other source that i can learn from? Thanks for all the
> suggestions.
> Best,
> Chungwen
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