[gmx-users] Short how-to for installing GROMACS with CUDA ...

Szilárd Páll pall.szilard at gmail.com
Thu Dec 17 12:16:56 CET 2015


On Wed, Dec 16, 2015 at 6:21 PM, Téletchéa Stéphane <
stephane.teletchea at univ-nantes.fr> wrote:

> Dear all,
> I have struggled recently in getting gromacs-aware of cuda capabilities.
> After searching for a "while" (one afternoon), I removed the
> ubuntu-provided
> drivers and packages (which worked in the past) and installed everything
> "from scratch".

>From your article:
"It seems that with very recent revisions of gromacs it is not possible
anymore to use the bundled NVIDIA packages from the official Ubuntu
repositories. "

The "incompatibility" can only come from a driver-runtime mismatch or
broken installation, IMO. There is no incompatibility, at least not that I
know of.

If your installation works, e.g. if i) nvidia-smi works and lists your GPU
(meaning that the driver works) ii) you can compile and run CUDA SDK
examples (meaning that the CUDA runtime works and it's compatible with the
driver) , GROMACS should work too!

I suggest you add these two steps to your article because they are quite
essential in diagnosing whether there is something wrong with the driver or
the runtime (/runtime-driver combo).

> It seems this is both coming from NVIDIA requiring the
> "GPU deployment kit" in addition to the cuda toolkit, and from GROMACS
> only warning about the missing NVML (but not failing while asking for GPU
> compilation).

Note that NVML is *recommended* but not mandatory and used to control the
application clocks on the GPU. Note that you can set the applicaiton clocks
manually with nvidia-smi.
(For more details see this blog post by Jiri Kraus:


In short, I have put the executive commands there:
> http://www.steletch.org/spip.php?article89
> As some messages on the list are about this "problem", I thought it would
> be
> helpful to all.
> Best,
> Stéphane
> --
> Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
> Nantes cedex 03, France
> Tél : +33 251 125 636 / Fax : +33 251 125 632
> http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
> --
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