[gmx-users] gromacs 5.1.2 mdrun can't detect GPU

Szilárd Páll pall.szilard at gmail.com
Fri Apr 22 21:33:05 CEST 2016


Don't get me wrong, I don't think anyone was angry at your post - I
certainly was not. On the contrary, describing this (rather annoying)
problem and suggesting a solution is of good use for the GROMACS community
-- and CUDA application user community in general.

However, it is important to make the correct assessments and draw the
correct conclusions. Therefore, in order to clarify things, I simply meant
to point out that the behavior is not a GPU *detection* issue, but a
software dependency issue. I suggested clarifying this assessment because a
correct diagnosis will allow the readers of your post (both on this list
and on your blog) to better understand the problem and seek the appropriate
solution (to avoid conclusions like GROMACS+CUDA on Ubuntu is problematic
hence one should use Fedora).

If you wish to pinpoint the issue at hand, I suggest the following:
- install an older CUDA version along 7.5, e.g. 6.5
- grab a simple sample code that uses the CUDA runtime (e.g. from the SDK)
- compile it with both nvcc's, older and newer,
- try running both and you'll likely see that the one compiled with the
newer compiler may fail while the other one will work.

I hope this helps, let me know if you want to dig further but you get stuck.


On Fri, Apr 22, 2016 at 6:40 PM, Téletchéa Stéphane <
stephane.teletchea at univ-nantes.fr> wrote:

> Le 22/04/2016 14:33, Szilárd Páll a écrit :
>> Additionally, I suggest amending the post to note that the GDK and NVML
>> that's picked up from it is optional and it is only useful with
>> Quadro/Tesla cards.
> Dear Szilárd,
> I hope I'll find time to produce a proper bug report, but using the Ubuntu
> binaries
> with the ubuntu cuda runtime (so exact same version) 352.xx (same for cuda
> and nvidia driver),
> gromacs failed to detect the GPU. Up-to-now I have not traced down where
> the problems lies.
> This was I think already stated in the previous entry (section at the end:
> To sum up*
> avoid ubuntu packages and install upstream drivers and dependencies*.)
> But since it seems not clear enough I have corrected some typos and added
> the disclaimer
> as requested. I hope Gromacs developper do not feel "angry", this was not
> my goal, I am a long
> term GNU/Linux contributor and keen to echaustive bug reports. This
> article was more a short recipe
> to get it working and not a complaint.
> I hope the clarifications on the web site are now better, and this it may
> help others
> in getting a proprely working installation ...
> Best,
> Stéphane
> --
> Assistant Professor in BioInformatics, 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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