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

Stéphane Téletchéa stephane.teletchea at univ-nantes.fr
Thu Dec 17 16:49:52 CET 2015

Le 17/12/2015 12:16, Szilárd Páll a écrit :

Dear Szilárd,
> Stéphane,
> 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.

Well, this is what I thought also, but nvidia-smi worked correctly, and 
cuda examples
too, so it seems gromacs is more sensitive to the minor number (352.63 
in ubuntu repositories,
352.39 in the cuda driver bundled with the cuda package).

If you wish I can try to reproduce with more debug information, but this 
is what led me to
the article, because other cuda-aware codes seemed to not be affected.

> 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!

Well, no. We can dig on this if you wish, it seemed gromacs for more 
to other cuda codes, but I can provide details if you wish (and open a 
bug report).

> 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).

Well, this seemed weird to me also, but the point is that previously I 
could use
the binaries from the ubuntu repositories and get the proper cuda-aware 
and with the recent packages this is no more the case.
I'm building gromacs with the same scripts as I'm using since 2007, just 
adjusting paths
or option as they evolve, but this is the first time I have to dig that 
much. It may be a
side effect (from the ubuntu packages), but from their repository the 
files were properly
package I think. Again, I can go into details in a bug report if needed.

>> >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:
> http://devblogs.nvidia.com/parallelforall/increase-performance-gpu-boost-k80-autoboost/
> )

Many thanks for the link, i only read the NVML description page, and got 
more or less
to the conclusion that it *should* be helpful, this may also lead to 
more lock-up I think in real
scenarios where dust enter the fan (on personal workstations like in my 
case for instance),
but I'll see from experience.

I'll add a note about this, thanks for the feedback

> Cheers,
> --
> Szilárd



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