[gmx-users] Does GPU support ATI card?

Szilárd Páll szilard.pall at cbr.su.se
Fri Nov 30 00:40:59 CET 2012

Hi Justin,

First of all, thanks for the feedback. I find in unfortunate that this
information got public in the form of a "by the way". More official wording
should follow. I wish it happened differently, but unfortunately things did
not come together as we thought they would. Dragging along code that for
the outsider seems supported, but in reality it is not properly maintained
is not beneficial to anyone. Therefore, we decided to demote mdrun-openmm
from "core" to "contrib" feature status. However, as we don't have a
maintainer for the code yet, the official state is "not fully supported"
contrib feature -- unless we find someone to help with at least minimal
support for 4.6.

I don't like to leave behind my own code, but the situation requires us to
focus our efforts on other things. The plan is to include native GPU
accelerated GB kernels in the next GROMACS release. While there is a good
chance that the code itself will become available in a development branch
rather soon, you will not be able to use this code in release version
before the next release, 5.0.

On Thu, Nov 29, 2012 at 7:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 11/29/12 12:51 PM, Albert wrote:
>> On 11/29/2012 06:44 PM, Szilárd Páll wrote:
>>> Hi Albert,
>>> That claim is false. The current mdrun-opnemm version only supports the
>>> CUDA OpenMM plugin and even that is not fully supported as we don't have
>>> enough resources to maintain the code.
>>> We will make sure to get the false claim of ATI GPU support removed from
>>> the OpenMM website.
>>> Cheers,
>>> --
>>> Szilárd
>>> PS: we are looking for volunteers to maintain the Gromacs OpenMM
>>> integration and in the lack of such people we will have to resort to
>>> dropping OpenMM support post-4.6.
>> Hello Szilard:
>>    thanks for kind comments. If there are not so much people use openMM,
>> probably you can consider give it up. Currently I am using NVIDIA GTX590
>> GPU
>> acceleration with Gromacs4.6 without openMM support, and it works fine (I
>> did
>> some tests comparing with CPU running results for my system). If I were
>> you, I
>> will save my time and energy focus on current version and road.

>  This would be very unfortunate, I think, but I understand the need to
> focus on the most feasible development, using the time people have to
> commit to it, and perhaps priorities are elsewhere.  We invested heavily in
> a few GPU workstations in recent years with the intent of doing a lot of
> GPU-enabled implicit solvent simulations.  Without the GPU, the implicit
> solvent code is severely limited without fixes to the parallelization on
> CPU.

To be honest I am not aware of the limitations you are referring to, nor
the current difference between CPU and GPU implicit solvent performance.

> It seems that the same issues (i.e. one cannot use more than 2 processors
> for a run) still persist thus far in the development of 4.6, with the focus
> of using GPU's in a more

I'm especially not aware of such a limitation and it sounds more like a bug
than a feature.

> generalized way, but without OpenMM, implicit solvent simulations (in my
> hands at least) are not worth it.  Of course, running explicit-solvent
> simulations on GPU is quite nice, but still, the point stands that the
> implicit code is rendered largely obsolete without GPU.

As you rely heavily on implicit solvent code in GROMACS, we could use some
help from you. First and foremost, could you please report in form of a
redmine issue and/or a mail to the dev-list the current issues you are
having/you know of with both CPU and GPU implicit solvent code? We can
continue the discussion on on those topic then.


> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
> --
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