[gmx-users] Problem with gromacs-4.6 compilation on Debian

[Szilárd Páll]

Let me add two more things.

Note that we *always* compare performance and acceleration to our
super-tuned state-of-the-art CPU code, which I can confidently say that is
among the fastest if not the fastest to date, and never to some slow (CPU)
implementation. Therefore, while other codes might be able to get 10-20x
with GPUs and many x-es even with pre-Fermi (CC <2.0) cards, for obvious
reasons we simply can't.

Still you'll get high *absolute performance* regardless whether you can use
CPU only or CPU+GPU, so this should be a decent deal, right?

If anybody volunteers to add software-based floating point atomic
operations for CC <2.0 and try running the current kernels on earlier
hardware, I'm willing to give pointers, but I simply had no time to try it
myself. This would enable using earlier cards, with a considerable
performance penalty of emulated atomic ops (plus these cards are anyway
slower), but it *might* be worth a try!

Feel free to drop me a mail if anybody is interested.

Cheers,

--
Szilárd


On Thu, Jan 24, 2013 at 3:48 PM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:

> On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/24/13 9:23 AM, James Starlight wrote:
>>
>>> oh that was simply solved by upgrading of G++ :)
>>>
>>> the only problem which remains is the missing of support of mu GPU :(
>>> That time I've tried to start simulation on simply 2 cores CPU + geforce
>>> 9500
>>>
>>>  From md run I've obtained
>>>>
>>>
>>> NOTE: Error occurred during GPU detection:
>>>        CUDA driver version is insufficient for CUDA runtime version
>>>        Can not use GPU acceleration, will fall back to CPU kernels.
>>>
>>> ED sampling will be performed!
>>> ED: Reading edi file new_a2a_pca_biased.edi
>>> ED: Note: Reference and average structure are composed of the same atom
>>> indices.
>>> ED: Found 1 ED group.
>>> Using 1 MPI thread
>>> Using 2 OpenMP threads
>>>
>>> No GPUs detected
>>>
>>>
>>> I've installed cuda-5.0 with driver
>>> NVRM version: NVIDIA UNIX x86_64 Kernel Module  304.54  Sat Sep 29
>>> 00:05:49 PDT 2012
>>>
>>> that system works fine with the recent nvidia GPU's but has no support
>>> for GeForce 9500.
>>>
>>>
>> GeForce 9500 cards have a compute capability of 1.1.  The minimum
>> required for Gromacs is 2.0 (noted in the installation instructions).
>
>
> Exactly! Anything below CC 2.0 lacks certain features that make those
> devices rather  slow for our algorithms and therefore pretty much
> impractical.
>
> Cheers,
> --
> Szilárd
>
>
>
>
>
>>
>>
>> -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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