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

[Christoph Junghans]

> Date: Thu, 24 Jan 2013 15:55:13 +0100
> From: Szil?rd P?ll <szilard.pall at cbr.su.se>
> Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
>         Debian
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <CANnYEw7Q3U_8aMyY=Bzds0vveb_DG7FVC+pbkAcoPH8JZm4YFA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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.
Always check the following 10 points before believing the speed-up of any code:
<http://www.hpcwire.com/hpcwire/2011-12-13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus.html>

And Gromacs does a pretty fair comparison.
>
> 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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>>
>>
>
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> End of gmx-users Digest, Vol 105, Issue 119
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--
Christoph Junghans
Web: http://www.compphys.de