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

[James Starlight]

Justin, Szilárd, thanks for suggestion!

It will be easily for me to found a better card :)

By the way in other topics some developments told me that the Plumed
plugin for methadynamics will be realised in gromacs 4.6. I've checked
for it in manual but could not find any notions about it . Have it
been included in newest Gromacs?


James

2013/1/24 Szilárd Páll <szilard.pall at cbr.su.se>:
> 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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>>
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