On Thu, Jan 24, 2013 at 6:48 PM, James Starlight <jmsstarli...@gmail.com>wrote:
> 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? > I said in that thread there would not be such a feature. Something being a plug-in means it is not standard. There's never been any mention of PLUMED (or any other plug-in) in the GROMACS manual, which documents the standard features. That's because the authors of GROMACS don't write PLUMED. Other people write plug-ins and document them :-) One of the PLUMED authors wrote that it would be implemented *for* GROMACS 4.6, not *in* GROMACS 4.6. Mark > > James > > 2013/1/24 Szilárd Páll <szilard.p...@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.p...@cbr.su.se > >wrote: > > > >> On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul <jalem...@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> > >>> > >>> ==============================**========== > >>> > >>> -- > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > >>> * Please search the archive at http://www.gromacs.org/** > >>> Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > >>> * Please don't post (un)subscribe requests to the list. Use the www > >>> interface or send it to gmx-users-requ...@gromacs.org. > >>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > >>> > >> > >> > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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