Hi Carsten, Thank you so much for the invaluable advice, I'll go for the GTX 980 then.
JJ -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Kutzner, Carsten Sent: Saturday, April 25, 2015 5:03 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5 > On 25 Apr 2015, at 03:39, Jingjie Yeo (IHPC) <ye...@ihpc.a-star.edu.sg> wrote: > > Hi Carsten, > > Thank you so much for the information! Seems like the GTX is the way to go. > One last question, regarding the Maxwell architecture, would there be any > kind of backward compatibility issue, say if I need to use both Gromacs 4.6 > and 5.0, since it is the newest architecture? No problem there. Both 4.6 and 5.0 work fine with GTX 980. Carsten > > JJ > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf > Of Kutzner, Carsten > Sent: Friday, April 24, 2015 5:51 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Optimal GPU setup for workstation with > Gromacs 5 > > Hi JJ, > >> On 24 Apr 2015, at 10:53, Jingjie Yeo (IHPC) <ye...@ihpc.a-star.edu.sg> >> wrote: >> >> Hi Carsten, >> >> Thank you so much for the information! I checked with my vendor on his >> opinions on the GTX and his reply was that GTX cards will not minimize >> calculation errors the way Tesla and Quadro cards will. Do you think this is >> an issue? > The GeForce cards do not offer ECC memory, so they cannot pick up > memory errors occurring on the GPU, which are however very unlikely. > Run an extensive memory check (e.g. memtestCL) before first usage of > the cards. We have tested nearly > 300 GeForce cards, and only 7 of them had problems with memory, so we > replaced them. > > Carsten > > >> >> JJ >> >> -----Original Message----- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf >> Of Kutzner, Carsten >> Sent: Friday, 24 April, 2015 16:40 >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Optimal GPU setup for workstation with >> Gromacs 5 >> >> Hi JJ, >> >>> On 24 Apr 2015, at 03:02, Jingjie Yeo (IHPC) <ye...@ihpc.a-star.edu.sg> >>> wrote: >>> >>> Hi Carsten, >>> >>> In this case of 2 x GTX980, as far as I can tell, the clock speed >>> and GPU ram is significantly lower. For simulations of more >> The GTX 980s have a clock rate of about 1200 MHz, whereas the clock rate of >> the Tesla K40 is 732 MHz. The latter has more CUDA cores, however. >> A rough estimate on how well the GROMACS short-ranged kernels perform on a >> card is the product of clock rate and CUDA cores. In this metric, the GTX >> 980 is slightly better than the K40. In addition, the GTX 980 also has the >> newer Maxwell generation chip, yielding somewhat higher performance due to >> better instruction scheduling. >> >> The amount of GPU memory is almost never an issue with GROMACS unless you >> want to run enormously large MD systems. The largest system that we >> benchmarked had 12 million atoms and this was using 1.2 GB of GPU memory, so >> you could even run a couple of these on a 980. >> >> In our tests with a 2 million atom system on a node with 2x E5-2680v2 >> processors, using two 980s resulted in a 14% increased GROMACS performance >> when compared to using two K40s. >> >> Note that from the money you save by buying GTX instead of Tesla >> cards you can get another node to run another simulation on :) >> >> Carsten >> >> >>> than a million atoms, would it be advisable to go for more cores or more >>> clock speed, or having both is the best case scenario? >>> >>> JJ >>> >>> -----Original Message----- >>> Date: Thu, 23 Apr 2015 08:03:46 +0000 >>> From: "Kutzner, Carsten" <ckut...@gwdg.de> >>> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> >>> Subject: Re: [gmx-users] Optimal GPU setup for workstation with >>> Gromacs 5 >>> Message-ID: <fe42569f-159b-49b1-a644-86a866aaa...@mpibpc.mpg.de> >>> Content-Type: text/plain; charset="us-ascii" >>> >>> Hi, >>> >>>> On 23 Apr 2015, at 08:03, Jingjie Yeo (IHPC) <ye...@ihpc.a-star.edu.sg> >>>> wrote: >>>> >>>> Dear all, >>>> >>>> My workstation specs are 2 x Intel Xeon E5-2695v2 2.40 GHz, 12 Cores. I >>>> would like to combine this with an optimal GPU setup for Gromacs 5 running >>>> simulations with millions of atoms. May I know what are the recommended >>>> setups? My vendor proposed doing a dual K40 Tesla GPU setup, would that be >>>> optimal? >>> I would propose to put two GTX 980 into that machine instead. >>> This will give you the same GROMACS performance at a fraction of the price. >>> >>> Carsten >>> >>>> >>>> Best Regards, >>>> JJ >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >>>> a mail to gmx-users-requ...@gromacs.org. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >>> a mail to gmx-users-requ...@gromacs.org. >> >> -- >> Dr. Carsten Kutzner >> Max Planck Institute for Biophysical Chemistry Theoretical and >> Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany >> Tel. +49-551-2012313, Fax: +49-551-2012302 >> http://www.mpibpc.mpg.de/grubmueller/kutzner >> http://www.mpibpc.mpg.de/grubmueller/sppexa >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry Theoretical and > Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/grubmueller/kutzner > http://www.mpibpc.mpg.de/grubmueller/sppexa > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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