I'm curious what are the conditions under which you get such a exceptional speedup. Can you share your input files and/or log files?
-- Szilárd On Thu, Jul 2, 2015 at 2:18 AM, Alex <nedoma...@gmail.com> wrote: > Yup, about 7-8 times between with and without GPU acceleration, not making > this up: I had 11 ns/day and now ~80-87 ns/day, the numbers vary a bit. > I've been getting a similar boost on our GPU-accelerated cluster node (dual > core i7, 8 cores each) with two Tesla C2075 cards (I am directing my > simulations to one of them via -gpu_id). > All runs are -ntomp 4, with or without GPU. The physics in all cases is > perfectly acceptable. So far I only tested my new box on vacuum > simulations, about to run the solvated version (~30K particles). > > Alex > > > On Wed, Jul 1, 2015 at 6:09 PM, Szilárd Páll <pall.szil...@gmail.com> > wrote: > >> Hmmm, 8x sounds rather high, are you sure you are comparing to CPU-only >> runs that use proper SIMD optimized kernels? >> >> Because of the way offload-based acceleration works, the CPU and GPU will >> inherently be executing concurrently only part of the runtime and as a >> consequence the GPU is idle part of the run-time (during >> integration+constraints). You can make use of this idle time by running >> multiple independent simulations concurrently. This can yield serious >> improvements in terms of _aggregate_ simulation performance especially with >> small inputs and many cores (see slide 51 https://goo.gl/7DnSri)/ >> >> -- >> Szilárd >> >> On Wed, Jul 1, 2015 at 4:16 AM, Alex <nedoma...@gmail.com> wrote: >> >>> I am happy to say that I am getting an 8-fold increase in simulation >>> speeds for $200. >>> >>> >>> An additional question: normally, how many simulations (separate mdruns >>> on separate CPU cores) can be performed simultaneously on a single GPU? >>> Say, for 20-40K particle sized simulations. >>> >>> The coolers are not even spinning during a single test (mdrun -ntomp 4), >>> and I get massive acceleration. They aren't broken, the card is just cool >>> (small system, ~3K particles). >>> >>> >>> Thanks, >>> >>> >>> Alex >>> >>> >>> >>> > >>> >>> >>> >>> >>> > >>> >>> Ah, ok, so you can get a 6-pin from the PSU and another from a converted >>> molex connector. That should be just fine, especially as the card should >>> will not pull more than ~155W (under heavy graphics load) based on the >>> Tomshardware review* and you are providing 225W max. >>> >>> >>> >>> * >>> http://www.tomshardware.com/reviews/evga-super-super-clocked-gtx-960,4063-3.html >>> >>> >>> >>> >>> -- >>> >>> Szilárd >>> >>> >>> >>> On Tue, Jun 30, 2015 at 7:31 PM, Alex <nedoma...@gmail.com> wrote: >>> >>> >>> Well, I don't have one like this. What I have instead is this: >>> >>> >>> 1. A single 6-pin directly from the PSU. >>> >>> 2. A single molex to 6-pin (my PSU does provide one molex). >>> >>> 3. Two 6-pins to a single 8-pin converter going to the card. >>> >>> >>> In other words, I can populate both 6-pins on the 6-8 converter, just >>> not sure about the pinouts in this case. >>> >>> >>> Not good? >>> >>> >>> Alex >>> >>> >>> >>> > >>> >>> What I meant is this: http://goo.gl/8o1B5P >>> >>> >>> That is 2x molex -> 8pin PCI-E. A single molex may not be enouhg. >>> >>> >>> >>> -- >>> >>> Szilárd >>> >>> >>> >>> On Tue, Jun 30, 2015 at 7:10 PM, Alex <nedoma...@gmail.com> wrote: >>> >>> >>> It is a 4-core CPU, single GPU box, so I doubt I will be running more >>> >>> than one at a time. We will very likely get a different PSU, unless... >>> >>> I do have a molex to 6 pin concerter sitting on this very desk. Do you >>> >>> think it will satisfy the card? I just don't know how much a single >>> >>> molex line delivers. If you feel this should work, off to installing >>> >>> everything I go. >>> >>> >>> Thanks a bunch, >>> >>> Alex >>> >>> >>> SP> First of all, unless you run multiple independent simulations on the >>> same >>> >>> SP> GPU, GROMACS runs alone will never get anywhere near the peak power >>> >>> SP> consumption of the GPU. >>> >>> >>> SP> The good news is that NVIDIA has gained some sanity and stopped >>> blocking >>> >>> SP> GeForce GPU info in nvidia-smi - although only for newer cars, but >>> it does >>> >>> SP> work with the 960 if you use a 352.xx driver: >>> >>> SP> +------------------------------------------------------+ >>> >>> >>> SP> | NVIDIA-SMI 352.21 Driver Version: 352.21 | >>> >>> >>> SP> >>> |-------------------------------+----------------------+----------------------+ >>> >>> SP> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile >>> Uncorr. >>> >>> SP> ECC | >>> >>> SP> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util >>> Compute >>> >>> SP> M. | >>> >>> SP> >>> |===============================+======================+======================| >>> >>> SP> | 0 GeForce GTX 960 Off | 0000:01:00.0 On | >>> >>> SP> N/A | >>> >>> SP> | 8% 45C P5 15W / 130W | 1168MiB / 2044MiB | 31% >>> >>> SP> Default | >>> >>> SP> >>> +-------------------------------+----------------------+----------------------+ >>> >>> >>> >>> SP> A single 6-pin can deliver 75W, an 8-pin 150W, so in your case, the >>> hard >>> >>> SP> limits of what your card can pull is 75W from the PCI-E slow + 150W >>> from >>> >>> SP> the cable = 225 W. With a single 6-pin cable you'll only get ~150W >>> max. >>> >>> SP> That can be OK if your card does not pull more power (e.g. the above >>> >>> SP> non-overclocked card would be just fine), but as your card is >>> overclocked, >>> >>> SP> I'm not sure it won't peak above 150W. >>> >>> >>> SP> You can try to get a molex -> PCI-E power cable converter. >>> >>> >>> >>> SP> -- >>> >>> SP> Szilárd >>> >>> >>> >>> SP> On Mon, Jun 29, 2015 at 9:56 PM, Alex <nedoma...@gmail.com> wrote: >>> >>> >>> >> Hi all, >>> >>> >> >>> >>> >> I have a bit of a gromacs-unrelated question here, but I think this >>> is a >>> >>> >> better place to ask it than, say, a gaming forum. The Nvidia GTX 960 >>> card >>> >>> >> we got here came with an 8-pin AUX connector on the card side, which >>> >>> >> interfaces _two_ 6-pin connectors to the PSU. It is a factory >>> superclocked >>> >>> >> card. My 525W PSU can only populate _one_ of those 6-pin connectors. >>> The >>> >>> >> EVGA website states that I need at least 400W PSU, while I have 525. >>> >>> >> >>> >>> >> At the same time, I have a dedicated high-power PCI-e slot, which on >>> the >>> >>> >> motherboard says "75W PCI-e". Do I need a different PSU to populate >>> the AUX >>> >>> >> power connector completely? Are these runs equivalent to drawing max >>> power >>> >>> >> during gaming? >>> >>> >> >>> >>> >> Thanks! >>> >>> >> >>> >>> >> Alex >>> >>> >> -- >>> >>> >> 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. >>> >>> >>> >>> >>> >>> -- >>> >>> Best regards, >>> >>> Alex mailto:nedoma...@gmail.com >>> <nedoma...@gmail.com> >>> >>> >>> >>> >>> >>> -- >>> >>> Best regards, >>> >>> Alex mailto:nedoma...@gmail.com >>> <nedoma...@gmail.com> >>> >>> >>> >>> >>> >>> -- >>> >>> Best regards, >>> >>> Alex mailto:nedoma...@gmail.com >>> <nedoma...@gmail.com> >>> >>> -- >>> 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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