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? 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.
