Thanks for the info. I tried with GMX_EMULATE_GPU=1 preceding the mdrun line, crashed after 100 steps. Is that the expected behavior?
On Fri, Jun 5, 2015 at 2:46 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: > On Fri, Jun 5, 2015 at 10:39 PM, Alex <nedoma...@gmail.com> wrote: > > In that case, I am a bit lost, as I was sure GMXRC needed modification. > > :)). Since I never ran anything on GPU and have an mdrun line that looks > > like > > > > mdrun -nt 4 -s <tpr> -c <final structure> > > gmx mdrun -ntomp 4 > > No need to do domain decomposition. Even with CPU runs it'll be faster > if you don't. > > > what should be added to trigger the behavior you're suggesting? I > > understand that it will likely blow up the system, but for the heck of > > it... > > those environment variables I mentioned. Plus timer resetting, e.g. > with -resethway if you want reliable timings. > > > I am now looking at the stats and see that (NxN QSTab + LJ) and (NxN > QSTab > > [F]) take up about 86% of all flops in my simulation. Which of those get > > offloaded? > > All of that will be offloaded. However, those are theoretical (useful) > flops, the timing table on the bottom is more relevant. Set the > GMX_CYCLE_SUBCOUNTER=ON breakdown of the "Force". > > However, if you just follow the previous emulate+skip non-bondeds > advise, you'll get a run that does the offload except that it skips > calculating - which is useful because you have no GPU to calculate > with. > > > Thank you, > > > > Alex > > > > > > On Fri, Jun 5, 2015 at 2:26 PM, Szilárd Páll <pall.szil...@gmail.com> > wrote: > > > >> Hi Alex, > >> > >> Why do you think GMXRC needs to be changed? You simply need to set > >> those env. vars to trigger the GPU code-path - and you will likely > >> have to freeze the system, otherwise it will probably not run more > >> than a few steps without seeing an explosion. Based on this you'll > >> know how fast you can run with GPU offload, but you can also > >> guesstimate how fast of a GPU you need (based on the PME+Bonded force > >> calculation time + publicly available CUDA kernel performance). > >> > >> Cheers, > >> -- > >> Szilárd > >> > >> > >> On Fri, Jun 5, 2015 at 10:13 PM, Alex <nedoma...@gmail.com> wrote: > >> > Hi Szilárd, > >> > > >> > Well, yes, it is an old CPU, but I am actually quite content with the > >> > ns/day performance it churns out on all four cores. I'm looking at > >> > > >> > http://manual.gromacs.org/documentation/5.1-beta1/user-guide/environment-variables.html > >> > and it is my understanding that GMXRC needs to be changed to include > >> those > >> > flags, but no recompiling is required. Is that correct? > >> > > >> > Thanks, > >> > > >> > Alex > >> > > >> > > >> > On Fri, Jun 5, 2015 at 1:52 PM, Szilárd Páll <pall.szil...@gmail.com> > >> wrote: > >> > > >> >> Hi Alex, > >> >> > >> >> That's a quite old CPU so it's hard to tell how fast is it, you'll > >> >> have to try. There are ways to "guesstimate" how fast does your GPU > >> >> have to be to keep up with your CPU cores (hint search for > >> >> GMX_EMULATE_GPU / GMX_NO_NONBONDED on the list). > >> >> > >> >> In any case, unless your CPU is so slow that it balances well with > the > >> >> 750Ti, I would strongly recommend that you get a GTX 960 which will > >> >> cost just a bit more, but it will be 1.6-1.8x faster at computing > >> >> non-bonded interactions. > >> >> > >> >> On Fri, Jun 5, 2015 at 9:08 PM, Alex <nedoma...@gmail.com> wrote: > >> >> > Hi all, > >> >> > > >> >> > We're about to start a bit of a toy project to test GPU-accelerated > >> GMX. > >> >> > What I have here is my old workstation (Dell Precision T3500: > >> Quad-core > >> >> > Xeon W3530 @ 2.8 GHz, 12 gigs of RAM) running Linux Mint 17.1. The > >> plan > >> >> is > >> >> > to get something like GeForce GTX 750 ( > >> >> > > >> >> > >> > http://www.amazon.com/GeForce-750Ti-GDDR5-Graphics-GTX750TI-OC-2GD5/dp/B00IB9P1KG/ref=sr_1_3?ie=UTF8&qid=1433529993&sr=8-3&keywords=Nvidia+GTX750 > >> >> > ) > >> >> > and maybe a new PSU. > >> >> > > >> >> > Questions: > >> >> > > >> >> > 1. With a card like this, how much acceleration (very > approximately) > >> can > >> >> we > >> >> > expect in a "standard" simulation (protein+lipid+water, PME > >> >> electrostatics)? > >> >> > >> >> In PME simulations you should see about 3x speedup, more if you are > >> >> lucky and possibly a little less if you are not so lucky with the > >> >> computational workload. What FF are you using? > >> >> > >> >> > 2. Should we put any extra considerations into cooling? We expect > >> >> week-long > >> >> > runs, and I am not sure these cards have this type of hardcore > gaming > >> in > >> >> > mind. :) > >> >> > >> >> I don't think so, but it depends how stuffed or dusty is that Dell > >> >> workstation. These Maxwell generation (96x) GPUs run quite cool. > >> >> > >> >> > Any additional comments are highly appreciated. Please keep in mind > >> that > >> >> > this is a toy project to utilize an old workstation. > >> >> > >> >> There is a GPU fan speed issue with desktop NVIDIA cards, the fan > >> >> rotation is limited to 60% and cards can overheat. You can force the > >> >> fan speed higher using nvidia-settings (you'll need an X server > >> >> running, though). For more details you can check slide 28 here: > >> >> https://goo.gl/7DnSri > >> >> > >> >> Cheers, > >> >> -- > >> >> Szilárd > >> >> > >> >> > Thank you, > >> >> > > >> >> > 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. > >> > -- > >> > 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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