Alex, The motherboard I am using with the 9900K is the ASUS WS Z390 PRO. The PRO version has the extra PCIe controller. I am using two RTX 1070ti GPUs, and I can hear everyone snorting with derision, but with this configuration I get performance with 100,000 atoms of about 72 ns/day with 2019.1 which is adequate for my needs. I’ll upgrade to the 2080ti when the price drops to <$1000. Another tip is to get the highest speed memory that the motherboard will handle. It doesn’t make a huge difference, maybe 2-3% over the cheapest memory but it is something that is easy and low cost to do.
Mike Sent from my iPhone > On Jul 17, 2019, at 11:16 AM, Alex <nedoma...@gmail.com> wrote: > > Gentlemen, thank you both! > > Michael, would you be able to suggest a specific motherboard that removes the > bottleneck? We aren't really limited by price in this case and would prefer > to get every bit of benefit out of the processing components, if possible. > > Thanks, > > Alex > >> On 7/17/2019 10:44 AM, Moir, Michael (MMoir) wrote: >> This is not quite true. I certainly observed this degradation in >> performance using the 9900K with two GPUs as Szilárd states using a >> motherboard with one PCIe controller, but the limitation is from the >> motherboard not from the CPU. It is possible to obtain a motherboard that >> contains two PCIe controllers which overcomes this obstacle for not a whole >> lot more money. >> >> Mike >> >> -----Original Message----- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Szilárd Páll >> Sent: Wednesday, July 17, 2019 8:14 AM >> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> >> Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000 >> >> Hi Alex, >> >> I've not had a chance to test the new 3rd gen Ryzen CPUs, but all >> public benchmarks out there point to the fact that they are a major >> improvement over the previous generation Ryzen -- which were already >> quite competitive for GPU-accelerated GROMACS runs compared to Intel, >> especially in perf/price. >> >> One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is >> that they don't have enough PCI lanes for peak CPU-GPU transfer (x8 >> for both of the GPUs) which will lead to a slightly less performance >> (I'd estimate <5-10%) in particular compared to i) having a single GPU >> plugged in into the machine ii) compare to CPUs like Threadripper or >> the i9 79xx series processors which have more PCIe lanes. >> >> However, if throughput is the goal, the ideal use-case especially for >> small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU, >> hence 4 runs on a 2-GPU system case in which the impact of the >> aforementioned limitation will be further decreased. >> >> Cheers, >> -- >> Szilárd >> >> >>> On Tue, Jul 16, 2019 at 7:18 PM Alex <nedoma...@gmail.com> wrote: >>> That is excellent information, thank you. None of us have dealt with AMD >>> CPUs in a while, so would the combination of a Ryzen 3900X and two >>> Quadro 2080 Ti be a good choice? >>> >>> Again, thanks! >>> >>> Alex >>> >>> >>>> On 7/16/2019 8:41 AM, Szilárd Páll wrote: >>>> Hi Alex, >>>> >>>>> On Mon, Jul 15, 2019 at 8:53 PM Alex <nedoma...@gmail.com> wrote: >>>>> Hi all and especially Szilard! >>>>> >>>>> My glorious management asked me to post this here. One of our group >>>>> members, an ex-NAMD guy, wants to use Gromacs for biophysics and the >>>>> following basics have been spec'ed for him: >>>>> >>>>> CPU: Xeon Gold 6244 >>>>> GPU: RTX 5000 or 6000 >>>>> >>>>> I'll be surprised if he runs systems with more than 50K particles. Could >>>>> you please comment on whether this is a cost-efficient and reasonably >>>>> powerful setup? Your past suggestions have been invaluable for us. >>>> That will be reasonably fast, but cost efficiency will be awful, to be >>>> honest: >>>> - that CPU is a ~$3000 part and won't perform much better than a >>>> $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which >>>> would be significantly faster. >>>> - Quadro cards also pretty low in bang for buck: a 2080 Ti will be >>>> close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit >>>> slower for at least another 1.5x less. >>>> >>>> Single run at a time or possibly multiple? The proposed (or any 8+ >>>> core) workstation CPU is fast enough in the majority of the >>>> simulations to pair well with two of those GPUs if used for two >>>> concurrent simulations. If that's a relevant use-case, I'd recommend >>>> two 2070 Super or 2080 cards. >>>> >>>> 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? 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.
