Hi Ross,
Thanks. I will try get the data center folks make some modifications and
see what performance gains i can get.
Regards
Abhilash
On Thu, Feb 27, 2020 at 12:45 PM Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Abhilash,
>
> Since it is in a data center I highly recommend asking your data center
> folk to set the case fans in the bios to be maximum speed. This should help
> a lot.
>
> All the best
> Ross
>
> > On Feb 27, 2020, at 12:42 PM, Abhilash J <md.scfbio.gmail.com> wrote:
> >
> > Hi Ross,
> >
> > Thanks for the insight. I am using CUDA Version: 10.2. nvidia smi
> > output is attached below.
> > As you say the AMBER 16 is not optimized for RTX2XXX cards. I will try
> > to work the problem out by trying to get AMBER 18 there.
> > The new RTX 2080 Super cards are housed in a data center they have 4
> > cards per node. The MD test was carried out with 3 cards being idle and 1
> > card running the simulation, so i hoped heating would not be an issue.
> > My local workstation has 4 cards (1080 Ti) and the output has been
> > around 36 ns/day (+- 1-2ns/day) in all different combinations.
> >
> > ======================================
> >
> >
> +-----------------------------------------------------------------------------+
> > | NVIDIA-SMI 440.31 Driver Version: 440.31 CUDA Version:
> 10.2 |
> >
> |-------------------------------+----------------------+----------------------+
> > | GPU Name Persistence-M| Bus-Id Disp.A | Volatile
> Uncorr. ECC |
> > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
> Compute M. |
> >
> |===============================+======================+======================|
> > | 0 GeForce RTX 208... Off | 00000000:3B:00.0 Off |
> N/A |
> > | 24% 24C P8 8W / 250W | 275MiB / 7981MiB | 0%
> Default |
> >
> +-------------------------------+----------------------+----------------------+
> > | 1 GeForce RTX 208... Off | 00000000:5E:00.0 Off |
> N/A |
> > | 25% 24C P8 10W / 250W | 12MiB / 7982MiB | 0%
> Default |
> >
> +-------------------------------+----------------------+----------------------+
> > | 2 GeForce RTX 208... Off | 00000000:AF:00.0 Off |
> N/A |
> > | 24% 23C P8 4W / 250W | 12MiB / 7982MiB | 0%
> Default |
> >
> +-------------------------------+----------------------+----------------------+
> > | 3 GeForce RTX 208... Off | 00000000:D8:00.0 Off |
> N/A |
> > | 25% 22C P8 13W / 250W | 12MiB / 7982MiB | 0%
> Default |
> >
> +-------------------------------+----------------------+----------------------+
> >
> >
> +-----------------------------------------------------------------------------+
> > | Processes: GPU
> Memory |
> > | GPU PID Type Process name
> Usage |
> >
> |=============================================================================|
> > | 0 3127 C python
> 115MiB |
> > | 0 5715 G /usr/bin/X
> 84MiB |
> > | 0 6307 G /usr/bin/gnome-shell
> 70MiB |
> >
> +-----------------------------------------------------------------------------+
> > =======================================
> >
> >
> >
> >
> >
> > On Thu, Feb 27, 2020 at 12:14 PM Ross Walker <ross.rosswalker.co.uk>
> wrote:
> >
> >> Hi Abhilash
> >>
> >> It's most likely the difference in AMBER version although the difference
> >> is bigger than I'd expect. The RTX architecture did not exist when
> AMBER 16
> >> came out so there is no optimization for it. Also what CUDA compiler
> >> version are you using? You ideally need to use 10.0 or later for RTX2XXX
> >> cards.
> >>
> >> A stock RTX2080 should be a little bit faster than a stock 1080TI. The
> >> RTX2080 Super is really just an overclocked RTX2080, in my experience
> it's
> >> about 5 to 10% faster than a stock 2080 depending on the simulation
> >> parameters. The small difference in 2080 vs 2080 Super performance is
> why
> >> I never bothered to update the benchmarks on the AMBER website.
> >>
> >> Note the other possibility is that you are seeing throttling of the
> >> RTX2080 due to heat issues. If you have more than 1 GPU in a box this
> can
> >> be a big issue with RTX cards. NVIDIA's reference design is not great
> for
> >> cooling. The ducted systems that blow air out of the back of the case
> are
> >> better but if you have multiple cards next to each other you have to
> remove
> >> the backplate on the cards so there is room for airflow. As a quick
> test I
> >> would recommend going into the machine bios and setting the case fan
> speeds
> >> to maximum (it may sound like a jet engine). Then rerun the benchmark.
> That
> >> will tell you if it's a thermal throttling issue.
> >>
> >> You can monitor the GPU temperature during a run using nvidia-smi. I
> >> forget the exact number but it's something like 80C that the RTX2080 is
> >> capped at so if the temperature pegs at that it means the clock speed is
> >> likely being reduced to prevent overheating.
> >>
> >> All the best
> >> Ross
> >>
> >>
> >>> On Feb 27, 2020, at 11:06 AM, Abhilash J <md.scfbio.gmail.com> wrote:
> >>>
> >>> Hi Everyone,
> >>>
> >>> I tried my hands on RTX 2080 Super today. I used AMBER 16. I got 17
> >>> ns/day for a system of 172K atoms.
> >>> This was quite disappointing as i get 36 ns/day from my 1080 ti cards
> >>> using AMBER 18 using the same 172K atoms system.
> >>> I don't know if it is the variation in the GPU cards or the one lower
> >>> AMBER version responsible.
> >>> Both machines were built by Exxact corporation.
> >>> I hope some developers can weigh in on this.
> >>>
> >>> Regards
> >>>
> >>> Abhilash
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Sat, Feb 22, 2020 at 8:05 AM Pietro Amodeo <pamodeo.icb.cnr.it>
> >> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> since NVidia RTX 3XXX cards are not expected before Q4 2020, and
> rumored
> >>>> RTX 2080 Super Ti models have not been confirmed, RTX 2080 Super,
> >>>> costing between 3/5 and 2/3 of Ti, could represent a good interim
> >>>> solution, especially because both all-in-one and integrated-block
> >>>> water-cooled cards based on this chip exist (a potentially critical
> >>>> issue for such a clock-boosted solution).
> >>>>
> >>>> In this view, info about RTX 2080 Super performances with AMBER 18
> (and,
> >>>> possibly, 20) would allow a proper cost/benefit ratio comparison
> between
> >>>> Super and Ti versions.
> >>>>
> >>>> Thank you in advance for any info.
> >>>>
> >>>> Best,
> >>>>
> >>>> Pietro
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
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> >>
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Received on Thu Feb 27 2020 - 10:00:03 PST
