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
> >> _______________________________________________
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> >>
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>
>
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Received on Thu Feb 27 2020 - 10:00:02 PST
