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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Feb 27 2020 - 09:30:02 PST
