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