Does GPU calc bonded terms? I the topology diff is more of these, and
CPU could/does handle those bond-related terms, could a faster CPU keep
the GPU busy?
Bill
On 8/6/20 2:02 AM, David Cerutti wrote:
> Agreed, the topology for a membrane system may be denser in terms of atoms
> that a protein in water system. If that is the case, the non-bonded
> kernels are going to run slower, but there is no way around this. If you
> are seeing the benchmarks run at about the right pace then it's your
> system. You also have a 10A cutoff in there, versus a 9A used in the
> benchmarks.
>
> Dave
>
>
> On Thu, Aug 6, 2020 at 2:52 AM Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> It might help more-informed people to mention your topology.
>>
>> AMBER Cuda is after my time, but I'll go ahead and speculate that the
>> nonbonded ops on cuda itself should be the same-ish for any N atoms, but
>> that if your topology is off the developers' beaten track, maybe there's
>> a bottleneck in collecting the data. What does nvidia-smi say about GPU
>> usage?
>>
>> Bill
>>
>> (I play cuda for tensorflow.)
>>
>>
>> On 8/5/20 11:43 PM, 李奕言 wrote:
>>> Thanks again for your kind reply.
>>>
>>> As much as I wish to get an upgrade, I am still wondering if there is
>> any solution within Amber16.
>>> The benchmark tests went well, but the actual system with similar number
>> of atoms got much slower -- Is this a general problem in Amber16 that can
>> only be fixed in newer versions? Does the performance of pmemd.cuda differ
>> among systems, or does it simply depend on the atom number?
>>> I would be grateful if you could help.
>>>
>>>> -----Original Messages-----
>>>> From: "David Cerutti" <dscerutti.gmail.com>
>>>> Sent Time: 2020-08-06 10:48:36 (Thursday)
>>>> To: "AMBER Mailing List" <amber.ambermd.org>
>>>> Cc:
>>>> Subject: Re: [AMBER] Reduced Performance with pmemd.cuda Compared With
>> Benchmarks.
>>>> We made some performance improvements in Amber18 that will carry over to
>>>> Amber20 once the patch hits. The sooner you can upgrade, the better,
>> but
>>>> the performance of Amber20 will probably still be better than Amber16
>> on a
>>>> GTX-1080Ti even without the patch.
>>>>
>>>> Dave
>>>>
>>>>
>>>> On Wed, Aug 5, 2020 at 9:59 PM 李奕言 <liyiyan.pku.edu.cn> wrote:
>>>>
>>>>> Thank you for the information.
>>>>> Unfortunately I was using Amber16. Does the same problem occur in
>> Amber16?
>>>>>
>>>>>> -----Original Messages-----
>>>>>> From: "David Cerutti" <dscerutti.gmail.com>
>>>>>> Sent Time: 2020-08-04 12:40:51 (Tuesday)
>>>>>> To: "AMBER Mailing List" <amber.ambermd.org>
>>>>>> Cc:
>>>>>> Subject: Re: [AMBER] Reduced Performance with pmemd.cuda Compared With
>>>>> Benchmarks.
>>>>>> This is a known problem in Amber20, which has yet to be fixed pending
>>>>> some
>>>>>> other developments in the master branch. We know the solution, but
>> the
>>>>>> release version for now is taking precautions that will only become
>>>>>> necessary in CUDA11 and later. There is nothing wrong with the code,
>> but
>>>>>> we are still deliberating what patch to make.
>>>>>>
>>>>>> Dave
>>>>>>
>>>>>>
>>>>>> On Sun, Aug 2, 2020 at 11:22 PM 李奕言 <liyiyan.pku.edu.cn> wrote:
>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Here is a new Amber user, who has been doing MD simulations on GTX
>>>>> 1080 Ti
>>>>>>> using pmemd.cuda in Amber 16 and have encountered considerable
>>>>> reduction in
>>>>>>> performance.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> First I ran the benchmark sets of AMBER 16 GPU acceleration. For NPT
>>>>>>> simulation of Factor IX with 90,906 atoms, I have got ~89 ns/day on
>>>>> single
>>>>>>> GPU, slightly less than the benchmark performance (92.08 ns/day),
>>>>> which is
>>>>>>> acceptable. Since the benchmark results were OK, I was not suspecting
>>>>> any
>>>>>>> problem with the GPU.
>>>>>>>
>>>>>>> When it came to my membrane protein system, which contains a GPCR
>> dimer
>>>>>>> protein (ffSB14), POPC lipids (lipid 14), waters (TIP3P) and ions,
>> and
>>>>> has
>>>>>>> a fairly similar atom number of 95,096, I was getting ~65 ns/day on
>>>>> single
>>>>>>> GPU. This was not what I was expecting, seeing that 95,096 was not
>> THAT
>>>>>>> larger than 90,906.
>>>>>>>
>>>>>>> My input file for the NPT simulation is as follows. I have tried to
>>>>> get
>>>>>>> as close as possible to the benchmark input.
>>>>>>>
>>>>>>> NPT Production Run
>>>>>>>
>>>>>>> &cntrl
>>>>>>> nstlim=250000000, dt=0.002, ntx=5, irest=1, ntpr=50000,
>> ntwr=50000000,
>>>>>>> ntwx=50000,
>>>>>>> temp0=300.0, ntt=1, tautp=10.0,
>>>>>>> ntb=2, ntp=1, barostat=2,
>>>>>>> ntc=2, ntf=2,
>>>>>>> ioutfm=1,
>>>>>>> &end
>>>>>>> /
>>>>>>> 1/ I have even cut down the writing of output and trajectories for
>>>>> better
>>>>>>> performance by raising ntpr and ntwx values, at the cost of
>> inadequate
>>>>>>> trajectory snapshots. Is this necessary?
>>>>>>>
>>>>>>> 2/ Also, currently I am running an aMD simulation with similar input
>>>>>>> settings, which resulted in ~42 ns/day. Is aMD performance destined
>> to
>>>>>>> drop compared to conventional MD?
>>>>>>>
>>>>>>> Production Run with Accelerated MD
>>>>>>> &cntrl
>>>>>>> nstlim=250000000, dt=0.002, ntx=5, irest=1, ntpr=1000,
>> ntwr=50000000,
>>>>>>> ntwx=1000, ntwprt=8873,
>>>>>>> temp0=300.0, ntt=1, tautp=10.0,
>>>>>>> ntb=2, ntp=1, barostat=2, cut=10.0,
>>>>>>> ntc=2, ntf=2,
>>>>>>> ioutfm=1,
>>>>>>> iamd=3,
>>>>>>> ethreshd=23916, alphad=1104,
>>>>>>> ethreshp=-187677, alphap=19011,
>>>>>>> &end
>>>>>>> /
>>>>>>>
>>>>>>> 3/ Does the performance of pmemd.cuda differ among systems, or does
>> it
>>>>>>> simply depend on the atom number?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I am hoping to get tips for improving the performance of my NPT runs.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Many thanks for any reply.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Ian
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>> _______________________________________________
>>>>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> --
>> Phobrain.com
>>
>> _______________________________________________
>> 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
>
--
Phobrain.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 06 2020 - 02:30:03 PDT
