From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Mon Feb 22 2021 - 18:35:35 CST
Hi Chathuranga,
(It looks like you replied to Lorenzo’s email by mistake, but I’ll go ahead and answer your lone pair question here.)
By looking at your BEN_water.psf and test.log files, I can see that NAMD is not recognizing atom 37 as a lone pair. To correctly designate a lone pair, the PSF file has to include a !NUMLP section that specifies the support atoms for each lone pair. Whatever you used to create the PSF file didn’t produce this information.
Best regards,
Dave
> On Feb 22, 2021, at 6:17 PM, Chathuranga Siriwardhana <ccs0019_at_mix.wvu.edu> wrote:
>
> Thank you for your response
> Here I ve attached all the files that I used.
>
>
>
>
> Chathuranga Siriwardhana
> Justin Legleiter Laboratory
> West Virginia University
> Department of chemistry
> Clark Hall, Room 561
> Morgantown, WV 26505
>
>
> On Mon, Feb 22, 2021 at 7:02 PM David Hardy <dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu>> wrote:
> Hi Lorenzo,
>
> Sorry, I have to follow up my previous email.
>
> I had thought that multi-GPU alpha 7 required NVLink. It happens to be recommended, but not required. I am not sure why you are seeing an error. If you are willing to share your data set with us, we could try to reproduce the issue locally. Also, it would be good to have the full log file from your failed run.
>
> Best regards,
> Dave
>
>> On Feb 22, 2021, at 4:26 PM, David Hardy <dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu>> wrote:
>>
>> Hi Lorenzo,
>>
>> The version of NAMD that you are running does require NVLink for multi-GPU support (see http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/ <http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/>). Our most recent improvements to multi-GPU support no longer require NVLink, however, scaling performance suffers without it. The next release (alpha 9) will include this new multi-GPU support. Until we get new builds posted, you will need to build from the GitLab “devel" branch to try it out. You can get access to the NAMD GitLab repo by following the posted directions (https://gitlab.com/tcbgUIUC/namd <https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!DZ3fjg!t09GZP2yKyUUuPIheBS0xLRYmQTrVUSsIv0ADtCu_nPxEzMjxpj4sdRGbrct4rMKkw$>).
>>
>> Best regards,
>> Dave
>>
>> --
>> David J. Hardy, Ph.D.
>> Beckman Institute
>> University of Illinois at Urbana-Champaign
>> 405 N. Mathews Ave., Urbana, IL 61801
>> dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu>, http://www.ks.uiuc.edu/~dhardy/ <http://www.ks.uiuc.edu/~dhardy/>
>>
>>> On Feb 19, 2021, at 9:24 PM, Lorenzo Casalino <lcasalino_at_ucsd.edu <mailto:lcasalino_at_ucsd.edu>> wrote:
>>>
>>> Hello,
>>>
>>> I am trying to use the multiGPU version of NAMD3 (NAMD_3.0alpha7_Linux-x86_64-multicore-CUDA-MultiGPU-SingleNode) to run plain MD on 2 GPUs on a single node on a local cluster using the following command:
>>>
>>> namd3 +p 2 +setcpuaffinity +idlepoll +devices 0,1 input.conf > input.log
>>>
>>> I added the following keywords to my configuration file:
>>> - CUDASOAintegrate on
>>> - margin 4
>>>
>>>> From the log file, it looks like the 2 GPUs are seen and activated:
>>> Info: Built with CUDA version 10010
>>> Pe 1 physical rank 1 binding to CUDA device 1 on tscc-gpu-5-0.sdsc.edu <https://urldefense.com/v3/__http://tscc-gpu-5-0.sdsc.edu/__;!!DZ3fjg!t09GZP2yKyUUuPIheBS0xLRYmQTrVUSsIv0ADtCu_nPxEzMjxpj4sdRGbrcXRgRvUg$>: 'GeForce RTX 3090' Mem: 24268MB Rev: 8.6 PCI: 0:24:0
>>> Pe 0 physical rank 0 binding to CUDA device 0 on tscc-gpu-5-0.sdsc.edu <https://urldefense.com/v3/__http://tscc-gpu-5-0.sdsc.edu/__;!!DZ3fjg!t09GZP2yKyUUuPIheBS0xLRYmQTrVUSsIv0ADtCu_nPxEzMjxpj4sdRGbrcXRgRvUg$>: 'GeForce RTX 3090' Mem: 24268MB Rev: 8.6 PCI: 0:1:0
>>>
>>> The startup phase finishes smoothly, and then, when the actual MD simulation starts, the following error is generated:
>>>
>>> Info: Finished startup at 34.7205 s, 0 MB of memory in use
>>>
>>> TCL: Running for 100000 steps
>>> FATAL ERROR: CUDA error cub::DeviceSelect::If(d_temp_storage, temp_storage_bytes, hgi, hgi, d_nHG, natoms, notZero(), stream) in file src/SequencerCUDAKernel.cu, function buildRattleLists, line 4461
>>> on Pe 1 (tscc-gpu-5-0.sdsc.edu <https://urldefense.com/v3/__http://tscc-gpu-5-0.sdsc.edu/__;!!DZ3fjg!t09GZP2yKyUUuPIheBS0xLRYmQTrVUSsIv0ADtCu_nPxEzMjxpj4sdRGbrcXRgRvUg$> device 1 pci 0:24:0): invalid device function
>>>
>>> A single node of the cluster has 32 cpus and 8 GPUs (GeForce RTX 3090).
>>> I point out that the GPUs are NOT connected by NVlink.
>>> Finally, this is the PBS argument I use to add the GPUs to the environment: #PBS -l nodes=1:ppn=8:gpus=2:gpu3090
>>>
>>> I was not able to work this error out. Is it possible that without NVlink I cannot use the multiGPU version?
>>> Any help or advises on this issue would be greatly appreciated.
>>>
>>> Thank you.
>>>
>>> Best regards,
>>> Lorenzo
>>
>
> <test.conf><BEN_water.pdb><BEN_water.psf><test.log><BEN.prm>
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