Re: [AMBER] problem about pmemd.cuda.MPI

From: ning via AMBER <amber.ambermd.org>
Date: Fri, 10 Nov 2023 09:03:34 +0800 (CST)

Thanks for you quick reply. Yes, as you said, I'm trying to make a single long trajectory. Maybe I should to try another enhanced sampling method for exploring more protein conformation.


Sincerely,
Ning


















At 2023-11-10 08:54:24, "PUJAN AJMERA" <pujanajmera1.g.ucla.edu> wrote:

Hi Ning,


Are you aiming to make a single long trajectory faster? Generally, GPUs will not run much faster beyond 1, due to communication overhead (GPUs are much faster than the communication between them), and unsurprisingly in your case, actually slow it down.


If you are looking to just get good sampling, I may suggest splitting your trajectory length into 8 runs, and running each on 1 GPU.


All the best,
Pujan Ajmera
PhD Student at UCLA


On Thu, Nov 9, 2023 at 4:46 PM ning via AMBER <amber.ambermd.org> wrote:

Hi amber experts,


      I have a question about how to use pmemd.cuda.MPI for long time simulation. Because, I found that if applying this command like "mpirun -np 8 pmemd.cuda.MPI .... to use 82080Ti GPU, the simulation performance had been decreased to 12.5% of one GPU. What's wrong about this I just compiled the parallel version as manual guidance. How to fix this problem? Thanks for any suggestions.


Best,
Ning
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Received on Thu Nov 09 2023 - 17:30:02 PST
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