Originally published at: https://developer.nvidia.com/blog/maximizing-gromacs-throughput-with-multiple-simulations-per-gpu-using-mps-and-mig/ In this post, we demonstrate the benefits of running multiple simulations per GPU for GROMACS and show how MPS can achieve up to 1.8X overall improvement …

Hello Alan and Szilárd, Thanks for the very useful post. I have tried implementing the MPS on V100s and have seen a massive improvement in the performance. I am facing an issue with using MPS on nodes with multiple GPUs (two GPUs). I would like your help with the same: I am using a job scheduler …

I am new to parallelization and cannot understand running the same job multiple times on the same GPU. I want to run multiple jobs on the same GPU and thus cannot comprehend $INPUT file manipulation. I hope you can help me.

Hi Akshay, In your simulation.sh script, are you setting the CUDA_VISIBLE_DEVICES environment variable? If so, please can you try removing that. When you launch each job with 1xV100, I expect that each device will be available as (the default) GPU 0 in each of the jobs (you can check this with nvid…

Hi Ravis, The relevant lines in the first script given in the blog are L45-51, where I create a new directory specific to each simulation, and copy the (same) input file into that directory. The directory naming structure I use is gpu${i}_sim${j}, such that e.g. for 2 simulations on each of 2 GPUs …

Hello Dr Alan, I appreciate your response to my queries. 1) No, I am not setting the CUDA_VISIBLE_DEVICES environment variable. (Though I had also tried running mdrun after setting this as detailed in your blog.) The simulation.sh file solely consists of: module load apps/gromacs/2021.4/gnu ex…

Hi Akshay, Thanks for the info. It looks like you just need to set a unique MPS pipe directory for each job, before launching MPS. To do this for your first job (using, e.g. /tmp/mps1 for the directory): export CUDA_MPS_PIPE_DIRECTORY=/tmp/mps1 mkdir -p $CUDA_MPS_PIPE_DIRECTORY nvidia-cuda-mps-…

Hello Dr Alan, Thank you very much for the suggestion. I will update you in case the problem remains unresolved. Regards, Akshay

I have almost reproduced the results that are given in this post for launching multiple simulations on the A100 GPU using MPS and MIG. Now, I am trying to use the Nvidia Nsights profiler to get a deeper understanding of the system state, GPUs, memory copies, kernel execution times etc. However I am …

Hi Dr. Alan, I am able to run the script and get an output of 32 .xtc files. I want to concatenate these separate files into one xtc file that covers the entire simulation. I’ve tried this using the gromacs trjcat utility as well as concatenating using VMD, but the xtc files do not appear to be in …

Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG

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ravis.bce16 July 12, 2022, 6:39pm 4

Hi Akshay, can you please provide me with your simulation.sh script

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Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG

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