Here’s a corrected and polished version of your text:
Hello,
I need to run a 5-microsecond simulation of my system containing 39,391 atoms.
I am using eight Tesla V100-SXM2 GPUs, running a job in SLURM with the following configuration:
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
#SBATCH --nodes=1
#SBATCH --ntasks=32
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:tesla:8
#SBATCH --time=168:00:00
…
mpirun -np 32 $AMBERHOME/bin/pmemd.MPI …
mpirun -np 8 $AMBERHOME/bin/pmemd.cuda.MPI ...
…
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
Based on the current timing information, the average performance is 762.52 ns/day, and the estimated runtime is approximately 160 hours. There are 5 systems in total, and I also wish to run 3 replicas for each system.
Is there anything else, aside from the HMR topology (which I have already applied), that I can use to further accelerate the job?
Thanks
———
Maciej Spiegel, MPharm PhD
assistant professor
.GitHub <
https://farmaceut.github.io/>
Department of Organic Chemistry and Pharmaceutical Technology,
Faculty of Pharmacy, Wroclaw Medical University
Borowska 211A, 50-556 Wroclaw, Poland
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Received on Sun Nov 24 2024 - 04:00:02 PST
