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calcoloscientifico:userguide:gromacs

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calcoloscientifico:userguide:gromacs [20/08/2025 17:24] – fabio.spatarocalcoloscientifico:userguide:gromacs [20/08/2025 18:00] (versione attuale) – [Job Gromacs CPU] fabio.spataro
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 ==== Examples ==== ==== Examples ====
  
-The following examples demonstrate using the NGC GROMACS container to run the STMV benchmark.+The following examples demonstrate using the [[https://catalog.ngc.nvidia.com/orgs/hpc/containers/gromacs|NGC GROMACS]] container to run the ''STMV'' benchmark.
  
 Download the ''STMV'' benchmark: Download the ''STMV'' benchmark:
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 ==== Job Gromacs CPU ==== ==== Job Gromacs CPU ====
  
-Script ''slurm-gromacs-2025.1-cpu.sh'' to request one node and start 8 MPI thread and 6 OpenMP threads for each MPI thread (48 threads overall):+Script ''slurm-gromacs-2025.1-cpu.sh'' to request one node and start 8 thread-MPI tasks and 6 OpenMP threads for each thread-MPI task (48 threads overall) and run the ''STMV'' benchmark:
  
 <code bash slurm-gromacs-2025.1-cpu.sh> <code bash slurm-gromacs-2025.1-cpu.sh>
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 #SBATCH --ntasks-per-node=8 #SBATCH --ntasks-per-node=8
 #SBATCH --cpus-per-task=6 #SBATCH --cpus-per-task=6
-#SBATCH --time=0-24:00:00 +#SBATCH --time=0-04:00:00 
-#SBATCH --mem=64G+#SBATCH --mem=16G
 #SBATCH --partition=cpu_guest #SBATCH --partition=cpu_guest
 #SBATCH --qos=cpu_guest #SBATCH --qos=cpu_guest
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 apptainer run \ apptainer run \
-    --nv \ 
     --bind "$PWD:/host_pwd" \     --bind "$PWD:/host_pwd" \
     --pwd /host_pwd \     --pwd /host_pwd \
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 ==== Job Gromacs GPU ==== ==== Job Gromacs GPU ====
  
-Script ''slurm-gromacs-2025.1-gpu.sh'' to request one node and start 8 MPI thread and 6 OpenMP threads for each MPI process (48 threads thread) with 8 CUDA GPU's:+Script ''slurm-gromacs-2025.1-gpu.sh'' to request one node and start 8 thread-MPI tasks and 6 OpenMP threads for each thread-MPI task (48 threads thread) with 8 CUDA GPU's and run the ''STMV'' benchmark:
  
 <code bash slurm-gromacs-2025.1-gpu.sh> <code bash slurm-gromacs-2025.1-gpu.sh>
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 #SBATCH --ntasks-per-node=8 #SBATCH --ntasks-per-node=8
 #SBATCH --cpus-per-task=6 #SBATCH --cpus-per-task=6
-#SBATCH --time=0-24:00:00 +#SBATCH --time=0-00:30:00 
-#SBATCH --mem=64G+#SBATCH --mem=8G
 #SBATCH --gres=gpu:a5000_mm1:8 #SBATCH --gres=gpu:a5000_mm1:8
 #SBATCH --partition=gpu_guest #SBATCH --partition=gpu_guest
calcoloscientifico/userguide/gromacs.1755703473.txt.gz · Ultima modifica: da fabio.spataro
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