Amber on Jean Zay

Amber is a suite of biomolecular simulation programs.

• Website
• GPU support
• Documentation
• Mailing List

• pmemd : OpenMP CPU version
• pmemd.MPI : MPI CPU version
• pmemd.cuda/pmemd.cuda_SPFP : mixed-precision OpenMP, Single GPU version
• pmemd.cuda_SPFP.MPI : mixed-precision MPI, Single GPU version
• pmemd.cuda_DPFP : double-precision OpenMP, Single-GPU version
• pmemd.cuda_DPFP.MPI : double-precision MPI, Multi-GPU version

pmemd_monogpu.slurm

#!/bin/bash
#SBATCH --nodes=1                   # 1 node is used
#SBATCH --ntasks-per-node=1         # 4 MPI tasks
#SBATCH --cpus-per-task=10          # Number of OpenMP threads per MPI task
#SBATCH --gres=gpu:1                # Number of GPUs per node
#SBATCH --hint=nomultithread        # Disable hyperthreading
#SBATCH --job-name=pmemd            # Jobname
#SBATCH --output=%x.%j              # Standard output file (%x is the job name, %j is the job number)
#SBATCH --error=%x.%j               # Standard error file
#SBATCH --time=10:00:00             # Expected runtime HH:MM:SS (max 100h for V100, 20h for A100)
##
## Please, refer to comments below for
## more information about these 4 last options.
##SBATCH --account=<account>@v100   # To specify gpu accounting: <account> = echo $IDRPROJ
##SBATCH --partition=<partition>    # To specify partition (see IDRIS web site for more info)
##SBATCH --qos=qos_gpu-dev          # Uncomment for job requiring less than 2 hours
##SBATCH --qos=qos_gpu-t4           # Uncomment for job requiring more than 20h (up to 16 GPU, V100 only)
 
# Cleans out the modules loaded in interactive and inherited by default
module purge
 
# Load needed modules
module load amber/20-mpi-cuda
 
 pmemd.cuda -O -i prod.in -o prod.out -p sys.prmtop -c sys.rst \
       -r sys.rst -ref sys.inpcrd -x sys.mdcrd