Amber on Jean Zay

Introduction

Amber is a suite of biomolecular simulation programs.

Available versions

Version Modules to load Comments
20 MPI, CUDA amber/20-mpi-cuda Contains Ambertools and pmemd for CPU and GPU

pmemd variants available

  • 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

Example of usage on the GPU partition

Submission script for the single 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)
##
## Please, refer to comments below for
## more information about these 4 last options.
##SBATCH --account=<account>@gpu       # 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 (only one node)
 
# 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