LAMMPS sur Jean Zay

LAMMPS est code de simulation de dynamique moléculaire classique spécialisé dans la modélisation de matériaux.

• Site web
• Documentation

lammps.in

#!/bin/bash
#SBATCH --nodes=1               # Number of Nodes
#SBATCH --ntasks-per-node=40    # Number of MPI tasks per node
#SBATCH --cpus-per-task=1       # Number of OpenMP threads
#SBATCH --hint=nomultithread    # Disable hyperthreading
#SBATCH --job-name=rhodo        # Jobname
#SBATCH --output=%x.o%j         # Output file %x is the jobname, %j the jobid
#SBATCH --error=%x.o%j          # 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>@cpu       # To specify cpu accounting: <account> = echo $IDRPROJ
##SBATCH --partition=<partition>       # To specify partition (see IDRIS web site for more info)
##SBATCH --qos=qos_cpu-dev      # Uncomment for job requiring less than 2 hours
##SBATCH --qos=qos_cpu-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 the module
module load lammps/20200721-mpi intel-mkl/2020.1
 
# Execute commands
srun lmp -i rhodo.in

lammps_gpu.slurm

#!/bin/bash
#SBATCH --nodes=1               # Number of Nodes
#SBATCH --ntasks-per-node=40    # Number of MPI tasks per node
#SBATCH --cpus-per-task=1       # Number of OpenMP threads
#SBATCH --gres=gpu:4                # Allocate 4 GPUs/node
#SBATCH --hint=nomultithread    # Disable hyperthreading
#SBATCH --job-name=rhodo        # Jobname
#SBATCH --output=%x.o%j         # Output file %x is the jobname, %j the jobid
#SBATCH --error=%x.o%j          # 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>@cpu       # To specify cpu accounting: <account> = echo $IDRPROJ
##SBATCH --partition=<partition>       # To specify partition (see IDRIS web site for more info)
##SBATCH --qos=qos_cpu-dev      # Uncomment for job requiring less than 2 hours
##SBATCH --qos=qos_cpu-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 the module
module load lammps/20200630-mpi-cuda-kokkos intel-mkl/2020.1 cuda/10.2
 
# Execute commands
srun lmp -i rhodo.in

• Les jobs ont tous des ressources définies dans Slurm par une partition et une “Qualité de Service” QoS (Quality of Service) par défaut. Vous pouvez en modifier les limites en spécifiant une autre partition et/ou une QoS comme indiqué dans notre documentation détaillant les partitions et les Qos.
• Pour les comptes multi-projets ainsi que ceux ayant des heures CPU et GPU, il est indispensable de spécifier l'attribution d'heures sur laquelle décompter les heures de calcul du job comme indiqué dans notre documentation détaillant la gestion des heures de calcul.