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Molecular Dynamics

COMSOL, LAMMPS, VASP, Wien2k

VASP

VASP

Modules

module purge
module load autotools 
module load gnu7/7.2.0 
module load openmpi3/3.0.0 
module load openblas/0.2.20
module load scalapack/2.0.2 
module load fftw/3.3.6 
module load prun

VASP

vasp.5.lib

ln -s makefile.linux_gfortran makefile
export CC=gcc
make

VASP 5.4.1/5.4.4

makefile.include

OFLAG      = -O2 -march=broadwell

LIBDIR     = /opt/ohpc/pub/libs/gnu7/openblas/0.2.20/lib

BLAS       = -L$(LIBDIR) -lopenblas

LAPACK     =

BLACS      =

SCALAPACK  = -L$(LIBDIR) -lscalapack $(BLACS)

FFTW       ?= /opt/ohpc/pub/libs/gnu7/openmpi3/fftw/3.3.6

VASP 5.4.1/5.4.4

Compile

make all

If you have to recompile

make veryclean
make all

To build only specific version

make std

VASP 5.4.1/5.4.4

Job script

/opt/ohpc/pub/examples/slurm/mul/vasp

#!/bin/bash
#
#SBATCH -J vasp
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --mem=16G

export OMP_NUM_THREADS=1

exe=/path/to/my/vasp/vasp.5.4.4/bin/vasp_std

time mpirun -np $SLURM_NPROCS $exe

LAMMPS

LAMMPS

/opt/ohpc/pub/examples/slurm/mul/lammps

#!/bin/bash
#
#SBATCH -J lammps 
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --mem=16G

module purge
module load lammps

mpirun -np $SLURM_NTASKS lmp_mul -in ./in.put

Wien2k


Wien2k

Example job script in:

/opt/ohpc/pub/examples/slurm/mul/wien2k

COMSOL


COMSOL 5.2a

Module

load module COMSOL/5.2a

COMSOL 5.2a

Job script threaded version (no MPI)

You can use only one node in this case. Create a job file called job_smp.sh:

/opt/ohpc/pub/examples/slurm/mul/comsol

#!/bin/bash
#
#SBATCH -J comsol
#SBATCH -N 1
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --time=04:00:00
#SBATCH --mem=16G

# Details of your input and output files
INPUTFILE=micromixer_cluster.mph
OUTPUTFILE=micromixer.out

# Load our comsol module
module purge
module load COMSOL/5.2a

# create tmpdir 
TMPDIR="/tmp1/comsol"
mkdir -p $TMPDIR

## Now, run COMSOL in batch mode with the input and output detailed above.
comsol batch -np $SLURM_NTASKS -inputfile $INPUTFILE -outputfile $OUTPUTFILE -tmpdir $TMPDIR

COMSOL 5.2a

Job script with MPI

You can use more than one node in this case. Create a job file called job_mpi.sh:

/opt/ohpc/pub/examples/slurm/mul/comsol

#!/bin/bash
#
#SBATCH -J comsol
#SBATCH -N 2
#SBATCH -o job.%j.out
#SBATCH -p E5-2690v4
#SBATCH -q E5-2690v4-batch
#SBATCH --ntasks-per-node=28
#SBATCH --threads-per-core=1
#SBATCH --time=04:00:00
#SBATCH --mem=16G

# Details of your input and output files
INPUTFILE=micromixer_cluster.mph
OUTPUTFILE=micromixer.out

# Load our comsol module
module purge
module load COMSOL/5.2a
module load intel-mpi/2018

# create tmpdir 
TMPDIR="/tmp1/comsol"
mkdir -p $TMPDIR

## Now, run COMSOL in batch mode with the input and output detailed above.
comsol -clustersimple batch \
-inputfile $INPUTFILE \
-outputfile $OUTPUTFILE \
-tmpdir $TMPDIR \
-mpiroot $MPIROOT -mpi intel -mpifabrics shm:dapl

COMSOL 5.2a

Submit job

sbatch job_xyz.sh

COMSOL 5.2a

Restarting jobs

To continue your calculation from the last saved state on use the options:

-recover -continue
doku/molecular_dynamics.txt · Last modified: 2020/04/23 19:21 by ir