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doku:molecular_dynamics [2020/04/23 08:45] – irdoku:molecular_dynamics [2020/04/23 19:21] – ir
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 ====== Molecular Dynamics ====== ====== Molecular Dynamics ======
- 
-under construction 
  
 COMSOL, LAMMPS, VASP,  Wien2k COMSOL, LAMMPS, VASP,  Wien2k
 +
 +====== VASP ======
 +
 +===== VASP =====
 +
 +==== Modules ====
 +
 +<code>
 +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
 +
 +</code>
 +
 +----
 +
 +===== VASP =====
 +
 +==== vasp.5.lib ====
 +
 +<code>
 +ln -s makefile.linux_gfortran makefile
 +export CC=gcc
 +make
 +</code>
 +
 +----
 +
 +===== VASP 5.4.1/5.4.4 =====
 +
 +==== makefile.include ====
 +
 +<code>
 +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
 +
 +</code>
 +
 +----
 +
 +===== VASP 5.4.1/5.4.4 =====
 +
 +==== Compile ====
 +
 +<code>
 +make all
 +</code>
 +==== If you have to recompile ====
 +
 +<code>
 +make veryclean
 +make all
 +</code>
 +==== To build only specific version ====
 +
 +<code>
 +make std
 +</code>
 +
 +----
 +
 +===== VASP 5.4.1/5.4.4 =====
 +
 +==== Job script ====
 +
 +''%%/opt/ohpc/pub/examples/slurm/mul/vasp%%''
 +
 +<code>
 +#!/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
 +
 +</code>
 +
 +----
 +
 +====== LAMMPS ======
 +
 +===== LAMMPS =====
 +
 +''%%/opt/ohpc/pub/examples/slurm/mul/lammps%%''
 +
 +<code>
 +#!/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
 +</code>
 +
 +----
 +
 +====== Wien2k ======
 +
 +
 +----
 +
 +===== Wien2k =====
 +
 +Example job script in:
 +
 +<code>
 +/opt/ohpc/pub/examples/slurm/mul/wien2k
 +</code>
 +
 +----
 +
 +====== COMSOL ======
 +
 +
 +----
 +
 +===== COMSOL 5.2a =====
 +
 +==== Module ====
 +
 +<code>
 +load module COMSOL/5.2a
 +</code>
 +
 +----
 +
 +===== 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%%''
 +
 +<code>
 +#!/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
 +</code>
 +
 +
 +----
 +
 +===== 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%%''
 +
 +<code>
 +#!/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
 +</code>
 +
 +
 +----
 +
 +===== COMSOL 5.2a =====
 +
 +==== Submit job ====
 +
 +<code>
 +sbatch job_xyz.sh
 +</code>
 +
 +----
 +
 +===== COMSOL 5.2a =====
 +
 +==== Restarting jobs ====
 +
 +To continue your calculation from the last saved state on use the options:
 +
 +<code>
 +-recover -continue
 +</code>
  • doku/molecular_dynamics.txt
  • Last modified: 2021/10/22 09:02
  • by ir