Quick Start and Tutorial

Quick Start

To use cmd_restarter you need:

• The input file for LAMMPS and any other file used by LAMMPS to perform the simulation, geometries for example
• The submission script that you will use on the cluster where you will run the jobs.

On your input file you need to add some comments that will instruct cmd_restarter about which portions of the Input will change in case you are running from scratch or restarting a previous calculation.

The input file needs to be modified to include one block like this:

# RST_BEGIN
# read_data ...
# read_restart ...
# read_restart ...
# RST_END

The lines inside the block will be commented or uncommented based on the existance or not of the restart files amd the restart file that will be activated is the newest file from the list of restart files.

There are a couple of more blocks to specify which parts of the input are activated only for the firts run or for restart runs The blocks are:

# INITONLY_BEGIN
...
...
# INITONLY_END

and:

# RESTONLY_BEGIN
...
...
# RESTONLY_END

cmd_restarter will comment or uncomment those blocks entirely so not real comments should be inside those blocks as cmd_restarter could uncomment them leaving a unproper LAMMPS input script.

Once those changes are done, cmd_restarter can be executed as:

cmd_restart.py -p <SUBMISSION_SCRIPT> -i <LAMMPS_INPUT> -d <DUMP_FILENAME> -m <MAX_ITERATIONS> -s <SLEEPING_TIME>

Tutorial: Lennard-Jones with 147 particles

Using cmd_restarter is really simple. You just need to add a few comments on your LAMMPS script file, prepare a basic submission script and the script will take the responsability of submit and resubmit jobs until the number of iterations is achieved.

We will present now a simple example using 147 particles interacting under a Lennard-Jones potential.

For this exercise we will use cmd_restarter to compute a simulation of 147 particles under a Lennard-Jones force field. This number of particles is still too low for modern computers, we have constrained the conditions to force multiple executions as it will be case with much bigger problems.

Conside the following LAMMPS input file (in.run):

# 147 LJ particles

units           lj
dimension       3
boundary        s s s
atom_style      atomic

region sbound sphere 0.00 0.00 0.00 25.000 units box side in

# RST_BEGIN
read_data LJ147.geo
# read_restart run_a.rest
# read_restart run_b.rest
# RST_END

include         LJ147.parm
timestep        0.005
run_style       verlet
velocity        all create 0.007 1298371 mom yes rot yes dist gaussian

fix             1 all nvt temp 0.007 0.007 100.0

dump            2 all dcd 100 rlx_0.5_LJ147.dcd
dump_modify  2 unwrap yes

thermo_style    multi
thermo          1000
variable sys_step equal step

fix 5 all wall/region sbound harmonic 1 1 25
compute 1 all gyration

fix Rgave all ave/time 100 5 1000 c_1 file Rg_rlx0.5_LJ147.dat
fix extra all print 1000 "${sys_step}" screen no append steps.dat
dump geometry all atom 1000 dump.atom
dump d0 all image 1000 dump.*.jpg type type
dump_modify d0 pad 8

restart         1000   run_a.rest run_b.rest
run             10000000

write_restart         rlx_0.5_LJ147.rest

This is a normal LAMMPS script file, the only special element is a block of commands enclosed in some comments:

# RST_BEGIN
read_data LJ147.geo
# read_restart run_a.rest
# read_restart run_b.rest
# RST_END

The actual state of the lines inside the block is irrelevant. You can perfectly keep all the lines read_... commented or uncommented. cmd_restarter will modify this input according to the presence or not of those restart files. If you start from scratch the files run_a.rest and run_b.rest do not exit, so the line with read_data is activated and the other lines are commented. After the first execution some or both of those restart files will be present, cmd_restarter will determine which one is newer and use it to prepare the input for restart and submit a new job to continue the simulation.

There is nothing special about the submission script, the LAMMPS input script in.run is always changed in-place, but keeping a backup copy on files eding on …BKPXXX. A very simple submission script will look like this (runjob.pbs):

#!/bin/bash

#PBS -l nodes=1:ppn=2,walltime=00:5:00
#PBS -m aeb
#PBS -q debug
#PBS -j oe

module purge
module load atomistic/lammps/2017.08.11

cd $PBS_O_WORKDIR
mpirun -np 2 -machinefile $PBS_NODEFILE lmp_mpi -in in.run

On this submission script we are just requesting 2 cores on the debug queue for 5 minutes. We are assuming that the only module needed to run LAMMPS is atomistic/lammps/2017.08.11 cmd_restater can be executed using this command line:

cmd_restart.py -p runjob.pbs -i in.run -d steps.dat -m 10000000 -s 30

The file steps.dat does not exist at the very begining, cmd_restarter just need a file that can be used to check how many iterations have been achieved in order to decide when the simulation is cosidered complete.