Common job script errors and issues

[balston]

Here is an example job script with a number of errors and issues on UCL clusters:

#!/bin/bash

# Batch script to run LAMMPS 29th September 2021 Update 2 GNU basic + FFTW version on Kathleen
# GNU 10.2.0 and OpenMPI module mpi/openmpi/4.0.5/gnu-10.2.0

# 1. Force bash as the executing shell.
#$ -S /bin/bash

# 2. Request twelve hours of wallclock time (format hours:minutes:seconds).
#$ -l h_rt=12:0:0

# 3. Request 1 gigabyte of RAM per process.
#$ -l mem=160G

# 4. Set the name of the job.
#$ -N LAMMPS-FFTW-rhodo80-12

# 5. Select the MPI parallel environment with 80 processes (2 nodes)
#$ -pe mpi 80

# 6. Set the working directory to somewhere in your scratch space.  This is
# a necessary step with the upgraded software stack as compute nodes cannot
# write to $HOME.
# Replace "<your_UCL_id>" with your UCL user ID :)
#$ -wd /home/<your_UCL_id>/Scratch/LAMMPS_examples/bench

module load beta-modules
module load gcc-libs/10.2.0
module load compilers/gnu/10.2.0
module load mpi/openmpi/4.0.5/gnu-10.2.0
module load python3/3.9-gnu-10.2.0
module load fftw/3.3.9/gnu-10.2.0
module load lammps/29sep21up2/basic-fftw/gnu-10.2.0


mpirun -np $NSLOTS lmp_mpi -var x 8 -var y 8 -var z 5 -in in.rhodo.long.scaled -log in.rhodo.long.log-$JOB_ID