HPC/Applications/nwchem

Introduction

• NWChem 6.1 User Documentation

Considerations on Carbon

SCRATCH_DIR

The *.nw input file is static, which makes it difficult to point to temporary directories that change from call to call. As a solution, I suggest to create a symbolic link in the job script prior to running NWChem, and use the name of the job script in your *.nw file. See $NWCHEM_HOME/sample.job for the full file.

cat $NWCHEM_HOME/sample.job

#!/bin/bash
#PBS ...

# Avoid quota overruns. 
# (1) Add the line "scratch_dir ./scratch" to the input file.
# (2) Provide this directory as local symlink; choose one of:
#   - $SANDBOX: distributed scratch (not auto-cleaned, shared file system)
#   - $TMPDIR node-local (auto-cleaned, slower)

dir=$SANDBOX/$PBS_JOBID
#dir=$TMPDIR

link=scratch
mkdir -p $dir
ln -snf $dir $link

mpirun -machinefile $PBS_NODEFILE -np $PBS_NP \
         nwchem foo.nw

# clean sandbox (won't be reached if job terminates for time)
[[ $dir =~ $SANDBOX/* ]] && rm -r $dir

cat job.nw

title "foo structure"
echo
scratch_dir ./scratch
geometry units angstroms
...

MEMORY

The default memory allocation is far smaller than useful on Carbon. Raise it using, e.g.:

memory total 3200 mb