HPC/Applications/nwchem

Introduction

• NWChem 6.1 User Documentation

Considerations on Carbon

Memory

• MEMORY

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

memory total 3200 mb

Disk space

• SCRATCH_DIR

NWChem might use a camparably large amount of disk space in volumes and bandwidth not suitable for your $HOME directory. To avoid quota overruns, use either $SANDBOX or $TMPDIR for NWChem scratch. The *.nw input file is static, which makes it difficult to point to temporary directories via their environment vairables. 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. To the following steps:

(1) In the job script, set up a job-specific scratch directory as symlink named "scratch" in the job's working directory. Choose one of:

• $SANDBOX: distributed scratch (not auto-cleaned, high bandwidth but shared file system)
• $TMPDIR: node-local (auto-cleaned, slower)

cat $NWCHEM_HOME/sample.job

#!/bin/bash
#PBS ...
...

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

(2) In the NWChem input file, add the line "scratch_dir ./scratch" near the beginning.

cat job.nw

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