157. Restarting gaussian (g09) job on an SGE system (qsub)

The Australian University I'm working at has a computational cluster where jobs are submitted using qsub. This post is more like a personal note to myself, but the point about resubmitting jobs may be of use to someone.

This page is useful reading for how these types of scripts with mixed shell and gaussian stuff work: http://www.gaussian.com/g_tech/g_ur/m_running.htm

0. The qsub header (Notes To Myself)

http://cf.ccmr.cornell.edu/cgi-bin/w3mman2html.cgi?qsub(1B)
#$ -S /bin/sh Shell. Can be csh, tcsh etc..
#$ -cwd execute in Current Working Directory
#$ -l h_rt=12:00:00 Maximum allowed run time in hours. -l is a list with resource limits.
#$ -l h_vmem=4G Memory limit. http://www.biostat.jhsph.edu/bit/cluster-usage.html#MemSpec. Should match %mem 4000mb

#$ -j y"-j join. Declares if the standard error stream of the job will be merged with the standard output stream of the job." It creates *.o* and *.p* files with what would've been echoed in the terminal.

#$ -pe g03_smpX XSeems to stand for parallel execution. X would be the number of slots it seems. The g03_smpX seems to be the message passing interface, but not entirely sure. 

1. Setting up simple jobs
First create a standard template, let's call it qsub.header

#!/bin/sh
#$ -S /bin/sh
#$ -cwd
#$ -l h_rt=12:00:00
#$ -l h_vmem=4G
#$ -j y
#$ -pe g03_smp2 2
module load gaussian/g09
time G09 << END > g09_output.log

and save it in your home folder ~.

Create an input file, e.g. water.in and put it in your work directory, e.g. ~/g09

%chk=water
#P ub3lyp/6-31G* opt

water energy

0  1
O
H  1  1.0
H  1  1.0  2  120.0

Put them together:
cat ~/qsub.header > water.qsub
cat ~/g09/water.in >>water.qsub

#!/bin/sh
#$ -S /bin/sh
#$ -cwd
#$ -l h_rt=12:00:00
#$ -l h_vmem=4G
#$ -j y
#$ -pe g03_smp2 2
module load gaussian/g09
time G09 << END > g09_output.log

%chk=water.chk
%nprocshared=6
#P ub3lyp/6-31G* opt

water energy

0  1
O
H  1  1.0
H  1  1.0  2  120.0

2. Restarting jobs

Most likely your home folder is shared across the nodes via nfs.

To find out, submit

#!/bin/sh
#$ -S /bin/sh
#$ -cwd
#$ -l h_rt=12:00:00
#$ -l h_vmem=4G
#$ -j y
#$ -pe g03_smp2 2
pwd
ls -lah
tree -L 1 -d

to get some directory information about the nodes.

Once you have that, just put the absolute path to your .chk file in your restart script, e.g.

#!/bin/sh
#$ -S /bin/sh
#$ -cwd
#$ -l h_rt=12:00:00
#$ -l h_vmem=4G
#$ -j y
#$ -pe g03_smp2 2
module load gaussian/g09
time G09 << END > g09_output.log

%chk=/nfs/home/hpcsci/username/g09/water.chk
%nprocshared=2
#P ub3lyp/6-31G* opt guess=read geom=allcheck