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/shand save it in your home folder ~.
#$ -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
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/shto get some directory information about the nodes.
#$ -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
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
