Shell Programming and Scripting

#!/bin/bash
#PBS -l nodes=1:ppn=8,walltime=48:00:00,os=centos53computeA

## To submit type: qsub x.sh

# If not an interactive job (i.e. -I), then cd into the directory where
# I typed qsub.
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then
  if [ -n "$PBS_O_WORKDIR" ]; then
    cd $PBS_O_WORKDIR
  fi
fi

# the input file is typically named something like "gamesjob.inp"
# so the script will be run like "$SCINET_RUNGMS gamessjob 00 8 8"

# find /scratch/mzd/gamess-scratch -type f -name ${NAME:-safety_net}\* -exec /bin/rm {} \;

# load the gamess module if not in .bashrc already
# actually, it MUST be in .bashrc
# module load gamess

# run the program

awk '/\ $VIB/{p=1}p;END{print " $END"}' /scratch/mzd/rungms/$NAME.rst >> job_name_restart.inp

awk: cmd. line:1 fatal: cannot open file '/scratch/mzd/gamess-scratch/.rst' for reading (No such file or directory)

#qsub x.sh -v NAME=job_name

#!/bin/bash
# script to add vibrational data for a hessian restart

awk '/\$VIB/{p=1}p;END{print " $END"}' /scratch/mzd/gamess-scratch/$NAME1.rst >> $NAME2.inp