Request for help with SGE submission script manipulation

Shell Programming and Scripting
1

Hi,

I have the following SGE submission (HPC calculation) script, which is just a Bash script:

#!/bin/bash -l

#$ -S /bin/bash
#$ -l h_rt=1:00:0
#$ -l mem=4G
#$ -N XXX
#$ -pe qlc 24
#$ -P XXX
#$ -wd /home/uccaxxx/Scratch/222PdT/3vac/c0001/

mpirun -m $TMPDIR/machines -np $NSLOTS $HOME/bin/new_vasp

What I'd like to do is take the following line within that script:

#$ -wd /home/uccaxxx/Scratch/222PdT/3vac/c0001/

... looking, specifically, at the 'c0001' element.

I'd then like to, for example, say that I want 101 new scripts like this with only the 'c0001' element in that line changing accordingly. So, I would have 101 scripts where that element changes from c0001 to c0002 ... c0033 ... all the way to c0101.

The script is currently called 'script_0001', and I'd like the new scripts' filenames to change to script_0002 etc. all the way through to script_0101 according to how the c0001 element in the line in question is changed.

Ideally I'd like to produce something that can do what I need in Python or Bash as these are languages I am familiar with.

I started writing something in Bash which fell down and this is what I have in Python so far, which is a long way off and which I have rather hit the wall with:

#!/usr/bin/python

from __future__ import print_function

with open('scriptnew', mode='w') as outfile:
    with open('script') as infile:
        for line in infile.readlines():
                    if line[4:6]=='-wd':
                            a = int(line[42])
                line = line[42] + int(a)
                        print(line, end='', file=outfile)

Any help (or statements informing me that this not at all simple) would be greatly appreciated.

2

By shell:

cat template

#!/bin/bash -l

#$ -S /bin/bash
#$ -l h_rt=1:00:0
#$ -l mem=4G
#$ -N XXX
#$ -pe qlc 24
#$ -P XXX
#$ -wd /home/uccaxxx/Scratch/222PdT/3vac/c0001/

mpirun -m $TMPDIR/machines -np $NSLOTS $HOME/bin/new_vasp

for (( i=1; i<=101; i++ ))
do 
  n=$(printf "c%04d" $i)
  f=$(printf "%04d" $i)
  sed "s/c0001/$n/" template > script_$f 
done
1 Like
3

Many thanks!