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I have the following Sun Grid Engine submission script:

#!/bin/sh
# sun grid engine cluster

# use current working directory
#$ -cwd

# merge error output into standard output stream
#$ -j yes
#$ -o generate_databases.log

# request to  cpu number
#$ -pe make 4

currentdir=`/bin/pwd`
echo "current working directory: $currentdir"

And here is my output

/home/eamorr/sge
currentdir: Undefined variable.

As you can see, the 'currentdir' variable returns undefined.

How to fix this?

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Your sure that /bin/pwd is correct? Does it work when invoked manually? –  Bobby Sep 19 '12 at 12:39
    
The fact that the script output the current directory (/home/eamorr/sge) suggests that it is finding pwd. And, even if not, it shouldn't cause this error; foo=`/no/such/command` should still either assign a null string to foo or abort the script. –  Scott Sep 19 '12 at 20:39

1 Answer 1

Are you sure it's bash? The backtick operator is not portable. There are several ways to (possibly) fix this:

  1. use #!/bin/bash in the first line to make dure it's bash not anything else
  2. avoid the backticks: currentdir=$(pwd) or currentdir=$(/bin/pwd)
  3. or even simpler currentdir=$PWD
share|improve this answer
    
Hi, thanks for the comment. I'm not sure it's bash... I tried currentdir=$(/bin/pwd), but it returned Illegal variable name –  Eamorr Sep 19 '12 at 12:00
    
So it's most likely not bash. Try option (1) then, but actually, it probably uses a proprietary SUN shell which just behaves completely different from other known shells. –  Stefan Seidel Sep 19 '12 at 12:04

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