[SOLVED] $variable in shell script

RudraB · 06-25-2013, 06:47 AM

Dear friends,
I am trying to write a pbs via a shell script as

Code:

 cat >Hutespot.pbs<<EOF
  #!/bin/bash
  #PBS -l nodes=64:ppn=1,pvmem=1900mb,walltime=1:00:00
  #PBS -V
 
  cd $PBS_O_WORKDIR
 
 
  mpirun ~/bin/kkr.run ${job}.inp >> ${job}.out
 EOF

Now, where, cd $PBS_O_WORKDIR should not be expanded to its value, I mean, in the working Hutespot.pbs, I should ha "cd $PBS_O_WORKDIR" as it is.
instead, while I am running this, as expected, I am having

Code:

  1  #!/bin/bash
  2  #PBS -l nodes=64:ppn=1,pvmem=1900mb,walltime=1:00:00
  3  #PBS -V
  4
  5  cd
  6
  7
  8  mpirun ~/bin/kkr.run input.inp >> input.out

instead of

Code:

 1  #!/bin/bash
  2  #PBS -l nodes=64:ppn=1,pvmem=1900mb,walltime=1:00:00
  3  #PBS -V
  4
  5  cd $PBS_O_WORKDIR
  6
  7
  8  mpirun ~/bin/kkr.run input.inp >> input.out

any help please?

NevemTeve · 06-25-2013, 07:23 AM

You are trying to say that you have a directory called $PBS_O_WORKDIR?
Unusual, but not illegal. There are a few possibilities, here is the simplest:

Code:

#!/bin/sh
...
export PBS_O_WORKDIR='$PBS_O_WORKDIR'
...
cd $PBS_O_WORKDIR
...

RudraB · 06-25-2013, 08:12 AM

Quote:

Originally Posted by NevemTeve

You are trying to say that you have a directory called $PBS_O_WORKDIR?

No, that file itself is a script, and take $PBS_O_WORKDIR from env.
I have managed it with escaping $ :

Code:

cd \$PBS_O_WORKDIR

NevemTeve · 06-25-2013, 08:55 AM

If this command works, then that "file" is actually a directory, and it's name is $PBS_O_WORKDIR.

David the H. · 06-28-2013, 04:48 AM

The proper way to keep a here document from expanding variables and command substitutions is simply to quote the opening string.

Also, if you use "<<-", then you can safely indent the content, and even the closing string if you want to, with tabs (and only tabs). They will be removed upon evaluation and won't appear in the final output.

Code:

#the heredoc contents are tab indented
cat >Hutespot.pbs <<-'EOF'
	#!/bin/bash
	#PBS -l nodes=64:ppn=1,pvmem=1900mb,walltime=1:00:00
	#PBS -V
 
	cd "$PBS_O_WORKDIR"
 
	mpirun "$HOME/bin/kkr.run" "$job.inp" >> "$job.out"
EOF

Of course, this will disable all variable expansions, so if you need some of them to expand and some not to, then you'll have to escape them individually, as you've already discovered.

It's more appropriate to use $HOME in scripts than "~". The latter is a kind of convenience alias designed more for interactive use, and is more limited than the preset shell variable.

QUOTE ALL OF YOUR VARIABLE EXPANSIONS. Note that the quotes inside the heredoc will not be directly evaluated, but will be passed literally to the target location, to be properly evaluated when the script is actually executed.

Finally, and this is just a bit of stylistic advice, I also recommend dropping the brackets around your variables. The full "${var}" form is usually unneeded (with some exceptions), and does nothing but add extra typing and clutter to your code, which can lead to an increased chance of errors. Take it from someone who's been there, you're better off without them.