perlbashgridperlbrewsungridengine

How can I control the Perl version used when submitting grid jobs?

I'm working with SGE (Sun Grid Engine) to submit jobs to a grid. I also use perlbrew to manage my installed Perl versions. I wrote some short sh scripts that I use to run a perl script which requires a specific Perl version (5.12.2), which look something like this:

#!/bin/bash
#$-S /bin/bash

source /home/dave/.bash_profile
/home/dave/perl5/perlbrew/bin/perlbrew switch perl-5.12.2

/home/dave/scripts/proc_12.pl --in=/home/dave/in/in.store --dir=/home/dave/in/dir2 --params=/home/dave/in/params.p

Now, when I submit a single job everything works fine, but when I submit many, I start getting perlbrew related error messages, like:

ln: creating symbolic link `current' to `perl-5.12.2': File exists
ln: creating symbolic link `/home/dave/perl5/perlbrew/bin/cpan' to `/home/dave/perl5/perlbrew/perls/current/bin/cpan': File exists
ln: creating symbolic link `/home/dave/perl5/perlbrew/bin/cpan2dist' to `/home/dave/perl5/perlbrew/perls/current/bin/cpan2dist': File exists
ln: cannot remove `/home/dave/perl5/perlbrew/bin/cpanp': No such file or directory
ln: cannot remove `/home/dave/perl5/perlbrew/bin/enc2xs': No such file or directory
ln: cannot remove `/home/dave/perl5/perlbrew/bin/find2perl': No such file or directory

So I guess the /home/dave/perl5/perlbrew/bin/perlbrew switch perl-5.12.2 line is causing the problems.

What can I do?

How can I make my script run using perl-5.12.2 (the default is 5.8.8)?

Solution

  • I don't recommend putting the perlbrew switch perl-5.12.2 in any script you run. Its really only for command line usage.

    If you need a script to use a specific version of Perl then either give it the full perlbrew path on the shebang:

    #!/home/dave/perl5/perlbrew/perls/perl-5.12.2/bin/perl

use 5.012;
use warnings;
...

    Then make sure its executable and run like so:

    chmod +x your_perl_program.pl
./your_perl_program.pl

    Or alternatively use the full pathname to the perl binary in your script:

    #!/bin/bash

/home/dave/perl5/perlbrew/perls/perl-5.12.2/bin/perl your_perl_program.pl


    BTW, you will have potential production and security issues if you run anything unqualified in your scripts or perl programs. For eg:

    #!/bin/sh

# security risk
perl some_script.pl

# and not just perl
tar cvf archive.tar *.txt

# production risk
/home/dave/perl5/perlbrew/bin/perl some_other_script.pl

    The first two are bad because it will pick up the first perl & tar it finds in your path. So this depends on $PATH setting and this could become a security risk. The last is also not good because its reliant on what perl perlbrew is currently switched to at the point in time its run :(

    So doing this can be a potential production & security nightmare. Instead the above should be written like this:

    #!/bin/sh

# fully qualified now.  Uses OS provided perl
/usr/bin/perl some_script.pl

# ditto
/usr/bin/tar cvf archive.tar *.txt

# this needs to run in perl 5.12.2
/home/dave/perl5/perlbrew/perls/perl-5.12.2/bin/perl some_other_script.pl

    Hope that all makes sense?