[GE users] Passing Arguments to Prolog Script

butters chris at pearit.co.uk
Wed May 27 13:38:46 BST 2009

Hi Everyone,

I was wondering if anyone could help me with a little puzzle please?
I'm trying to find a way to pass arguments to a prolog script in SGE. To be more precise, I'm working with Perl-Speaks-NONMEM (PsN). With PsN, the user submits a 'master' job, which then spawns lots of NONMEM jobs across the cluster via SGE. These 'child' jobs are completely separate from the master job, and aren't aware of the master job at all. They also don't inherit the environment from the master job when they're started.

This is fine, except our users sometimes need to run PsN jobs on data stored in Clearcase (an IBM version control system). Clearcase requires that the user 'login' with a special 'cleartool' command, before they can access the data stored in it. This command requires an argument specifying which 'view' to login to.
This creates a situation where the master job runs in a shell where the Clearcase login has already been performed (I have a script which can take care of this), but the child jobs then start in different shells, often on different nodes, where the Clearcase login hasn't been performed, causing them to fail.

To further complicate the situation, I have no control over the behaviour of Clearcase and I can't alter the way PsN spawns the child jobs (we're running a validated system (Pharma industry), so altering PsN would break months of validation work performed on it!).

I've tried to use environment variables to pass the arguments between the master job and the prolog scripts for the child jobs, but as I mentioned it seems they don't inherit the master's environment.

Is there any way to directly pass arguments to prolog scripts please? Or does anyone have any creative ideas how I could get round this please?

Thanks very much for any help anyone can give.


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