[Users] using PBS -V on kraken

[Roland Haas]

Hello Erik, Scott,

>  I've used -V on kraken using another code successfully, but not ET
> (haven't tried).
> 
>   One thing you could do as a compromise is limit your environment
> variables before submission, only setting the ones you need.
> 
>   I hope this helps.
At least it tells me that I am not the only one who does what NICS
recommends against :-). Thank you. I am not sure how to limit my
environment variables before submission though. They are already set at
that point. I don't add extra ones via (something equivalent to):
INITIAL_DATA=blah qsub Submit.qsub
rather they are set in .bashrc (otherwise I tended to forget to set them
and have the run abort after waiting for 24hr in queue).

>> Which variable do you want to set? Did you try -V on Kraken? If it
>> works, then let's use it. Modifying the submit script or run script
>> would also work; no need to provide a generic solution if there's only
>> a single use case.
I have used -V on kraken before (always did in the GT submit script and
for maybe 4 runs using a modified simfactory submit script). I never had
problems that I would blame on the environment variable.

The variable I would like to pass in is $INITIAL_DATA which is actually
a path to a directory containing ID files with LORENE data files. So it
is not a "general use" variable that is always defined. Expanding the
path by hand in the parameter file is awkward since it would likely
hard-code information about the user name and/or the cluster and whether
simfactory is used in the parameter file.

NICS suggests to use the -v (lowercase V) switch to pass only individual
environment variables (which is close to what you suggested, Scott,
isn't it?).

So the simfactory submit script does not not include "-V" because the
original author wanted to do what NICS suggests but he omission is
without explicit intent?

Yours,
Roland

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