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I am creating a python wrapper script and was wondering what'd be a good way to create it.

I want to run code serially. For example:

Step 1. Run same program (in parallel - the parallelization is easy because I work with an LSF system so I just submit three different jobs).

I run the program in parallel, and each run takes one fin.txt and outputs one fout.txt, i.e., when they all run they would produce 3 output files from the three input files, f1in.txt, f2in.txt, f3in.txt, f1out.txt, f2out.txt, f3out.txt.

(in the LSF system) When each run of the program is completed successfully, it produces a log file output, f1log.out, f2log.out, f3log.out.

The log files output are of this form, i.e., f1log.out would look something like this if it runs successfully.

------------------------------------------------------------
# LSBATCH: User input
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     86.20 sec.
    Max Memory :       103 MB
    Max Swap   :       881 MB

    Max Processes  :         4
    Max Threads    :         5

The output (if any) is above this job summary.

Thus, I'd like my wrapper to check (every 5 min or so) for each run (1,2,3) if the log file has been created, and if it has been created I'd like the wrapper to check if it was successfully completed (aka, if the string Successfully completed appears in the log file).

Also if the one of the runs finished and produces a log file that was not successfully completed I'd like my wrapper to end and report that run (k=1,2,3) was not completed.

After that,

Step2. If all three runs are successfully completed I would run another program that takes those three files as input... else I'd print an error.

Basically in my question I am looking for two things:

Does it sound like a good way to write a wrapper?

How in python I can check the existence of a file, and search for a pattern every certain time in a good way?

Note. I am aware that LSF has job dependencies but I find this way to be more clear and easy to work with, though may not be optimal.

Dnaiel
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1 Answers1

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I'm a user of an LSF system, and my major gripes are exit handling, and cleanup. I think a neat idea would be to send a batch job array that has for instance: Initialization Task, Legwork Task, Cleanup Task. The LSF could complete all three and send a return code to the waiting head node. Alot of times LSF works great to send one job or command, but it isn't really set up to handle systematic processing.

Other than that I wish you luck :)

Kevin R.
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