please use a workflow manager, support other job schedulers, or somehow otherwise provide a system-independent run option

Issue #8 new
Afif Elghraoui created an issue

It looks to me like this software only works as written for people who have SGE clusters. Using it to generate an SGE script and translating that to use with another job scheduler is not efficient.

I don't know of a good cross-scheduler solution (it's supposed to be DRMAA, but that's not practical), but if you could at least use a workflow manager, many of them have good ways of supporting different job schedulers or just direct execution.

Comments (1)

  1. Mehran Karimzadeh

    Hi Afif,

    Thanks a lot for your comment. You are absolutely right. For reasons you mentioned, I had already implemented some work arounds which of course are not ideal.

    All scripts accept a -var_id which is the environmental variable of job array. By default -var_id is set to SGE_TASK_ID and can be overwritten with your job scheduler.

    In addition, it is possible to run the program in a for loop or with GNU Parallel using -job_id argument which allows for setting the task manually for each script.

    Hope this helps.

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