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LANL-Bioinformatics / EDGE

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
https://lanl-bioinformatics.github.io/EDGE/
GNU General Public License v3.0
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Does command-line submission bypass the queue system on EDGE? #57

Closed aretchless closed 1 year ago

aretchless commented 1 year ago

Hello @chienchi et al. This is a question rather than a bug.

I am thinking of using EDGE command line tool to automate run analysis and to run datasets for testing purpose. This uses the 'runPipeline' command. My understanding is that this command occurs downstream of the queue that is created during batch submission from the GUI.

In that case, it would be up to my submission scripts to monitor resource availability and control how many jobs are running at once. Is that correct?

thanks

chienchi commented 1 year ago

It is correct. The runPipeline command is the main workflow execution script. The resource is monitored by the front-end javascript plus the server side cgi scripts. We also use command line version 'runPipeline' locally for large batch runs and testing purpose too and the jobs can be submitted to cluster. So, cluster scheduler can help us monitor the job resource usage.

aretchless commented 1 year ago

Thanks for the answer. And thanks for inviting me to the discussions forum.