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solutions for very long-running jobs #15

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tavareshugo opened this issue Mar 24, 2022 · 1 comment

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enhancement major

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tavareshugo commented Mar 24, 2022 •

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Could add something to the materials for very long jobs that timeout (e.g. on CSD3).

checkpoint:
- https://dmtcp.sourceforge.io/ (need to see how this works exactly)
- another one: https://criu.org/Main_Page
- this may sometimes break things -- make sure to test before you do a big job with it
use cases of breaking workflows into smaller pieces. For example, with GATK can use the new GenomicsDB format to add samples sequentially to the database.
parallelise your code

tavareshugo added the enhancement label

tavareshugo added the major label

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tavareshugo commented Dec 8, 2022

This could be part of a separate "advanced" module, together with #18

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Running workflows (Nextflow or Snakemake) #18

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