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TheEvergreenStateCollege / bioinformatics

Plant genome sequencing
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Ricard and Dom's work on low system memory in rusty-plants #46

Closed learner-long-life closed 1 month ago

learner-long-life commented 1 month ago

Does this compile and run the same as before? How would we test the desired behavior? (Program exists cleanly and drops the suffix tree if it reaches the magic number of 80% of system memory).

learner-long-life commented 1 month ago

I think I understand more about this task. The bounty and task was originally to just detect when system memory is low, print out a message, and gracefully exit, dropping the one big suffix tree.

I think this code implements the next step, along with low system memory detection, which is processing suffix trees in chunks from the transcriptome / genome, and perhaps sizing the chunk so that we never run out of memory. However, it appears we still drop them all in the end.

I'm merging it to the mozes-sysmem-branch for now to create an alternate binary, so we can close the pull requests, and Mozes can delete his private fork if he wishes. Thanks everyone for your work @AbyssalRemark @Mozes721