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fix error handling #19

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bluegenes merged 3 commits into main from err-handling

May 9, 2024

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bluegenes commented May 9, 2024 •

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In v0.2.1, if we encounter an issue with the md5sum file download, the error handling loop would cause us to hang / not continue to process sigs.
This fixes the issue by introducing an error_handler to receive errors and notify as we go.
because we can't bail from within the error_handler, I introduce and AtomicBool to monitor whether we need to bail because we expected sigs but didn't end up writing any

I just ran this on 95k protein downloads, and it took 2h54mins and 12GB of RAM

cat /home/ntpierce/database-releases/gtdb-rs214.protein/logs/gtdb-rs214.protein.download_and_sketch_missing.benchmark

s	h:m:s	max_rss	max_vms	max_uss	max_pss	io_in	io_out	mean_load	cpu_time
10476.4868	2:54:36	445.03	12946.43	456.79	457.60	86.62	25.43	1.27	133.17

bluegenes added 3 commits

May 8, 2024 20:58


          add error handler for timely err reporting

6a675ff


          restore bail if sigs expected but not written

2528cfc


          bump version

5b738fd

bluegenes merged commit 835b039 into main

1 check failed

bluegenes deleted the err-handling branch

July 15, 2024 18:48

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