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fix(k8s/prepro): reduce mpox batch size to 5, use 1 nextclade job, to not use more than 1GB of memory #1878

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merged 1 commit into from
May 11, 2024

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@corneliusroemer corneliusroemer commented May 11, 2024

https://update-limits.loculus.org

Use one processing thread for Nextclade to reduce memory consumption

We currently set limits to 1GB of memory for preprocessing. It gets hit by mpox with settings prior to this PR:

tmp/tmpryvdeuf4/input.fasta']
Traceback (most recent call last):
  File "/opt/conda/bin/prepro", line 8, in <module>
    sys.exit(cli_entry())
             ^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/loculus_preprocessing/__main__.py", line 16, in cli_entry
    run(config)
  File "/opt/conda/lib/python3.12/site-packages/loculus_preprocessing/prepro.py", line 378, in run
    processed = process_all(unprocessed, dataset_dir, config)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/loculus_preprocessing/prepro.py", line 315, in process_all
    nextclade_results = enrich_with_nextclade(unprocessed, dataset_dir, config)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/loculus_preprocessing/prepro.py", line 121, in enrich_with_nextclade
    raise Exception(msg)
Exception: nextclade failed with exit code -9

… of memory

Use one processing thread to reduce memory consumption
@corneliusroemer corneliusroemer added the preview Triggers a deployment to argocd label May 11, 2024
@corneliusroemer corneliusroemer changed the title fix(k8s/prepro): reducem pox batch size to 5 to not use more than 1GB of memory fix(k8s/prepro): reduce mpox batch size to 5, use 1 nextclade job, to not use more than 1GB of memory May 11, 2024
@corneliusroemer corneliusroemer merged commit 2d73e4c into main May 11, 2024
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@corneliusroemer corneliusroemer deleted the update-limits branch May 11, 2024 20:32
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2 participants