Create a Nextflow profile and workflow configuration for CCAM HPC#4
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AlexPatrie wants to merge 236 commits intomasterfrom
Open
Create a Nextflow profile and workflow configuration for CCAM HPC#4AlexPatrie wants to merge 236 commits intomasterfrom
AlexPatrie wants to merge 236 commits intomasterfrom
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GCSFS schedules future, which does not work in atexit callbacks, so we revert back to PyArrow. Additionally, we now use os._exit to explicitly set an exit code of 1 when an exception is raised during finalization because Python ignores exceptions in atexit callbacks by default.
Exceptions in atexit hooks are ignored and not reflected in the final exit code. Additionally, new futures cannot be scheduled in atexit hooks (after interpreter shutdown) so asyncio does not work.
Security updates
T2D spot VMs only available in standard sizes so retries would need to bump memory and CPU together, which is wasteful
Fixed memory request for GCP
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NOTE(please read first):
This PR may be expected to be open indefinitely, or at least as long as it takes to reconcile content between this branch, the fork's
masterand/or the origin'smaster. The final SMS deployment (non-"academic" API) must replicate this PR/branch in the secure vEcoli repo. (Not yet done).What does this PR do?:
ccamNextflow profile inrunscripts/nextflow/config.templaterunscripts/workflow.pyconfigs/sms_ccam.jsontextwrap.dedentwrapping to existing SLURM script generation string blocks for claritymessagesbranchdata-transformersbranch (which itself has been merged intomessages)