Add option to set default number of jobs/CPUs to use #138
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pcm32
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Jan 14, 2025
README.md
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| @@ -42,6 +42,7 @@ Usage: scanpy-cli [OPTIONS] COMMAND [ARGS]... | |||
| Options: | |||
| --debug Print debug information | |||
| --verbosity INTEGER Set scanpy verbosity | |||
| --njobs INTEGER Set scanpy default number of jobs/CPUs, defaults to all available | |||
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I would suggest that you keep the default as it was (1 job), then on updates of older scripts, you don't need to change anything (but you can always set the number of jobs explicitly as pursued). Probably also using all available CPUs by default might lead (when forgetting to set this) to some undesirable behaviour (abuse node beyond resources request, use more memory than requested and then get killed due to OOM, etc).
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Thanks, Pablo. Very much appreciate this commnent. Done in a50edfb. We were also planning on setting the number of jobs explicitly where applicable while the pipeline is still using an older version of scanpy-scripts.
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Add a
scanpy-clioption to set the default number of jobs/CPUs that scanpy uses, for parallel computing.