fix: n_jobs in cluster.cluster() not working#22
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wuwenrui555 wants to merge 2 commits intodpeerlab:masterfrom
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fix: n_jobs in cluster.cluster() not working#22wuwenrui555 wants to merge 2 commits intodpeerlab:masterfrom
n_jobs in cluster.cluster() not working#22wuwenrui555 wants to merge 2 commits intodpeerlab:masterfrom
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jpintar
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Sep 23, 2025
phenograph/core.py
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| row indices, column indices, and nonzero values for a sparse adjacency matrix | ||
| """ | ||
| if n_jobs == -1: | ||
| n_jobs = cpu_count() |
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I would not use multiprocessing.cpu_count() here – in HPC contexts it won't always correctly pick up how many cores your job has been allocated, but the total core count of the node. It's safer to use len(os.sched_getaffinity(0)) instead (there's also os.process_cpu_count() introduced in Python 3.13).
Hopefully this pull request gets incorporated... Not sure how actively Phenograph is being maintained...
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Thanks for the feedback! You're absolutely right about the HPC context issue.
I've updated the code to use len(os.sched_getaffinity(0)) instead.
…t() for HPC compatibility
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Fix bug that there are more processes than expected after setting n_jobs in phenograph.cluster() function.