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snkit's link_nodes_to_nearest_edge is called several times and takes a while for large networks. The function doing most of the work is split_edges_at_nodes. SNKIT_PARALLEL can be set to 1 or TRUE to enable parallelism in this function, but it is not constrained (uses os.cpu_count()), so open-gira's snakemake workflow.cores limit is not respected.
Change snkit parallelism to specify an integer number of processes via SNKIT_PARALLEL or SNKIT_PROCESSES?
Use rule.threads = to specify a maximum number for any given rule invocation. Then hopefully jobs could be submitted that respect the workflow cores limit (test this...).
The text was updated successfully, but these errors were encountered:
snkit's link_nodes_to_nearest_edge is called several times and takes a while for large networks. The function doing most of the work is split_edges_at_nodes. SNKIT_PARALLEL can be set to 1 or TRUE to enable parallelism in this function, but it is not constrained (uses os.cpu_count()), so open-gira's snakemake workflow.cores limit is not respected.
The text was updated successfully, but these errors were encountered: