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rename distance subcommand to phylo

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Rename the distance CLI subcommand to phylo across the codebase, documentation, and build configurations. Relocate source files from cmd/distance/ to a dedicated cmd/phylo/ module, update all internal routing references, and adjust benchmark scripts and Makefile targets to reflect the new command name.
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Eric Coissac
2026-08-15 10:07:03 +02:00
parent 79346c0c86
commit dd889854cb
19 changed files with 49 additions and 46 deletions
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UserDocMD/architecture.md
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@@ -20,7 +20,7 @@ An index directory is organized as `KmerIndex → partitions → layers`, with a
## Parallel execution and NUMA awareness
Partition-level work (index construction, `merge`, `filter`, `reindex`, `select`, `distance`'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:
Partition-level work (index construction, `merge`, `filter`, `reindex`, `select`, `phylo`'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:
- On a multi-socket / multi-NUMA-node machine, one thread pool is pinned per NUMA node, and each partition is processed entirely by threads pinned to one node — keeping the memory a partition touches local to that node's DRAM. This matters because touching kmer data across NUMA nodes without pinning can degrade throughput by an order of magnitude or more on large multi-socket machines.
- On a single-socket machine, Apple Silicon, or if hwloc cannot report NUMA topology, all cores are treated as one node with no pinning and negligible overhead — this is the default behavior on macOS.