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perf: make circle_map_realign more parallelized, try mem_mb dependent on thread number #22

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Merged
merged 1 commit into from
Jun 11, 2025
Merged

perf: make circle_map_realign more parallelized, try mem_mb dependent on thread number #22

merged 1 commit into from
Jun 11, 2025

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@dlaehnemann dlaehnemann commented Jun 11, 2025 •
edited by coderabbitai bot
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Summary by CodeRabbit

  • Chores
    • Updated resource allocation and threading configuration for improved performance during realignment steps.

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coderabbitai bot commented Jun 11, 2025 •
edited
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Walkthrough

The circle_map_realign rule in the workflow was updated to increase the number of threads from 4 to 16 and to modify the memory allocation logic. Memory is now calculated based on the number of threads rather than input file size. The shell command remains unchanged except for the updated thread count.

Changes

File(s) Change Summary
workflow/rules/circle_map.smk Increased threads from 4 to 16 in circle_map_realign rule; memory allocation now based on threads

Sequence Diagram(s)

sequenceDiagram
    participant Snakemake
    participant CircleMapRealign

    Snakemake->>CircleMapRealign: Run with threads=16, mem_mb=threads*5000
    CircleMapRealign-->>Snakemake: Processed output
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Poem

Sixteen threads now hop along,
Memory grows, robust and strong.
Circles realign with greater might,
Bunnies cheer through day and night.
With every tweak, the workflow gleams,
Hopping forward, chasing dreams! 🐇✨

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between f9eaafb and 9253a84.

📒 Files selected for processing (1)
  • workflow/rules/circle_map.smk (1 hunks)
⏰ Context from checks skipped due to timeout of 90000ms (2)
  • GitHub Check: Formatting
  • GitHub Check: Linting
🔇 Additional comments (1)
workflow/rules/circle_map.smk (1)

44-46:

❓ Verification inconclusive

Ensure the resource lambda’s signature & memory scaling are cluster-compatible

  1. Snakemake forwards several positional arguments to resource lambdas (wildcards, input, threads, resources, attempt).
    • On versions < 7.17, the second positional argument is input, not threads_. • If your production environment is pinned to an older Snakemake, this will raise TypeError: () got multiple values for argument 'threads'`.

    A safer definition is:

-    resources:
-        mem_mb=lambda wc, threads: threads * 5000,
+    resources:
+        mem_mb=lambda wc, threads, **kwargs: threads * 5000,

  1. threads * 5000 → 80 GB for 16 threads. Confirm your cluster profile advertises mem_mb and that nodes with ≥80 000 MB are available; otherwise jobs will stay in the queue indefinitely.

  2. The previous formula scaled with input.size_mb; switching to a fixed 5 GB / thread may over-allocate for small samples and under-allocate for large ones. Consider keeping a hybrid or configurable factor (e.g. via config["circle_map_mem_per_thread"]).

🏁 Script executed:

#!/bin/bash
# Display the first 200 lines of the rule to inspect existing memory‐scaling logic
sed -n '1,200p' workflow/rules/circle_map.smk

Length of output: 2873

Validate resource lambda signature & memory scaling

Please review the following before merging:

  • If your Snakemake version is < 7.17, resource lambdas receive (wildcards, input, threads, resources, attempt), so the existing
    lambda wildcards, threads: … will raise a TypeError. To support both old and new Snakemake, add a catch-all **kwargs.
  • Verify your cluster profile advertises mem_mb and can schedule ≥ 80 000 MB for a 16-thread job, or the job may queue indefinitely.
  • Using a fixed 5 GB/thread may over- or under-allocate; consider a hybrid formula or a config-driven factor (e.g. config["circle_map_mem_per_thread"]).

Location:

  • workflow/rules/circle_map.smk → rule circle_map_realign

Suggested diff:

 rule circle_map_realign:
     …
     threads: 16
     resources:
-        mem_mb=lambda wildcards, threads: threads * 5000,
+        mem_mb=lambda wildcards, threads, **kwargs: threads * 5000,
     shell:
         "Circle-Map Realign …"

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@dlaehnemann dlaehnemann merged commit 545be19 into main Jun 11, 2025
7 checks passed
@dlaehnemann dlaehnemann deleted the perf/improve-circle-map-realigner-resource-requests branch June 11, 2025 18:50
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