Reduce MMseqs2 split-memory-limit to prevent OOM kills

[dbolotin]

Summary

• Reduce --split-memory-limit from 80% to 60% of system RAM
• The flag only controls prefilter database splitting; actual peak usage is ~125% of the set value
• Clustering and alignment steps use additional uncontrolled memory on top
• At 80%, total memory could reach 100%+ of container RAM → OOM kills
• 60% leaves sufficient headroom for all MMseqs2 stages plus OS overhead

Test plan

• Run clonotype clustering on a dataset that previously OOM'd
• Verify clustering results are identical (only memory splitting changes, not algorithm)

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses Out-Of-Memory (OOM) issues encountered during MMseqs2 execution by strategically lowering the --split-memory-limit configuration. By reducing the allocated memory percentage, the system gains crucial headroom to accommodate peak memory demands from various MMseqs2 stages, ensuring more stable and reliable operation.

Highlights

• MMseqs2 Memory Limit Adjustment: The --split-memory-limit for MMseqs2 has been reduced from 80% to 60% of system RAM.
• OOM Prevention: This adjustment aims to prevent Out-Of-Memory (OOM) kills by providing sufficient memory headroom, considering that actual peak usage can exceed the set limit and additional memory is consumed by clustering and alignment steps.

Changelog

• workflow/src/clustering.tpl.tengo
  • Updated the calculation for memLimit to use 60% of system RAM instead of 80%.
  • Added a new comment explaining the rationale for this memory limit adjustment.

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[gemini-code-assist]

Code Review

This pull request reduces the MMseqs2 --split-memory-limit from 80% to 60% of system RAM to prevent out-of-memory errors. The change also introduces a minimum memory limit of 1GB and switches from ceil to int (truncation) for the calculation, which are sensible improvements. The code change is correct and aligns with the goal. I have one minor suggestion to improve code readability.

[gemini-code-assist]

For better readability and consistency with the previous code that used 0.8, it's clearer to use the floating-point literal 0.6 instead of the expression 60/100. While Tengo's division should handle this correctly, using 0.6 avoids any potential confusion about integer division for future maintainers.

	    memLimit := "{int(max(system.ram.gb * 0.6, 1))}" + "G"