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Reduce MMseqs2 split-memory-limit to prevent OOM kills #104

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Reduce MMseqs2 split-memory-limit to prevent OOM kills #104

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2748e0b
Reduce MMseqs2 --split-memory-limit from 80% to 60% of system RAM
dbolotin Mar 12, 2026
5847ef7
Add changeset for MMseqs2 memory fix
dbolotin Mar 12, 2026
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5 changes: 4 additions & 1 deletion workflow/src/clustering.tpl.tengo
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Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,10 @@ self.body(func(inputs) {
run()

// get split memory limit based on real system ram
memLimit := "{int(ceil(system.ram.gb * 0.8))}" + "G"
// --split-memory-limit controls only the prefilter database splitting;
// actual peak usage is ~125% of this value, plus uncontrolled memory
// from clustering and alignment steps; 60% leaves headroom for all of that
memLimit := "{int(max(system.ram.gb*60/100,1))}" + "G"

@gemini-code-assist gemini-code-assist Bot Mar 12, 2026

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medium

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"


mem := "32GiB" // @TODO: set based on the size of the input
cpu := 16
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