Enable GPU-accelerated translated search#1082
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KimBioInfoStudio wants to merge 1 commit intosoedinglab:masterfrom
Open
Enable GPU-accelerated translated search#1082KimBioInfoStudio wants to merge 1 commit intosoedinglab:masterfrom
KimBioInfoStudio wants to merge 1 commit intosoedinglab:masterfrom
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Pass GPU and MAKEPADDEDSEQDB_PAR variables to the translated search workflow. When GPU is enabled and the target is nucleotide, automatically create a padded database from the translated ORFs before the inner protein search. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
GPUandMAKEPADDEDSEQDB_PARenvironment variables fromSearch.cppto the translated search workflowmakepaddedseqdbon the translated ORF database before the inner protein searchREMOVE_TMPis setThis enables GPU acceleration for all three translated search modes: blastx (nucleotide query → protein target), tblastn (protein query → nucleotide target), and tblastx (nucleotide query → nucleotide target).
Benchmark (1,000 queries × 10,000 targets, DGX Spark)
GPU and CPU produce identical results in all tested cases.
Test plan
--gpu 1: verified GPU/CPU results identical--gpu 1 --mask 0: verified GPU/CPU results identical--gpu 1 --mask 0: verified GPU/CPU results identical (6/6 hits match)🤖 Generated with Claude Code