Optimize memory management and fix parallel deadlocks for HPC#28
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Lesky47 wants to merge 3 commits into
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Optimize memory management and fix parallel deadlocks for HPC#28Lesky47 wants to merge 3 commits into
Lesky47 wants to merge 3 commits into
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ASCAT expects data frames; convert SNPpos to data.frame. Deep copy of SNPpos to avoid modifying the original object by reference.
- Replaced DT sorting with setorder. Replaced 'foreach' + '.combine="rbind"' with 'lapply' + 'rbindlist' to avoid quadratic copying. Peak RAM dropped from >400GB to ~20GB with 16 cores in this step. Runtime dropped from 1.5 hrs to seconds. - Updated parallelization in allele counting with 'callr' package. Previous 'doParallel::stopImplicitCluster' creates OpenMP deadlocks for the second bam at allele counting step. Now using callr::r() to isolate per-sample processing. Reclaims memory and clears locks between BAM files. - Bugfix: Corrected invalid 'on=' argument to 'by=' in SNP data.table merge
NMNS93
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Mar 7, 2026
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NMNS93
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Other than the TODO, LGTM. Thanks!
| tsnps <- tsnps[BAF_n >= 0.08 & BAF_n <= 0.92] | ||
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| # Temporarily changed to 0.2 and 0.8 for high coverage WGBS data. | ||
| # TODO: fix this later !!! |
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Replaced DT sorting with setorder. Replaced 'foreach' + '.combine="rbind"' with 'lapply' + 'rbindlist' to avoid quadratic copying. Peak RAM dropped from >400GB to ~20GB with 16 cores in this step. Runtime dropped from 1.5 hrs to seconds.
Updated parallelization in allele counting with 'callr' package. Previous 'doParallel::stopImplicitCluster' creates OpenMP deadlocks for the second bam at allele counting step. Now using callr::r() to isolate per-sample processing. Reclaims memory and clears locks between BAM files.
Bugfix: Corrected invalid 'on=' argument to 'by=' in SNP data.table merge