Hi, I've using package DEXSeq that implements functions with nCores for speed-up. The functions work fine, but I found out that the children processes were not terminated, they still hold memory, and new command will start up new children processes. So if I don't manually kill those orphan processes, they will cause problem. I was qlogin to SGE cluster node to run R. From our administrator, I heard that at least another R package zinba, which based on parallel too, met the same problem. I tried to use functions from multicore, such as kill(children()) and collect(), they just return NULL, but didn't do anything. I was wondering if anyone has met this problem before? Beside kill in command line, is there any way in R that I can use to clean-up the orphan processes?
My session info is attached below. Thank you! Bin >sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DEXSeq_1.4.0 AnnotationDbi_1.20.3 Biobase_2.18.0 [4] BiocGenerics_0.4.0 RSQLite_0.11.2 DBI_0.2-5 loaded via a namespace (and not attached): [1] annotate_1.36.0 biomaRt_2.14.0 clusterProfiler_1.6.0 [4] colorspace_1.2-0 DESeq_1.10.1 dichromat_1.2-4 [7] digest_0.5.2 DO.db_2.5.0 DOSE_1.4.0 [10] genefilter_1.40.0 geneplotter_1.36.0 ggplot2_0.9.3 [13] GO.db_2.8.0 GOSemSim_1.16.1 grid_2.15.1 [16] gtable_0.1.2 hwriter_1.3 igraph_0.5.5-4 [19] IRanges_1.16.4 KEGG.db_2.8.0 labeling_0.1 [22] lattice_0.20-10 MASS_7.3-22 munsell_0.4 [25] parallel_2.15.1 plyr_1.8 proto_0.3-9.2 [28] qvalue_1.32.0 RColorBrewer_1.0-5 RCurl_1.95-3 [31] reshape2_1.2.2 scales_0.2.3 splines_2.15.1 [34] statmod_1.4.16 stats4_2.15.1 stringr_0.6.2 [37] survival_2.36-14 tcltk_2.15.1 tools_2.15.1 [40] XML_3.95-0.1 xtable_1.7-0 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
