Hi Alejandro, Yes, I think it's something with parallel. There's other user met similar problem with package zinba, which also based on parallel. I'll try r-help list, see if anyone there can help. Thank you! Bin On 1/29/13 12:57 PM, "Alejandro Reyes" <alejandro.reyes at="" embl.de=""> wrote: >Dear Bin Ye, > >I do not know exactly where the problem is coming from, but my guess >would be that it is a problem is from the parallel package. Does it >happen only when you use DEXSeq? Or it also happens when you use >parallel in general? > >Best regards, >Alejandro Reyes > >> Dear list, >> >> I've been using DEXSeq as describe in vignette on our SGE cluster which >> worked as expected, but I noticed that when any command with nCore=N (N >>> 1) >> called, there will be N orphan processes left in background. After the >> command finished, those N processes will be in sleep and hold certain >>amount >> of memory, but 0 cpu. These just keep adding up until it crashes the >>compute >> node. I've tried to clean-up with multicore command kill(children()) in >>R, >> it just return NULL without doing anything. I had to manually kill in >>linux >> command line. And I can't find in vignette how to deal with this. Is >>this an >> issue with package parallel/multicore? My session info is attached >>below. >> >> Is there a way to clean-up in R after calling those multi-processes >> commands? It will be really helpful if the vignette can be updated on >>this >> issue. >> >> 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 >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor >