Bin Ye | 28 Jan 22:06 2013

DEXSeq and parallel, orphan processes.

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

Thank you!


> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-redhat-linux-gnu (64-bit)

 [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

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

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