[BioC] DEXSeq and parallel, orphan processes.

[Alejandro Reyes]

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
>
>
>
>
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>
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