[BioC] DEXSeq and parallel, orphan processes.

[Bin Ye]

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]]
>>
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>