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
