Question: BiocParallel: zombie processes on FORK cluster
1
gravatar for assaron
15 months ago by
assaron150
assaron150 wrote:

Hello,

Is it a knwon issue that bplapply function leaves zombie processes on FORK cluster?

library(BiocParallel)
b <- MulticoreParam(workers=4)
bplapply(1:10, sqrt, BPPARAM=b)
# here 4 zombie processes appear
bplapply(1:10, sqrt, BPPARAM=b)
# here another 4 zombie processes appear

It could be realted to this issue: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15471 As far as I understand that bug was not yet fixed in R Core but it is more mild:

library(parallel)
mclapply(1:10, sqrt, mc.cores=4)
# here 3 zombie processes appear
mclapply(1:10, sqrt, mc.cores=4)
# no additional zombies

sessionInfo:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=ru_RU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=ru_RU.UTF-8        LC_COLLATE=ru_RU.UTF-8    
 [5] LC_MONETARY=ru_RU.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=ru_RU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=ru_RU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] BiocParallel_1.12.0

loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1    RCurl_1.95-4.8 bitops_1.0-6
biocparallel parallel • 456 views
ADD COMMENTlink modified 15 months ago by Martin Morgan ♦♦ 23k • written 15 months ago by assaron150
Answer: BiocParallel: zombie processes on FORK cluster
2
gravatar for Martin Morgan
15 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

I believe that this has been addressed in R-devel

------------------------------------------------------------------------
r73775 | kalibera | 2017-11-22 08:37:18 -0500 (Wed, 22 Nov 2017) | 3 lines

Do not leave zombie processes behind in parallel. Improvements to signal
handling and termination of forked processes in parallel.

and in NEWS.Rd

      \item (Package \pkg{parallel}.)  \code{mclapply()}, \code{pvec()}
      and \code{mcparallel()} (when \code{mccollect()} is used to
      collect results) no longer leave zombie processes behind.

so that zombies will be vanquished in the next release of R.

 

ADD COMMENTlink written 15 months ago by Martin Morgan ♦♦ 23k

Thanks for the info! I'll try to check R-devel version

ADD REPLYlink written 15 months ago by assaron150

Indeed, it is fixed in R-devel.

ADD REPLYlink written 15 months ago by assaron150
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