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

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.