How to stop R from leaving zombie processes behind

Question

Here is a little reproducible example:

library(doMC)
library(doParallel)
registerDoMC(4)
    timing <- system.time( fitall <- foreach(i=1:1000, .combine = "c") %dopar% {
                print(i)
            })

I start up R and look at the process table:

> system("ps -efl")
F S UID        PID  PPID  C PRI  NI ADDR SZ WCHAN  STIME TTY          TIME CMD
4 S chbr         1     0  5  80   0 - 21399 wait   10:58 ?        00:00:00 /usr/local/lib/R/bin/exec/R --no-save --no-restore
0 S chbr         9     1  0  80   0 -  1113 wait   10:58 ?        00:00:00 sh -c ps -efl
0 R chbr        10     9  0  80   0 -  4294 -      10:58 ?        00:00:00 ps -efl

If I use the aformentioned simple for loop doMC or doParallel leave a zombie process behind. Output of ps -efl after running the loop:

> system("ps -efl")
F S UID        PID  PPID  C PRI  NI ADDR SZ WCHAN  STIME TTY          TIME CMD
4 S chbr         1     0  4  80   0 - 25256 wait   11:00 ?        00:00:00 /usr/local/lib/R/b
1 Z chbr        10     1  0  80   0 -     0 exit   11:00 ?        00:00:00 [R] <defunct>
0 S chbr        12     1  0  80   0 -  1113 wait   11:00 ?        00:00:00 sh -c ps -efl
0 R chbr        13    12  0  80   0 -  4294 -      11:00 ?        00:00:00 ps -efl

If I repeat the loop without issuing registerDoMC(4) again no additional zombie process gets created. However, if I issue registerDoMC(4) an additional zombie process gets created:

> system("ps -efl")
F S UID        PID  PPID  C PRI  NI ADDR SZ WCHAN  STIME TTY          TIME CMD
4 S chbr         1     0  0  80   0 - 25554 wait   11:00 ?        00:00:01 /usr/local/lib/R/b
1 Z chbr        21     1  0  80   0 -     0 exit   11:02 ?        00:00:00 [R] <defunct>
1 Z chbr        22     1  0  80   0 -     0 exit   11:02 ?        00:00:00 [R] <defunct>
0 S chbr        26     1  0  80   0 -  1113 wait   11:03 ?        00:00:00 sh -c ps -efl
0 R chbr        27    26  0  80   0 -  4294 -      11:03 ?        00:00:00 ps -efl

That's how I figured it could be doMC which is doing something that should not be done. If doMC is causing this is there a way to stop doMC from leaving zombie processes behind? (stopCluster() does not work as no cluster gets created in the first place.)

> sessionInfo()
R Under development (unstable) (2014-08-16 r66404)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] doParallel_1.0.8 doMC_1.3.3       iterators_1.0.7  foreach_1.4.2   

loaded via a namespace (and not attached):
[1] codetools_0.2-8 compiler_3.2.0

Answer 1

This really has nothing to do with foreach or doMC; as Steve Weston has pointed out in answer to other StackOverflow queries, doMC is essentially just a wrapper for mclapply, and you can see zombie processes created with a simple call to mclapply:

library(parallel)
mclapply(rep(5,4), rnorm)

On my system, this leaves two zombie processes:

[richcalaway@richcalaway-pc ~]$ ps -efl | grep defunct
1 Z 1660945517 28701 28624  0 77  0 -     0 exit   12:00 pts/1    00:00:00 [R] <defunct>
1 Z 1660945517 28702 28624  0 78  0 -     0 exit   12:00 pts/1    00:00:00 [R] <defunct>
0 S 1660945517 28704 28308  0 78  0 - 15306 pipe_w 12:00 pts/2    00:00:00 grep defunct

Under normal circumstances, these zombie processes won't cause any trouble, and they do disappear when the R session ends. You can avoid them by using doParallel and a fork cluster instead of using doMC.

Cheers,

Rich Calaway

Principal Program Manager

Revolution Analytics