Good day,
I haven't been able to make a small and reproducible example, but I am using
bpstart and bpstop to run a loop with 25 workers multiple times on a large
bioinformatics dataset. After a few times of running the loop successfully, a
small number of the R workers use 100% CPU endlessly :
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
3300 dario 20 0 1190832 837212 17988 R 100.0 0.2 3848:00 R
5014 dario 20 0 1194528 829084 8224 R 99.8 0.2 3843:44 R
5015 dario 20 0 1194532 829088 8224 R 99.8 0.2 3843:44 R
There are also three connections belonging to the R processes waiting to close :
~$ lsof -i | grep CLOSE
R 3300 dario 1025u IPv4 160778259 0t0 TCP
localhost:11881->localhost:49379 (CLOSE_WAIT)
R 5014 dario 1025u IPv4 160778259 0t0 TCP
localhost:11881->localhost:49379 (CLOSE_WAIT)
R 5015 dario 1025u IPv4 160778259 0t0 TCP
localhost:11881->localhost:49379 (CLOSE_WAIT)
~$ lsof -i | grep -c R
256
I use :
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
with BiocParallel 1.5.12
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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