[Bioc-devel] bplapply Processes Sometimes Stall

[Dario Strbenac]

Good day,

Today, I can't reproduce the stalling. It runs all 20 iterations to completion. When the loop finishes, I see many R processes shown in the output of top as zombies, though. I killed all R processes before running the test, so these are originating from the test command I used.

26853 dario     20   0       0      0      0 Z   0.0  0.0   0:00.25 R
26857 dario     20   0       0      0      0 Z   0.0  0.0   0:00.25 R
26860 dario     20   0       0      0      0 Z   0.0  0.0   0:00.25 R
26861 dario     20   0       0      0      0 Z   0.0  0.0   0:00.22 R
26863 dario     20   0       0      0      0 Z   0.0  0.0   0:00.22 R
          ...                             ...

Do you observe this on your server, too ?

On the ninth try, however, I did manage to completely crash R :

...                    ...
Variety12
Variety13
Variety14
*** buffer overflow detected ***: /usr/lib/R/bin/exec/R terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x731ff)[0x7fc1619ad1ff]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7fc161a304c7]
/lib/x86_64-linux-gnu/libc.so.6(+0xf46e0)[0x7fc161a2e6e0]
/lib/x86_64-linux-gnu/libc.so.6(+0xf6437)[0x7fc161a30437]
...                    ...
7ffeee1f8000-7ffeee23a000 rw-p 00000000 00:00 0                          [stack]
7ffeee29c000-7ffeee29d000 r-xp 00000000 00:00 0                          [vdso]
7ffeee29d000-7ffeee29f000 r--p 00000000 00:00 0                          [vvar]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia