[maker-devel] maker leaving large numbers of defunct zombies

[Carson Holt]

MAKER uses IPC::Open3 to open almost all external applications, including
a helper script called every once in a while that helps check file locks
on NFS.

MAKER then calls waitpid to reap the processes, as IPC::Open3 doesn't
auto-reap.  The only time previously I've seen issues with zombie
accumulation was with MPICH2 when it moved from the MPD process manager to
Hydra.  Hydra had certain broken signal handling issues that I had to bug
the MPICH2 developers about and they fixed it.  It is possible that the
issue you are having may be with OpenMPI or with perl 5.16.  I currently
use perl 5.12.  Perl instituted something called safe signals in either
5.6 or 5.8 and there may be some updates in 5.16 where they've been
changing those around again.

I can try installing a copy of 5.16 to test with and OpenMPI to see if I
can replicate the error.

Thanks,
Carson



On 12-05-31 8:25 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been working lately to set up maker for annotation work on a few
>fungal genomes. I've got mpi maker up and running now, however, I notice
>that maker is leaving a lot of <defunct> perl processes behind. This
>happens to the extent that the process table on the system gets filled up
>after a few hours run time. Right now the process tree after three hours
>running looks like this:
>
>    |-sge_execd-+-sge_shepherd---bash---mpirun-+-maker-+-maker
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1371*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1348*[perl]
>     |           |                              |       `-perl
>     |           |                              |-maker-+-maker
>     |           |                              |
>|-maker---1384*[perl]
>     |           |                              |       `-perl
>
>...and so on for all mpi processes, except for the controlling processes.
>
>What perl programs is maker calling, that might end up as zombies? I've
>had a brief look at the source to no avail, but would be happy to dig
>further with some pointers for where to look.
>
>This is run with the 2.25-beta from the web page, perl 5.16.0 and openmpi
>1.4.5. 
>
>Thanks,
>Mikael
>
>
>
>
>
>
>
>
>
>
>-------------------------------------
>Mikael Brandström Durling, PhD
>Assistant Professor
>
>Sveriges lantbruksuniversitet
>Swedish University of Agricultural Sciences
>
>Uppsala BioCenter
>Dept of Forest Mycology and Plant Pathology
>Box 7026, 75007 Uppsala
>Visiting address: Almas Allé 5
>Telefon: 018-671512
>mikael.durling at slu.se, www.slu.se/mykopat
>
>
>
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