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

[Mikael Brandström Durling]

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