[Bioperl-l] Remote blast fork errors / Process limit restrictions

Robert Bradbury robert.bradbury at gmail.com
Thu Dec 17 15:23:38 EST 2009

Oh, yes, in case it was not clear, the fork calls which fails is in
DB/WebDBSeqI.pm: line 722
     defined(my $pid = fork)
          or $self->throw("'Couldn't fork: $!");

And of course that is because Linux has reached the process limits for the
user (due to accumulated background processes which are uncollected).

And they could be resolved by simply executing a simple waitpid call for
prior orphaned children before forking [1] But such a succinct solution
would violate "functional" programming rules -- clean up what you create --
instead they would tend to fall into the OO camp -- "Oh don't worry the
garbage collector will take care of it".  Green programming is a little less


1. IMO, a very very real problem with programming today is that there is no
connection between programmers and the cost of their programs.  How many
programmers know the instruction cycle time of their computers, what does an
instruction cost in terms of W consumed, W wasted (heat generation),
fruitless scanning over uncollected zombie processes, etc.  It may be that
only that programmers who grew up in the era when CPU cycles were expensive
(300 ns/cycle) who know what each instruction required in terms of cycles
consider these perspectives.  Now things (cpu use, processor use, etc) tend
to be swept under the rug and it appears that that is the case with the
standard implementation of bioper.  The documentation does not clearly state
that additional sub-processes may be created and need to be collected.  You
are providing a utility that only works "this much".  And guess what -- I
happen to have run into the "this".

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