So, your real question is "How can I make my program use less memory?" There are some answers to that in general terms in the Perl documentation and other places. For specific advice, try to narrow down a small section that grows a lot over time, and post it here for help.

A perl program can use more memory after running a while even if nothing is wrong. For example, if you load a 10MB file into a scalar, that scalar will hang onto that memory, even if it goes out of scope.

Shouldn't these situations be handled by garbage collection. If a scalar (or array/hash) gets out of scope (eg. subroutines internal variables) they should be freed when memory is needed before asking memory from system?

AFAIK memory asked from system won't shrink.

Shouldn't these situations be handled by garbage collection.

Maybe, but mostly they aren't, for performance reasons:

sub bla {
  my $arg = shift;
  my $big_string = $arg x 1000;
}
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Perl will in general keep the memory for $big_string allocated and reserved, because then it doesn't need to allocate the memory again next time the sub is called.

Explicitly undef()ing or resizing variables before they go out of scope sometimes helps, though - on some systems, it might even free the memory back to the system.

Usually, you don't need to do this, exactly because the memory gets reused anyway. If your program grows a lot, it's more likely you're using an inefficient algorithm, or you're creating circular references somewhere.

"What should it profit a man, if he should win a flame war, yet lose his cool?"

That's what I was thinking too. The fact that memory usage slowly grows until the OS kills it is not good. The files I am processing have fairly short lines and it processes the files line by line in a loop. All of the variables inside that loop should be "reusing" the same space, right? Otherwise, what is the point of scoping at all.

Scott
Project coordinator of the Generic Model Organism Database Project

No, the memory is not freed. Perl keeps it as an optimization since you would need to allocate it again the next time this chunk of code runs. Of course that doesn't help you any if that code doesn't run again in your program... We have discussed this at length on the mod_perl list and it is covered in the mod_perl docs.

my @outfile;
while (<INFILE>) {
    # Process stuff here.
    push @outfile, $newline;
}

foreach my $line (@outfile) {
    print OUTFILE $line;
}
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Why not just do something like:

while (<INFILE>) {
    # Process stuff here.
    print OUTFILE $newline;
}
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I can't imagine code like that working in this application since the files can be quite large. Here is an outline of how the script works:
• Prepare several DB SELECT statement handles that will be used inside the loop to get useful information.
• Create tied hashes for caching that information so that I don't have to hit the database everytime I need the id of some frequenly used term.
• Create an IO object that will parse the file line by line and hand back information about the line in an OO way.
• Loop using the IO object's next_feature method. Do lots of bookkeeping using the tied hashes. Write output to several (about 10) files that will later be loaded into postgres using COPY FROM STDIN.
• Close open files, destroy DB statement handles, and load data into database.

Scott
Project coordinator of the Generic Model Organism Database Project

Create tied hashes for caching that information so that I don't have to hit the database everytime I need the id of some frequenly used term.

Did you benchmark this? Repeatedly asking the database for the same thing might not be so bad if your database is good in caching. But tied hashes in Perl are slow. There are many factors involved, and what's best will vary from setup to setup, but don't dismiss something for tied hashes too easily if it's performance you care about.

Of course, this has nothing to do with your memory problem.

Create tied hashes for caching that information so that I don't have to hit the database everytime I need the id of some frequenly used term.

And you're wondering why your memory usage is increasing? Why don't you try a run with caching disabled and see if that fixes your problem.

---

My wife's blog

Of course, the leak may also be in perl, or in a library perl is using. Or in a module your program is using.

Thanks to all of you for your suggestions,