in reply to MLDBM tie fails

You don't show the rest of your code (i.e., the 'use' statements and the other necessary modules); I suspect that this is where the failure is coming from. Example of working code: 

#!/usr/bin/perl -w
use strict;
use Fcntl;
use MLDBM qw/DB_File Storable/;

tie my %positions_hash, 'MLDBM', 'positions.db', O_CREAT|O_RDWR, 0640 
+or die "positions.db: $!\n";

%positions_hash = (
    foo     =>  1,
    bar     =>  2,
    qux     =>  3,
);

untie %positions_hash;

[download]

On my system (Ubuntu Linux, AMD64), this creates three files - 'positions.db{,dir,pag}' - exactly as expected.


--
"Language shapes the way we think, and determines what we can think about."
-- B. L. Whorf

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Re^2: MLDBM tie fails
by greigite (Novice) on Dec 17, 2008 at 00:14 UTC
    Thanks for your response. I included the use statements at the top of my post. Sorry, but I don't understand how these are incorrect- can you specify? They look quite similar to yours. Here is the relevant code in my program: 
    #!/usr/bin/perl -w
use strict;
use Fcntl qw(O_RDWR O_CREAT); 
use MLDBM qw(DB_File Storable);
....
tie(%positions_hash, 'MLDBM', 'positions.db', O_CREAT|O_RDWR, 0640) or
+ die "Could not create db file\n"; #write positions hash to db file
untie %positions_hash;

    [download]

    The hash is a large, complex multi-level structure created in several subroutines which I didn't post. I suspect the problem has something to do with its size (> 1G). Your code, which is basically identical to mine except that the tied hash is a single-level small structure, also works fine on my system.
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      I don't recall seeing them in your original post; did I just miss them, or did you do a "stealth" update? In any case, given that additional datum, my response would be the same as tilly's: MLDBM is reputed to suffer "mysterious failures" when stressed (I tend to avoid it, myself.) Again, echoing tilly, DBM::Deep is a good recommendation.


      --
      "Language shapes the way we think, and determines what we can think about."
      -- B. L. Whorf
[reply]
        Thanks, I'll try DBM::Deep. BTW there were no stealth updates on the first post :-)
        UPDATE: Tried DBM::Deep. I'm getting this error:
        Use of uninitialized value in -e at /usr/local/share/perl/5.8.8/DBM/Deep/File.pm line 55
        Here is the code snippet: 
        #!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
use Bio::SeqIO;
use Fcntl qw(O_RDWR O_CREAT);
use DBM::Deep;
require Variation::RecombConfig;
use Variation::Recomb;
use POSIX qw(ceil floor);
use DirHandle;
use File::Temp;
use Data::Dumper;
# do lots of stuff to create a big complex hash, %positions_hash

my $db = DBM::Deep->new( -filename =>"positions.db", pack_size => 'lar
+ge');
$db->import(\%positions_hash);
$db->optimize();

        [download]
        From the DBM::Deep code it seems that it is not properly creating the new file positions.db. Is there a way around this?
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