Here is an easy way to make the bulk-update for DB_File work a lot faster -- preprocess the input data before going near the database. What you can do is very dependent on the nature of your data, but you initial example implies you will always append to existing entries in the DB. So here is an example that show the gains that can be made by preprocessing - I've assumes there are 1000 unique keys in the database, and I'm adding 50k records.

First, note the performance gain from preprocessing.

           s/iter   original preprocess
original     3.26         --       -93%
preprocess  0.221      1375%         --
[download]

And here is the code

#!/usr/bin/perl

use strict;
use warnings;

use Benchmark ':hireswallclock';
use DB_File ();

my $DB_FILE1;
my $DB_FILE2;


my $NUM_RECORDS = 50_000;
my $NUM_KEYS    = 1000;

setup_dbfile();

Benchmark::cmpthese(
    10,
    {
        'original' => \&benchmark_dbfile1,
        'preprocess'   => \&benchmark_dbfile2
    }
);



sub benchmark_dbfile1 {

    foreach my $value ( 1 .. $NUM_RECORDS ) {

        my $key = int(rand($NUM_KEYS));

        if ( exists $DB_FILE1->{$key} ) {
            $DB_FILE1->{$key} .= ",$value";
        }
        else {
            $DB_FILE1->{$key} = $value;
        }

    }
}

sub benchmark_dbfile2 {

    my %preprocess = ();
    foreach my $value ( 1 .. $NUM_RECORDS ) {

        my $key = int(rand($NUM_KEYS));
        push @{ $preprocess{$key} }, $value ;
    }

    while (my ($key, $val_list) = each %preprocess) {

        my $value = join ",", @$val_list;

        if ( exists $DB_FILE2->{$key} ) {
            $DB_FILE1->{$key} .= ",$value";
        }
        else {
            $DB_FILE2->{$key} = $value;
        }

    }
}

sub setup_dbfile {

  {
    unlink 'berkeley.db1';  
    my %data;
    tie %data, 'DB_File', 'berkeley.db1' or die "$!";
    $DB_FILE1 = \%data;
  }
  {
    unlink 'berkeley.db2';  
    my %data;
    tie %data, 'DB_File', 'berkeley.db2' or die "$!";
    $DB_FILE2 = \%data;
  }
}
[download]