Where in your program do you loop over your input file?

You are talking about 100,000 inserts but your program is only ever doing one insert.

Maybe you can show us a real program that does more than one insert.

My suggestion for doing more than one insert is to use a loop and to prepare the statement handles outside of the loop and to do the ->commit calls every 1000 inserts or something like that.

Also, consider using the native data loading functionality of MySQL instead of hand-feeding the data to your database.

OK I put that part back in:

use strict;
use warnings;
use DBI;

my $start = time();
my $data;
my ($version,$jobnumber);
my $file = "C:/temp/dump.txt";

open (FH, "$file") or die "$!";
while(<FH>){
   $data .= $_;
}

$version = substr($data,0,3);
$jobnumber = substr($data,4,5);

my $databaseName        =   "basedb";
my $connectHost         =   "127.0.0.1";
my $DSN                 =   "DBI:mysql:dbname=$databaseName;host=$conn
+ectHost";
my $db_username         =   'root';
my $db_password         =   'root';
my $dbh                 =   DBI->connect($DSN,$db_username,$db_passwor
+d,{RaiseError=>1,PrintWarn=>0,AutoCommit=>0}) || die "error connectin
+g: $!";

my $dump_sql = "INSERT INTO temp (version,jobnumber) VALUES(?,?);";
my $dump_sth = $dbh->prepare($dump_sql) or die "$DBI::errstr";
eval{
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    $dump_sth->execute($version,$jobnumber) or die "$DBI::errstr";
    ...
}
[download]

Have you heard that Perl has loops?

Also, you never change $version and $jobnumber.

Maybe you want to reconsider using one of the approaches I've already outlined.

Update: Performance Benchmark

To demonstrate my point that running a single transaction for all of the inserts will make a HUGE difference, I offer the following benchmark code that makes a test DB table with 170,568 records.

I used SQLite so that this can be run by anybody. If anything MySQL will be faster. I am using an ancient WinXP laptop.

Results:
Doing a commit after every insert = 4.9 hours! Doing a Single commit after all 170,568 inserts = 3 seconds!!! That is what I call a HUGE difference!

Since my laptop takes about 5 hours the OP's reported time of 4 hours sounds plausible. My guess is that a table creation like I show below will reduce the OP's execution time from 4 hours to 1-2 seconds. Nothing really fancy required, just some solid code.

#!/usr/bin/perl
use strict;
use warnings;

use Data::Dumper;
use DBI qw(:sql_types);

my $dbfile  = "./TestingInsert.sqlite";

if (-e $dbfile) {unlink $dbfile or die "Delete of $dbfile failed! $!\n
+";}

my $start_seconds = time();

my $dbh = DBI->connect("dbi:SQLite:dbname=$dbfile","","",{RaiseError =
+> 1})
    or die "Couldn't connect to database: " . DBI->errstr;

$dbh->do ("CREATE TABLE test
             (  id        integer PRIMARY KEY AUTOINCREMENT,
                version   integer,
                jobnumber integer
             );
          ");
          
$dbh->do("BEGIN");  #running one transaction is needed for speed!!!
import_data();
$dbh->do("COMMIT"); 

my $end_time = time();
print "Total elasped time: ", $end_time-$start_seconds, "\n";


sub import_data
{
   my $jobnumber = 1;
   
   my $add = $dbh->prepare("INSERT INTO test ( version, jobnumber )
                            VALUES(?,?)");
  
   while ($jobnumber < 170568)
   {     
       $add->execute($jobnumber, $jobnumber++);    #DBI insert   
   }
   
   return; 
}   

__END__
Using a comitt for each insert:
Total elasped time: 17833  => 297 min => 4.9 hours

Using a single transaction for 170,568 inserts:
Total elasped time: 3  seconds
[download]

Do you want the load to be all or nothing. i.e. if one records fails then rollback all the previous inserts ?

Our requirement is that but data be there, but we do not concern what that data is only if there.