Suspect your problem is that while(<perlIN>) is causing it to read the whole binary file, all at once, right there. Boom -- out of memory.

Instead, as noted by others, read only what you need -- one record at a time.

A common approach is to use a flag variable to indicate when you reach end of file; control the loop based on that.

Two ways to do this:

1. Read one record at the top of the loop (use read and your $recln value); use substr to extract the pieces, or;
2. Don't read anything at the top of the loop, but instead, read each variable like you do currently do; modify each one to check for end of file (sample below).

my    $TRUE    = 1;
my    $FALSE    = 0;
     [...]
my $EofFlag = $FALSE;
while(!$EofFlag)
{
     [...]
    my $cmtseq_cnt = read(perlIN,$cmtseq,5);
    if ($cmtseq_cnt < 5)
    {
        $EofFlag = $TRUE;    # Redundant, given what we do next, but h
+ere for example
        last;
    }
}
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