Scanning over your snippet, the other thing that jumped out is that you're using the single-argument form of exec(), which has a hidden performance penalty. (See perlfunc, and read carefully.)

But do you really need a fork()/exec() here? Wouldn't using system() give you the same effect with less hassle? Note, though, that system() has the same hidden overhead as exec() when called with a single argument.

Create an image tag for your html that looks something like this.

  <img src="imagename.ext?randomcode"......
[download]

You could try to make sure the image name is always different. Use a counter to increment a number, and use that as part of an image name. To delete old files, you could use a cron job; or you can have the parent do that, while it's waiting for the child to finish. You'll never have too many old files, that way. I hope. :-)

But my preference would be to invoke the image creating script directly from a separate CGI script (or equivalent), and send the image data directly to the browser instead of saving it to a file first. You do need to provide the appropriate content-type header, as others already have suggested, and then simply print out the image data. The parameters you now use on the command line, can be passed as part of the image URL, after a question mark, using the familiar GET URL syntax.

The image is saved to file and although this snippet doesn't show it, the image filename was manually changed each time the script was run, so the caching problem shouldn't really apply.

We did try to give the give the process ID as the filename.

Yes, I can see how it would be a good idea to send the image directly to the browser but I am curious to know why the current effort doesn't work Here is the full code:

#!/usr/bin/perl -w

$|=1;
use strict;
use CGI::Carp "fatalsToBrowser";
use CGI ":all";
use DBI;

print header,start_html(-title=>'Bright', -bgcolor=>'#BDBDB0');

print h1(font{-face=>'Futura Lt BT'}, "Genome view");
print font{-size=>'3', -color=>'#800000', -face=>'Futura Lt BT'};


my($tth,$sth,$dbh,@position,$start,$finish,@row,$i,$child_pid,@accessi
+on,$SQLstr,$imagename);



if(!param)
{
    $dbh = DBI->connect("DBI:mysql:database=dicty;host=localhost", "**
+**", "****");
    $sth=$dbh->prepare("select min(fstart),max(fstop) from fdata");
    $sth->execute;

    while(@row=$sth->fetchrow_array)
    {
        $position[0]=$row[0];
        $position[1]=$row[1];
    }

    $dbh->disconnect;
    print start_form;
    print textfield(-name=>'start',-value=>$position[0],-size=>15),br,
     textfield(-name=>'finish',-value=>$position[1],-size=>15);
    print submit(-name=>'submit'),end_form;
}

if(param("submit"))
{
    $imagename=$$;

    $start=param("start");
    $finish=param("finish");
    

    if(!defined($child_pid=fork()))
    {
        die "cannot fork $!";
    }
    elsif($child_pid==0)
    {
        
        my $query= "/usr/apache/cgi-bin/order/ldasdump.pl -png -d dict
+y chr5.1:$start,$finish --user root --pass mysqladmin > /usr/apache/h
+tdocs/imagename.png";
        exec($query);
        
    }
    else
    {
        
        waitpid($child_pid,0);
        
        print img({src=>"../../imagename.png",align=>'LEFT'});
    
    }

}
[download]

I am curious to know why the current effort doesn't work

The problems start with this line   print header,start_html(-title=>'Bright', -bgcolor=>'#BDBDB0'); which sends a MIME type of "text/html" back to the browser, then starts an HTML page. At this point, it's a bit late to start printing image bits and expect the browser to display an image.

Read the description of header() in the CGI.pm POD, and note how to override the MIME type (aka Content-type). You want to send "image/png".

I should have given up and gone to bed hours ago.

Is it possible that there's something in $start or $finish that is fouling up the shell meta-character expansion that happens when you use the single-argument form of exec(), preventing the command from generating an image?

Try using the list form of exec(), which doesn't trigger shell meta-character expansion.