alternatively, use the OPEN function with a pipe like so

open(GNUPLOT,"gnuplot $cmd |") or die;
@output = <GNUPLOT>;
close GNUPLOT or die "error reading GNUPLOT";
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this is my preferred way. The close function makes sure that buffers are flushed. From my experience as programmer...the complex lines in a program are usually not at fault...instead it's the simple lines that cause problems. print $cmd to stdout just to make sure it has what you think it has. regarding apache user permissions...you can replicate how it works on the webserver by su - nobody, or whatever the apache user is, and try to run the program on the command line, i.e. gnuplot $whatever_your_cmd_is