Advanced Solution 1

For this solution, I wrote a giant Condor submit file to submit a hundred different jobs that are nearly identical. It looked like this:

Universe   = java
Executable = condor_shapes.jar
jar_files  = condor_shapes.jar
Log        = explorer.log
Output     = explorer.$(Process).output
Error      = explorer.$(Process).error

Arguments  = uk.ac.nesc.training.sfk.RegularExplorer 0 0 10 10 2000
Queue

Arguments  = uk.ac.nesc.training.sfk.RegularExplorer 0 10 10 20 2000
Queue

Arguments  = uk.ac.nesc.training.sfk.RegularExplorer 0 20 10 30 2000
Queue

... [extra deleted]

I wrote a Perl script to write this submit file, because it's tedious:

#!/usr/bin/env perl

open(SUBMIT, ">submit-big");
print SUBMIT "Universe   = java\n";
print SUBMIT "Executable = condor_shapes.jar\n";
print SUBMIT "jar_files  = condor_shapes.jar\n";
print SUBMIT "Log        = explorer.log\n";
print SUBMIT "Output     = explorer.\$(Process).output\n";
print SUBMIT "Error      = explorer.\$(Process).error\n";
print SUBMIT "\n";

my $x, $y;

for ($x = 0; $x < 100; $x += 10) {
    for ($y = 0; $y < 100; $y += 10) {
        my $xx = $x + 10;
        my $yy = $y + 10;
        print SUBMIT "Arguments  = uk.ac.nesc.training.sfk.RegularExplorer ";
        print SUBMIT "$x $y $xx $yy 2000\n";
        print SUBMIT "Queue\n";
        print SUBMIT "\n";
    }
}
close(SUBMIT);

exit 0;

There are a few things to notice here:

1. Each of the jobs shares a log file. This works just fine in Condor, and it keeps the number of files smaller.
2. I used $(Process) to make separate output and error files for each job.

When all of these finished, I simply did:

> cat *.output > large.dat
> gnuplot

        G N U P L O T
        Version 3.7 patchlevel 3
        last modified Thu Dec 12 13:00:00 GMT 2002
        System: Linux 2.4.21-27.0.2.EL.cernsmp

        Copyright(C) 1986 - 1993, 1998 - 2002
        Thomas Williams, Colin Kelley and many others

        Type `help` to access the on-line reference manual
        The gnuplot FAQ is available from
        http://www.gnuplot.info/gnuplot-faq.html

        Send comments and requests for help to 
        Send bugs, suggestions and mods to 


Terminal type set to 'x11'
gnuplot> splot "large.dat"