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

my $g = GraphViz->new();

my @default_attrs = (
                     fontsize => '8',
                     fontname => 'arial',
                    );

my $eurocluster = {name=>'Europe',
                   style=>'filled',
                   fillcolor=>'lightgray',
                   fontname=>'arial',
                   fontsize=>'12',
                   };
$g->add_node('London', cluster=>$eurocluster, @default_attrs);
$g->add_node('Paris', cluster=>$eurocluster, @default_attrs);
$g->add_node('New York', @default_attrs);

$g->add_edge('London' => 'Paris', @default_attrs);
$g->add_edge('London' => 'New York', label => 'Far', @default_attrs);
$g->add_edge('Paris' => 'London', @default_attrs);

$g->as_gif("nodes.gif");
$g->as_dot("nodes.dot");
[download]

digraph test {
    graph [ratio=fill];
    node [label="\N"];
    graph [bb="0,0,150,174"];
    subgraph cluster_Europe {
        graph [fillcolor=lightgray,
            fontname=arial,
            fontsize=12,
            label=Europe,
            style=filled,
            bb="8,8,78,166"];
        London [label=London, fontname=arial, fontsize=8, pos="43,118"
+, width="0.75", height="0.5"];
        Paris [label=Paris, fontname=arial, fontsize=8, pos="43,34", w
+idth="0.75", height="0.5"];
        London -> Paris [fontname=arial, fontsize=8, pos="e,37.367,51.
+789 37.364,100.19 36.203,89.049 35.949,74.471 36.604,61.831"];
        Paris -> London [fontname=arial, fontsize=8, pos="e,48.636,100
+.19 48.633,51.789 49.796,62.92 50.051,77.497 49.398,90.14"];
    }
    "New York" [label="New York", fontname=arial, fontsize=8, pos="119
+,34", width="0.86111", height="0.5"];
    London -> "New York" [fontname=arial, fontsize=8, label=Far, pos="
+e,104.51,50.015 57.295,102.2 68.687,89.609 84.811,71.787 97.72,57.52"
+, lp="91.5,76"];
}
[download]

I've never used GraphViz, since the example you link to is named 'clusters', the GraphViz documentation has examples for 'clusters':

"Nodes can be clustered together with the "cluster" attribute, which is drawn by having a labelled rectangle around all the nodes in a cluster. An empty string means not clustered...."