Depending on how you want to deal with any nested groups, either:
myDiagram.commit(function(d) {
d.findTopLevelGroups().each(function(g) { g.collapseSubGraph(); });
});
Or:
myDiagram.commit(function(d) {
d.nodes.each(function(g) {
if (g instanceof go.Group) g.collapseSubGraph();
});
});