Ответ 1
Попробуйте префикс ваших подграфов "cluster _":
digraph dataflow {
subgraph cluster_pipeline {
relations;
synonyms;
articles;
}
subgraph cluster_lucene {
index;
search;
}
training_data -> index;
relations -> search;
synonyms -> index;
articles -> index;
training_data -> evaluation;
}