subgraph cluster ranking in dot

Answer 1

This will produce the graph you are looking for:

digraph d {
  subgraph cluster0 {
    A -> {B1 B2}
    B2 -> {C1 C2 C3}
    C1 -> D;
  }

  subgraph {
    rankdir="TB"
    subgraph cluster1 {
      C2 -> dll1_A;
      dll1_A -> B1;
    }

    subgraph cluster2 {
      C3 -> dll2_A;
    }
  }
  dll1_A -> dll2_A;
}

What this does is creat a subgraph that is used only for layout purposes to provide the top to bottom ordering that you desire.

Answer 2

The layout is an attempt by Dot to minimise the overall size during layout of the graph.

One reason for the more compact than required layout is the use of the edge that goes in the reverse direction from dll1_a to B1. It tries to pull the cluster as close back to the destination node as possible. To avoid this edge affecting the graph, either relax the constraint on the upwards edges as shown, or draw the edge in the forward direction and use the dir attribute to reverse the arrow.

This will help with many layouts but it alone is not sufficient to fix the example given. To prevent Dot from maintaining the compact layout it prefers you can add a minlen attribute to edges that should remain (near) vertical. This may be difficult to calculate in general but is practical for manually tuned laoyouts.

digraph d {
    subgraph cluster0 {
        A -> {B1 B2}    
        B2 -> {C1 C2 C3}
        C1 -> D;
    }
    subgraph cluster1 {
        C2 -> dll1_A [minlen = 2];
        dll1_A -> B1 [constraint = false];
        /* B1 -> dll1_A [dir = back]; */
    }
    subgraph cluster2 {
        C3 -> dll2_A;
    }
    dll1_A -> dll2_A;
}