Index: graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java =================================================================== --- graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java (revision 1427035) +++ graph/src/main/java/org/apache/hama/graph/GraphJobRunner.java (working copy) @@ -179,6 +179,7 @@ BSPPeer peer) throws IOException { int activeVertices = 0; + int i = 0; for (Vertex vertex : vertices) { List msgs = messages.get(vertex.getVertexID()); // If there are newly received messages, restart. @@ -202,6 +203,15 @@ activeVertices++; } } + + messages.remove(vertex.getVertexID()); + int min = 10; + if(vertices.size() < min) + min = vertices.size(); + if((i % (vertices.size() / min)) == 0) { + System.gc(); + } + i++; } aggregationRunner.sendAggregatorValues(peer, activeVertices);