At 2015-01-22 02:06:37 -0800, NicolasC <nicolas.ch...@inria.fr> wrote:
> I try to execute a simple program that runs the ShortestPaths algorithm
> (org.apache.spark.graphx.lib.ShortestPaths) on a small grid graph.
> I use Spark 1.2.0 downloaded from spark.apache.org.
>
> This program runs more than 2 hours when the grid size is 70x70 as above, and
> is then killed
> by the resource manager of the cluster (Torque). After a 5-6 minutes of
> execution, the
> Spark master UI does not even respond.
>
> For a grid size of 30x30, the program terminates in about 20 seconds, and for
> a grid size
> of 50x50 it finishes in about 80 seconds. The problem appears for a grid size
> of 70x70 and
> above.
Unfortunately this problem is due to a Spark bug. In later iterations of
iterative algorithms, the lineage maintained for fault tolerance grows long and
causes Spark to consume increasing amounts of resources for scheduling and task
serialization.
The workaround is to checkpoint the graph periodically, which writes it to
stable storage and interrupts the lineage chain before it grows too long.
If you're able to recompile Spark, you can do this by applying the patch to
GraphX at the end of this mail, and before running graph algorithms, calling
sc.setCheckpointDir("/tmp")
to set the checkpoint directory as desired.
Ankur
=== patch begins here ===
diff --git a/graphx/src/main/scala/org/apache/spark/graphx/Pregel.scala
b/graphx/src/main/scala/org/apache/spark/graphx/Pregel.scala
index 5e55620..1fbbb87 100644
--- a/graphx/src/main/scala/org/apache/spark/graphx/Pregel.scala
+++ b/graphx/src/main/scala/org/apache/spark/graphx/Pregel.scala
@@ -126,6 +126,8 @@ object Pregel extends Logging {
// Loop
var prevG: Graph[VD, ED] = null
var i = 0
+ val checkpoint = g.vertices.context.getCheckpointDir.nonEmpty
+ val checkpointFrequency = 25
while (activeMessages > 0 && i < maxIterations) {
// Receive the messages. Vertices that didn't get any messages do not
appear in newVerts.
val newVerts = g.vertices.innerJoin(messages)(vprog).cache()
@@ -139,6 +141,14 @@ object Pregel extends Logging {
// get to send messages. We must cache messages so it can be
materialized on the next line,
// allowing us to uncache the previous iteration.
messages = g.mapReduceTriplets(sendMsg, mergeMsg, Some((newVerts,
activeDirection))).cache()
+
+ if (checkpoint && i % checkpointFrequency == checkpointFrequency - 1) {
+ logInfo("Checkpointing in iteration " + i)
+ g.vertices.checkpoint()
+ g.edges.checkpoint()
+ messages.checkpoint()
+ }
+
// The call to count() materializes `messages`, `newVerts`, and the
vertices of `g`. This
// hides oldMessages (depended on by newVerts), newVerts (depended on by
messages), and the
// vertices of prevG (depended on by newVerts, oldMessages, and the
vertices of g).
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