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Out-of-core messages

Review Request #6013 - Created July 17, 2012 and submitted

Maja Kabiljo
GIRAPH-45
Reviewers
giraph
giraph
This patch introduces out-of-core messages support for Giraph. Some ideas are taken from discussion in https://issues.apache.org/jira/browse/GIRAPH-45. 

We keep messages in MessageStore, from which they will be flushed to disk when necessary. Messages are separated by partition. In moments we only flush single partition to disk so we would still keep things in memory in case it's time for next superstep. When flushing to disk, we write in the following format:
numberOfVertices
vertexId1 numberOfMessages1 messagesForVertexId1
vertexId2 numberOfMessages2 messagesForVertexId2
...
Vertex ids are sorted. We don't require enough memory to fit all the messages for partition, but we require that messages for a single vertex fit in memory. 
In the end we potentially have several files for each partition. When reading messages, all the files are read sequentially.

DiskBackedMessageStoreByPartition handles all messages, DiskBackedMessageStore is then used for a single partition, and SequentialFileMessageStore handles single file.
There is also SimpleMessageStore which doesn't use disk at all.

Options available to user:
- whether or not to use out-of-core messaging
- number of messages to keep in memory - this should probably be changed (explained below)
- size of buffer when reading from and writing to disk

ServerData now has two instances of message stores: one which is consumed in current superstep with messages from previous superstep, and one in which it will keep incoming messages for next superstep.

Other things which had to be changed:
- Checkpointing - since messages are not kept in the vertex anymore, they need to be stored separately.
- Partition exchange between workers - same reasons as above - added SendMessagesRequest
- Messages are not assigned to vertex, they are just passed in compute
- compute methods are now executed in order of vertex id inside of partition, so we could have fast reading from disk

For memory check I only have the number of messages which I allow in memory. This should be done better, but there is a problem since Alessandro's patch for out-of-core graph also has memory checks. We don't want one of those parts to use all the memory and leave too little space for the other, but I'm not aware of a way to separately check memory usage of different data structures.

I didn't integrate this with RPC, that's why there are some checks for useNetty, those can be removed once the RPC is removed. Also, since vertex doesn't keep messages in itself anymore, once RPC is removed we should also remove getMessages/putMessages/getNumMessages from vertex, change initialize to (id, value, edges, hasMessages) and just give messages to vertex when calling compute.

I'll fix the part when partitions are sent around before superstep, since that's the only part now which requires that all the messages for single partition fit in memory.
Run mvn verify and tests in pseudo-distributed mode, all apart from this one https://issues.apache.org/jira/browse/GIRAPH-259 pass.
Total:
12
Open:
12
Resolved:
0
Dropped:
0
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Review request changed
Updated (Aug. 24, 2012, 1:34 p.m.)
  • changed from pending to submitted