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From Claudio Martella <claudio.marte...@gmail.com>
Subject Re: Review Request: Out-of-core messages
Date Wed, 18 Jul 2012 13:23:27 GMT
Cool!

Nice to see you got to implement the stuff as discussed on the JIRA, I
was going to dig into this again soon :). I'm in favor of your
approach 100%, just one thing, as I mentioned also on the JIRA about
out-of-core graph, the spill to disk threshold should be something
simple, deterministic and reliable, leading to a predictable behavior,
leaving control to the user. By this I suggest an absolute size based
approach, something like mapreduce buffer size parameters for sorting
(e.g., spill to disk when the memstore gets over 2GB). Users already
define their heap size and the rest, so they should have a fairly
accurate estimate of their memory distribution. This is also how HBase
handles the memstore size before it gets spill to disk into a Sequence
file.
What do you think?

On Tue, Jul 17, 2012 at 6:57 PM, Maja Kabiljo <majakabiljo@fb.com> wrote:
>
> -----------------------------------------------------------
> This is an automatically generated e-mail. To reply, visit:
> https://reviews.apache.org/r/6013/
> -----------------------------------------------------------
>
> Review request for giraph.
>
>
> Description
> -------
>
> 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.
>
>
> This addresses bug GIRAPH-45.
>     https://issues.apache.org/jira/browse/GIRAPH-45
>
>
> Diffs
> -----
>
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/bsp/CentralizedServiceWorker.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/BasicRPCCommunications.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/NettyServer.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/NettyWorkerClient.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/NettyWorkerClientServer.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/NettyWorkerServer.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/RPCCommunications.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/RequestRegistry.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/SendPartitionMessagesRequest.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/ServerData.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/WorkerServer.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/BasicMessageStore.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/DiskBackedMessageStore.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/DiskBackedMessageStoreByPartition.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/FlushableMessageStore.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/MessageStore.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/MessageStoreByPartition.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/MessageStoreFactory.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/SendMessagesRequest.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/SequentialFileMessageStore.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/SimpleMessageStore.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/comm/messages/package-info.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/graph/BasicVertexResolver.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/graph/BspServiceWorker.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/graph/GiraphJob.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/graph/GraphMapper.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/graph/VertexResolver.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/graph/partition/Partition.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/main/java/org/apache/giraph/utils/CollectionUtils.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/test/java/org/apache/giraph/comm/ConnectionTest.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/test/java/org/apache/giraph/comm/RequestTest.java
1362202
>   http://svn.apache.org/repos/asf/giraph/trunk/src/test/java/org/apache/giraph/comm/TestMessageStores.java
PRE-CREATION
>   http://svn.apache.org/repos/asf/giraph/trunk/src/test/java/org/apache/giraph/utils/MockUtils.java
1362202
>
> Diff: https://reviews.apache.org/r/6013/diff/
>
>
> Testing
> -------
>
> Run mvn verify and tests in pseudo-distributed mode, all apart from this one https://issues.apache.org/jira/browse/GIRAPH-259
pass.
>
>
> Thanks,
>
> Maja Kabiljo
>



-- 
   Claudio Martella
   claudio.martella@gmail.com

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