Thanks,
I was not sure if it really works as I described.
> Facebook can't be using it like this if, as described, they have
billions of vertices and a trillion edges.
Yes, its strange. I guess configuration does not help so much on large
cluster. What might help are properties of input data.
> So do you, or Avery, have any idea how you might initialize this is a
more reasonable way, and how???
Fast workaround is to set number of partitions to from W^2 to W or 2*W
. It will help if you dont have very large number of workers.
I would not change MAX_*_REQUEST_SIZE much since it may hurt performance.
You can do some preprocessing before loading data to Giraph.
How to change Giraph:
The caches could be flushed if total sum of vertexes/edges in all caches
exceeds some number. Ideally, it should prevent not only OutOfMemory
errors but also raising high water mark. Not sure if it (preventing
raising HWM) is easy to do.
I am going to use almost-prebuild partitions. For my use case it would
be ideal to detect if some cache is abandoned and i would not be used
anymore. It would cut memory usage in caches from ~O(n^3) to ~O(n). It
could be done by counting number of cache flushes or cache insertions
and if some cache was not touched for long time it would be flushed.
There could be separated configuration MAX_*_REQUEST_SIZE for per
partition caches during loading data.
I guess there should be simple but efficient way how to trace memory
high-water mark. It could look like:
Loading data: Memory high-water mark: start: 100 Gb end: 300 Gb
Iteration 1 Computation: Memory high-water mark: start: 300 Gb end: 300 Gb
Iteration 1 XYZ ....
Iteration 2 Computation: Memory high-water mark: start: 300 Gb end: 300 Gb
.
.
.
Lukas
On 09/04/13 01:12, Jeff Peters wrote:
Thank you Lukas!!! That's EXACTLY the kind of model I was building in
my head over the weekend about why this might be happening, and why
increasing the number of AWS instances (and workers) does not solve
the problem without increasing each worker's VM. Surely Facebook can't
be using it like this if, as described, they have billions of vertices
and a trillion edges. So do you, or Avery, have any idea how you might
initialize this is a more reasonable way, and how???
On Mon, Sep 2, 2013 at 6:08 AM, Lukas Nalezenec
<lukas.naleze...@firma.seznam.cz
<mailto:lukas.naleze...@firma.seznam.cz>> wrote:
Hi
I wasted few days on similar problem.
I guess the problem was that during loading - if you have got W
workers and W^2 partitions there are W^2 partition caches in each
worker.
Each cache can hold 10 000 vertexes by default.
I had 26 000 000 vertexes, 60 workers -> 3600 partitions. It means
that there can be up to 36 000 000 vertexes in caches in each
worker if input files are random.
Workers were assigned 450 000 vertexes but failed when they had
900 000 vertexes in memory.
Btw: Why default number of partitions is W^2 ?
(I can be wrong)
Lukas
On 08/31/13 01:54, Avery Ching wrote:
Ah, the new caches. =) These make things a lot faster (bulk data
sending), but do take up some additional memory. if you look at
GiraphConstants, you can find ways to change the cache sizes
(this will reduce that memory usage).
For example, MAX_EDGE_REQUEST_SIZE will affect the size of the
edge cache. MAX_MSG_REQUEST_SIZE will affect the size of the
message cache. The caches are per worker, so 100 workers would
require 50 MB per worker by default. Feel free to trim it if
you like.
The byte arrays for the edges are the most efficient storage
possible (although not as performance as the native edge stores).
Hope that helps,
Avery
On 8/29/13 4:53 PM, Jeff Peters wrote:
Avery, it would seem that optimizations to Giraph have,
unfortunately, turned the majority of the heap into "dark
matter". The two snapshots are at unknown points in a superstep
but I waited for several supersteps so that the activity had
more or less stabilized. About the only thing comparable between
the two snapshots are the vertexes, 192561 X "RecsVertex" in the
new version and 191995 X "Coloring" in the old system. But with
the new Giraph 672710176 out of 824886184 bytes are stored as
primitive byte arrays. That's probably indicative of some very
fine performance optimization work, but it makes it extremely
difficult to know what's really out there, and why. I did notice
that a number of caches have appeared that did not exist before,
namely SendEdgeCache, SendPartitionCache, SendMessageCache
and SendMutationsCache.
Could any of those account for a larger per-worker footprint in
a modern Giraph? Should I simply assume that I need to force AWS
to configure its EMR Hadoop so that each instance has fewer map
tasks but with a somewhat larger VM max, say 3GB instead of 2GB?
On Wed, Aug 28, 2013 at 4:57 PM, Avery Ching <ach...@apache.org
<mailto:ach...@apache.org>> wrote:
Try dumping a histogram of memory usage from a running JVM
and see where the memory is going. I can't think of
anything in particular that changed...
On 8/28/13 4:39 PM, Jeff Peters wrote:
I am tasked with updating our ancient (circa 7/10/2012)
Giraph to giraph-release-1.0.0-RC3. Most jobs run fine
but our largest job now runs out of memory using the
same AWS elastic-mapreduce configuration we have always
used. I have never tried to configure either Giraph or
the AWS Hadoop. We build for Hadoop 1.0.2 because that's
closest to the 1.0.3 AWS provides us. The 8 X m2.4xlarge
cluster we use seems to provide 8*14=112 map tasks
fitted out with 2GB heap each. Our code is completely
unchanged except as required to adapt to the new Giraph
APIs. Our vertex, edge, and message data are completely
unchanged. On smaller jobs, that work, the aggregate
heap usage high-water mark seems about the same as
before, but the "committed heap" seems to run higher. I
can't even make it work on a cluster of 12. In that case
I get one map task that seems to end up with nearly
twice as many messages as most of the others so it runs
out of memory anyway. It only takes one to fail the job.
Am I missing something here? Should I be configuring my
new Giraph in some way I didn't used to need to with the
old one?