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From "Scruggs, Matt" <matt.scru...@bronto.com>
Subject Re: spark-itemsimilarity scalability / Spark parallelism issues (SimilarityAnalysis.cooccurrencesIDSs)
Date Tue, 15 Aug 2017 13:21:44 GMT
Hi Pat,

I've taken some screenshots of my Spark UI to hopefully shed some light on the behavior I'm
seeing. Do you mind if I send you a link via direct email (would rather not post it here)?
It's just a shared Dropbox folder.


Thanks,
Matt



On 8/14/17, 11:34 PM, "Scruggs, Matt" <matt.scruggs@bronto.com> wrote:

>I'm running a custom Scala app (distributed in a shaded jar) directly calling SimilarityAnalysis.cooccurrenceIDSs(),
not using the CLI.
>
>The input data already gets explicitly repartitioned to spark.cores.max (defaultParallelism)
in our code. I'll try increasing that by the factor of 4 that you suggest, but all our cores
are already utilized so I'm not sure that will help. It gets bogged down in the post-shuffle
(shuffle read / combine / reduce) phase even with all cores busy the whole time, which is
why I've been playing around with various values for spark.sql.shuffle.partitions. The O(log
n) operations I mentioned seem to take >95% of runtime.
>
>Thanks,
>Matt
>________________________________
>From: Pat Ferrel <pat@occamsmachete.com>
>Sent: Monday, August 14, 2017 11:02:42 PM
>To: user@mahout.apache.org
>Subject: Re: spark-itemsimilarity scalability / Spark parallelism issues (SimilarityAnalysis.cooccurrencesIDSs)
>
>Are you using the CLI? If so it’s likely that there is only one partition of the data.
If you use Mahout in the Spark shell or using it as a lib, do a repartition on the input data
before passing it into SimilarityAnalysis.cooccurrencesIDSs. I repartition to 4*total cores
to start with and set max parallelism for spark to the same. The CLI isn’t really production
worthy, just for super easy experiments with CSVs.
>
>
>On Aug 14, 2017, at 2:31 PM, Scruggs, Matt <matt.scruggs@bronto.com> wrote:
>
>Howdy,
>
>I'm running SimilarityAnalysis.cooccurrencesIDSs on a fairly small dataset (about 870k
[user, item] rows in the primary action IDS…no cross co-occurrence IDS) and I noticed it
scales strangely. This is with Mahout 0.13.0 although the same behavior happens in 0.12.x
as well (haven't tested it before that).
>
>TLDR - regardless of the Spark parallelism (CPUs) I throw at this routine, every Spark
task within the final / busy stage seems to take the same amount of time, which leads me to
guess that every shuffle partition contains the same amount of data (perhaps the full dataset
matrix in shape/size, albeit with different values). I'm reaching out to see if this is a
known algorithmic complexity issue in this routine, or if my config is to blame (or both).
>
>Regarding our hardware, we have identical physical machines in a Mesos cluster with 6
workers and a few masters. Each worker has ~500GB of SSD, 32 cores and 128g RAM. We run lots
of Spark jobs and have generally ironed out the kinks in terms of hardware and cluster config,
so I don't suspect any hardware-related issues.
>
>Here are some timings for SimilarityAnalysis.cooccurrencesIDSs on this dataset with maxNumInteractions
= 500, maxInterestingItemsPerThing = 20, randomSeed = default, parOpts = default (there's
lots of other Spark config, this is just what I'm varying to check for effects). In particular,
notice how the ratio of (spark.sql.shuffle.partitions / spark.cores.max) affects the runtime:
>
> * 8 executors w/8 cores each, takes about 45 minutes
> * note that spark.sql.shuffle.partitions > spark.cores.max
> spark.cores.max = 64
> spark.executor.cores = 8
> spark.sql.shuffle.partitions = 200 (default)
>
> * 1 executors w/24 cores, takes about 65 minutes
> * note that spark.sql.shuffle.partitions >>> spark.cores.max
> spark.cores.max = 24
> spark.executor.cores = 24
> spark.sql.shuffle.partitions = 200 (default)
>
> * 1 executor w/8 cores, takes about 8 minutes
> * note that spark.sql.shuffle.partitions = spark.cores.max
> spark.cores.max = 8
> spark.executor.cores = 8 (1 executor w/8 cores)
> spark.sql.shuffle.partitions = 8
>
> * 1 executor w/24 cores, takes about 8 minutes (same as 8 cores!)
> * note that spark.sql.shuffle.partitions = spark.cores.max
> spark.cores.max = 24
> spark.executor.cores = 24 (1 executor w/24 cores)
> spark.sql.shuffle.partitions = 24
>
> * 32 executors w/2 cores each, takes about 8 minutes (same as 8 cores!)
> * note that spark.sql.shuffle.partitions = spark.cores.max
> spark.cores.max = 64
> spark.executor.cores = 2
> spark.sql.shuffle.partitions = 88 (results in 64 tasks for final stage)
>
>Adjusting the "maxNumInteractions" parameter down to 100 and 50 results in a minor improvement
(5-10%). I've also played around with removing [user, item] rows from the input dataset for
users with only 1 interaction…I read to try that in another thread…that yielded maybe
a 40-50% speed improvement, but I'd rather not toss out data (unless it truly is totally useless,
of course :D ).
>
>When I look at the thread dump within the Spark UI's Executors -> thread dump pages,
it seems all the executors are very busy in the code pasted below for >95% of the run.
GC throughput is very good so we're not bogged down there...it's just super busy doing running
the code below. I am intrigued about the comments on the SequentialAccessSparseVector methods
I see being called (getQuick and setQuick), which state they take O(log n) time (https://github.com/apache/mahout/blob/08e02602e947ff945b9bd73ab5f0b45863df3e53/math/src/main/java/org/apache/mahout/math/SequentialAccessSparseVector.java).
>
>
>Thanks all for your time and feedback!
>
>Matt Scruggs
>
>org.apache.mahout.math.OrderedIntDoubleMapping.find(OrderedIntDoubleMapping.java:105)
>org.apache.mahout.math.OrderedIntDoubleMapping.get(OrderedIntDoubleMapping.java:110)
>org.apache.mahout.math.SequentialAccessSparseVector.getQuick(SequentialAccessSparseVector.java:157)
>org.apache.mahout.math.SparseRowMatrix.getQuick(SparseRowMatrix.java:90)
>org.apache.mahout.math.AbstractMatrix.assign(AbstractMatrix.java:240)
>org.apache.mahout.math.scalabindings.MatrixOps.$plus$eq(MatrixOps.scala:45)
>org.apache.mahout.sparkbindings.blas.AtA$$anonfun$19.apply(AtA.scala:258)
>org.apache.mahout.sparkbindings.blas.AtA$$anonfun$19.apply(AtA.scala:258)
>org.apache.spark.util.collection.ExternalAppendOnlyMap$$anonfun$3.apply(ExternalAppendOnlyMap.scala:151)
>org.apache.spark.util.collection.ExternalAppendOnlyMap$$anonfun$3.apply(ExternalAppendOnlyMap.scala:150)
>org.apache.spark.util.collection.AppendOnlyMap.changeValue(AppendOnlyMap.scala:144)
>org.apache.spark.util.collection.SizeTrackingAppendOnlyMap.changeValue(SizeTrackingAppendOnlyMap.scala:32)
>org.apache.spark.util.collection.ExternalAppendOnlyMap.insertAll(ExternalAppendOnlyMap.scala:163)
>org.apache.spark.Aggregator.combineCombinersByKey(Aggregator.scala:50)
>org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:85)
>org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:109)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79)
>org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47)
>org.apache.spark.scheduler.Task.run(Task.scala:86)
>org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
>java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>java.lang.Thread.run(Thread.java:745)
>
>……or this code……
>
>org.apache.mahout.math.SparseRowMatrix.setQuick(SparseRowMatrix.java:105)
>org.apache.mahout.math.AbstractMatrix.assign(AbstractMatrix.java:240)
>org.apache.mahout.math.scalabindings.MatrixOps.$plus$eq(MatrixOps.scala:45)
>org.apache.mahout.sparkbindings.blas.AtA$$anonfun$19.apply(AtA.scala:258)
>org.apache.mahout.sparkbindings.blas.AtA$$anonfun$19.apply(AtA.scala:258)
>org.apache.spark.util.collection.ExternalAppendOnlyMap$$anonfun$3.apply(ExternalAppendOnlyMap.scala:151)
>org.apache.spark.util.collection.ExternalAppendOnlyMap$$anonfun$3.apply(ExternalAppendOnlyMap.scala:150)
>org.apache.spark.util.collection.AppendOnlyMap.changeValue(AppendOnlyMap.scala:144)
>org.apache.spark.util.collection.SizeTrackingAppendOnlyMap.changeValue(SizeTrackingAppendOnlyMap.scala:32)
>org.apache.spark.util.collection.ExternalAppendOnlyMap.insertAll(ExternalAppendOnlyMap.scala:163)
>org.apache.spark.Aggregator.combineCombinersByKey(Aggregator.scala:50)
>org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:85)
>org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:109)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
>org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
>org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79)
>org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47)
>org.apache.spark.scheduler.Task.run(Task.scala:86)
>org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
>java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>java.lang.Thread.run(Thread.java:745)
>
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