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From Benjamin Kim <bbuil...@gmail.com>
Subject Re: Performance Question
Date Thu, 28 Jul 2016 05:41:42 GMT
JD,

I checked the WARNING logs and found this.

W0728 05:36:25.453966 22452 consensus_peers.cc:326] T 377e17bb8a93493993cec74f72c2d7a5 P cb652bf9e56347beb93039802c26085f
-> Peer da37b6f955184aa68f0cde68f85c5e03 (prod-dc1-datanode163.pdc1i.gradientx.com:7050):
Couldn't send request to peer da37b6f955184aa68f0cde68f85c5e03 for tablet 377e17bb8a93493993cec74f72c2d7a5.
Status: Remote error: Service unavailable: Soft memory limit exceeded (at 100.06% of capacity).
Retrying in the next heartbeat period. Already tried 93566 times.

In Cloudera Manager, the CGroup Soft Memory Limit is set to -1. How can I fix this? Is it
Linux related? Also, the Kudu Tablet Server Hard Memory Limit is set to 4GB.

Thanks,
Ben

> On Jul 27, 2016, at 11:12 AM, Jean-Daniel Cryans <jdcryans@apache.org> wrote:
> 
> Hey Ben,
> 
> I fixed a few hangs in the Java client over the past few weeks, so you might be hitting
that. To confirm if it's the case, set a timeout that's way higher, like minutes. If it still
times out, might be the hang in which case there are some workarounds.
> 
> Otherwise, it might be that your cluster is getting slammed? Have you checked the usuals
like high iowait, swapping, etc? Also take a look at the WARNING log from the tservers and
see if they complain about long Write RPCs.
> 
> FWIW I've been testing non-stop inserts on a 6 nodes cluster (of which one is just a
master) here and I have 318B (318,852,472,816) rows inserted, 43TB on disk post-replication
and compression, so I'm not too worried about 800M rows unless they're hundreds of KB each
:P
> 
> J-D
> 
> On Tue, Jul 26, 2016 at 5:15 PM, Benjamin Kim <bbuild11@gmail.com <mailto:bbuild11@gmail.com>>
wrote:
> I have reached over 800M rows (813,997,990), and now it’s starting to timeout when
UPSERTing data.
> 
> 16/07/27 00:04:58 WARN scheduler.TaskSetManager: Lost task 0.0 in stage 17.0 (TID 87,
prod-dc1-datanode163.pdc1i.gradientx.com <http://prod-dc1-datanode163.pdc1i.gradientx.com/>):
com.stumbleupon.async.TimeoutException: Timed out after 30000ms when joining Deferred@1592877776(state=PENDING,
result=null, callback=org.kududb.client.AsyncKuduSession$ConvertBatchToListOfResponsesCB@154c94f8
-> wakeup thread Executor task launch worker-2, errback=passthrough -> wakeup thread
Executor task launch worker-2)
> 	at com.stumbleupon.async.Deferred.doJoin(Deferred.java:1177)
> 	at com.stumbleupon.async.Deferred.join(Deferred.java:1045)
> 	at org.kududb.client.KuduSession.close(KuduSession.java:110)
> 	at org.kududb.spark.kudu.KuduContext.writeRows(KuduContext.scala:181)
> 	at org.kududb.spark.kudu.KuduContext$$anonfun$writeRows$1.apply(KuduContext.scala:131)
> 	at org.kududb.spark.kudu.KuduContext$$anonfun$writeRows$1.apply(KuduContext.scala:130)
> 	at org.apache.spark.rdd.RDD$$anonfun$foreachPartition$1$$anonfun$apply$33.apply(RDD.scala:920)
> 	at org.apache.spark.rdd.RDD$$anonfun$foreachPartition$1$$anonfun$apply$33.apply(RDD.scala:920)
> 	at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1869)
> 	at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1869)
> 	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
> 	at org.apache.spark.scheduler.Task.run(Task.scala:89)
> 	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
> 	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> 	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> 	at java.lang.Thread.run(Thread.java:745)
> 
> 
> Thanks,
> Ben
> 
> 
>> On Jul 18, 2016, at 10:32 AM, Todd Lipcon <todd@cloudera.com <mailto:todd@cloudera.com>>
wrote:
>> 
>> On Mon, Jul 18, 2016 at 10:31 AM, Benjamin Kim <bbuild11@gmail.com <mailto:bbuild11@gmail.com>>
wrote:
>> Todd,
>> 
>> Thanks for the info. I was going to upgrade after the testing, but now, it looks
like I will have to do it earlier than expected.
>> 
>> I will do the upgrade, then resume.
>> 
>> OK, sounds good. The upgrade shouldn't invalidate any performance testing or anything
-- just fixes this important bug.
>> 
>> -Todd
>> 
>> 
>>> On Jul 18, 2016, at 10:29 AM, Todd Lipcon <todd@cloudera.com <mailto:todd@cloudera.com>>
wrote:
>>> 
>>> Hi Ben,
>>> 
>>> Any chance that you are running Kudu 0.9.0 instead of 0.9.1? There's a known
serious bug in 0.9.0 which can cause this kind of corruption.
>>> 
>>> Assuming that you are running with replication count 3 this time, you should
be able to move aside that tablet metadata file and start the server. It will recreate a new
repaired replica automatically.
>>> 
>>> -Todd
>>> 
>>> On Mon, Jul 18, 2016 at 10:28 AM, Benjamin Kim <bbuild11@gmail.com <mailto:bbuild11@gmail.com>>
wrote:
>>> During my re-population of the Kudu table, I am getting this error trying to
restart a tablet server after it went down. The job that populates this table has been running
for over a week.
>>> 
>>> [libprotobuf ERROR google/protobuf/message_lite.cc:123] Can't parse message of
type "kudu.tablet.TabletSuperBlockPB" because it is missing required fields: rowsets[2324].columns[15].block
>>> F0718 17:01:26.783571   468 tablet_server_main.cc:55] Check failed: _s.ok() Bad
status: IO error: Could not init Tablet Manager: Failed to open tablet metadata for tablet:
24637ee6f3e5440181ce3f20b1b298ba: Failed to load tablet metadata for tablet id 24637ee6f3e5440181ce3f20b1b298ba:
Could not load tablet metadata from /mnt/data1/kudu/data/tablet-meta/24637ee6f3e5440181ce3f20b1b298ba:
Unable to parse PB from path: /mnt/data1/kudu/data/tablet-meta/24637ee6f3e5440181ce3f20b1b298ba
>>> *** Check failure stack trace: ***
>>>     @           0x7d794d  google::LogMessage::Fail()
>>>     @           0x7d984d  google::LogMessage::SendToLog()
>>>     @           0x7d7489  google::LogMessage::Flush()
>>>     @           0x7da2ef  google::LogMessageFatal::~LogMessageFatal()
>>>     @           0x78172b  (unknown)
>>>     @       0x344d41ed5d  (unknown)
>>>     @           0x7811d1  (unknown)
>>> 
>>> Does anyone know what this means?
>>> 
>>> Thanks,
>>> Ben
>>> 
>>> 
>>>> On Jul 11, 2016, at 10:47 AM, Todd Lipcon <todd@cloudera.com <mailto:todd@cloudera.com>>
wrote:
>>>> 
>>>> On Mon, Jul 11, 2016 at 10:40 AM, Benjamin Kim <bbuild11@gmail.com <mailto:bbuild11@gmail.com>>
wrote:
>>>> Todd,
>>>> 
>>>> I had it at one replica. Do I have to recreate?
>>>> 
>>>> We don't currently have the ability to "accept data loss" on a tablet (or
set of tablets). If the machine is gone for good, then currently the only easy way to recover
is to recreate the table. If this sounds really painful, though, maybe we can work up some
kind of tool you could use to just recreate the missing tablets (with those rows lost).
>>>> 
>>>> -Todd
>>>> 
>>>>> On Jul 11, 2016, at 10:37 AM, Todd Lipcon <todd@cloudera.com <mailto:todd@cloudera.com>>
wrote:
>>>>> 
>>>>> Hey Ben,
>>>>> 
>>>>> Is the table that you're querying replicated? Or was it created with
only one replica per tablet?
>>>>> 
>>>>> -Todd
>>>>> 
>>>>> On Mon, Jul 11, 2016 at 10:35 AM, Benjamin Kim <bkim@amobee.com <mailto:bkim@amobee.com>>
wrote:
>>>>> Over the weekend, a tablet server went down. It’s not coming back up.
So, I decommissioned it and removed it from the cluster. Then, I restarted Kudu because I
was getting a timeout  exception trying to do counts on the table. Now, when I try again.
I get the same error.
>>>>> 
>>>>> 16/07/11 17:32:36 WARN scheduler.TaskSetManager: Lost task 468.3 in stage
0.0 (TID 603, prod-dc1-datanode167.pdc1i.gradientx.com <http://prod-dc1-datanode167.pdc1i.gradientx.com/>):
com.stumbleupon.async.TimeoutException: Timed out after 30000ms when joining Deferred@712342716(state=PAUSED,
result=Deferred@1765902299, callback=passthrough -> scanner opened -> wakeup thread
Executor task launch worker-2, errback=openScanner errback -> passthrough -> wakeup
thread Executor task launch worker-2)
>>>>> at com.stumbleupon.async.Deferred.doJoin(Deferred.java:1177)
>>>>> at com.stumbleupon.async.Deferred.join(Deferred.java:1045)
>>>>> at org.kududb.client.KuduScanner.nextRows(KuduScanner.java:57)
>>>>> at org.kududb.spark.kudu.RowResultIteratorScala.hasNext(KuduRDD.scala:99)
>>>>> at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>>>>> at org.apache.spark.sql.execution.aggregate.TungstenAggregate$$anonfun$doExecute$1$$anonfun$2.apply(TungstenAggregate.scala:88)
>>>>> at org.apache.spark.sql.execution.aggregate.TungstenAggregate$$anonfun$doExecute$1$$anonfun$2.apply(TungstenAggregate.scala:86)
>>>>> at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710)
>>>>> at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710)
>>>>> at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>>>>> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
>>>>> at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
>>>>> at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
>>>>> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
>>>>> at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
>>>>> at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
>>>>> at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
>>>>> at org.apache.spark.scheduler.Task.run(Task.scala:89)
>>>>> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
>>>>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>>>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>> 
>>>>> Does anyone know how to recover from this?
>>>>> 
>>>>> Thanks,
>>>>> Benjamin Kim
>>>>> Data Solutions Architect
>>>>> 
>>>>> [a•mo•bee] (n.) the company defining digital marketing.
>>>>> 
>>>>> Mobile: +1 818 635 2900 <tel:%2B1%20818%20635%202900>
>>>>> 3250 Ocean Park Blvd, Suite 200  |  Santa Monica, CA 90405  |  www.amobee.com
<http://www.amobee.com/>
>>>>>> On Jul 6, 2016, at 9:46 AM, Dan Burkert <dan@cloudera.com <mailto:dan@cloudera.com>>
wrote:
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Wed, Jul 6, 2016 at 7:05 AM, Benjamin Kim <bbuild11@gmail.com
<mailto:bbuild11@gmail.com>> wrote:
>>>>>> Over the weekend, the row count is up to <500M. I will give it
another few days to get to 1B rows. I still get consistent times ~15s for doing row counts
despite the amount of data growing.
>>>>>> 
>>>>>> On another note, I got a solicitation email from SnappyData to evaluate
their product. They claim to be the “Spark Data Store” with tight integration with Spark
executors. It claims to be an OLTP and OLAP system with being an in-memory data store first
then to disk. After going to several Spark events, it would seem that this is the new “hot”
area for vendors. They all (MemSQL, Redis, Aerospike, Datastax, etc.) claim to be the best
"Spark Data Store”. I’m wondering if Kudu will become this too? With the performance I’ve
seen so far, it would seem that it can be a contender. All that is needed is a hardened Spark
connector package, I would think. The next evaluation I will be conducting is to see if SnappyData’s
claims are valid by doing my own tests.
>>>>>> 
>>>>>> It's hard to compare Kudu against any other data store without a
lot of analysis and thorough benchmarking, but it is certainly a goal of Kudu to be a great
platform for ingesting and analyzing data through Spark.  Up till this point most of the Spark
work has been community driven, but more thorough integration testing of the Spark connector
is going to be a focus going forward.
>>>>>> 
>>>>>> - Dan
>>>>>> 
>>>>>>  
>>>>>> Cheers,
>>>>>> Ben
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Jun 15, 2016, at 12:47 AM, Todd Lipcon <todd@cloudera.com
<mailto:todd@cloudera.com>> wrote:
>>>>>>> 
>>>>>>> Hi Benjamin,
>>>>>>> 
>>>>>>> What workload are you using for benchmarks? Using spark or something
more custom? rdd or data frame or SQL, etc? Maybe you can share the schema and some queries
>>>>>>> 
>>>>>>> Todd
>>>>>>> 
>>>>>>> Todd
>>>>>>> 
>>>>>>> On Jun 15, 2016 8:10 AM, "Benjamin Kim" <bbuild11@gmail.com
<mailto:bbuild11@gmail.com>> wrote:
>>>>>>> Hi Todd,
>>>>>>> 
>>>>>>> Now that Kudu 0.9.0 is out. I have done some tests. Already,
I am impressed. Compared to HBase, read and write performance are better. Write performance
has the greatest improvement (> 4x), while read is > 1.5x. Albeit, these are only preliminary
tests. Do you know of a way to really do some conclusive tests? I want to see if I can match
your results on my 50 node cluster.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> Ben
>>>>>>> 
>>>>>>>> On May 30, 2016, at 10:33 AM, Todd Lipcon <todd@cloudera.com
<mailto:todd@cloudera.com>> wrote:
>>>>>>>> 
>>>>>>>> On Sat, May 28, 2016 at 7:12 AM, Benjamin Kim <bbuild11@gmail.com
<mailto:bbuild11@gmail.com>> wrote:
>>>>>>>> Todd,
>>>>>>>> 
>>>>>>>> It sounds like Kudu can possibly top or match those numbers
put out by Aerospike. Do you have any performance statistics published or any instructions
as to measure them myself as good way to test? In addition, this will be a test using Spark,
so should I wait for Kudu version 0.9.0 where support will be built in?
>>>>>>>> 
>>>>>>>> We don't have a lot of benchmarks published yet, especially
on the write side. I've found that thorough cross-system benchmarks are very difficult to
do fairly and accurately, and often times users end up misguided if they pay too much attention
to them :) So, given a finite number of developers working on Kudu, I think we've tended to
spend more time on the project itself and less time focusing on "competition". I'm sure there
are use cases where Kudu will beat out Aerospike, and probably use cases where Aerospike will
beat Kudu as well.
>>>>>>>> 
>>>>>>>> From my perspective, it would be great if you can share some
details of your workload, especially if there are some areas you're finding Kudu lacking.
Maybe we can spot some easy code changes we could make to improve performance, or suggest
a tuning variable you could change.
>>>>>>>> 
>>>>>>>> -Todd
>>>>>>>> 
>>>>>>>> 
>>>>>>>>> On May 27, 2016, at 9:19 PM, Todd Lipcon <todd@cloudera.com
<mailto:todd@cloudera.com>> wrote:
>>>>>>>>> 
>>>>>>>>> On Fri, May 27, 2016 at 8:20 PM, Benjamin Kim <bbuild11@gmail.com
<mailto:bbuild11@gmail.com>> wrote:
>>>>>>>>> Hi Mike,
>>>>>>>>> 
>>>>>>>>> First of all, thanks for the link. It looks like an interesting
read. I checked that Aerospike is currently at version 3.8.2.3, and in the article, they are
evaluating version 3.5.4. The main thing that impressed me was their claim that they can beat
Cassandra and HBase by 8x for writing and 25x for reading. Their big claim to fame is that
Aerospike can write 1M records per second with only 50 nodes. I wanted to see if this is real.
>>>>>>>>> 
>>>>>>>>> 1M records per second on 50 nodes is pretty doable by
Kudu as well, depending on the size of your records and the insertion order. I've been playing
with a ~70 node cluster recently and seen 1M+ writes/second sustained, and bursting above
4M. These are 1KB rows with 11 columns, and with pretty old HDD-only nodes. I think newer
flash-based nodes could do better.
>>>>>>>>>  
>>>>>>>>> 
>>>>>>>>> To answer your questions, we have a DMP with user profiles
with many attributes. We create segmentation information off of these attributes to classify
them. Then, we can target advertising appropriately for our sales department. Much of the
data processing is for applying models on all or if not most of every profile’s attributes
to find similarities (nearest neighbor/clustering) over a large number of rows when batch
processing or a small subset of rows for quick online scoring. So, our use case is a typical
advanced analytics scenario. We have tried HBase, but it doesn’t work well for these types
of analytics.
>>>>>>>>> 
>>>>>>>>> I read, that Aerospike in the release notes, they did
do many improvements for batch and scan operations.
>>>>>>>>> 
>>>>>>>>> I wonder what your thoughts are for using Kudu for this.
>>>>>>>>> 
>>>>>>>>> Sounds like a good Kudu use case to me. I've heard great
things about Aerospike for the low latency random access portion, but I've also heard that
it's _very_ expensive, and not particularly suited to the columnar scan workload. Lastly,
I think the Apache license of Kudu is much more appealing than the AGPL3 used by Aerospike.
But, that's not really a direct answer to the performance question :)
>>>>>>>>>  
>>>>>>>>> 
>>>>>>>>> Thanks,
>>>>>>>>> Ben
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>> On May 27, 2016, at 6:21 PM, Mike Percy <mpercy@cloudera.com
<mailto:mpercy@cloudera.com>> wrote:
>>>>>>>>>> 
>>>>>>>>>> Have you considered whether you have a scan heavy
or a random access heavy workload? Have you considered whether you always access / update
a whole row vs only a partial row? Kudu is a column store so has some awesome performance
characteristics when you are doing a lot of scanning of just a couple of columns.
>>>>>>>>>> 
>>>>>>>>>> I don't know the answer to your question but if your
concern is performance then I would be interested in seeing comparisons from a perf perspective
on certain workloads.
>>>>>>>>>> 
>>>>>>>>>> Finally, a year ago Aerospike did quite poorly in
a Jepsen test: https://aphyr.com/posts/324-jepsen-aerospike <https://aphyr.com/posts/324-jepsen-aerospike>
>>>>>>>>>> 
>>>>>>>>>> I wonder if they have addressed any of those issues.
>>>>>>>>>> 
>>>>>>>>>> Mike
>>>>>>>>>> 
>>>>>>>>>> On Friday, May 27, 2016, Benjamin Kim <bbuild11@gmail.com
<mailto:bbuild11@gmail.com>> wrote:
>>>>>>>>>> I am just curious. How will Kudu compare with Aerospike
(http://www.aerospike.com <http://www.aerospike.com/>)? I went to a Spark Roadshow and
found out about this piece of software. It appears to fit our use case perfectly since we
are an ad-tech company trying to leverage our user profiles data. Plus, it already has a Spark
connector and has a SQL-like client. The tables can be accessed using Spark SQL DataFrames
and, also, made into SQL tables for direct use with Spark SQL ODBC/JDBC Thriftserver. I see
from the work done here http://gerrit.cloudera.org:8080/#/c/2992/ <http://gerrit.cloudera.org:8080/#/c/2992/>
that the Spark integration is well underway and, from the looks of it lately, almost complete.
I would prefer to use Kudu since we are already a Cloudera shop, and Kudu is easy to deploy
and configure using Cloudera Manager. I also hope that some of Aerospike’s speed optimization
techniques can make it into Kudu in the future, if they have not been already thought of or
included.
>>>>>>>>>> 
>>>>>>>>>> Just some thoughts…
>>>>>>>>>> 
>>>>>>>>>> Cheers,
>>>>>>>>>> Ben
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> -- 
>>>>>>>>>> --
>>>>>>>>>> Mike Percy
>>>>>>>>>> Software Engineer, Cloudera
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> -- 
>>>>>>>>> Todd Lipcon
>>>>>>>>> Software Engineer, Cloudera
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> -- 
>>>>>>>> Todd Lipcon
>>>>>>>> Software Engineer, Cloudera
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> Todd Lipcon
>>>>> Software Engineer, Cloudera
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> Todd Lipcon
>>>> Software Engineer, Cloudera
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Todd Lipcon
>>> Software Engineer, Cloudera
>> 
>> 
>> 
>> 
>> -- 
>> Todd Lipcon
>> Software Engineer, Cloudera
> 
> 


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