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From Sheriffo Ceesay <sneceesa...@gmail.com>
Subject Re: Week 2 Report and A Question
Date Wed, 12 Jun 2019 16:54:08 GMT
Hi All,

Further to my previous email, I have now updated the code to reflect the
code optimisations proposed by Alfonso. I have completely removed the
reflection approach. @Alfonso Nishikawa <alfonso.nishikawa@gmail.com> , the
reason I did not use *SpecificRecordBase.get(int index)* and
*SpecificRecordBase.put(int
index, Object o)* in my first implementation was due to this comment
" //Used by DatumWriter.  Applications should not call." just before the
methods in the generated class. I have now changed the implementation to
use these two methods.

@Renato Marroquín Mogrovejo <renatoj.marroquin@gmail.com> , I forgot to
answer your question about how I run the code, please see below.

First Step: From the gora-benchmark directory execute

*mvn clean install*

Second Step:

*java -cp
.:bmstuff/core-0.1.4.jar:target/gora-benchmark-0.9-SNAPSHOT.jar:bmstuff/sources-dist-0.9-SNAPSHOT.jar:lib/*
*
* com.yahoo.ycsb.Client *
*-load *
*-db org.apache.gora.benchmark.GoraBenchmarkClient *
*-threads 10 -s *
*-P bmstuff/workloads/workloada > bmstuff/out.log*

The following switches or command line option are YCSB specific.

 com.yahoo.ycsb.Client is YCSB implementation that will load our DB class.
-load will load the database
-db Specify our benchmark implementation
-threads specify the number of client threads to start.
-P  the workload to execute, the file *bmstuff/workloads/workloada* contains
various key-value pairs e.g. number of records to count, number of records
to read and update.
> bmstuff/out.log send standard out and logs to out.log.

YCSB is highly configurable, we can pass a lot of KV pairs as a property
file or command line options. See [1] and [2] for more information. In the
end, we can write an executable script like ycsb.sh to automate the entire
benchmark process of Gora. This would range from creating the Avro files to
producing the benchmarking results.

 Please let me know if that makes sense.

Thank you.

[1] https://github.com/brianfrankcooper/YCSB/wiki/Running-a-Workload
[2] https://github.com/brianfrankcooper/YCSB/wiki/Core-Properties


**Sheriffo Ceesay**


On Wed, Jun 12, 2019 at 11:50 AM Sheriffo Ceesay <sneceesay77@gmail.com>
wrote:

> Hi Renato,
>
> I will follow Alfonso's recommendations about reusing objects as much as I
> can. I will push those changes to the branch by the end of this week.
>
> To answer your questions.
>
> Yes, you are right I am using a clean cold JVM. If necessary, I can also
> have a look at warming the JVM down the line.
>
> Yes, I have tried setting *gora.hbasestore.scanner.caching* to different
> values but there was no significant difference. Also, I may be wrong but  I
> think this setting has to do with scan operation and not insert operation?
>
> As for flushing, I tried but it quickly throws an error and hence I
> commented that line of code. I think this is due to the fact that the
> insert operation inserts a single user object for each call, so calling
> dataStore.flush() within that method would mean calling flush on every
> object insertion. Is that not the case? There should be a way to track the
> progress of inserts then that can be used to call flush after N insert
> calls. So I used *gora.hbasestore.hbase.client.autoflush.enabled=true *which
> would automatically call flush at some point. However, like I mentioned in
> my previous email, enabling autoflush decreases write performance [1].
>
> [1] https://gora.apache.org/current/gora-hbase.html
>
> Thank you.
>
> **Sheriffo Ceesay**
>
>
> On Tue, Jun 11, 2019 at 10:52 PM Renato Marroquín Mogrovejo <
> renatoj.marroquin@gmail.com> wrote:
>
>> Hey Sheriffo,
>>
>> Cool to hear you are making progress! :) and great to see that we have
>> some numbers already! :)
>> Regarding optimization point (1), regardless that this was not he
>> cause of the issue or not, Alfonso suggestions are something we should
>> follow, many objects with a short life in java might create a
>> performance problem sooner or later. Also about your comment:
>>
>> "Also, I may be wrong but the way I understand YCSB framework is, it
>> will execute an insert operation for each user object, so I thought it
>> was right to create a user object within the insert method."
>>
>> As you pointed out, YCSB is about inserting the objects, and NOT about
>> creating them, so it doesn't matter if we reuse the objects, as long
>> as the values that we insert are actually correct. We don't want to
>> end up measuring object creation+gc. I think Alfonso's comment was
>> hinting on that direction (please feel free to correct me @Alfonso if
>> I am misunderstanding you) and I think his comments are just on the
>> spot.
>> I have some other questions regarding the numbers you sent around:
>> - are you running YCSB for each data store with warm JVM? or are these
>> numbers each with a clean cold JVM? I suppose the latter, right?
>> - did you try setting gora.hbasestore.scanner.caching to a lower value?
>> - which is the command that you are using to run/start this code?
>> - did you try flushing the commits more regularly in:
>>
>> https://github.com/sneceesay77/gora/blob/GORA-532/gora-benchmark/src/main/java/org/apache/gora/benchmark/GoraBenchmarkClient.java#L142
>> let's say every 1000 elements? or something like that? I mean instead
>> of at the end of the 1M elements?
>>
>> Thanks a lot for the report Sheriffo!
>>
>>
>> Best,
>>
>> Renato M.
>>
>> El mar., 11 jun. 2019 a las 16:12, Sheriffo Ceesay
>> (<sneceesay77@gmail.com>) escribió:
>> >
>> > Hello,
>> >
>> > I have taken a proper look at the recommendations from @Alfonso and
>> @Renato and below are the outcomes.
>> >
>> > Failed Attempts
>> > 1. Optimisation, for the insert operation, to avoid the concatenation
>> issue, I have just taken the quickest route by calling the methods directly
>> without reflection. Below are those calls. Note: I have moved all reusable
>> codes to the init method.
>> >
>> >> public int insert(String table, String key, HashMap<String,
>> ByteIterator> values) {
>> >>       user.setField0(values.get("field0").toString());
>> >>       user.setField1(values.get("field1").toString());
>> >>       user.setField2(values.get("field2").toString());
>> >>       user.setField3(values.get("field3").toString());
>> >>       user.setField4(values.get("field4").toString());
>> >>       user.setField5(values.get("field5").toString());
>> >>       user.setField6(values.get("field6").toString());
>> >>       user.setField7(values.get("field7").toString());
>> >>       user.setField8(values.get("field8").toString());
>> >>       user.setField9(values.get("field9").toString());
>> >>       dataStore.put(user.getUserId().toString(), user);
>> >>     } catch (Exception e) {
>> >>       return FAILED;
>> >>     }
>> >>     return SUCCESS;
>> >>   }
>> >
>> >
>> > if the above had worked, I would have changed the code as suggested by
>> Alfonso. Also, I may be wrong but the way I understand YCSB framework is,
>> it will execute an insert operation for each user object, so I thought it
>> was right to create a user object within the insert method.
>> >
>> >
>> > 2. I used different config values for -Xmx (256MB, 512MB, 1GB, 2GB) and
>> even disabled GC checking using -XX:-UseGCOverheadLimit but they all failed
>> with the same GC error.
>> >
>> > Successful Attempt -- There may be room for improvement
>> > Using the configurations below worked but I think it is not the best
>> for write performance.
>> >
>> > First, I read from [1] related to [2] that the following oneliner code
>> should be executed for better HBase performance when using YCSB. It
>> basically avoids overloading a single region server.
>> >
>> > hbase(main):001:0> n_splits = 200 # HBase recommends (10 * number of
>> regionservers)
>> > hbase(main):002:0> create 'users', 'info', {SPLITS => (1..n_splits).map
>> {|i| "user#{1000+i*(9999-1000)/n_splits}"}}
>> >
>> > Second, as suggested by @Renato Marroquín Mogrovejo , it only works
>> when I set
>> >
>> > hbase.client.autoflush.default=true
>> >
>> > However, from [3], I found "HBase autoflushing. Enabling autoflush
>> decreases write performance. Available since Gora 0.2. Defaults to
>> disabled.". So I am of the opinion that the problem is not entirely solved.
>> >
>> > I have done the following testing to insert 1M records into MongoDB and
>> HBase, so I think this may not be bad after all but more benchmarks may be
>> required to validate this. HBase in Gora has almost the same performance as
>> vanilla YCSB to benchmark it.
>> >
>> > Backend          Ave Time Taken (sec)
>> > MongoDB                      ~90
>> > HBase in Gora              ~160
>> > HBase YCSB                ~160
>> >
>> >
>> > [1] https://github.com/brianfrankcooper/YCSB/tree/master/hbase098
>> > [2] https://issues.apache.org/jira/browse/HBASE-4163
>> > [3] https://gora.apache.org/current/gora-hbase.html
>> >
>> > Comments are welcomed.
>> >
>> > Thank you.
>> > *Sheriffo Ceesay*
>> >
>> >
>> >
>> > On Tue, Jun 11, 2019 at 12:04 AM Sheriffo Ceesay <sneceesay77@gmail.com>
>> wrote:
>> >>
>> >> Hello Alfonso and Renato,
>> >>
>> >> Thank you for getting in touch and thanks for the detailed replies.
>> >>
>> >> I will have proper look at this tomorrow morning. I did some
>> troubleshooting yesterday (mostly playing with Xmx and zookeeper timeout
>> settings), that improved the conditions, but it did not entirely solve the
>> problem. Preliminary, it seems the problem has to do with configuration or
>> how HBaseStore is implemented (this may not be entirely true).
>> >>
>> >> I will keep you all posted whenever I thoroughly have a look at your
>> suggestions.
>> >>
>> >> Thanks again.
>> >>
>> >> *Sheriffo Ceesay*
>> >>
>> >>
>> >>
>> >> On Mon, Jun 10, 2019 at 11:14 PM Alfonso Nishikawa <
>> alfonso.nishikawa@gmail.com> wrote:
>> >>>
>> >>> Hi!
>> >>>
>> >>> My hypothesis is taht that the difference between MongoDB and HBase
>> is that
>> >>> HBase put more stress serializing with avro. It could affect too that
>> if
>> >>> the HBase's test is performed after MongoDB's ones, then the GC
>> starts from
>> >>> a "bad" situation.
>> >>>
>> >>> From [A] linked by @Renato, if the error was OutOfMemoryException I
>> would
>> >>> have recommended lowering gora.hbasestore.scanner.caching to 100, 10
>> or
>> >>> even 1, but with a GC error I am not that much sure. In anycase,
>> @Sheriffo:
>> >>> you can try this if with the optimizations still doesn't work :)
>> >>>
>> >>> @Renato: Thx for the links!
>> >>>
>> >>> Regards,
>> >>>
>> >>> Alfonso Nishikawa
>> >>>
>> >>>
>> >>>
>> >>> El lun., 10 jun. 2019 a las 22:02, Renato Marroquín Mogrovejo (<
>> >>> renatoj.marroquin@gmail.com>) escribió:
>> >>>
>> >>> > @Alfonso,
>> >>> > Thank you very much for the suggestions! you are totally right
about
>> >>> > all of your points! Sheriffo, please benefit from them ;)
>> >>> >
>> >>> > Also what is strange is this (although it can be optimized as
>> Alfonso
>> >>> > pointed out) is that it works for the MongoDB backend. So I would
>> also
>> >>> > suspect on the configuration of the Gora-HBase client. Have you
>> taken
>> >>> > a look at [A] for example? or other Gora-HBase assumed
>> configurations
>> >>> > [B]? Maybe there you can specify some Xmx / Xms config.
>> >>> >
>> >>> >
>> >>> > Best,
>> >>> >
>> >>> > Renato M.
>> >>> >
>> >>> > [A]
>> >>> >
>> https://github.com/sneceesay77/gora/blob/master/gora-hbase/src/test/conf/gora.properties
>> >>> > [B]
>> >>> >
>> https://github.com/sneceesay77/gora/blob/master/gora-hbase/src/test/conf/hbase-site.xml
>> >>> >
>> >>> > El lun., 10 jun. 2019 a las 23:39, Alfonso Nishikawa
>> >>> > (<alfonso.nishikawa@gmail.com>) escribió:
>> >>> > >
>> >>> > > Hi again, Sheriffo.
>> >>> > >
>> >>> > > More improvements to [1] over the last email:
>> >>> > >
>> >>> > > - fields.toArray() doesn't need a full array like in [6].
You
>> should do
>> >>> > > just fields.toArray(new String[0]), and better if you create
an
>> array [0]
>> >>> > > and reuse it. That call only needs the type.
>> >>> > > - I guess the class at [2] will always be the same, so you
don't
>> need to
>> >>> > > set it on every insert call.
>> >>> > > - The string concatenation is overkilling for the jvm on the
1M
>> calls * N
>> >>> > > fields at [3] and same for [4]. Precalculate the names in
a list
>> or array
>> >>> > > and reuse then for the 1M*N calls.
>> >>> > > - Other optimization for [3] is, given that PersistentBase
[5]
>> exctends
>> >>> > > SpecificRecordBase, you can access the fields by index with
>> >>> > > SpecificRecordBase.get(int) and SpecificRecordBase.put(int,
>> Object).
>> >>> > >
>> >>> > > [1] -
>> >>> > >
>> >>> >
>> https://github.com/sneceesay77/gora/blob/GORA-532/gora-benchmark/src/ma1in/java/org/apache/gora/benchmark/GoraBenchmarkClient.java#L127
>> >>> > > [2] -
>> >>> > >
>> >>> >
>> https://github.com/sneceesay77/gora/blob/GORA-532/gora-benchmark/src/main/java/org/apache/gora/benchmark/GoraBenchmarkClient.java#L134
>> >>> > > [3] -
>> >>> > >
>> >>> >
>> https://github.com/sneceesay77/gora/blob/GORA-532/gora-benchmark/src/main/java/org/apache/gora/benchmark/GoraBenchmarkClient.java#L136
>> >>> > > [4] -
>> >>> > >
>> >>> >
>> https://github.com/sneceesay77/gora/blob/GORA-532/gora-benchmark/src/main/java/org/apache/gora/benchmark/GoraBenchmarkClient.java#L139
>> >>> > > [5] -
>> >>> > >
>> >>> >
>> https://github.com/sneceesay77/gora/blob/GORA-532/gora-core/src/main/java/org/apache/gora/persistency/impl/PersistentBase.java#L3
>> >>> > > [6] -
>> >>> > >
>> >>> >
>> https://github.com/sneceesay77/gora/blob/GORA-532/gora-benchmark/src/main/java/org/apache/gora/benchmark/GoraBenchmarkClient.java#L163
>> >>> > >
>> >>> > > Let's see if with that optimizations we free the jvm memory
>> management
>> >>> > from
>> >>> > > much stress.
>> >>> > >
>> >>> > > Regards,
>> >>> > >
>> >>> > > Alfonso Nishikawa
>> >>> > >
>> >>> > >
>> >>> > >
>> >>> > >
>> >>> > >
>> >>> > >
>> >>> > >
>> >>> > >
>> >>> > >
>> >>> > >
>> >>> > > El lun., 10 jun. 2019 a las 21:18, Alfonso Nishikawa (<
>> >>> > > alfonso.nishikawa@gmail.com>) escribió:
>> >>> > >
>> >>> > > > Hi, Sheriffo.
>> >>> > > >
>> >>> > > > You can try reusing the Persistent instances [1] to insert
the
>> data. I
>> >>> > > > don't know all the backends, but they should be reusable,
at
>> least in
>> >>> > > > mongoDB and HBase.
>> >>> > > >
>> >>> > > > [1] -
>> >>> > > >
>> >>> >
>> https://github.com/sneceesay77/gora/blob/GORA-532/gora-benchmark/src/main/java/org/apache/gora/benchmark/GoraBenchmarkClient.java#L130
>> >>> > > >
>> >>> > > > Regards,
>> >>> > > >
>> >>> > > > Alfonso Nishikawa
>> >>> > > >
>> >>> > > > El lun., 10 jun. 2019 a las 21:14, Alfonso Nishikawa
(<
>> >>> > > > alfonso.nishikawa@gmail.com>) escribió:
>> >>> > > >
>> >>> > > >> Hi, Sheriffo.
>> >>> > > >>
>> >>> > > >> I really don't know how to solve it, but are you
setting any
>> Xmx / Xms
>> >>> > > >> configuration values?
>> >>> > > >>
>> >>> > > >> Regards,
>> >>> > > >>
>> >>> > > >> Alfonso NIshikawa
>> >>> > > >>
>> >>> > > >>
>> >>> > > >> El sáb., 8 jun. 2019 a las 16:02, Sheriffo Ceesay
(<
>> >>> > sneceesay77@gmail.com>)
>> >>> > > >> escribió:
>> >>> > > >>
>> >>> > > >>> Hi All,
>> >>> > > >>>
>> >>> > > >>> Week 2 progress update is available at
>> >>> > > >>>
>> >>> > > >>>
>> >>> >
>> https://cwiki.apache.org/confluence/display/GORA/%5BGORA-532%5D+Apache+Gora+Benchmark+Module+Weekly+Report
>> >>> > > >>>
>> >>> > > >>> I have one question that I would like my mentors
to advise
>> on, I am
>> >>> > still
>> >>> > > >>> working it but thought it would be good to report
it because
>> it is
>> >>> > HBase
>> >>> > > >>> specific.
>> >>> > > >>>
>> >>> > > >>> So the problem has to do with an OutOfMemory
error when
>> inserting 1M
>> >>> > +
>> >>> > > >>> record in HBase.  This happens when I try to
run the actual
>> >>> > benchmark by
>> >>> > > >>> first loading HBase with 1 million plus records.
It works
>> perfectly
>> >>> > for
>> >>> > > >>> MongoDB but not HBase
>> >>> > > >>>
>> >>> > > >>> So I am assuming this problem is specific to
HBase.  The
>> stack trace
>> >>> > is
>> >>> > > >>> given below.
>> >>> > > >>>
>> >>> > > >>> Exception in thread "Thread-1" java.lang.OutOfMemoryError:
GC
>> >>> > overhead
>> >>> > > >>> limit exceeded
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> >>> > > >>>
>> java.lang.StringCoding$StringEncoder.encode(StringCoding.java:300)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> java.lang.StringCoding.encode(StringCoding.java:344)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at java.lang.String.getBytes(String.java:918)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> org.apache.hadoop.hbase.util.Bytes.toBytes(Bytes.java:733)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> >>> > > >>>
>> >>> > > >>>
>> >>> >
>> org.apache.gora.hbase.util.HBaseByteInterface.toBytes(HBaseByteInterface.java:225)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> >>> > > >>>
>> >>> > > >>>
>> >>> >
>> org.apache.gora.hbase.store.HBaseStore.addPutsAndDeletes(HBaseStore.java:383)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> >>> > > >>>
>> >>> > > >>>
>> >>> >
>> org.apache.gora.hbase.store.HBaseStore.addPutsAndDeletes(HBaseStore.java:348)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> >>> > > >>>
>> org.apache.gora.hbase.store.HBaseStore.put(HBaseStore.java:319)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> >>> > org.apache.gora.hbase.store.HBaseStore.put(HBaseStore.java:84)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> >>> > > >>>
>> >>> > > >>>
>> >>> >
>> org.apache.gora.benchmark.GoraBenchmarkClient.insert(GoraBenchmarkClient.java:141)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at com.yahoo.ycsb.DBWrapper.insert(DBWrapper.java:148)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at
>> >>> > > >>>
>> com.yahoo.ycsb.workloads.CoreWorkload.doInsert(CoreWorkload.java:461)
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>         at com.yahoo.ycsb.ClientThread.run(Client.java:269)
>> >>> > > >>>
>> >>> > > >>> The insert implementation of the module available
at
>> >>> > > >>>
>> https://github.com/sneceesay77/gora/tree/GORA-532/gora-benchmark  in
>> >>> > > >>> GoraBenchmarkClient.java is very straight forward.
I have had
>> a brief
>> >>> > > >>> look
>> >>> > > >>> at HBaseStore.java put() implementation but could
not find an
>> issue
>> >>> > with
>> >>> > > >>> that.
>> >>> > > >>>
>> >>> > > >>> If I solve this problem, then I will do run more
workloads to
>> verify
>> >>> > that
>> >>> > > >>> the module is stable for the basic implementation.
Then I
>> will go
>> >>> > ahead
>> >>> > > >>> and
>> >>> > > >>> work on suggestions made by Renato last week.
>> >>> > > >>>
>> >>> > > >>> Please let me know what your thoughts are.
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>> Thank you.
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>>
>> >>> > > >>> **Sheriffo Ceesay**
>> >>> > > >>>
>> >>> > > >>
>> >>> >
>>
>

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