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From alchemist <alchemistsrivast...@gmail.com>
Subject Re: Upsert is EXTREMELY slow
Date Wed, 11 Jul 2018 14:53:04 GMT
Thanks so much for all your help and response.  Here are the recommended
details.

I have deployed Hbase backed by S3 on EMR cluster.  And performing upsert
from EC2 node outside EMR using simple java multithreaded client to perform
atomic update.

I have created a table like following

CREATE TABLE IF NOT EXISTS VBQL_PHOENIX_TRANSCRIPT ( PK VARCHAR NOT NULL
PRIMARY KEY, IMMUTABLES.VBMETAJSON VARCHAR, IMMUTABLES.ACCOUNTID VARCHAR,
IMMUTABLES.DATECREATED VARCHAR, IMMUTABLES.DATEFINISHED VARCHAR,
IMMUTABLES.MEDIAID VARCHAR, IMMUTABLES.JOBID VARCHAR, IMMUTABLES.STATUS
VARCHAR, UPDATABLE.METADATA VARCHAR, CATEGORIES.C_ACOUNTID_CATEGORYNAME
VARCHAR, COMPUTED.ADDITIONALMETRICS VARCHAR) SALT_BUCKETS =100;

with secondary index like this:

CREATE INDEX  VBQL_PHOENIX_TRANSCRIPT_INDEX5  ON  VBQL_PHOENIX_TRANSCRIPT5
(IMMUTABLES.MEDIAID) ;


Sample Upsert
UPSERT INTO VBQL_PHOENIX_TRANSCRIPT2  ( PK , IMMUTABLES.ACCOUNTID ,
IMMUTABLES.DATECREATED , IMMUTABLES.DATEFINISHED ,
IMMUTABLES.MEDIAID , IMMUTABLES.JOBID , IMMUTABLES.STATUS  ) 
VALUES
('5DAD32BA-9656-41F3-BD38-BBF890B85CD62018-05-18T18:09:38.60700005D681A95C-8CDA-47B2-93BE-C165B1DEC7D8',
'AAAAAAAAAAAAAAA5DAD32BA-9656', 
'2018-04-18T18:09:38.607+0000',
'2018-05-18T18:09:38.607+0000','5D681A95C-8CDA-47B2-93BE-C165B1DEC7D8',
'JOB123', 'FINISHED');


HBASE IS INSTALLED ON EMR CLUSTER HERE TABLE IS CREATED USING ABOVE CREATE
TABLE COMMANDS

EMR Cluster is 4 node m4.4xlarge cluster (32 vCore, 64 GiB memory, EBS only
storage
EBS Storage:32 GiB)

Client is a Java program running in EC2 (m4.10xlarge m4.10xlarge	40 CPU	160 
RAM 10 GiB Network EBS Only	10 Gbps	4,000 Mbps) Client is a multithreaded
program that creates atomic connection to Hbase and performs inserts.


CLIENT hbase-site.xml looks like following:

<?xml version="1.0"?>
<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>

<configuration>
  <property>
  <name>hbase.regionserver.wal.codec</name>
 
<value>org.apache.hadoop.hbase.regionserver.wal.IndexedWALEditCodec</value>
</property>

  <property>
    <name>hbase.cluster.distributed</name>
    <value>true</value>
  </property>

  <property>
    <name>hbase.zookeeper.quorum</name>
    <value>10.16.129.55</value>
  </property>

  <property>
    <name>hbase.rootdir</name>
    <value>s3://dev-mock-transcription/</value>
  </property>

  <property>
    <name>dfs.support.append</name>
    <value>true</value>
  </property>

  <property>
    <name>hbase.rest.port</name>
    <value>8070</value>
  </property>


  <property>
    <name>hbase.replication</name>
    <value>false</value>
  </property>

  <property>
    <name>hbase.balancer.tablesOnMaster</name>
    <value>hbase:meta</value>
  </property>

  <property>
    <name>hbase.bucketcache.size</name>
    <value>8192</value>
  </property>

  <property>
    <name>hbase.master.balancer.uselocality</name>
    <value>false</value>
  </property>

  <property>
    <name>hbase.master.startup.retainassign</name>
    <value>false</value>
  </property>

  <property>
    <name>hbase.wal.dir</name>
    <value>hdfs://10.16.129.55:8020/user/hbase/WAL</value>
  </property>

  <property>
    <name>hbase.bulkload.retries.retryOnIOException</name>
    <value>true</value>
  </property>

  <property>
    <name>hbase.bucketcache.ioengine</name>
    <value>files:/mnt1/hbase/bucketcache</value>
  </property>

   <property>
      <name>hbase.rpc.timeout</name>
      <value>1800000</value>
    </property>


  <property>
      <name>phoenix.query.timeoutMs</name>
      <value>18000000</value>
                    </property>
     <property>
      <name>phbase.regionserver.lease.period</name>
      <value>18000000</value>
    </property>

      <property>
      <name>hbase.client.scanner.caching</name>
      <value>180000</value>
    </property>

      <property>
      <name>phbase.client.scanner.timeout.period</name>
      <value>18000000</value>
    </property>

 <property>
      <name>index.writer.threads.max</name>
      <value>30</value>
 </property>
 <property>
      <name>index.builder.threads.max</name>
      <value>30</value>
 </property>
 <property>
      <name>phoenix.query.threadPoolSize</name>
      <value>256</value>
 </property>
 <property>
      <name>index.builder.threads.keepalivetime</name>
      <value>90000</value>
 </property>
<property>
      <name>phoenix.query.timeoutMs</name>
      <value>90000</value>
 </property>


</configuration>



HBASE ENV LOOKS LIKE FOLLOWING:

[ec2-user@ip-10-16-129-55 conf]$ cat hbase-env.sh 
#
#/**
# * Licensed to the Apache Software Foundation (ASF) under one
# * or more contributor license agreements.  See the NOTICE file
# * distributed with this work for additional information
# * regarding copyright ownership.  The ASF licenses this file
# * to you under the Apache License, Version 2.0 (the
# * "License"); you may not use this file except in compliance
# * with the License.  You may obtain a copy of the License at
# *
# *     http://www.apache.org/licenses/LICENSE-2.0
# *
# * Unless required by applicable law or agreed to in writing, software
# * distributed under the License is distributed on an "AS IS" BASIS,
# * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# * See the License for the specific language governing permissions and
# * limitations under the License.
# */

# Set environment variables here.

# This script sets variables multiple times over the course of starting an
hbase process,
# so try to keep things idempotent unless you want to take an even deeper
look
# into the startup scripts (bin/hbase, etc.)

# The java implementation to use.  Java 1.7+ required.
# export JAVA_HOME=/usr/java/jdk1.6.0/

# Extra Java CLASSPATH elements.  Optional.
export HBASE_CLASSPATH=/etc/hadoop/conf

# The maximum amount of heap to use. Default is left to JVM default.
# export HBASE_HEAPSIZE=1G
export HBASE_HEAPSIZE=1024

# Uncomment below if you intend to use off heap cache. For example, to
allocate 8G of 
# offheap, set the value to "8G".
# export HBASE_OFFHEAPSIZE=1G

# Extra Java runtime options.
# Below are what we set by default.  May only work with SUN JVM.
# For more on why as well as other possible settings,
# see http://wiki.apache.org/hadoop/PerformanceTuning
export HBASE_OPTS="$HBASE_OPTS -XX:+UseConcMarkSweepGC -XX:+UseParNewGC
-XX:CMSInitiatingOccupancyFraction=70 -Dsun.net.inetaddr.ttl=60
-Dnetworkaddress.cache.ttl=60"


# Uncomment one of the below three options to enable java garbage collection
logging for the server-side processes.

# This enables basic gc logging to the .out file.
# export SERVER_GC_OPTS="-verbose:gc -XX:+PrintGCDetails
-XX:+PrintGCDateStamps"

# This enables basic gc logging to its own file.
# If FILE-PATH is not replaced, the log file(.gc) would still be generated
in the HBASE_LOG_DIR .
# export SERVER_GC_OPTS="-verbose:gc -XX:+PrintGCDetails
-XX:+PrintGCDateStamps -Xloggc:<FILE-PATH>"

# This enables basic GC logging to its own file with automatic log rolling.
Only applies to jdk 1.6.0_34+ and 1.7.0_2+.
# If FILE-PATH is not replaced, the log file(.gc) would still be generated
in the HBASE_LOG_DIR .
# export SERVER_GC_OPTS="-verbose:gc -XX:+PrintGCDetails
-XX:+PrintGCDateStamps -Xloggc:<FILE-PATH> -XX:+UseGCLogFileRotation
-XX:NumberOfGCLogFiles=1 -XX:GCLogFileSize=512M"

# Uncomment one of the below three options to enable java garbage collection
logging for the client processes.

# This enables basic gc logging to the .out file.
# export CLIENT_GC_OPTS="-verbose:gc -XX:+PrintGCDetails
-XX:+PrintGCDateStamps"

# This enables basic gc logging to its own file.
# If FILE-PATH is not replaced, the log file(.gc) would still be generated
in the HBASE_LOG_DIR .
# export CLIENT_GC_OPTS="-verbose:gc -XX:+PrintGCDetails
-XX:+PrintGCDateStamps -Xloggc:<FILE-PATH>"

# This enables basic GC logging to its own file with automatic log rolling.
Only applies to jdk 1.6.0_34+ and 1.7.0_2+.
# If FILE-PATH is not replaced, the log file(.gc) would still be generated
in the HBASE_LOG_DIR .
# export CLIENT_GC_OPTS="-verbose:gc -XX:+PrintGCDetails
-XX:+PrintGCDateStamps -Xloggc:<FILE-PATH> -XX:+UseGCLogFileRotation
-XX:NumberOfGCLogFiles=1 -XX:GCLogFileSize=512M"

# See the package documentation for org.apache.hadoop.hbase.io.hfile for
other configurations
# needed setting up off-heap block caching. 

# Uncomment and adjust to enable JMX exporting
# See jmxremote.password and jmxremote.access in $JRE_HOME/lib/management to
configure remote password access.
# More details at:
http://java.sun.com/javase/6/docs/technotes/guides/management/agent.html
# NOTE: HBase provides an alternative JMX implementation to fix the random
ports issue, please see JMX
# section in HBase Reference Guide for instructions.

# export HBASE_JMX_BASE="-Dcom.sun.management.jmxremote.ssl=false
-Dcom.sun.management.jmxremote.authenticate=false"
# export HBASE_MASTER_OPTS="$HBASE_MASTER_OPTS $HBASE_JMX_BASE
-Dcom.sun.management.jmxremote.port=10101"
# export HBASE_REGIONSERVER_OPTS="$HBASE_REGIONSERVER_OPTS $HBASE_JMX_BASE
-Dcom.sun.management.jmxremote.port=10102"
# export HBASE_THRIFT_OPTS="$HBASE_THRIFT_OPTS $HBASE_JMX_BASE
-Dcom.sun.management.jmxremote.port=10103"
# export HBASE_ZOOKEEPER_OPTS="$HBASE_ZOOKEEPER_OPTS $HBASE_JMX_BASE
-Dcom.sun.management.jmxremote.port=10104"
# export HBASE_REST_OPTS="$HBASE_REST_OPTS $HBASE_JMX_BASE
-Dcom.sun.management.jmxremote.port=10105"

# File naming hosts on which HRegionServers will run. 
$HBASE_HOME/conf/regionservers by default.
# export HBASE_REGIONSERVERS=${HBASE_HOME}/conf/regionservers

# Uncomment and adjust to keep all the Region Server pages mapped to be
memory resident
#HBASE_REGIONSERVER_MLOCK=true
#HBASE_REGIONSERVER_UID="hbase"

# File naming hosts on which backup HMaster will run. 
$HBASE_HOME/conf/backup-masters by default.
# export HBASE_BACKUP_MASTERS=${HBASE_HOME}/conf/backup-masters

# Extra ssh options.  Empty by default.
# export HBASE_SSH_OPTS="-o ConnectTimeout=1 -o SendEnv=HBASE_CONF_DIR"

# Where log files are stored.  $HBASE_HOME/logs by default.
# export HBASE_LOG_DIR=${HBASE_HOME}/logs

# Enable remote JDWP debugging of major HBase processes. Meant for Core
Developers 
# export HBASE_MASTER_OPTS="$HBASE_MASTER_OPTS -Xdebug
-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8070"
# export HBASE_REGIONSERVER_OPTS="$HBASE_REGIONSERVER_OPTS -Xdebug
-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8071"
# export HBASE_THRIFT_OPTS="$HBASE_THRIFT_OPTS -Xdebug
-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8072"
# export HBASE_ZOOKEEPER_OPTS="$HBASE_ZOOKEEPER_OPTS -Xdebug
-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8073"

# A string representing this instance of hbase. $USER by default.
# export HBASE_IDENT_STRING=$USER

# The scheduling priority for daemon processes.  See 'man nice'.
# export HBASE_NICENESS=10

# The directory where pid files are stored. /tmp by default.
# export HBASE_PID_DIR=/var/hadoop/pids

# Seconds to sleep between slave commands.  Unset by default.  This
# can be useful in large clusters, where, e.g., slave rsyncs can
# otherwise arrive faster than the master can service them.
# export HBASE_SLAVE_SLEEP=0.1

# Tell HBase whether it should manage it's own instance of Zookeeper or not.
# export HBASE_MANAGES_ZK=true

# The default log rolling policy is RFA, where the log file is rolled as per
the size defined for the 
# RFA appender. Please refer to the log4j.properties file to see more
details on this appender.
# In case one needs to do log rolling on a date change, one should set the
environment property
# HBASE_ROOT_LOGGER to "<DESIRED_LOG LEVEL>,DRFA".
# For example:
# HBASE_ROOT_LOGGER=INFO,DRFA
# The reason for changing default to RFA is to avoid the boundary case of
filling out disk space as 
# DRFA doesn't put any cap on the log size. Please refer to HBase-5655 for
more context.

export HBASE_MANAGES_ZK=false
export HBASE_DAEMON_DEFAULT_ROOT_LOGGER=INFO,DRFA
export HBASE_DAEMON_DEFAULT_SECURITY_LOGGER=INFO,DRFAS
export HBASE_CLASSPATH=${HBASE_CLASSPATH}${HBASE_CLASSPATH:+:}$(ls -1
/usr/lib/phoenix/phoenix-*-HBase-*-server.jar)

AND SERVER SIDE hbase-site.xmllooks like this:
<configuration>
  <property>
    <name>hbase.cluster.distributed</name>
    <value>true</value>
  </property>

  <property>
    <name>hbase.zookeeper.quorum</name>
    <value>ip-10-16-129-55.ec2.internal</value>
  </property>

  <property>
    <name>hbase.rootdir</name>
    <value>s3://dev-mock-transcription/</value>
  </property>

  <property>
    <name>dfs.support.append</name>
    <value>true</value>
  </property>

  <property>
    <name>hbase.rest.port</name>
    <value>8070</value>
  </property>

  <property>
    <name>hbase.replication</name>
    <value>false</value>
  </property>

  <property>
    <name>hbase.balancer.tablesOnMaster</name>
    <value>hbase:meta</value>
  </property>

  <property>
    <name>hbase.bucketcache.size</name>
    <value>8192</value>
  </property>

  <property>
    <name>hbase.master.balancer.uselocality</name>
    <value>false</value>
  </property>

  <property>
    <name>hbase.master.startup.retainassign</name>
    <value>false</value>
  </property>

  <property>
    <name>hbase.wal.dir</name>
    <value>hdfs://ip-10-16-129-55.ec2.internal:8020/user/hbase/WAL</value>
  </property>

  <property>
    <name>hbase.bulkload.retries.retryOnIOException</name>
    <value>true</value>
  </property>

  <property>
    <name>hbase.bucketcache.ioengine</name>
    <value>files:/mnt1/hbase/bucketcache</value>
  </property>

  

<property>
      <name>hbase.rpc.timeout</name>
      <value>180000</value>
    </property> 
  <property>
      <name>index.writer.threads.max</name>
      <value>30</value>
 </property>
 <property>
      <name>index.builder.threads.max</name>
      <value>30</value>
 </property>
 </configuration>




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