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Amazon EC2 memory configuration

To: dhis2-users@xxxxxxxxxxxxxxxxxxx, dhis2-devs@xxxxxxxxxxxxxxxxxxx
From: David Huser <david.huser@xxxxxxxxxxxx>
Date: Wed, 2 Sep 2015 12:11:11 +0200
User-agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:38.0) Gecko/20100101 Thunderbird/38.2.0

Hi

I registered for a free tier EC2 instance (t2.micro) on Amazon withUbuntu 14.04 AMD64 http://aws.amazon.com/ec2/instance-types/

I have set it up according to the DHIS2 implementation manual.

I'm aware that this low hardware specifications are not ready fornational use, I'd like to use it as prototyping resource. However, theserver responds to pings but is not accessible through the browser. Isuspect the memory configuration. Please find the relevantconfigurations / error messages in red below.


*Hardware:*
RAM: 1GB memory
CPU: 1 CPU, spike balancing (t2.micro tier from amazon)
Disk: 20GB

Basically, I just divided the RAM specs from the implementation manual(2x 8GB) for each attribute by 16 (I have 1GB).

*$ cat /etc/postgresql/9.3/main/postgresql.conf* shared_buffers = 128MBwork_mem = 1MB maintenance_work_mem = 32MB effective_cache_size = 128MB*$ java -version* java version "1.7.0_79" OpenJDK Runtime Environment(IcedTea 2.5.6) (7u79-2.5.6-0ubuntu1.14.04.1) OpenJDK 64-Bit Server VM(build 24.79-b02, mixed mode)




*$ cat /tomcat-dhis/bin/setenv.sh*
#!/bin/sh
#

CATALINA_HOME=/usr/share/tomcat7

# The first existing directory is used for JAVA_HOME (if JAVA_HOME is not
# defined in $DEFAULT)

JDK_DIRS="/usr/lib/jvm/java-6-openjdk /usr/lib/jvm/java-6-sun/usr/lib/jvm/java-1.5.0-sun /usr/lib/j2sdk1.5-sun /usr/lib/j2sdk1.5-ibm"


# Look for the right JVM to use
for jdir in $JDK_DIRS; do
    if [ -r "$jdir/bin/java" -a -z "${JAVA_HOME}" ]; then
        JAVA_HOME_TMP="$jdir"
        # checks for a real JDK like environment, needed to check if
        # really the java-gcj-compat-dev package is installed
        if [ -r "$jdir/bin/jdb" ]; then
            JAVA_HOME="$JAVA_HOME_TMP"
        fi
    fi
done

# Default Java options
if [ -z "$JAVA_OPTS" ]; then
        JAVA_OPTS="-Djava.awt.headless=true -Xmx128M"
fi

export JAVA_HOME='/usr/lib/jvm/java-7-openjdk-amd64'
export JAVA_OPTS='-Xmx768m -Xms256m -XX:MaxPermSize=128m -XX:PermSize=32m'
export DHIS2_HOME='/home/dhis/config'




after restarting tomcat:
*$ cat catalina.out *

Sep 02, 2015 11:59:08 AM org.apache.catalina.startup.ClassLoaderFactoryvalidateFileWARNING: Problem with directory [/usr/share/tomcat7/common/classes],exists: [false], isDirectory: [false], canRead: [false]Sep 02, 2015 11:59:08 AM org.apache.catalina.startup.ClassLoaderFactoryvalidateFileWARNING: Problem with directory [/usr/share/tomcat7/common], exists:[false], isDirectory: [false], canRead: [false]Sep 02, 2015 11:59:08 AM org.apache.catalina.startup.ClassLoaderFactoryvalidateFileWARNING: Problem with directory [/usr/share/tomcat7/server/classes],exists: [false], isDirectory: [false], canRead: [false]Sep 02, 2015 11:59:08 AM org.apache.catalina.startup.ClassLoaderFactoryvalidateFileWARNING: Problem with directory [/usr/share/tomcat7/server], exists:[false], isDirectory: [false], canRead: [false]Sep 02, 2015 11:59:08 AM org.apache.catalina.startup.ClassLoaderFactoryvalidateFileWARNING: Problem with directory [/usr/share/tomcat7/shared/classes],exists: [false], isDirectory: [false], canRead: [false]Sep 02, 2015 11:59:08 AM org.apache.catalina.startup.ClassLoaderFactoryvalidateFileWARNING: Problem with directory [/usr/share/tomcat7/shared], exists:[false], isDirectory: [false], canRead: [false]

Sep 02, 2015 11:59:09 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Sep 02, 2015 11:59:09 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 1007 ms

Sep 02, 2015 11:59:09 AM org.apache.catalina.core.StandardServicestartInternal

INFO: Starting service Catalina

Sep 02, 2015 11:59:09 AM org.apache.catalina.core.StandardEnginestartInternal

INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Sep 02, 2015 11:59:09 AM org.apache.catalina.startup.HostConfig deployWAR

INFO: Deploying web application archive/home/dhis/tomcat-dhis/webapps/ROOT.war* INFO 2015-09-02 11:59:35,400 System property dhis2.home not set(DefaultLocationManager.java [localhost-startStop-1])* INFO 2015-09-02 11:59:35,402 Environment variable DHIS2_HOME pointsto /home/dhis/config (DefaultLocationManager.java [localhost-startStop-1])* INFO 2015-09-02 11:59:37,945 Hibernate configuration loaded, usingdialect: org.hibernate.dialect.PostgreSQLDialect(DefaultHibernateConfigurationProvider.java [localhost-startStop-1])* INFO 2015-09-02 11:59:57,732 Found the following message senders:[org.hisp.dhis.message.EmailMessageSender@68b059dc,org.hisp.dhis.sms.SmsMessageSender@5e5f2c88] (DefaultMessageService.java[localhost-startStop-1])* INFO 2015-09-02 12:00:09,471 Detected apps: [](DefaultAppManager.java [localhost-startStop-1])* INFO 2015-09-02 12:00:13,236 Added logger:org.hisp.dhis.resourcetable using file:/home/dhis/config/logs/dhis-analytics-table.log(Log4JLogConfigInitializer.java [localhost-startStop-1])* INFO 2015-09-02 12:00:13,236 Added logger:org.hisp.dhis.analytics.table using file:/home/dhis/config/logs/dhis-analytics-table.log(Log4JLogConfigInitializer.java [localhost-startStop-1])* INFO 2015-09-02 12:00:13,237 Added logger: org.hisp.dhis.dxf2 usingfile: /home/dhis/config/logs/dhis-data-exchange.log(Log4JLogConfigInitializer.java [localhost-startStop-1])* INFO 2015-09-02 12:00:13,237 Added logger: org.hisp.dhis.dxf2.synchusing file: /home/dhis/config/logs/dhis-data-sync.log(Log4JLogConfigInitializer.java [localhost-startStop-1])* INFO 2015-09-02 12:00:13,237 Added root logger using file:/home/dhis/config/logs/dhis.log (Log4JLogConfigInitializer.java[localhost-startStop-1])* WARN 2015-09-02 12:00:14,817 RP discovery / realm validationdisabled; (RealmVerifier.java [localhost-startStop-1])* INFO 2015-09-02 12:00:15,654 Executing startup routine [1 of 15,runlevel 1]: InitTableAlteror (DefaultStartupRoutineExecutor.java[localhost-startStop-1])* INFO 2015-09-02 12:00:15,774 Executing startup routine [2 of 15,runlevel 2]: PeriodTypePopulator (DefaultStartupRoutineExecutor.java[localhost-startStop-1])* INFO 2015-09-02 12:00:15,811 Executing startup routine [3 of 15,runlevel 2]: DataElementDefaultDimensionPopulator(DefaultStartupRoutineExecutor.java [localhost-startStop-1])* INFO 2015-09-02 12:00:15,860 Linked default category with defaultconcept (DataElementDefaultDimensionPopulator.java [localhost-startStop-1])* INFO 2015-09-02 12:00:16,005 Executing startup routine [4 of 15,runlevel 3]: ReportingIdentityPopulator(DefaultStartupRoutineExecutor.java [localhost-startStop-1])* INFO 2015-09-02 12:00:16,180 Executing startup routine [5 of 15,runlevel 3]: TableAlteror (DefaultStartupRoutineExecutor.java[localhost-startStop-1])* INFO 2015-09-02 12:00:20,284 Tables updated (TableAlteror.java[localhost-startStop-1])* INFO 2015-09-02 12:00:20,285 Executing startup routine [6 of 15,runlevel 3]: TrackerIdentityPopulator(DefaultStartupRoutineExecutor.java [localhost-startStop-1])* INFO 2015-09-02 12:00:20,294 1 last updated set on trackedentity(IdentityPopulator.java [localhost-startStop-1])* INFO 2015-09-02 12:00:20,296 1 created timestamps set ontrackedentity (IdentityPopulator.java [localhost-startStop-1])* INFO 2015-09-02 12:00:20,424 Executing startup routine [7 of 15,runlevel 4]: TrackedEntityTableAlteror(DefaultStartupRoutineExecutor.java [localhost-startStop-1])* INFO 2015-09-02 12:00:21,370 Executing startup routine [8 of 15,runlevel 4]: IdentityPopulator (DefaultStartupRoutineExecutor.java[localhost-startStop-1])* INFO 2015-09-02 12:00:21,488 Executing startup routine [9 of 15,runlevel 5]: TableCreator (DefaultStartupRoutineExecutor.java[localhost-startStop-1])* INFO 2015-09-02 12:00:21,582 Executing startup routine [10 of 15,runlevel 7]: MapViewUpgrader (DefaultStartupRoutineExecutor.java[localhost-startStop-1])* INFO 2015-09-02 12:00:21,690 Executing startup routine [11 of 15,runlevel 7]: FavoriteDataItemUpgrader(DefaultStartupRoutineExecutor.java [localhost-startStop-1])* INFO 2015-09-02 12:00:21,698 Executing startup routine [12 of 15,runlevel 7]: FavoriteDataItemUpgrader(DefaultStartupRoutineExecutor.java [localhost-startStop-1])* INFO 2015-09-02 12:00:21,707 Upgraded custom case entry formidentifiers (DataEntryFormUpgrader.java [localhost-startStop-1])* INFO 2015-09-02 12:00:21,708 Executing startup routine [13 of 15,runlevel 8]: ExpressionUpgrader (DefaultStartupRoutineExecutor.java[localhost-startStop-1])* INFO 2015-09-02 12:00:21,725 Executing startup routine [14 of 15,runlevel 9]: ConfigurationPopulator (DefaultStartupRoutineExecutor.java[localhost-startStop-1])* INFO 2015-09-02 12:00:21,729 Executing startup routine [15 of 15,runlevel 9]: I18nLocalePopulator (DefaultStartupRoutineExecutor.java[localhost-startStop-1])* INFO 2015-09-02 12:00:21,743 All startup routines done(DefaultStartupRoutineExecutor.java [localhost-startStop-1])

Sep 02, 2015 12:00:31 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Sep 02, 2015 12:00:31 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 82000 ms
Sep 02, 2015 12:01:37 PM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]

Sep 02, 2015 12:01:37 PM org.apache.catalina.core.StandardServicestopInternal

INFO: Stopping service Catalina

* INFO 2015-09-02 12:01:37,676 De-registering jdbc driver:org.postgresql.Driver@7e306ed7 (StartupListener.java[localhost-startStop-2])Sep 02, 2015 12:01:37 PM org.apache.catalina.loader.WebappClassLoaderclearReferencesThreadsSEVERE: The web application [] appears to have started a thread named[GT authority factory disposer] but has failed to stop it. This is verylikely to create a memory leak.Sep 02, 2015 12:01:37 PM org.apache.catalina.loader.WebappClassLoaderclearReferencesThreadsSEVERE: The web application [] appears to have started a thread named[WeakCollectionCleaner] but has failed to stop it. This is very likelyto create a memory leak.

Sep 02, 2015 12:01:37 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Sep 02, 2015 12:01:37 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]

Follow ups

Re: Amazon EC2 memory configuration
From: Knut Staring, 2015-09-02