dhis2-users team mailing list archive

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Re: Amazon EC2 memory configuration

To: David Huser <david.huser@xxxxxxxxxxxx>
From: Knut Staring <knutst@xxxxxxxxx>
Date: Wed, 2 Sep 2015 12:56:13 +0200
Cc: "dhis2-users@xxxxxxxxxxxxxxxxxxx" <dhis2-users@xxxxxxxxxxxxxxxxxxx>, DHIS 2 developers <dhis2-devs@xxxxxxxxxxxxxxxxxxx>
In-reply-to: <55E6CB3F.8090407@swisstph.org>
Hi David,

1 GB is probably pushing it a bit, AFAIK. Possible, but not too easy....2
GB should be fine.

Knut

On Wed, Sep 2, 2015 at 12:11 PM, David Huser <david.huser@xxxxxxxxxxxx>
wrote:

> Hi
>
> I registered for a free tier EC2 instance (t2.micro) on Amazon with Ubuntu
> 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 for national
> use, I'd like to use it as prototyping resource. However, the server
> responds to pings but is not accessible through the browser. I suspect the
> memory configuration. Please find the relevant configurations / 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 = 128MB
> work_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.ClassLoaderFactory
> validateFile
> WARNING: 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.ClassLoaderFactory
> validateFile
> WARNING: Problem with directory [/usr/share/tomcat7/common], exists:
> [false], isDirectory: [false], canRead: [false]
> Sep 02, 2015 11:59:08 AM org.apache.catalina.startup.ClassLoaderFactory
> validateFile
> WARNING: 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.ClassLoaderFactory
> validateFile
> WARNING: Problem with directory [/usr/share/tomcat7/server], exists:
> [false], isDirectory: [false], canRead: [false]
> Sep 02, 2015 11:59:08 AM org.apache.catalina.startup.ClassLoaderFactory
> validateFile
> WARNING: 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.ClassLoaderFactory
> validateFile
> WARNING: 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.StandardService
> startInternal
> INFO: Starting service Catalina
> Sep 02, 2015 11:59:09 AM org.apache.catalina.core.StandardEngine
> startInternal
> 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 points to
> /home/dhis/config (DefaultLocationManager.java [localhost-startStop-1])
> * INFO  2015-09-02 11:59:37,945 Hibernate configuration loaded, using
> dialect: 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 using
> file: /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.synch
> using 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 validation disabled;
> (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 default
> concept (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 on trackedentity
> (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 form
> identifiers (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.StandardService
> stopInternal
> 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.WebappClassLoader
> clearReferencesThreads
> SEVERE: The web application [] appears to have started a thread named [GT
> authority factory disposer] but has failed to stop it. This is very likely
> to create a memory leak.
> Sep 02, 2015 12:01:37 PM org.apache.catalina.loader.WebappClassLoader
> clearReferencesThreads
> SEVERE: The web application [] appears to have started a thread named
> [WeakCollectionCleaner] but has failed to stop it. This is very likely to
> 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"]
>
> _______________________________________________
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>
>


-- 
Knut Staring
Dept. of Informatics, University of Oslo
Norway: +4791880522
Skype: knutstar
http://dhis2.org
Follow ups

Re: [Dhis2-devs] Amazon EC2 memory configuration
From: Jason Pickering, 2015-09-02
References

Amazon EC2 memory configuration
From: David Huser, 2015-09-02