dhis2-devs team mailing list archive

[David Huser <david.huser@xxxxxxxxxxxx>]

Thanks all for your suggestions. I got an instance from a simpler VPS 
service (DigitalOcean) with 2GB/2CPU and it's running well without any 
complex configurations needed.

Initially I followed the Implementation Guides' minimal requirements 
from 
https://www.dhis2.org/doc/snapshot/en/implementer/html/dhis2_implementation_guide_en_full.html#d3606e413
and suggest adding the mentioned implications to it, may help other 
implementers, too (or should I add it to 
https://github.com/dhis2/dhis2-docs/blob/master/src/docbkx/en/dhis2_implementation_guide_installation.xml#L17 
myself?)

Best
David


On 02.09.2015 23:38, Bob Jolliffe wrote:
> Hi David
>
> The log file does seem to indicate that the startup was successful.
> It does look like an orderly shutdown rather than any sign of
> out-of-memory exceptions.  Which happens about 1 minute after the
> successful startup.  Did you shut it down yourself or it just
> collapsed without you doing anything?
>
> if you started it then couldn't access it, so you shut it down, it
> might well be related to a firewall issue as per Lars's suggestion.
>
> Don't pay the SEVERE memory leak exceptions too much mind.  These are
> important if you are starting and stopping individual web applications
> in a (continuous) running tomcat.  They don't mean much at all if you
> are bringing down the whole tomcat server.
>
> Running in 1G is a challenge and you might be able to get dhis up and
> running but barely functional.  There are a few things to try:
>
> 1.  Don't try to optimize postgres settings at all.  Let it run in the
> bare minimum out-of-the-box default.  If I add up all your java and
> postgres allocations you are already over 1G without even considering
> kernel memory and the like.
>
> 2.  You could (in server.xml) reduce the max size of tomcat threadpool
> to maybe 4 or 5.
>
> 3.  There are some dhis internal threadpool configs you can also
> reduce but its a bit more fiddly (and I don't have the details at
> hand)
>
> The sensible thing (depending on what you are trying to achieve) is to
> increase your available RAM to 2G or more.  getting it to run in 1G is
> an interesting challenge which I've achieved once or twice but really
> not all that useful.
>
> Bob
>
> On 2 September 2015 at 17:52, Lars Helge Øverland<larshelge@xxxxxxxxx>  wrote:
> > Hi David,
> >
> > INFO: Pausing ProtocolHandler ["http-bio-8080"]
> >
> > you are running on port 8080, this might be related to firewalls on aws. Try
> > running on port 80 (conf/server.xml).
> >
> > Alternatively check if firewalls are active and blocks 8080.
> >
> > regards,
> >
> > Lars
> >
> >
> >
> >
> >
> > On Wed, Sep 2, 2015 at 3:47 PM, Dan Cocos<dcocos@xxxxxxxxxxxxxx>  wrote:
> > > At BAO we've found we could only reliably support DHIS 2 with a minimum of
> > > 2GB.
> > >
> > >
> > > Dan Cocos
> > > BAO Systems
> > > www.baosystems.com
> > > T: +1 202-569-8751 | gchat:dcocos@xxxxxxxxxxxxxx
> > >
> > > On Sep 2, 2015, at 7:33 AM, Jason Pickering<jason.p.pickering@xxxxxxxxx>
> > > wrote:
> > >
> > >
> > > Are you sure that Tomcat actually shut down ?
> > >
> > > Be sure Tomcat is dead by invoking ps -ef | grep tomcat and killing any
> > > processes(es) which may be running, and then start it again. If you get that
> > > memory leak error again, then something else is not right.
> > >
> > > Having said that, I agree with Knut. 1GB will really be pushing it, but
> > > you might be able to get it to work.
> > >
> > > Regards,
> > > Jason
> > >
> > >
> > >
> > >
> > > On Wed, Sep 2, 2015 at 12:56 PM, Knut Staring<knutst@xxxxxxxxx>  wrote:
> > > > 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 AMD64http://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"]
> > > > >
> > > > > _______________________________________________
> > > > > Mailing list:https://launchpad.net/~dhis2-users
> > > > > Post to     :dhis2-users@xxxxxxxxxxxxxxxxxxx
> > > > > Unsubscribe :https://launchpad.net/~dhis2-users
> > > > > More help   :https://help.launchpad.net/ListHelp
> > > >
> > > > --
> > > > Knut Staring
> > > > Dept. of Informatics, University of Oslo
> > > > Norway: +4791880522
> > > > Skype: knutstar
> > > > http://dhis2.org
> > > >
> > > > _______________________________________________
> > > > Mailing list:https://launchpad.net/~dhis2-devs
> > > > Post to     :dhis2-devs@xxxxxxxxxxxxxxxxxxx
> > > > Unsubscribe :https://launchpad.net/~dhis2-devs
> > > > More help   :https://help.launchpad.net/ListHelp
> > >
> > > --
> > > Jason P. Pickering
> > > email:jason.p.pickering@xxxxxxxxx
> > > tel:+46764147049
> > > _______________________________________________
> > > Mailing list:https://launchpad.net/~dhis2-devs
> > > Post to     :dhis2-devs@xxxxxxxxxxxxxxxxxxx
> > > Unsubscribe :https://launchpad.net/~dhis2-devs
> > > More help   :https://help.launchpad.net/ListHelp
> > >
> > >
> > >
> > > _______________________________________________
> > > Mailing list:https://launchpad.net/~dhis2-users
> > > Post to     :dhis2-users@xxxxxxxxxxxxxxxxxxx
> > > Unsubscribe :https://launchpad.net/~dhis2-users
> > > More help   :https://help.launchpad.net/ListHelp
> >
> > --
> > Lars Helge Øverland
> > Lead developer, DHIS 2
> > University of Oslo
> > Skype: larshelgeoverland
> > http://www.dhis2.org
> >
> >
> > _______________________________________________
> > Mailing list:https://launchpad.net/~dhis2-devs
> > Post to     :dhis2-devs@xxxxxxxxxxxxxxxxxxx
> > Unsubscribe :https://launchpad.net/~dhis2-devs
> > More help   :https://help.launchpad.net/ListHelp
> _______________________________________________
> Mailing list:https://launchpad.net/~dhis2-devs
> Post to     :dhis2-devs@xxxxxxxxxxxxxxxxxxx
> Unsubscribe :https://launchpad.net/~dhis2-devs
> More help   :https://help.launchpad.net/ListHelp

--
*David Huser*
Informatics Specialist
Swiss Centre for International Health
Tel: +41 79 740 63 41
Skype: dafhus
david.huser@xxxxxxxxxxxx

*Swiss Tropical and Public Health Institute*
Socinstrasse 57, P.O. Box
4002 Basel, Switzerland
www.swisstph.ch