DHIS-live 2.12 problem

Support - Assistance technique
1

OK, I have given up on DHIS-live and am headed in a ubuntu12.-4/32bit-tomcat6-postgres1.9-dhis2.12 direction. I have basically followed the directions at http://www.dhis2.org/doc/snapshot/en/implementer/html/ch08s02.html with the following difficulties:
(1) in Operating System Kernel Tuning, setting kernel.shmmax does not work, see postgresql - Postgres - could not create shared memory segment: Invalid argument - Ask Ubuntu. I am able to set the parameter thusly (output from sysctl):
kernel.shmmax = 42949672
kernel.shmmni = 4096
(2) in Install Tomcat, did not rename to ROOT.war. Also, there was no location specified for bin/setenv.sh, so I added the lines to /etc/bash.bashrc. They can be seen from the command line, e.g.
JAVA_HOME=/usr/lib/jvm/java-6-openjdk
JAVA_OPTS=‘-Xmx512m -Xms768m -XX:MaxPermSize=500m -XX:PermSize=300m’

At this point, free returns
total used free shared buffers cached
Mem: 4079068 2761100 1317968 0 423824 1192504
-/+ buffers/cache: 1144772 2934296
Swap: 19398480 0 19398480

I can start the Tomcat manager application and dhis is shown as having started, but it appears that actually Java has run out of heap space (log below) and the connection just times out.

Suggestions?

Saludos, Roger

Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/server], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/shared], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:14 AM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Jun 21, 2013 11:30:14 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2532 ms
Jun 21, 2013 11:30:14 AM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Jun 21, 2013 11:30:14 AM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.35
Jun 21, 2013 11:30:14 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor dhis.xml
Jun 21, 2013 11:30:22 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/var/lib/tomcat6/webapps/dhis/WEB-INF/lib/geronimo-servlet_2.5_spec-1.1.2.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Jun 21, 2013 11:47:43 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor manager.xml
Jun 21, 2013 11:47:47 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor host-manager.xml
Jun 21, 2013 11:47:49 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor docs.xml
Jun 21, 2013 11:47:52 AM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Jun 21, 2013 11:47:53 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 1059093 ms
Jun 21, 2013 11:50:04 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error processing request
java.lang.OutOfMemoryError: Java heap space
Jun 21, 2013 11:50:08 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error finishing response
java.lang.OutOfMemoryError: Java heap space
Jun 21, 2013 11:50:20 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error processing request
java.lang.OutOfMemoryError: Java heap space
Jun 21, 2013 11:50:23 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error finishing response
java.lang.OutOfMemoryError: Java heap space

···
2

Hello Dear!

First it is advisable to use 64 bits. But anyway we can use 32bit.

Second do not mess up java in ubuntu using those enviroment settings; Use update-alternatives command. Check the doccumentation for that.

In my experience the Linux kernel settings by default are fine. And the it is important to set those when you are in a production server. The most important one is the java and postgres section. Install OpenJDK at least 1.6. and then tomcat at least 6.

Hope it helps

Caveman

···

On Fri, Jun 21, 2013 at 6:02 PM, r.friedman@mindspring.com wrote:

OK, I have given up on DHIS-live and am headed in a ubuntu12.-4/32bit-tomcat6-postgres1.9-dhis2.12 direction. I have basically followed the directions at http://www.dhis2.org/doc/snapshot/en/implementer/html/ch08s02.html with the following difficulties:

(1) in Operating System Kernel Tuning, setting kernel.shmmax does not work, see http://askubuntu.com/questions/286852/postgres-could-not-create-shared-memory-segment-invalid-argument. I am able to set the parameter thusly (output from sysctl):

kernel.shmmax = 42949672
kernel.shmmni = 4096
(2) in Install Tomcat, did not rename to ROOT.war. Also, there was no location specified for bin/setenv.sh, so I added the lines to /etc/bash.bashrc. They can be seen from the command line, e.g.

JAVA_HOME=/usr/lib/jvm/java-6-openjdk
JAVA_OPTS=‘-Xmx512m -Xms768m -XX:MaxPermSize=500m -XX:PermSize=300m’

At this point, free returns
total used free shared buffers cached

Mem: 4079068 2761100 1317968 0 423824 1192504
-/+ buffers/cache: 1144772 2934296
Swap: 19398480 0 19398480

I can start the Tomcat manager application and dhis is shown as having started, but it appears that actually Java has run out of heap space (log below) and the connection just times out.

Suggestions?

Saludos, Roger

Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/server/classes], exists: [false], isDirectory: [false], canRead: [false]

Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/server], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat6/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/shared], exists: [false], isDirectory: [false], canRead: [false]

Jun 21, 2013 11:30:14 AM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Jun 21, 2013 11:30:14 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2532 ms

Jun 21, 2013 11:30:14 AM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Jun 21, 2013 11:30:14 AM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.35

Jun 21, 2013 11:30:14 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor dhis.xml
Jun 21, 2013 11:30:22 AM org.apache.catalina.loader.WebappClassLoader validateJarFile

INFO: validateJarFile(/var/lib/tomcat6/webapps/dhis/WEB-INF/lib/geronimo-servlet_2.5_spec-1.1.2.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Jun 21, 2013 11:47:43 AM org.apache.catalina.startup.HostConfig deployDescriptor

INFO: Deploying configuration descriptor manager.xml
Jun 21, 2013 11:47:47 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor host-manager.xml
Jun 21, 2013 11:47:49 AM org.apache.catalina.startup.HostConfig deployDescriptor

INFO: Deploying configuration descriptor docs.xml
Jun 21, 2013 11:47:52 AM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Jun 21, 2013 11:47:53 AM org.apache.catalina.startup.Catalina start

INFO: Server startup in 1059093 ms
Jun 21, 2013 11:50:04 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error processing request
java.lang.OutOfMemoryError: Java heap space
Jun 21, 2013 11:50:08 AM org.apache.coyote.http11.Http11Processor process

SEVERE: Error finishing response
java.lang.OutOfMemoryError: Java heap space
Jun 21, 2013 11:50:20 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error processing request
java.lang.OutOfMemoryError: Java heap space

Jun 21, 2013 11:50:23 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error finishing response
java.lang.OutOfMemoryError: Java heap space

Mailing list: https://launchpad.net/~dhis2-users

Post to : dhis2-users@lists.launchpad.net

Unsubscribe : https://launchpad.net/~dhis2-users

More help : https://help.launchpad.net/ListHelp

3

Hi Roger,

The manual is very misleading, as the kernel memory paramaters are very much going to depend on the size of the machine, which in the manual, are for a machine with more memory than you have.

I would suggest you try this first though

JAVA_OPTS=‘-Xmx2048m -Xms512m’

for now…and see if it starts. With 2.12, the need for memory has shifted to the database, so we really need to rewrite much of this in the manual. Try this though and see if it works. After you get it up, you can tune the memory usage a bit more.

The setenv.sh file should be in your tomcat /bin/ directory, and this will depend a lot on how you installed it.

Regards,

Jason

···

On Fri, Jun 21, 2013 at 6:02 PM, r.friedman@mindspring.com wrote:

OK, I have given up on DHIS-live and am headed in a ubuntu12.-4/32bit-tomcat6-postgres1.9-dhis2.12 direction. I have basically followed the directions at http://www.dhis2.org/doc/snapshot/en/implementer/html/ch08s02.html with the following difficulties:

(1) in Operating System Kernel Tuning, setting kernel.shmmax does not work, see http://askubuntu.com/questions/286852/postgres-could-not-create-shared-memory-segment-invalid-argument. I am able to set the parameter thusly (output from sysctl):

kernel.shmmax = 42949672
kernel.shmmni = 4096
(2) in Install Tomcat, did not rename to ROOT.war. Also, there was no location specified for bin/setenv.sh, so I added the lines to /etc/bash.bashrc. They can be seen from the command line, e.g.

JAVA_HOME=/usr/lib/jvm/java-6-openjdk
JAVA_OPTS=‘-Xmx512m -Xms768m -XX:MaxPermSize=500m -XX:PermSize=300m’

At this point, free returns
total used free shared buffers cached

Mem: 4079068 2761100 1317968 0 423824 1192504
-/+ buffers/cache: 1144772 2934296
Swap: 19398480 0 19398480

I can start the Tomcat manager application and dhis is shown as having started, but it appears that actually Java has run out of heap space (log below) and the connection just times out.

Suggestions?

Saludos, Roger

Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/server/classes], exists: [false], isDirectory: [false], canRead: [false]

Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/server], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat6/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/shared], exists: [false], isDirectory: [false], canRead: [false]

Jun 21, 2013 11:30:14 AM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Jun 21, 2013 11:30:14 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2532 ms

Jun 21, 2013 11:30:14 AM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Jun 21, 2013 11:30:14 AM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.35

Jun 21, 2013 11:30:14 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor dhis.xml
Jun 21, 2013 11:30:22 AM org.apache.catalina.loader.WebappClassLoader validateJarFile

INFO: validateJarFile(/var/lib/tomcat6/webapps/dhis/WEB-INF/lib/geronimo-servlet_2.5_spec-1.1.2.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Jun 21, 2013 11:47:43 AM org.apache.catalina.startup.HostConfig deployDescriptor

INFO: Deploying configuration descriptor manager.xml
Jun 21, 2013 11:47:47 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor host-manager.xml
Jun 21, 2013 11:47:49 AM org.apache.catalina.startup.HostConfig deployDescriptor

INFO: Deploying configuration descriptor docs.xml
Jun 21, 2013 11:47:52 AM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Jun 21, 2013 11:47:53 AM org.apache.catalina.startup.Catalina start

INFO: Server startup in 1059093 ms
Jun 21, 2013 11:50:04 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error processing request
java.lang.OutOfMemoryError: Java heap space
Jun 21, 2013 11:50:08 AM org.apache.coyote.http11.Http11Processor process

SEVERE: Error finishing response
java.lang.OutOfMemoryError: Java heap space
Jun 21, 2013 11:50:20 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error processing request
java.lang.OutOfMemoryError: Java heap space

Jun 21, 2013 11:50:23 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error finishing response
java.lang.OutOfMemoryError: Java heap space

4

Hi,

the server setup in manual assumes a server with 16 GB of RAM.

That is fairly well described in this section, saying:

For this guide we assume that 8 Gb RAM is allocated for PostgreSQL and 8 GB RAM is allocated for Tomcat/JVM, and that a 64-bit operating system is used. If you are running a different configuration please adjust the suggested values accordingly!

http://www.dhis2.org/doc/snapshot/en/implementer/html/ch08s02.html

regards,

Lars

···

On Fri, Jun 21, 2013 at 6:16 PM, Jason Pickering jason.p.pickering@gmail.com wrote:

Hi Roger,

The manual is very misleading, as the kernel memory paramaters are very much going to depend on the size of the machine, which in the manual, are for a machine with more memory than you have.

I would suggest you try this first though

JAVA_OPTS=‘-Xmx2048m -Xms512m’

for now…and see if it starts. With 2.12, the need for memory has shifted to the database, so we really need to rewrite much of this in the manual. Try this though and see if it works. After you get it up, you can tune the memory usage a bit more.

The setenv.sh file should be in your tomcat /bin/ directory, and this will depend a lot on how you installed it.

Regards,

Jason

Mailing list: https://launchpad.net/~dhis2-users

Post to : dhis2-users@lists.launchpad.net

Unsubscribe : https://launchpad.net/~dhis2-users

More help : https://help.launchpad.net/ListHelp

On Fri, Jun 21, 2013 at 6:02 PM, r.friedman@mindspring.com wrote:

OK, I have given up on DHIS-live and am headed in a ubuntu12.-4/32bit-tomcat6-postgres1.9-dhis2.12 direction. I have basically followed the directions at http://www.dhis2.org/doc/snapshot/en/implementer/html/ch08s02.html with the following difficulties:

(1) in Operating System Kernel Tuning, setting kernel.shmmax does not work, see http://askubuntu.com/questions/286852/postgres-could-not-create-shared-memory-segment-invalid-argument. I am able to set the parameter thusly (output from sysctl):

kernel.shmmax = 42949672
kernel.shmmni = 4096
(2) in Install Tomcat, did not rename to ROOT.war. Also, there was no location specified for bin/setenv.sh, so I added the lines to /etc/bash.bashrc. They can be seen from the command line, e.g.

JAVA_HOME=/usr/lib/jvm/java-6-openjdk
JAVA_OPTS=‘-Xmx512m -Xms768m -XX:MaxPermSize=500m -XX:PermSize=300m’

At this point, free returns
total used free shared buffers cached

Mem: 4079068 2761100 1317968 0 423824 1192504
-/+ buffers/cache: 1144772 2934296
Swap: 19398480 0 19398480

I can start the Tomcat manager application and dhis is shown as having started, but it appears that actually Java has run out of heap space (log below) and the connection just times out.

Suggestions?

Saludos, Roger

Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/server/classes], exists: [false], isDirectory: [false], canRead: [false]

Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/server], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile

WARNING: Problem with directory [/usr/share/tomcat6/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Jun 21, 2013 11:30:11 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat6/shared], exists: [false], isDirectory: [false], canRead: [false]

Jun 21, 2013 11:30:14 AM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Jun 21, 2013 11:30:14 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2532 ms

Jun 21, 2013 11:30:14 AM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Jun 21, 2013 11:30:14 AM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.35

Jun 21, 2013 11:30:14 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor dhis.xml
Jun 21, 2013 11:30:22 AM org.apache.catalina.loader.WebappClassLoader validateJarFile

INFO: validateJarFile(/var/lib/tomcat6/webapps/dhis/WEB-INF/lib/geronimo-servlet_2.5_spec-1.1.2.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Jun 21, 2013 11:47:43 AM org.apache.catalina.startup.HostConfig deployDescriptor

INFO: Deploying configuration descriptor manager.xml
Jun 21, 2013 11:47:47 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor host-manager.xml
Jun 21, 2013 11:47:49 AM org.apache.catalina.startup.HostConfig deployDescriptor

INFO: Deploying configuration descriptor docs.xml
Jun 21, 2013 11:47:52 AM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Jun 21, 2013 11:47:53 AM org.apache.catalina.startup.Catalina start

INFO: Server startup in 1059093 ms
Jun 21, 2013 11:50:04 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error processing request
java.lang.OutOfMemoryError: Java heap space
Jun 21, 2013 11:50:08 AM org.apache.coyote.http11.Http11Processor process

SEVERE: Error finishing response
java.lang.OutOfMemoryError: Java heap space
Jun 21, 2013 11:50:20 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error processing request
java.lang.OutOfMemoryError: Java heap space

Jun 21, 2013 11:50:23 AM org.apache.coyote.http11.Http11Processor process
SEVERE: Error finishing response
java.lang.OutOfMemoryError: Java heap space