DHIS2 Server setup

Here is a useful chapter of DHIS2 official documentation on how to setup a DHIS2 server. You ca find the article at this address:
http://www.dhis2.org/doc/snapshot/en/implementer/html/ch08s02.html

Server setup
This section describes how to set up a server instance of DHIS 2 on Ubuntu 12.04 64 bit with PostgreSQL as database system and Tomcat as Servlet container. The term invoke refers to executing a given command in a terminal.

For a national server the recommended configuration is a quad-core 2 Ghz processor or higher and 12 Gb RAM or higher. Note that a 64 bit operating system is required for utilizing more than 4 Gb of RAM, the Ubuntu 12.04 64 bit edition is thus recommended.

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! We recommend that the available memory is split roughly equally between the database and the JVM. Remember to leave some of the physical memory to the operating system for it to perform its tasks, for instance around 2 GB. The steps marked as optional, like the step for performance tuning, can be done at a later stage.

Create new user (optional)

You might want to create a dedicated user for running DHIS - it is not recommended to run as the root user. Create a new user called dhis by invoking useradd -d /home/dhis -m dhis -s /bin/bash If there is no admin group already you must create it by invoking groupadd admin Then make the user able to perform operations temporarily as root by invoking usermod -G admin dhis Then invoke passwd dhis to set the password for your account. Make sure you set a strong password with at least 15 random characters. You might want to disable remote login for the root account for improved security by invoking sudo passwd -l root

Operating system kernel tuning

These settings are optional except for the shared memory setting which is required for PostgreSQL memory allocation. Open the kernel configuration file by invoking sudo nano /etc/sysctl.conf At the end of the file add the following lines and save.

kernel.shmmax = 4294967296
net.core.rmem_max = 8388608
net.core.wmem_max = 8388608
Make the changes take effect by invoking sudo sysctl -p

Install Java

Install Java by invoking the following:

sudo apt-get install openjdk-7-jdk
Check that your installation is okay by invoking java -version

Install PostgreSQL

To install PostgreSQL version 9.2 we first need to add a Ubuntu package repository to our system.

sudo apt-get install python-software-properties

sudo add-apt-repository ppa:pitti/postgresql

sudo apt-get update
Now install PostgreSQL by invoking sudo apt-get install postgresql-9.2

Switch to the postgres user by invoking sudo su postgres

Create a non-privileged user called dhis by invoking createuser -SDRP dhis. Enter a secure password at the prompt. Create a database by invoking createdb -O dhis dhis2. Return to your session by invoking exit You now have a PostgreSQL user called dhis and a database called dhis2.

Do performance tuning by opening the following file by invoking

sudo nano /etc/postgresql/9.2/main/postgresql.conf

and set the following properties:

shared_buffers = 3200MB

Determines how much memory should be allocated exclusively for PostgreSQL caching. This setting controls the size of the kernel shared memory which should be reserved for PostgreSQL. Should be set to around 40% of total memory dedicated for PostgreSQL.

work_mem = 20MB

Determines the amount of memory used for internal sort and hash operations. This setting is per connection, per query so a lot of memory may be consumed if raising this too high. Setting this value correctly is essential for DHIS 2 aggregation performance.

maintenance_work_mem = 256MB

Determines the amount of memory PostgreSQL can use for maintenance operations such as creating indexes, running vacuum, adding foreign keys. Incresing this value might improve performance of index creation during the analytics and data mart generation processes.

effective_cache_size = 8000MB

An estimate of how much memory is available for disk caching by the operating system (not an allocation) and is used by PostgreSQL to determine whether a query plan will fit into memory or not. Setting it to a higher value than what is really available will result in poor performance. This value should be inclusive of the shared_buffers setting. PostgreSQL has two layers of caching: The first layer uses the kernel shared memory and is controlled by the shared_buffers setting. PostgreSQL delegates the second layer to the operating system disk cache and the size of available memory can be given with the effective_cache_size setting.

checkpoint_segments = 32

PostgreSQL writes new transactions to a log file called WAL segments which are 16MB in size. When a number of segments have been written a checkpoint occurs. Setting this number to a larger value will thus improve performance for write-heavy systems such as DHIS 2.

checkpoint_completion_target = 0.8

Determines the percentage of segment completion before a checkpoint occurs. Setting this to a high value will thus spread the writes out and lower the average write overhead.

wal_buffers = 16MB

Sets the memory used for buffering during the WAL write process. Increasing this value might improve throughput in write-heavy systems.

synchronous_commit = off

Specifies whether transaction commits will wait for WAL records to be written to the disk before returning to the client or not. Setting this to off will improve performance considerably. It also implies that there is a slight delay between the transaction is reported successful to the client and it actually being safe, but the database state cannot be corrupted and this is a good alternative for performance-intensive and write-heavy systems like DHIS 2.

wal_writer_delay = 10000ms

Specifies the delay between WAL write operations. Setting this to a high value will improve performance on write-heavy systems since potentially many write operations can be executed within a single flush to disk.

Restart PostgreSQL by invoking sudo /etc/init.d/postgresql restart

Set the database configuration

The database connection information is provided to DHIS 2 through a configuration file called hibernate.properties. Create this file and save it in a convenient location. A file corresponding to the above setup has these properties:

hibernate.dialect = org.hibernate.dialect.PostgreSQLDialect
hibernate.connection.driver_class = org.postgresql.Driver
hibernate.connection.url = jdbc:postgresql:dhis2
hibernate.connection.username = dhis
hibernate.connection.password = xxxx
hibernate.hbm2ddl.auto = update
A common mistake is to have a white-space after the last property value - make sure there is no white-space at the end of any line. Also remember that this file contains the clear text password for your dhis2 database so needs to be protected from unauthorized access. To do this invoke chmod 0600 hibernate.properties which ensures that only the dhis user which owns the file is allowed to read or write to it.

Install Tomcat

Download the Tomcat binary distribution from http://tomcat.apache.org/download-70.cgi A useful tool for downloading files from the web is wget. Extract to a convenient location. This guide assumes that you have navigated to the root directory of the extracted archive. Download the latest stable DHIS WAR file by invoking:

wget stable.dhis2.org
Clear the pre-installed web applications by invoking rm -rf webapps/* Move the DHIS WAR file to the webapps directory and rename it to ROOT.war.

Create a file bin/setenv.sh and add the lines below. The first will set the location of your Java Runtime Environment, the second will dedicate memory to Tomcat and the third will set the location for where DHIS 2 will search for the hibernate.properties configuration file. Please check that the path the Java binaries are correct as they might vary from system to system, e.g. on AMD systems you might see /java-7-openjdk-amd64 Note that you should adjust this to your environment:

export JAVA_HOME='/usr/lib/jvm/java-7-openjdk'
export JAVA_OPTS='-Xmx7500m -Xms4000m -XX:MaxPermSize=500m -XX:PermSize=300m'
export DHIS2_HOME='/home/dhis/config'
If you need to change the port of which Tomcat listens for requests you can open the Tomcat configuration file /conf/server.xml, locate the element which is not commented out and change the port attribute value to the desired port number.

To monitor the behavior of Tomcat the log is the primary source of information. The log can be easily viewed with the command tail -f logs/catalina.out

Set server time

Remember to set the server date correctly according to the time zone of which the main part of the users of the system are located. This will affect e.g. when scheduled tasks are executed. For instance, to the set time to 22:45, October 17, 2012, invoke sudo date 101722452012

Run DHIS 2

Make the startup script executable by invoking chmod 755 bin/* DHIS 2 can now be started by invoking bin/startup.sh The log can be monitored by invoking tail -f logs/catalina.out DHIS 2 can be stopped by invoking bin/shutdown.sh Assuming that the WAR file is called ROOT.war, you can now access your DHIS instance at http://localhost:8080