Users of GCJ and OS-provided packages (linux) for Java and/or Tomcat may want to reference the THREDDS mailing list for installation help.
While there are different distributors of Java and servlet containers, Unidata develops, uses and tests the THREDDS Data Server using Sun Java and the Apache Tomcat servlet container.
At the time of this workshop, that is version Java SE 7u9. We will be using the Linux x64-bit tar.gz file:
jdk-7u9-linux-x64.tar.gz
Copy the binary tar.gz file into the installation directory (/home/tds/GettingStarted/ in this example):
$ pwd /home/tds $ ls -l drwxr-xr-x 2 tds ustaff 4096 Oct 9 14:02 Desktop drwxr-xr-x 2 tds ustaff 4096 Oct 9 12:55 Documents drwxr-xr-x 2 tds ustaff 4096 Oct 19 17:49 Downloads drwxr-xr-x 14 tds ustaff 4096 Oct 19 16:02 epd drwxr-xr-x 2 tds ustaff 4096 Oct 8 15:52 GettingStarted drwxr-xr-x 2 tds ustaff 4096 Oct 9 12:55 Music drwxr-xr-x 2 tds ustaff 4096 Oct 9 13:48 netcdf-java-4.3 drwxr-xr-x 2 tds ustaff 4096 Oct 9 12:55 Pictures drwxr-xr-x 2 tds ustaff 4096 Oct 9 12:55 Public drwxr-xr-x 2 tds ustaff 4096 Oct 9 12:55 Templates drwxr-xr-x 2 tds ustaff 4096 Oct 9 12:55 Videos drwxr-xr-x 2 tds ustaff 4096 Oct 19 17:52 workshop $ cp Downloads/jdk-7u9-linux-x64.tar.gz GettingStarted/ $ ls -l GettingStarted/ -rw-r--r-- 1 tds ustaff 96043498 Oct 19 17:56 jdk-7u9-linux-x64.tar.gz
Move into the installation directory and unpack the archive file:
$ cd GettingStarted/ $ pwd /home/tds/GettingStarted $ ls -l -rw-r--r-- 1 tds ustaff 96043498 Oct 19 17:56 jdk-7u9-linux-x64.tar.gz $ tar zxvf jdk-7u9-linux-x64.tar.gz
This will extract the JDK in the installation directory:
$ ls -l drwxr-xr-x 8 tds ustaff 4096 Sep 24 21:38 jdk1.7.0_09 -rw-r--r-- 1 tds ustaff 96043498 Oct 19 17:56 jdk-7u9-linux-x64.tar.gz
Depending on your OS you may need install either the 32-bit or 64-bit version of the JDK.
For more information about installing Tomcat on Windows OS, see the Tomcat setup guide for installation on different platforms.
At the time of this workshop, that is version 7.0.32. We will be using the binary tar.gz file:
apache-tomcat-7.0.32.tar.gz
Copy the binary tar.gz file into the installation directory (/home/tds/GettingStarted/ in this example):
$ pwd /home/tds/GettingStarted $ cp ~/Downloads/apache-tomcat-7.0.32.tar.gz . $ ls -l -rw-r--r-- 1 tds ustaff 7701019 Oct 19 17:59 apache-tomcat-7.0.32.tar.gz drwxr-xr-x 8 tds ustaff 4096 Sep 24 21:38 jdk1.7.0_09 -rw-r--r-- 1 tds ustaff 96043498 Oct 19 17:56 jdk-7u9-linux-x64.tar.gz
Unpack the archive file:
$ tar xvzf apache-tomcat-7.0.32.tar.gz
This will create a Tomcat directory:
$ ls -l drwxr-xr-x 9 tds ustaff 4096 Oct 19 18:00 apache-tomcat-7.0.32 -rw-r--r-- 1 tds ustaff 7701019 Oct 19 17:59 apache-tomcat-7.0.32.tar.gz drwxr-xr-x 8 tds ustaff 4096 Sep 24 21:38 jdk1.7.0_09 -rw-r--r-- 1 tds ustaff 96043498 Oct 19 17:56 jdk-7u9-linux-x64.tar.gz
Using the steps outlined in the above sections, install the JDK and Tomcat in /home/tds/GettingStarted
${tomcat_home}. Move into ${tomcat_home} and do a long listing:
$ cd apache-tomcat-7.0.32 $ ls -l drwxr-xr-x 2 tds ustaff 4096 Oct 19 18:00 bin drwxr-xr-x 2 tds ustaff 4096 Oct 3 01:52 conf drwxr-xr-x 2 tds ustaff 4096 Oct 19 18:00 lib -rw-r--r-- 1 tds ustaff 56812 Oct 3 01:52 LICENSE drwxr-xr-x 2 tds ustaff 4096 Oct 3 01:51 logs -rw-r--r-- 1 tds ustaff 1192 Oct 3 01:52 NOTICE -rw-r--r-- 1 tds ustaff 8826 Oct 3 01:52 RELEASE-NOTES -rw-r--r-- 1 tds ustaff 15557 Oct 3 01:52 RUNNING.txt drwxr-xr-x 2 tds ustaff 4096 Oct 19 18:00 temp drwxr-xr-x 7 tds ustaff 4096 Oct 3 01:52 webapps drwxr-xr-x 2 tds ustaff 4096 Oct 3 01:51 work
bin/
startup.sh, shutdown.sh and other scripts/programs.*.sh files (for Unix systems) are functional duplicates of the *.bat files (for Windows systems).conf/
server.xml and tomcat-users.xml to adjust logging, authentication and access control, enable SSL, etc.webapps/
manager application that comes with Tomcat during this workshop.logs/
catalina.out, catalina.yyyy-mm-dd.log and localhost_access_log.yyyy-mm-dd.log files by the end of this workshop.Run the startup.sh script in the Tomcat bin/ directory:
$ pwd /home/tds/GettingStarted/apache-tomcat-7.0.32 $ bin/startup.sh
Look and see if you have a Tomcat process running:
$ ps -ef | grep tomcat tds 2688 1 5 11:01 pts/1 00:00:02 /usr/bin/java -Djava.util.logging.config.file=/home/tds/GettingStarted/apache-tomcat-7.0.32/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.endorsed.dirs=/home/tds/GettingStarted/apache-tomcat-7.0.32/endorsed -classpath /home/tds/GettingStarted/apache-tomcat-7.0.32/bin/bootstrap.jar:/home/tds/GettingStarted/apache-tomcat-7.0.32/bin/tomcat-juli.jar -Dcatalina.base=/home/tds/GettingStarted/apache-tomcat-7.0.32 -Dcatalina.home=/home/tds/GettingStarted/apache-tomcat-7.0.32 -Djava.io.tmpdir=/home/tds/GettingStarted/apache-tomcat-7.0.32/temp org.apache.catalina.startup.Bootstrap start tds 2711 2197 0 11:02 pts/1 00:00:00 grep tomcat
Open a new browser window/tab and go to http://localhost:8080/ to verify Tomcat is running:
Run the shutdown.sh script in the Tomcat bin/ directory:
$ bin/shutdown.sh
Which Java is Tomcat currently using? (Hint: what was sent to STDOUT when running the startup.sh and shutdown.sh?)
logs for clues about why Tomcat failed to start or stop.catalina.out. $JAVA_HOME, $JAVA_OPTS and $CATALINA_BASEIf you're running Tomcat on an instance of Windows OS, you will want to create a setenv.bat file.
We are going to create a file called setenv.sh in the Tomcat bin/ directory to:
$JAVA_HOME and $CATALINA_BASE) during startup and shutdown;$JAVA_OPTS; and $JAVA_OPTS to enable more advanced services we will be learning about later on in this workshop.setenv.sh file.Using your favorite text editor (gedit, vi, emacs, etc.), create a new file called setenv.sh in the Tomcat bin/ directory:
$ pwd /home/tds/GettingStarted/apache-tomcat-7.0.32 $ cd bin $ vi setenv.sh
Add the following information and save your setenv.sh file:
#!/bin/sh # # ENVARS for Tomcat and TDS environment # JAVA_HOME="/home/tds/GettingStarted/jdk1.7.0_09" export JAVA_HOME CATALINA_BASE="/home/tds/GettingStarted/apache-tomcat-7.0.32" export CATALINA_BASE JAVA_OPTS="-Xmx4096m -Xms512m -server -Djava.awt.headless=true -Djava.util.prefs.systemRoot=$CATALINA_BASE/content/thredds/javaUtilPrefs" export JAVA_OPTS
Whenever possible, Unidata recommends -Xmx1500m for 32-bit systems, and-Xmx4096m (or more) for 64-bit systems.
You will learn more about the TDS Web Map Service (WMS) later on in this workshop.
The parameters we pass to $JAVA_OPTS:
-Xms is the initial allocated memory of the JVM (for performance).-Xmx the maximum allocated memory of the JVM (for performance).-server tells the Hostspot compiler to run the JVM in "server" mode.-Djava.awt.headless=true is needed to prevent graphics rendering code from assuming a graphics console exists. Without this, WMS code will crash the server in some circumstances.-Djava.util.prefs.systemRoot=$CATALINA_BASE/content/thredds/javaUtilPrefs allows the java.util.prefs of the TDS WMS to write system preferences to a location that is writable by the Tomcat user.Restart Tomcat and examine the output generated to the terminal window by the startup script:
$ ./startup.sh Using CATALINA_BASE: /home/tds/GettingStarted/apache-tomcat-7.0.32 Using CATALINA_HOME: /home/tds/GettingStarted/apache-tomcat-7.0.32 Using CATALINA_TMPDIR: /home/tds/GettingStarted/apache-tomcat-7.0.32/temp Using JRE_HOME: /home/tds/GettingStarted/jdk1.7.0_09 Using CLASSPATH: /home/tds/GettingStarted/apache-tomcat-7.0.32/bin/bootstrap.jar:/home/tds/GettingStarted/apache-tomcat-7.0.32/bin/tomcat-juli.jar
Did you notice any difference in the what is being reported to STDOUT during startup?
Take a look at the running Tomcat process to see the new $JAVA_OPTS settings:
$ ps -ef | grep tomcat tds 2819 1 28 11:17 pts/1 00:00:02 /home/tds/GettingStarted/jdk1.7.0_09/bin/java -Djava.util.logging.config.file=/home/tds/GettingStarted/apache-tomcat-7.0.32/conf/logging.properties -Xmx4096m -Xms512m -server -Djava.awt.headless=true -Djava.util.prefs.systemRoot=/home/tds/GettingStarted/apache-tomcat-7.0.32/content/thredds/javaUtilPrefs -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.endorsed.dirs=/home/tds/GettingStarted/apache-tomcat-7.0.32/endorsed -classpath /home/tds/GettingStarted/apache-tomcat-7.0.32/bin/bootstrap.jar:/home/tds/GettingStarted/apache-tomcat-7.0.32/bin/tomcat-juli.jar -Dcatalina.base=/home/tds/GettingStarted/apache-tomcat-7.0.32 -Dcatalina.home=/home/tds/GettingStarted/apache-tomcat-7.0.32 -Djava.io.tmpdir=/home/tds/GettingStarted/apache-tomcat-7.0.32/temp org.apache.catalina.startup.Bootstrap start
For more information on the environment variable prerequisites used by Tomcat, consult ${tomcat_home}/bin/catalina.sh (or catalina.bat) file.
What allows us to create the setenv.sh file and have its contents read? (Hint: have a look at the catalina.sh file in the Tomcat bin/ directory at lines 24 and 133).
m' in your -Xms and -Xmx settings.catalina.out:Error occurred during initialization of VM Could not reserve enough space for object heap
setenv.sh file, it will be reported to catalina.out:Error occurred during initialization of VM Incompatible minimum and maximum heap sizes specified
catalina.out:May 25, 2010 6:28:22 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush system prefs: java.util.prefs.BackingStoreException: /etc/.java/.systemPrefs/org create failed.
You will need to set the java.util.prefs.systemRoot system property in $JAVA_OPTS to a location that is writable by the user that Tomcat, e.g.:
#!/bin/sh # # ENVARS for Tomcat and TDS environment # JAVA_HOME="/home/tds/GettingStarted/jdk1.7.0_09" export JAVA_HOME CATALINA_BASE="/home/tds/GettingStarted/apache-tomcat-7.0.32" export CATALINA_BASE JAVA_OPTS="-Xmx4096m -Xms512m -server -Djava.awt.headless=true -Djava.util.prefs.systemRoot=$CATALINA_BASE/content/thredds/javaUtilPrefs" export JAVA_OPTS
$JAVA_HOME, $JAVA_OPTS and $CATALINA_BASEsetenv.sh file in the Tomcat bin/ and set $JAVA_HOME, $JAVA_OPTS and $CATALINA_BASE.thredds.warA maintenance checklist and contains helpful information about upgrading the TDS. New features and configuration changes made between TDS versions are listed for each release.
We will be using the current TDS 4.3 (release candidate) version for this workshop:
thredds.war
Put thredds.war in the Tomcat webapps/ directory:
$ pwd /home/tds/GettingStarted/apache-tomcat-7.0.32/bin $ cd ../webapps $ cp ~/Downloads/thredds.war . $ ls -l drwxr-xr-x 13 tds ustaff 4096 Oct 19 18:00 docs drwxr-xr-x 6 tds ustaff 4096 Oct 19 18:00 examples drwxr-xr-x 5 tds ustaff 4096 Oct 19 18:00 host-manager drwxr-xr-x 5 tds ustaff 4096 Oct 19 18:00 manager drwxr-xr-x 3 tds ustaff 4096 Oct 19 18:00 ROOT -rw-r--r-- 1 tds ustaff 40444990 Oct 19 18:10 thredds.war
If Tomcat is already running, wait a couple of seconds after placing the WAR file in the Tomcat webapps/ and then verify the thredds.war file was unpacked:
$ ls -l drwxr-xr-x 13 tds ustaff 4096 Oct 19 18:00 docs drwxr-xr-x 6 tds ustaff 4096 Oct 19 18:00 examples drwxr-xr-x 5 tds ustaff 4096 Oct 19 18:00 host-manager drwxr-xr-x 5 tds ustaff 4096 Oct 19 18:00 manager drwxr-xr-x 3 tds ustaff 4096 Oct 19 18:00 ROOT drwxr-xr-x 8 tds ustaff 4096 Oct 19 18:10 thredds -rw-r--r-- 1 tds ustaff 40444990 Oct 19 18:10 thredds.war
Go to http://localhost:8080/thredds/ in your browser to verify the TDS has been deployed:
catalina.out file of the Tomcat logs/ directory. ~/GettingStarted/apache-tomcat-7.0.32. Do you notice anything new?logs/logs/ directory.Move into the logs/ directory to see the type of information being logged:
$ pwd /home/tds/GettingStarted/apache-tomcat-7.0.32/webapps $ cd ../logs $ ls -l -rw-r--r-- 1 tds ustaff 10635 Oct 19 18:10 catalina.2012-10-19.log -rw-r--r-- 1 tds ustaff 10748 Oct 19 18:10 catalina.out -rw-r--r-- 1 tds ustaff 0 Oct 19 18:02 host-manager.2012-10-19.log -rw-r--r-- 1 tds ustaff 2820 Oct 19 18:10 localhost.2012-10-19.log -rw-r--r-- 1 tds ustaff 0 Oct 19 18:02 localhost_access_log.2012-10-19.txt -rw-r--r-- 1 tds ustaff 0 Oct 19 18:02 manager.2012-10-19.log
Do you see a correspondence between some of the web applications in the Tomcat webapps/ directory and the naming of certain log files?
Is there a difference in the information being logged to catalina.out versus catalina.yyyy-mm-dd.log?
Are some log files more verbose than others?
catalina.out.Open another terminal window (hereafter referred to as terminal #2) and run the following command in the new terminal:
$ tail -f /home/tds/GettingStarted/apache-tomcat-7.0.32/logs/catalina.out
In your original terminal window, start/stop and start Tomcat and watch what is being logged to catalina.out in the terminal #2 window.
Is it only errors messages being reported to catalina.out?
What messages in catalina.out are from the TDS?
catalina.outcatalina.outThe Tomcat Users mailing list has seen a lot of traffic dedicated to catalina.out logging and rotation.
System.out and System.err gets appended to catalina.out. catalina.out can quickly grow large if the hosted web applications are not specifically catching and logging System.out and System.err to designated files.catalina.out is not automatically rotated in Tomcat.logadm or logrotate) to rotate catalina.out.catalina.out files and other log files out of the Tomcat logs/ on a regular basis.catalina.out file is not automatically created. Instead only the catalina.yyyy-mm-dd.log files are used. These have equivalent content.server.xml Tomcat's configuration files, including server.xml can be found in in the Tomcat conf/ directory.
server.xml do not take effect until Tomcat is restarted.server.xmlserver.xml.Move into the Tomcat conf/ directory and examine the server.xml file:
$ pwd /home/tds/GettingStarted/apache-tomcat-7.0.32/logs $ cd ../conf $ less server.xml
Reference the table below to see how the server.xml elements relate to configuring TDS (mouse-over the element for a description):
tomcat-users.xml tomcat-users.xml do not take effect until Tomcat is restarted.tomcat-users.xmltomcat-users.xml.Open the tomcat-users.xml file:
$ pwd /home/tds/GettingStarted/apache-tomcat-7.0.32/conf $ less tomcat-users.xml
Reference the table below to see how the tomcat-users.xml elements relate to configuring TDS (mouse-over the element for a description):
| Tag Name | Instances | How it relates to the TDS |
|---|---|---|
<tomcat-users>Description: The tomcat-users element represents the single outermost element in tomcat-users.xml
|
1...1 | Not modified. (The only tag you get by default.) |
<role>Description: The role element defines one role or group a user can belong to.
|
1...* |
You will have at least two of these: one for the Tomcat manager application and one for the TDS. (You will need to add if you want to enable role-based authentication.)
|
<user>Description: The user element represents one valid user.
|
1...* |
You will need to create an entry for each user who needs access to the Tomcat manager application and/or the restricted areas of the TDS. (You will need to add if you want to enable user authentication.)
|
manager Applicationmanager applicationmanagerFor more information about the Tomcat manager application, see the Tomcat Manager App HOW-TO documentation.
manager directory in the Tomcat webapps/ directory. server.xml.manager applicationmanager applicationThe manager application URLs and roles has been re-structured. See the Tomcat Migration guide for more information.
Attempt to access the Tomcat manager application in your browser: http://localhost:8080/manager/html/. You will be prompted to login via BASIC authentication, which will end in failure since we do not yet have permission to access the manager application:
Based on what we know about Tomcat configuration, which file in the Tomcat conf/ directory should we edit to grant ourselves access to the manager application?
Changes to tomcat-users.xml do not take effect until Tomcat is restarted.
manager applicationtomcat-users.xml to add role and user elements.Using your favorite editor, open ${tomcat_home}/conf/tomcat-users.xml:
$ vi tomcat-users.xml
Between the <tomcat-users> tags, add a role element and specify the rolename attribute as manager:
<tomcat-users>
<role rolename="manager-gui"/>
</tomcat-users>
Now add a new user by adding a user element. Create a username and password for the new user and specify manager-gui as one of the roles (in this example we are creating a user called 'admin' with a corresponding password of 'secret'):
<tomcat-users>
<role rolename="manager-gui"/>
<user username="admin" password="secret" roles="manager-gui"/>
</tomcat-users>
manager application.To gain access to restricted parts of the TDS, you will perform the same steps you used to grant yourself access to the manager application.
Attempt to access the manager application again (http://localhost:8080/manager/html/), this time logging in using the name and password specified in tomcat-users.xml:
Voilà! You should have access to the manager application.
tomcat-users.xml to make sure it is well-formed and without error.tomcat-users.xml?logs/catalina.out file. manager applicationtomcat-users.xml to grant yourself access to the Tomcat manager application.manager applicationmanager application to undeploy the TDS.Find the TDS in the list of web application on the Applications page. Stop and then Undeploy the TDS:

List the contents of the Tomcat webapps/ directory to verify that both thredds.war and the unpacked thredds/ directory have been removed:
$ pwd /home/tds/GettingStarted/apache-tomcat-7.0.32/conf $ cd ../webapps $ ls -l drwxr-xr-x 13 tds ustaff 4096 Oct 19 18:00 docs drwxr-xr-x 6 tds ustaff 4096 Oct 19 18:00 examples drwxr-xr-x 5 tds ustaff 4096 Oct 19 18:00 host-manager drwxr-xr-x 5 tds ustaff 4096 Oct 19 18:00 manager drwxr-xr-x 3 tds ustaff 4096 Oct 19 18:00 ROOT
manager application.Upload the TDS WAR file using the Deploy section of the manager application:
Confirm the deployment went as planned by accessing the TDS using your browser: http://localhost:8080/thredds/
manager applicationmanager application.You will need to enable Enable SSL encryption to access TDS remote management tool.