![](media/image1.jpeg){width="2.4194444444444443in"
height="0.8986111111111111in"}

**Table of Contents**

[Introduction 1](#introduction)

[UPT 3.2.0 Software and Technology Requirements
1](#upt-3.2.0-software-and-technology-requirements)

[Java SDK Installation 2](#java-sdk-installation)

[Apache Ant Installation 3](#apache-ant-installation)

[Apache Ant Environment Variables 3](#apache-ant-environment-variables)

[Installing UPT 3.2.0 Application and Services
6](#__RefHeading___Toc212625675)

[Downloading UPT 3.2.0 files 6](#__RefHeading___Toc212625676)

[Installing a New UPT 7](#installing-a-new-upt)

[Running GUI installer in Headless Environment
7](#running-gui-installer-in-headless-environment)

[Command-Line Installation 8](#command-line-installation)

[JBoss Errors During Installation 8](#jboss-errors-during-installation)

[Configuring JBoss 8](#__RefHeading___Toc212625681)

[Configuring JBoss to Run as a Service 9](#__RefHeading___Toc212625682)

[Running JBoss as a Service 9](#running-jboss-as-a-service)

[Contacting Application Support 10](#contacting-application-support)

#### 

#  {#section-1 .unnumbered}

# Introduction 

> This UPT 3.2.0 installation Guide provides you with the instructions
> to install and configure the UPT 3.2.0 application in your
> environment. The UPT installation installs and configures the JBoss
> application servers.

+------------+---------------------------------------------------------+
| > **NOTE** | > Published UPT documentation can be found on the UPT   |
| >          | > section of the LSD GForge site:                       |
| > !        | >                                                       |
| [](media/i | > <https://gforge.nci.nih.gov/frs/?group_id=450>        |
| mage2.wmf) |                                                         |
+------------+---------------------------------------------------------+

+-------------+--------------------------------------------------------+
| #####       | > The process for installing UPT includes the          |
|             | > following tasks described in this document:          |
| #           |                                                        |
| #### Overvi | a.  Downloading and installing required software       |
| ew of UPT I |                                                        |
| nstallation | b.  Setting environment variables                      |
|             |                                                        |
|             | c.  Downloading UPT 3.2.0 distribution files           |
|             |                                                        |
|             | d.  Installing UPT                                     |
|             |                                                        |
|             | e.  Configuring JBoss                                  |
+-------------+--------------------------------------------------------+

+------------+---------------------------------------------------------+
| Before You | -   Please contact us directly with any questions:\     |
| Proceed    |     > E-mail: <ncicb@pop.nci.nih.gov>\                  |
|            |     > Telephone: 301-451-4384\                          |
|            |     > Toll free: 888-478-4423                           |
|            |                                                         |
|            | ```{=html}                                              |
|            | <!-- -->                                                |
|            | ```                                                     |
|            | -   Directions are given in this document for both      |
|            |     Linux and Windows operating systems.                |
+------------+---------------------------------------------------------+

# UPT 3.2.0 Software and Technology Requirements

+-------------+--------------------------------------------------------+
| #####       | > The UPT 3.2.0 installation has been tested on Linux  |
|             | > Red Hat Enterprise Linux AS 4 64/32-bit (for AMD     |
| ###         | > chipset) and the Windows XP/2003 environments. While |
| ## Tested E | > the installation may work in other Linux and Windows |
| nvironment  | > environments, it has only been tested in these       |
|             | > environments.                                        |
+-------------+--------------------------------------------------------+

+-------------+--------------------------------------------------------+
| #####       | > Many of the servers and services that make up UPT    |
|             | > 3.2.0 are automatically installed as part of this    |
| #           | > installation. However, certain tools that you must   |
| #### Requir | > manually install and configure are listed in         |
| ed Software | > Table 1. The software name, version, description,    |
| ---Not Incl | > and URL hyperlinks (for download) are indicated in   |
| uded in UPT | > the table.                                           |
+-------------+--------------------------------------------------------+

> Prior to the UPT 3.2.0 installation, you must download and install the
> following tools and recommended versions in the order they are listed.
> Complete the directions for installing each, as directed on the
> corresponding website.

+-------------------------------------------------+--------------------+
| ***Required Software Name***                    | ***Description***  |
|                                                 |                    |
| ***Version***                                   |                    |
+=================================================+====================+
| Java 2 Platform Standard Edition 5.0 Update 10  | The J2SE           |
| (J2SE 5.0)                                      | Develop­ment Kit    |
|                                                 | (JDK) supports     |
| <http                                           | creat­ing J2SE      |
| ://java.sun.com/products/archive/j2se/5.0_10/.> | applications.      |
|                                                 |                    |
| Be sure to download the correct Java SDK for    |                    |
| your operating environment. For example, for    |                    |
| Linux AMD 64, you would download                |                    |
| jdk-1_5_0_10-linux-amd64-rpm.bin. For Windows,  |                    |
| you might download                              |                    |
| jdk-1_5_0_10-windows-i586-p.exe.                |                    |
+-------------------------------------------------+--------------------+
| Apache Ant, 1.7.0                               | Apache Ant is a    |
|                                                 | Java-based build   |
| <https://gforge.nci.nih.gov/sv                  | tool.              |
| nroot/lsd/trunk/tools/apache-ant-1.7.0-bin.zip> |                    |
+-------------------------------------------------+--------------------+

Table 1 Required Software

+------------+---------------------------------------------------------+
| #####      | As you install each application, record the             |
|            | installation directory path.                            |
| #####      |                                                         |
|  IMPORTANT | Also, if you plan to install caArray and/or NCI         |
|            | locally, do these installs first and record the         |
| ![](media/ | hostname, application port, and grid port for each.     |
| image3.wmf |                                                         |
| ){width="0 |                                                         |
| .594444444 |                                                         |
| 4444444in" |                                                         |
| height="0  |                                                         |
| .59375in"} |                                                         |
+------------+---------------------------------------------------------+

## Java SDK Installation

When you install the Java SDK, you will be prompted to select the
installation directory. Record the path, as this directory will be used
when you set the environment variables.

## Apache Ant Installation

> Unzip the Apache Ant distribution files using a command line unzip
> tool or a zip utility, such as WinZip.
>
> After extracting the zip, you must set the environment variables,
> described in the following section, so that Ant is available in the
> system PATH.

### Apache Ant Environment Variables

+--------------+-------------------------------------------------------+
| NOTE         | > The purpose of setting operating system environment |
|              | > variables is so that the Java SDK and Ant build     |
| ![](media    | > tool are available to run from anywhere in the      |
| /image4.wmf) | > system.                                             |
+--------------+-------------------------------------------------------+

#### Linux

To set the environmental variables in Linux, follow these steps:

+--------------+-------------------------------------------------------+
| NOTE         | > The JAVA_HOME, ANT_HOME and PATH environment        |
|              | > variables are set in /etc/profile. You may need to  |
| ![](media    | > create the variables, or modify them if they        |
| /image5.wmf) | > already exist.                                      |
+--------------+-------------------------------------------------------+

+--------+-------------------------------------------------------------+
| Step   | Action                                                      |
+========+=============================================================+
| 1      | As the root user (or sudo w/ privileges), enter the         |
|        | following in the /etc/profile file. A PATH variable should  |
|        | already be created in this file, so be sure to define the   |
|        | JAVA_HOME and ANT_HOME export before the PATH export.       |
|        | Replace \<installation_directory\> with the directory where |
|        | you have installed the Java SDK and Ant.                    |
|        |                                                             |
|        | (The location example in the Apache Ant installation is     |
|        | /usr/java.)                                                 |
|        |                                                             |
|        | export JAVA_HOME=\<installation_directory\>/jdk1.5.0_10     |
|        |                                                             |
|        | export ANT_HOME=\<installation_directory\>/apache-ant-1.7.0 |
|        |                                                             |
|        | export PATH=\$JAVA_HOME/bin:\$ANT_HOME/bin:\$PATH           |
|        |                                                             |
|        | []{.mark}                                                   |
+--------+-------------------------------------------------------------+
| > []{  | Log out and log back in so that the system recognizes your  |
| .mark} | changes.                                                    |
|        |                                                             |
| 2      |                                                             |
+--------+-------------------------------------------------------------+

#### Verifying the Environment Variables in Linux

> To verify that environment variables have been set correctly, follow
> these steps:

+--------+-------------------------------------------------------------+
| Step   | Action                                                      |
+========+=============================================================+
| 1      | From the command line, enter:                               |
|        |                                                             |
|        | ***echo \$JAVA_HOME***                                      |
|        |                                                             |
|        | ***echo \$ANT_HOME***                                       |
|        |                                                             |
|        | Both of these commands should return the location where you |
|        | installed these tools.                                      |
+--------+-------------------------------------------------------------+
| 2      | To verify your Java SDK installation, enter ***java         |
|        | --version*** from a command prompt. You should see java     |
|        | version \"1.5.0_10\".                                       |
+--------+-------------------------------------------------------------+
| 3      | To verify your Ant installation, enter: ***ant --version*** |
|        | from a command prompt. You should see: Apache Ant version   |
|        | 1.7.0 compiled on December 13 2006.                         |
+--------+-------------------------------------------------------------+

#### Windows

To set the environmental variables in Windows, follow these steps:

+--------------+-------------------------------------------------------+
| NOTE         | > The JAVA_HOME, ANT_HOME and PATH environment        |
|              | > variables are set in the Systems Properties.        |
| ![](media    |                                                       |
| /image6.wmf) |                                                       |
+--------------+-------------------------------------------------------+

+--------+-------------------------------------------------------------+
| Step   | Action                                                      |
+========+=============================================================+
| 1      | In Windows, select **Control Panel**, then select the       |
|        | **Systems** application. In the Systems window, select the  |
|        | **Advanced** tab.                                           |
+--------+-------------------------------------------------------------+
| 2      | On the **Advanced** tab, click the **Environment            |
|        | Variables** button. To add a new system variable, select    |
|        | the **New** button.                                         |
|        |                                                             |
|        | a.  In the **Variable [n]{.underline}ame** text box, enter  |
|        |     ***JAVA_HOME***.                                        |
|        |                                                             |
|        | b.  In the **Variable [v]{.underline}alue** text box, enter |
|        |     the location of your Java installation.                 |
+--------+-------------------------------------------------------------+
| 3      | Click the **New** button again.                             |
|        |                                                             |
|        | a.  In the **Variable [n]{.underline}ame** text box, enter  |
|        |     ***ANT_HOME.***                                         |
|        |                                                             |
|        | b.  In the **Variable [v]{.underline}alue** text box, enter |
|        |     the location of your Ant installation.                  |
+--------+-------------------------------------------------------------+
| 4      | Select the PATH system environment variable, and select the |
|        | **Edit** button. This opens the Edit System Variable dialog |
|        | box, displayed here as an example.                          |
|        |                                                             |
|        | ![](media/image7.png){width="3.613888888888889in"           |
|        | height="1.53125in"}                                         |
+--------+-------------------------------------------------------------+
| 5      | In the Variable value text box, prepend the following text  |
|        | in front of the text that already exists in the **Variable  |
|        | Value** field.                                              |
|        |                                                             |
|        | ***%JAVA_HOME%\\bin;%ANT_HOME%\\bin;***                     |
|        |                                                             |
|        | Click **OK**.                                               |
+--------+-------------------------------------------------------------+

#### Verifying the Environment Variables in Windows

> To verify the environment variables have been set correctly, follow
> these steps:

+--------+-------------------------------------------------------------+
| Step   | Action                                                      |
+========+=============================================================+
| 1      | From the command line, enter:                               |
|        |                                                             |
|        | ***echo %JAVA_HOME%***                                      |
|        |                                                             |
|        | ***echo %ANT_HOME%***                                       |
|        |                                                             |
|        | Both of these commands should return the location where you |
|        | installed these tools.                                      |
+--------+-------------------------------------------------------------+
| 2      | To verify your Java SDK installation, enter ***java         |
|        | --version*** from a command prompt. You should see java     |
|        | version \"1.5.0_10\"**.**                                   |
+--------+-------------------------------------------------------------+
| 3      | To verify your Ant installation, enter ***ant --version***  |
|        | from a command prompt.                                      |
|        |                                                             |
|        | You should see: Apache Ant version 1.7.0 compiled on        |
|        | December 13 2006.                                           |
+--------+-------------------------------------------------------------+

+--------------+-------------------------------------------------------+
| NOTES        | > Environment variables for UPT will be modified and  |
|              | > set in those sections of this document: Installing  |
| ![](media    | > a New [UPT]{.underline} on page                     |
| /image8.wmf) | > [8](#installing-a-new-upt).                         |
+--------------+-------------------------------------------------------+

# Installing UPT 3.2.0 Application and Services

> To install the UPT 3.2.0 application and services, follow the steps in
> this section:

-   [Downloading UPT 3.2.0 files from
    > GForge](#_Downloading_caArray_2.0_files)

-   [Installing a New]{.underline}

-   [Configuring JBoss to Run as a
    > Service](#_Configuring_JBoss_and_MySQL_to_Run__1)

+------------+---------------------------------------------------------+
| #####      | > > Before running the installers, be sure your         |
|  IMPORTANT | > > Database Administrator has created an empty         |
|            | > > database (if installing the software for the first  |
| ![](media/ | > > time) and a database user with full access to this  |
| image3.wmf | > > database. Once the database has been created and    |
| ){width="0 | > > permissions granted, you will need the following    |
| .594444444 | > > information before beginning the install:           |
| 4444444in" |                                                         |
| height="0  | -   Database Name                                       |
| .59375in"} |                                                         |
|            | -   Database User                                       |
|            |                                                         |
|            | -   Database Password                                   |
|            |                                                         |
|            | -   Port where MySQL is installed                       |
+------------+---------------------------------------------------------+

[]{#__RefHeading___Toc212625676 .anchor}

### Downloading UPT 3.2.0 files

> To download the UPT 3.2.0 files, follow this step:

+--------+-------------------------------------------------------------+
| Step   | Action                                                      |
+========+=============================================================+
| 1      | The installation file for UPT 3.2.0 is over 100MB.          |
|        |                                                             |
|        | -   For a new installation, from the                        |
|        |     <https://gforge.nci.nih.gov/frs/?group_id=450>          |
|        |     directory in GForge, download the                       |
|        |     upt_gui_distribution_3_2_0.jar file.                    |
|        |                                                             |
|        | Remember the download location as you will be using this    |
|        | file to run the installation in the steps that follow.      |
+--------+-------------------------------------------------------------+

+-------------+--------------------------------------------------------+
| #####       | These server components are installed and configured   |
|             | as part of the UPT 3.2.0 installation. You do not need |
| ###         | to do anything further to download or install these    |
| ## Server C | components.                                            |
| omponents i |                                                        |
| n UPT 3.2.0 | -   JBoss 4.0.5 (hosts the UPT application)            |
+-------------+--------------------------------------------------------+

## Installing a New UPT  {#installing-a-new-upt .unnumbered}

> For performing a new installation of UPT, v. 3.2.0, follow these
> steps:

+--------+-------------------------------------------------------------+
| Step   | Action                                                      |
+========+=============================================================+
| 1      | From the directory where you downloaded the                 |
|        | upt_gui_distribution_3_2_0.jar from [Downloading UPT 3.2.0  |
|        | files](#important-1), open a command prompt and type:       |
|        |                                                             |
|        | java --jar upt_gui_distribution_3_2_0.jar                   |
+--------+-------------------------------------------------------------+
| 2      | A graphic user interface (GUI) wizard-based installer will  |
|        | prompt you for information. Follow the instructions.        |
+--------+-------------------------------------------------------------+
| 3      | Configuring property values is an important step in the     |
|        | installation process. For detailed information on the       |
|        | property values you will enter during the installation      |
|        | process, see <https://wiki.nci.nih.gov/x/Baml>              |
+--------+-------------------------------------------------------------+

The GUI installer generates installation files into the \${user.home}
directory. (For example, in Windows, this might be something like
C:\\Documents and Settings\\nate.greene\\.installer-upt). In particular,
the installer generates a file called **antlog_installer.txt** in this
directory that can be useful when troubleshooting.

### Running GUI installer in Headless Environment {#running-gui-installer-in-headless-environment .unnumbered}

+--------------+-------------------------------------------------------+
| NOTE         | If you are attempting to use the GUI installers in an |
|              | environment that has no GUI (such as a headless Linux |
| ![](media    | operating system), you can install a tool on your     |
| /image9.wmf) | Windows workstation to install in a remote headless   |
|              | environment. See <https://wiki.nci.nih.gov/x/gq6l>    |
|              | for more information.                                 |
+--------------+-------------------------------------------------------+

###   {#section-7 .unnumbered}

### Command-Line Installation {#command-line-installation .unnumbered}

+--------------+-------------------------------------------------------+
| NOTE         | []{.mark}                                             |
|              |                                                       |
| ![](media/   | An alternative to using the GUI-based installer is to |
| image10.wmf) | install UPT via the command line. See                 |
|              | <https://wiki.nci.nih.gov/x/taql> for detailed        |
|              | instructions on installing from the command line.     |
|              |                                                       |
|              | []{.mark}                                             |
+--------------+-------------------------------------------------------+

### JBoss Errors During Installation {#jboss-errors-during-installation .unnumbered}

+--------------+-------------------------------------------------------+
| NOTE         | You may receive an error such as Exception in thread  |
|              | \"main\" java.lang.NoClassDefFoundError:              |
| ![](media/   | org/jboss/Shutdown. This should not be a problem, as  |
| image11.wmf) | the installer attempts to remove previously installed |
|              | servers to prevent problems during the installation.  |
|              | If this is your first time installing UPT, you may    |
|              | receive and disregard this error message.             |
+--------------+-------------------------------------------------------+

## Configuring JBoss

+--------------+-------------------------------------------------------+
| NOTE         | For optimal performance, you must modify your JBoss   |
|              | 4.0.5 configuration to increase the amount of         |
| ![](media/   | available memory for the UPT application. Directions  |
| image12.wmf) | for doing this in Windows are in the following step   |
|              | 1.                                                    |
+--------------+-------------------------------------------------------+

> To configure JBoss in **Windows**, follow these steps:

+--------+-------------------------------------------------------------+
| Step   | Action                                                      |
+========+=============================================================+
| 1      | Add the following entry to the JBoss run.bat file which is  |
|        | located will be located at                                  |
|        | \<application_root_directory\>/jboss-4.0.5.GA/bin/run.bat.  |
|        | Add the text right after the line "rem Add -server to the   |
|        | JVM options, if supported".                                 |
|        |                                                             |
|        | -server --Xms1024m --Xmx1024m -XX:ThreadStackSize=128       |
|        | -XX:SurvivorRatio=10 -XX:PermSize=128m -XX:MaxPermSize=128m |
|        | -Dsun.rmi.dgc.client.gcInterval=3600000                     |
|        | -Dsun.rmi.dgc.server.gcInterval=3600000                     |
|        | -Djava.awt.headless=true                                    |
|        |                                                             |
|        | **Warning**: Be careful when copying and pasting from this  |
|        | document, whether PDF or MS Word. No spaces must come       |
|        | before and after the columns. A safe way to ensure that the |
|        | text has no unwanted space and unwanted characters is to    |
|        | copy the text into a blank NotePad first. Correct the       |
|        | spacing, then copy and paste back into the run.bat file.    |
+--------+-------------------------------------------------------------+
| 2      | Restart your JBoss 4.0.5 server for the changes to take     |
|        | effect. The method of doing this may depend on the          |
|        | start/stop/restart scripts you created after the            |
|        | installation. Most commonly, you can execute shutdown.bat   |
|        | and then run.bat under \$JBOSS_HOME/bin. Refer to the       |
|        | publicly available JBoss user's guide at                    |
|        | [www.jboss.org](http://www.jboss.org/) for more             |
|        | information.                                                |
+--------+-------------------------------------------------------------+

# Configuring JBoss to Run as a Service

+--------------+-------------------------------------------------------+
| NOTE         | > The JBoss server that runs UPT must run continually |
|              | > as a service. The instructions in this section      |
| ![](media/   | > covers this scenario. For UPT 3.2.0, there are is a |
| image13.wmf) | > single server:                                      |
|              |                                                       |
|              | -   JBoss 4.0.5 (for UPT application)                 |
+--------------+-------------------------------------------------------+

### Running JBoss as a Service

+------------+---------------------------------------------------------+
| NOTE       | > The default UPT installation runs JBoss as a command  |
|            | > line process using the user currently logged on.      |
| ![         | > Therefore, when you log out as this user, JBoss will  |
| ](media/im | > no longer be available for UPT. For that reason, it   |
| age14.wmf) | > is recommended that you configure your JBoss servers  |
|            | > to run as a Linux or Windows service. The             |
|            | > instructions are contained in this section.           |
+------------+---------------------------------------------------------+

To run JBoss as a service, follow these steps:

+--------+-------------------------------------------------------------+
| Step   | Action                                                      |
+========+=============================================================+
| 1      | ##### Linux                                                 |
|        |                                                             |
|        | See                                                         |
|        | <http://wi                                                  |
|        | ki.jboss.org/wiki/Wiki.jsp?page=StartJBossOnBootWithLinux>. |
+--------+-------------------------------------------------------------+
| 2      | ##### Windows                                               |
|        |                                                             |
|        | To run an existing JBoss command line installation as a     |
|        | service, follow the directions for creating a user-defined  |
|        | service at <http://support.microsoft.com/kb/137890/EN-US/>  |
|        |                                                             |
|        | **Note:** You need to have access to the Windows Resource   |
|        | Kit.                                                        |
+--------+-------------------------------------------------------------+

# Contacting **Application** Support

+-----------+----------------------------------------------------------+
| **NCICB   | <http://ncicb.nci.nih.gov/NCICB/support>                 |
| Ap        |                                                          |
| plication | Telephone: 301-451-4384                                  |
| Support** |                                                          |
|           | Toll free: 888-478-4423                                  |
+-----------+----------------------------------------------------------+