Generalities

Once the prerequisite for your system are installed (see below) you can run Shape via the Launch Shape 2010 link on the start page of the ShapeSite. When you click on that link a file named Shape_it.jnlp is downloaded to a temporary folder and is run by Java Webstart. The first time you do that, webstart downloads the Shape code and starts the program. The next time, it will only check whether the code has been updated. If not, webstart runs the local version. Otherwise it downloads and runs the new version. This makes it easy to keep the code up-to-date.

If you are going to run complex, memory intensive physical models, then the default memory settings for Java may not be sufficient to achieve a suitable spatial resolution. Then it is recommendable to increase the RAM that Java is allowed to access.

Java runs with a certain RAM memory limit, since it is embedded into what is called the Java Virtual Machine. The maximum recommendable memory for that is approximately 1.5 GB for 32 bit processors.

The maximum memory to be claimed by Java is set in the Shape_it.jnlp file. If you have more than 2 GB for a 32 bit system, you can manually increase the default maximum memory of 1000 KB to 1500 KB. To do that save the Shape_it.jnlp file on your desktop and open it in a text editor as an ascii file. Change the following code section:

max-heap-size="1000M"

to

max-heap-size="1500M"

Similarly, on 64 bit systems you can take advantage of its higher address space to increase the spatial resolution of your models. Increase the max-heap-size to a value suitable for your system, say 2/3 of the available RAM.

Now that you have saved and modified the Shape_it.jnlp file, you can run Shape by opening this file with webstart (click or double-click on the file icon). Shape will then open with the new settings.

As of October 2010, the Java Advanced Imaging (JAI) and Java Media Framework (JMF) are included directly in Shape. So, you do not have to install them anymore. Since most systems these days already include Java Runtime Environment, you probably only have to install Java3D, which is system dependent. This should be true for all operating systems.

Windows

Linux

Ubuntu 8.04 Hardy I) Installing Java 1. Download JDK from the Sun website: http://java.sun.com/javase/downloads/index.jsp
2. Select JDK in Java Platform, Standard Edition
3. Select “Linux” from the platform option
4. Select Linux self-extracting file jdk-6u18-linux-i586.bin
5. Set the downloaded file executable first:
sudo chmod +x jdk-6u6-linux-i586-rpm.bin
6. Allow JDK to run:
sudo sh ./jdk-6u2-linux-i586.bin
Then follow instruction:
Do you agree to the above license terms? [yes or no]
yes
The package jdk1.6.0_18 is created
7. Configure Java:
a)the new java is the new first alternative (when you enable Java):
sudo update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jvm/jdk1.6.0_18/bin/java" 1
b)Select the new alternative as the real Java:
sudo update-alternatives --set java /usr/lib/jvm/jdk1.6.0_18/bin/java
Output: Using '/usr/lib/jvm/jdk1.6.0_18/bin/java' to provide 'java'
8- Check that the version of Java is the one just installed:
java -version
Output: java version "1.6.0_18"
Java(TM) SE Runtime Environment (build 1.6.0_18-b07)
Java HotSpot(TM) Server VM (build 16.0-b13, mixed mode) 9- Configure JAVAC (idem Java):
sudo update-alternatives --install "/usr/bin/javac" "javac" "/usr/lib/jvm/jdk1.6.0_18/bin/javac" 1
sudo update-alternatives --set javac /usr/lib/jvm/jdk1.6.0_18/bin/javac
II) Installing Java3D
1- Get the latest j3d version for linux from https://java3d.dev.java.net/ (e.g. j3d-1_5_2-linux-i586.bin)

2- Move the file to the JRE directory (e.g. “mv j3d-1_5_2-linux-i586.bin /usr/lib/jvm/jdk1.6.0_18/jre/”)

3- Make the file executable: (e.g. “chmod +x j3d-1_5_2-linux-i586.bin”)

4- Run the file. sudo sh ./j3d-1_5_2-linux-i586.bin
(This will place the necessary .jar files into the proper places: j3dcore.jar, j3dutils.jar, vecmath.jar in /usr/lib/jvm/jdk1.6.0_18/jre/lib/ext and libj3dcore-ogl.so, libj3dcore-ogl-cg.so in /usr/lib/jvm/jdk1.6.0_18/jre/lib/i386.)

5- To detect if you have a suitable Java Runtime environment and Java 3D installed on your system go to http://www.chemgapedia.de/vsengine/info/en/help/requirements/java.html , you should see a 3D cube rotating !Note: Firefox may act in a weird way if Flash player is not properly installed so one can use Opera to check if Java3D is working. To set Opera properly: * Go to Tools > Preferences > Advanced > Content.
* Click the "Java options" button. Check the "Enable Java" option.
* Click the "Choose" button for the "Java path" field.
* Navigate to the Java directory and click "OK".
In our case, the path is: /usr/lib/jvm/jdk1.6.0_18/jre/lib/i386
* Click the "Validate Java path" button.
* Click "OK" to save your changes and exit the Java dialog.
* Click "OK" to save your changes and exit the Preferences dialog.III) Installing JAI 1. Get the latest JDK jai version for linux from http://java.sun.com/products/java-media/jai/downloads/download-1_1_2.html (e.g. jai-1_1_3-lib-linux-i586-jdk.bin)
2. Move the file to the JDK directory (e.g. “sudo mv jai-1_1_3-lib-linux-i586-jdk.bin /usr/lib/jvm/jdk1.6.0_18/”)
3. Make the file executable: (e.g. “chmod +x jai-1_1_3-lib-linux-i586-jdk.bin”)
4. Run the file:
sudo sh ./jai-1_1_3-lib-linux-i586-jdk.bin This will place the necessary .jar files into the proper places.
IV) Download Shape

You should now be able to run Shape using javaws: Open Shape with /usr/lib/jvm/jdk1.6.0_18/jre/bin/javaws or /usr/lib/jvm/jdk1.6.0_18/bin/javaws. Jawaws will be used as default except if set otherwise. This is it !!!!Thanks for letting us know any issues with these instructions or variants for other types of Linux systems.

Instructions kindly contributed by Laurence Sabin, Instituto de Astronomía, UNAM, Ensenada

2. Fedora 9, NVIDIA video card Installing Java on Linux (http://www.wikihow.com/Install-Java-on-Linux):

Installing Java3D (https://j3d-core.dev.java.net/j3d1_4_0_01/HOW-TO-INSTALL.html)

Installing JAI

You should now be able to run Shape using webstart.  If webstart is not installed you will have to download it and install it, but it should be already installed.If you get an error about the GLX version being too low when you try to open the 3d module (or perhaps Shape itself) you will need to install the latest drivers for you video card.  Shape used Java3d v1.5 which required Glx > 1.3.  Upgrading your video driver varies depending on what video driver you have.  If you have an nvidia card you can upgrade using RPM packages.  I can only give you the example of my system (Fedora 9, NVIDIA card) in which the following worked:NVIDIA driver upgrade on RedHat/Fedora: (http://www.brandonhutchinson.com/NVIDIA_drivers_with_Red_Hat_Linux.html)

Mac OSX

Here is how I install the required libraries to let Shape run on a macbook:

1) Be sure you have installed the Java SE 6, available with the Java Update 2 from Apple:
http://support.apple.com/downloads/Java_for_Mac_OS_X_10_5_Update_2

2) In the Application/Utilities/Java/Preferences, choose the SE 6 version as default.

3) download the 1.5.2 version of J3D at:
https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=java3d-1.5.1-oth-JPR@CDS-CDS_Developer

unpack it, and move the contents of j3d-1_5_2-macosx/lib/ext into /System/Library/Java/Extensions
It's 3 jar files: j3dcore.jar, j3dutils.jar and vecmath.jar; you may find usefull to save the original versions of these files somewhere, in case of willing coming back to your previous installation.

4) download the package JOGL from https://jogl.dev.java.net/, and move the contents of jogl-1.1.1-macosx-universal/lib into /System/Library/Java/Extensions.IMPORTANT ADDITIONAL INFORMATION FOR NEWER SYSTEMS WITH SnowLeopard: You can download the necessary files HERE:

The procedure described above has problems for the most recent systems.
The main problem is to install the various libraries and to be sure that Java uses the ones we want.
There are 3 places for Java to look for libraries:
/Library/Java/Extensions
/Users/YOURHOME/Extensions
/System/Library/Java/ExtensionsThe problem was that there were files with the same names in various directories. I thus just removed everything from the first two directories, and just copied all the necessary libraries from the other Mac (Leopard one) to the /System/... directory and it works now!Shape need the following:
-rw-r--r--@ 1 root wheel 1704635 28 avr 22:23 j3dutils.jar
-rw-r--r--@ 1 root wheel 2957997 28 avr 22:23 j3dcore.jar
-rw-r--r--@ 1 root wheel 318956 28 avr 22:23 vecmath.jar
-rw-r--r--@ 1 root wheel 1126370 28 avr 22:24 jogl.jar
-rw-r--r--@ 1 root wheel 470352 28 avr 22:24 libjogl_cg.jnilib
-rw-r--r--@ 1 root wheel 50312 28 avr 22:24 libjogl_awt.jnilib
-rw-r--r--@ 1 root wheel 2838744 28 avr 22:24 libjogl.jnilib
-rw-r--r--@ 1 root wheel 49800 28 avr 22:24 libgluegen-rt.jnilib
-rw-r--r--@ 1 root wheel 18416 28 avr 22:24 gluegen-rt.jar
-rwxr-xr-x 1 root wheel 409568 28 avr 22:26 libJ3D.jnilib
-rwxr-xr-x 1 root wheel 54768 28 avr 22:27 libJ3DUtils.jnilib

It should work fine.

Known problems: There may be problems with saving movie files in the Movie Module.