Installing HYDRA

Note: These instructions are too brief. Feel free to email questions, suggestions--or better yet, an improved version.

Step 1: Download the Hydra package.

• Hydra_1.0.0.jar Jar archive (2295 KB)
• Hydra_1.0.0.tgz gzipped tar archive (1620 KB)
• Hydra_1.0.0.zip ZIP archive (2313 KB)

Each file contains source code, javadoc documentation, example files, and two additional java packages (the JAMA Matrix package, and Merlin Hughes' DataReader package).

You will also need to download and install Visual Numerics' JNL package.

Step 2: Unpack

Move the package file you downloaded to the directory where you wish installation to occur. The un-archiving program will create a directory named "Hydra" that contains all of the Hydra files.

On Unix-like systems

• Using GNU tar (and gzip)
  

  tar -xvzf filename.tgz

• Using non-GNU tar
  

  gzip -c filename.tgz | tar -xvf -

• Unpacking using the Java "jar" command
  

  jar -xvf filename.jar

On Microsoft Windows Systems

Use your favorite unarchiving program (WinZip, or whatever). Make sure to specify that directories should be created (this should be the default). Otherwise you will end up with a million files in one directory and things won't work.

Step 3: Download and install the Java Numerics Library (JNL) from VisualNumerics.

Step 4: Add the Hydra package to your classpath

1. The directory where you installed Hydra
2. the Jama jar file (included with Hydra),
3. the DataReader jar file (included with Hydra), and
4. the location of the VisualNumerics classes (installed in Step 3).

On Unix-like Systems

I unpacked Hydra in my home directory, so that the Hydra directory is $HOME/Hydra. I installed the JNL package in $HOME/Java/jnl, so that the JNL classes are located under $HOME/Java/jnl/JNL/Classes.

Thus my CLASSPATH variable needs to contain:

$HOME/Hydra:$HOME/Hydra//Jama-1.0.1.jar:$HYDRA_DIR/DataReader.jar:$HOME/Java/jnl/JNL/Classes

With a sh-compatible shell (sh,bash) this can be added to the CLASSPATH variable using the command:

export CLASSPATH=$CLASSPATH:$HOME/Hydra:$HOME/Hydra//Jama-1.0.1.jar:$HYDRA_DIR/DataReader.jar:$HOME/Java/jnl/JNL/Classes

With a csh-compatible shell (csh,tcsh,ksh) this can be added to the CLASSPATH variable using the command:

setenv CLASSPATH $CLASSPATH:$HOME/Hydra:$HOME/Hydra//Jama-1.0.1.jar:$HYDRA_DIR/DataReader.jar$HOME/Java/jnl/JNL/Classes

You will probably want to add the command that sets your classpath to your shell inialization file (usually one or more of $HOME/.cshrc, $HOME/.tcshrc, $HOME/.bashrc, $HOME/.profile, etc.)

On Microsft Windows Systems

I installed Hydra in C:\Pfizer\My Stuff\Hydra. I installed the VisualNumerics classes in C:\Pfizer\My Stuff\jnl,  so the path to the class files is C:\Pfizer\My Stuff\jnl\Jnl\Classes

Thus, my CLASSPATH variable needs to contain:

C:\Pfizer\My Stuff\Hydra;C:\Pfizer\My Stuff\Hydra\Jama-1.0.1.jar;C:\Pfizer\My Stuff\Hydra\DataReader.jar;C:\Pfizer\My Stuff\jnl\Jnl\Classes

At the MSDOS prompt, or in a batch file, this can be accomplished using the command

SET CLASSPATH=C:\Pfizer\My Stuff\Hydra;C:\Pfizer\My Stuff\Hydra\Jama-1.0.1.jar;C:\Pfizer\My Stuff\Hydra\DataReader.jar;C:\Pfizer\My Stuff\jnl\Jnl\Classes

For information on other methods for setting your class path permenantly see http://java.sun.com/j2se/1.3/docs/tooldocs/win32/classpath.html.

Step 5: Run the example programs

I've include several example programs in the directory org/omegahat/Simulations/MCMC/NKC/Examples. These are

• Binomial_BetaBinomialExample,
• Binomial_BetaBinomial_Example,
• Binomial_BetaBinomial_Example_II,
• Binomial_BetaBinomial_Example_III,
• Binomial_BetaBinomial_Example_NKC,
• Binomial_BetaBinomial_Example_NKC_BiMode

I've created batch/script files for both Unix-like systems and Windows systems that will set the CLASSPATH variable and then run each of these examples. Before using either script, you will need to edit it to use the correct paths.

• For Unix-like systems the shell script is

  RunExamples.sh.

• For Microsoft Windows Systems, the shell script is

  RUN.BAT.

Step 6: Read the documentation

1. A technical report showing describing the features of Hydra and giving a brief tutorial using an example problem is provided in the file UsingHydra.pdf.
2. Javadoc documentation is HTML format stored in the doc directory.
3. There is additional documentation on the individual classes stored in the source *.jweb files.

Step 7: Start Experimenting

Once you have the examples working, you can start modifying them (they live under Hydra/org.omegahat/Simulations/MCMC/NKC/Examples) to change how they work.

To do this, first copy one of the files, say Binomial_BetaBinomial_Example.java to a new name, say, BBE.java, edit the file so that the class name matches the file name. Now you should be able to compile it by typing

javac BBE.java

You should be able to run this new class by typing

java Hydra/org.omegahat/Simulation/MCMC/NKC/Examples/BBE

Step 8: Give Feedback

I hope that you find Hydra useful, if so please send examples of how you are using it, what features you would like to see, and any problems or bugs you run into. Example data and programs will be particulary helpful.