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.
The Hydra package is provided in three forms:
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
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Using GNU tar (and gzip)
tar -xvzf filename.tgz
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Using non-GNU tar
gzip -c filename.tgz | tar -xvf -
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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.
The JNL package and installation instructions are available from http://www.vni.com/products/wpd/jnl/.
Step 4: Add the Hydra package to your classpath
For Hydra to work, four items must be listed in the CLASSPATH environment
variable.
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The directory where you installed Hydra
-
the Jama jar file (included with Hydra),
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the DataReader jar file (included with Hydra), and
-
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
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Binomial_BetaBinomialExample,
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Binomial_BetaBinomial_Example,
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Binomial_BetaBinomial_Example_II,
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Binomial_BetaBinomial_Example_III,
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Binomial_BetaBinomial_Example_NKC,
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Binomial_BetaBinomial_Example_NKC_BiMode
(There are other examples sprinkled around, go spelunking.)
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
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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.
-
Javadoc documentation is HTML format stored in the doc directory.
-
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
at the shell or MSDOS prompt (in the
Hydra/org/omegahat/Simulation/MCMC/NKC/Examplesdirectory).
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.
-Greg Warnesgreg@warnes.net
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