This document contains information regarding how to setup and use DOGMA3. It is not meant as an all encompassing tutorial or is by any means meant to be the only documentation on the system. Further documentation is being written and will be available at the DOGMA Wiki.
DOGMA is an opensource project that aims to allow easy use of idle machines for distributed computing. It was created and is maintained by the Computational Science Lab at Brigham Young University. Other individuals also participate in maintainance and development. DOGMA is licensed under the GNU General Public License found here.
We would like to acknowledge the hard work of individuals and projects that DOGMA3 makes use of. First we would like to thank Nathaniel G. Avul of
DownloadThe latest version of DOGMA can be downloaded here .
Setup and Install
First you will need to install JBoss version 3.2.5 on your server. DOGMA3 makes use of the jboss-net.sar so you will need copy/link the jboss-net.sar into the default server directory.
Once JBoss is installed you should decide which version of DOGMA3 Server to run. There should be at least 2 included in this distribution. One uses the default jboss datasource for its database backend the other uses PostgresDS. There should be an example Postgres Datasource XML file included in the same directory as the PostgresDS DOGMA3 server.
Copy the desired version of the dogma3.ear into the deploy directory of the jboss server you are using(eg. [jboss directory]/server/default/deploy). If you are using a version on than the DefaultDS one make sure the datasource is defined and working. For information on setting up other datasources consult the Jboss website. Now just launch JBoss and your DOGMA3 server should be ready to go.
Included in your distribution should be a file called "bootstrap.jar" and an executable install. The executable install is for Windows machines and installs a screen saver that launches the DOGMA3 client whenever the screen saver starts. Alternately you can launch a client directly by using the bootstrap.jar file. To launch using the jar file you will need to specify the class file to launch and the class repository to use. So as an example if your DOGMA3 server were at http://dogma.cs.byu.edu:8080 you would start up the client with the following command, java -jar bootstrap.jar http://dogma.cs.byu.edu:8080/dogma/classes/ edu.byu.cs.ncl.dng.launcher.Launcher.
For now you can just use the default configuration. For explenations on how to do more advanced server configurations please refer to the DOGMA Homepage for further documentation. You can access your server at http://yourmachine:8080/dogma3gui. Where yourmachine and 8080 are the machine address and port number that JBoss is running on. Click the help link on each page if you have questions.
Several applications have been built to run on the Dogma 3 system. They include a distributed ray tracer, a parallel phylogenetic tree search, and a random phylogenetic tree search. Their source code is available at their links. Further information regarding these projects is forth coming.
Dogma FundingThis research was funded in part by NSF grant #0120718 BIOCOMPLEXITY: Hexapod Phylogenomics - Bringing Phylogenetic Supercomputing to the Masses.
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