MPI-programming with Java

• Online documentation
• Installation
• Run your parallel program on Windows
  
• Run your parallel program on our Linux cluster
• MPJ Troubleshooting
  

 Documentation

The MPI standard: MPI reference manual & MPI 2.0 extensions

MPJ Express: the MPI implementation for java that we are using

MPJ API doc

List of MPJ Express methods

Blog with all the news

Usage documentation

MPI Quick Reference page 1, MPI Quick Reference page 2

   Installation

MPJ Express (or download directly from here) A new version (0.38) is out

    Under Windows (see Readme.html):

• extract zip-file to a folder (eg. C:).
• Right-click My Computer->Properties->Advanced tab->Environment Variables and export the following system variables (user variables are not enough)
• Set the value of variable MPJ_HOME as c:\mpj
• Add c:\mpj\bin to the value of variable PATH (all paths have to separated by a semicolon ';'). Through this variable Windows will find the executable.
  
• Make sure you can run java from the command line. Type java to see if Windows know this. Otherwise add the path of java.exe to the PATH variable. Java is in the C:\Program Files\Java\<java version>\bin
  
• Add c:\mpj\lib to the value of variable CLASSPATH (all paths have to separated by a semicolon ';'). Through this variable Java will find the jar-files.
• It seems that jar-files from the CLASSPATH are not always found, put the libraries in the lib\ext folder.
  
• Test the variables with echo %PATH% in the Windows command window (open one via Start -> Run -> type cmd). The SET command prints all variables.
  
• Note: you have to open a new cmd window to see the changed variables.
  
• On each machine that you want to use MPJ run c:\mpj\bin\installmpjd-windows.bat
• Goto Control-Panel->Administrative Tools->Services-> MPJ Daemon and start the service.
• It seems better to start the daemon as a user process instead of a SYSTEM process. Check the properties of the service and choose log in as... Fill in your user name and password.
• This fails on Vista 64-bit machines. Start the daemon manually by running mpjdaemon.bat of the mpj bin folder. You will have to start the daemon on all machines you want to use MPJ.
  
• If you want to do the MPI exercises, download parsysGeneralLibs.jar to the lib\ext of your java version (something like C:\Program Files\Java\<java version>\lib\ext).
• Normally you don't have to restart your computer.
• In order to be able to communicate with other computers, you have to switch off the computers' firewalls. You can do this in the Services window.
• Ports used: 10000, 15000 and 20000 (as explained here)
  
• To test MPI run: mpjrun.bat -np 2 -jar %MPJ_HOME%\lib\test.jar in a command window: Start -> Run -> type cmd
• this requires a machines file in the current directory. Create a new file, name it machines (withou an extension!) and add line localhost
• Add other machines by their ip-addresses, but put them before localhost.
  
• We are having problems on our Vista 64-bit machine. These fixes might solve it: change daemon.jar in the mpj lib folder with this one. Here is the source code in case you have to recompile it.
  

On our Linux cluster (see Readme.html)
   
Work on our cluster

• MPJ is installed under /home/parallel/software/mpj
• Set the following environment variables in .cshrc:
• setenv MPJ_HOME /home/parallel/mpj
• setenv PATH $MPJ_HOME/bin:$PATH
  
• 
  

 Run your parallel program on Windows machines

1. Open a CMD window (type cmd in "Search programs and files"), go to root directory of your program
• change directories with cd
  
• change drive with D:
  
2. Execute in the root directory of your program:
   
• mpjrun -np 4 <packagename.classname> <program arguments>
• create 4 processes that are distributed evenly among the available cores
• Add jar-file (you should explicitly mention the file!):
• mpjrun -classpath <path\mylibrary.jar> -np 4  <packagename.classname> <program arguments>
3. To stop your parallel program: Ctrl+C

1. open CMD window => start mpj daemon with C:\mpj\bin\mpjdaemon.bat
2. put a machines file in the folder containing your code.
3. Open a CMD window, go to root directory of your program
• change directories with cd
  
• change drive with D:
  
4. Execute in the root directory of your program:
   
• mpjrun -np 4 <packagename.classname> <arguments>
• create 4 processes that are distributed evenly among the available processors
• Code that is used but not located at that location should be added as jar-files to the lib/ext folder of your current java
• Add jar-file (you should explicitly mention the file!):
• mpjrun -classpath <path\mylibrary.jar> -np 4 -dev niodev <packagename.classname> <program arguments>
• mpjrun -np 4 -jar <jar-file.jar> <arguments>
• if the class is in a jar-file
• it should be the application entry point (indicating which main the jar-file should execute)(this is the last option when creating a jar-file in eclipse)
  
5. To stop your parallel program: Ctrl+C

• CLASSPATH points to all folders with jar-files the virtual machine will look into
• print it with echo %CLASSPATH%
• alternatively put the jar-files in the lib\ext folder of your java folder (in C:\Program Files\java\jrexxx), they will then automatically be loaded.
  

 Run your parallel program on our Linux cluster

• Put the computers you want to use in a machines file.
• Start the mpj deamons with mpjboot machines
• Run a program:
• mpjrun.bat -np 4 <packagename.classname> <arguments>
• mpjrun.bat -np 4 -jar <jar-file.jar> <arguments>
• Stop the mpj deamons with mpjhalt machines   (don't forget)
  

 Troubleshooting