From Genesis II Wiki

Main: General Network Setup

Refer to the wiki for a list of the General machines.

Starting a Net from Scratch

I have chosen Cicero to be the root of the UVa net. Log into Cicero using the gbg account. I have indicated the required directory for each step and noted the duration if it is significant.

Checkout Source from SVN

We start in /home/gbg/GeniiNet/GenesisII-src (which is a link to the local disk location: /localtmp/gbg/GenesisII-src). Checkout latest GenesisII trunk from SVN (3 mins)

  GenesisII-src>svn checkout  
  svn:// <>

Note: I will refer to the <> location as GenesisII. Build using Ant (2 mins)

  GenesisII-src>cd <>

Create Installer with Correct Security for UVa Grid

(create script that do these steps) Populate keystores, Create trust stores. This script takes following seven parameters: <deployment path> <net root CA pass> <container group CA pass> <admin pass> <installer pass> <container pass> <trust store pass>

  netroot containergrp admin installer container trusted

Copy above created public+private key stores

  GenesisII>cd deployments/GeniiNetFullContainer/security
  security>ls (ensure dir is empty)
  security>cp ../../GeniiNetBootstrapContainer/security/trusted.pfx trusted.pfx
  security>cp ../../GeniiNetBootstrapContainer/security/installer.pfx installer.pfx

Check the installer release number and update appropriately

  security>cd ../../../installer

Edit the number as desired. For this change to be persistent, you need to check it into SVN.

Build installer for the UVa net with the newly added credentials (2 mins)


Copy created installer to shared FS

  installer>cd installers
  installers>cp GenesisII-GeniiNetFullContainer-installer-0.x.0.jar 

Upload the installer onto the webpage:

Create a directory for the build if needed:

 ssh -l vcgr
 cd public_html/genesisII/downloads
 mkdir Build_<BuildNumer>

Transfer installer file:

 cd Build_<BuildNumer>
 scp gbg@cicero:~/GeniiNet/*.jar installer.jar

Starting a Net From an Installer

Once you have created a GenesisII installer as specified above or if you already have one...

Install Root Net

To run the installer in this phase you will need to be able to view the GUI installer pop-up. (Create .xml install description in the future to automate this.) Make sure no java process is already running

  ps auxww | grep java 

Delete old files


Run installer

  GeniiNet>java -jar UvaNetInstaller-0.x.0.jar

At this point the GUI installer will pop-up. Select to install

   *Example JSDL Documents

Be sure to set the install path to


(You should be notified that this directory does already exist.)

Start Root Container and Bootstrap

We start the container by running the install container wrapper script. It takes the following two arguments: <deployment name> <container service name>

  GeniiNet>cd GeniiNetInstall
   GeniiNetBootstrapContainer GeniiNetContainer

Check that the log file indicates that the Container Started

  GeniiNetInstall>tail -f ~/.genesisII/GeniiNetContainer/wrapper.log

We bootstrap the grid with the appropriate UVa net settings by running the script tool with the following arguments to specify the GENII_INSTALL_DIR, DEPLOYMENT_NAME, and location of the bootstrap.xml script. (2 mins)

  vcgr:$>script GENII_INSTALL_DIR=/home/gbg/GeniiNet/GeniiNetInstall 

We need to copy the context.xml file that was created to be publicly available for other who may want to connect to this UVa net. (create script for this)

  GeniiNetInstall>scp context.xml  

Leave the connection to the root node up while you add other nodes so that you can monitor success.

Adding Linux Containers

Connect to another Linux general (Titus, Sulla, or Camillus). Make sure no java process is already running

  >ps auxww | grep java 

Delete old files


Run the installer. Note the install options differ from the install for the root container. (5 mins)

  GeniiNet>java -jar UvaNetInstaller-0.x.0.jar install-desc.xml

A new smaller popup window will appear after about 30 seconds. You will be prompted to enter a password. It is imperative you type this correctly as there is no backspace. If you do mistype something, you will need to wipe the state for this container entirely (see the uninstall steps) and restart at the beginning. After this, you will be asked to enter the installer password a second time. Please do so as before.

  Password for the installer.pfx:installer

As the script finishes, a good sign that the container setups correctly is if 'setting security' takes some time for each step.

To test if the new container has been properly hooked into the UVa Net, go back to the connection on the root and check if the newly added container appears.

  vcgr:$>ls /containers
  vcgr:$>ls -ls /container/<container name>

Adding Windows Containers

To add a Windows Container to the UVa net, you need to get the installer for the net, run it, and make sure everything looks good. If the correct options are selected, the installer will do all the work!

First we check that no Genesis II service is up and running on this machine already. This is a good check if there is any chance that Genesis II has been run on this machine before. Go to

  Start->All Programs->Administrative Tools->Services.  

Make sure that no service starting with the name "Genesis II" appears.

Next we need to get the installer jar with all the security settings for the current UVa net. To do this you can get the installer from the Downloads] section of the website if it has been updated or bring up Cygwin and scp directly from the gbg home folder:

  >cd Desktop
  >scp gbg@cicero:~/GeniiNet/*.jar installer.jar

Run the installer (double-click!). Note the install options differ from the install above for the root container. The installation will take around 5 minutes.

Select to install the following:

   *Example JSDL Documents
   *Start GeniiFullContainer

Make sure the install path contains no parens:

  Program Files/Genesis II(You should be notified that this directory does not yet exist.)

A new smaller popup window will appear. When prompted, enter:

  Password for the installer.pfx:installer

Then you will be prompted again to enter the password for the machine you are on. This is referring to the windows password you used to log into that machine. If you mistype either of these passwords, you will need to uninstall GenesisII and then start the installation from the beginning. You will be asked a second time for the installer password. Use the same value that you typed in the first time (not the windows user password). You can uninstall with the following command:

  Genesis II>uninstall-container.bat GeniiNetFullContainer GeniiNetContainer

Make sure the container setups correctly. A good sign is if 'setting security' takes some time for each step.

To test if the new container has been properly hooked into the UVa Net, open up the net and check if the newly added container appears.

  Genesis II>grid.bat
  vcgr:$>ls /containers
  vcgr:$>ls -ls /container/<container name>

Testing the Net

Once the UVa net is setup, running some of the example jobs is a good way to test if things are working. One way to do this is to start up a net on your own machine and connect to the UVa net to run the jobs. For these instructions I'll be assuming you're creating a net on a Windows machine.

Get a copy of the installer used above to setup a local net.

  scp*.jar startup.jar

Install the net via the GUI. Make sure to select the example files for download. Do not select to start the NetFullContainer.

Go to where you installed the net and run the grid by selecting the grid.bat file.

Connect to the UVa net:

  vcgr:$>connect "" "deployments/GeniiNetFullContainer"

Login using your UVa certificate.

  vcgr:$>login --file=<filename.pfx> --password=<> --no-gui 

When you ls now you should see the net with all the containers.


Running a job will create output. Go to your personal directory so that you will have the needed permissions to save a file.

  vcgr:$>cd /home/<personaldir>

For each Linux container, you can run the following job:

  vcgr:$>run --jsdl=example-jsdl/example-posix-jsdl.xml /bes-containers/<linux_container_name>

A file, sum.dat, should be created.

  vcgr:$>cat sum.dat

The value 49 should appear.

For each Windows container, you can run the following job:

  vcgr:$>run --jsdl=example-jsdl/win-posix-jsdl.xml /bes-containers/<windows_container_name>

A file, job1.stdout, should be created.

  vcgr:$>cat job1.stdout

The value 7 should appear.

Tearing Down a Net

The following instructions describe how to nicely tear down the net. The root container should be torn down last. If after following these steps, the containers are still running, feel free to:

  kill -9 -1

Tearing Down Linux Containers

The GeniiNetContainer-manage-script is used to tear down a Linux container.

  GeniiNet/GeniiNetInstall>./GeniiNetContainer-manage-script stop

When run, the script should display "Stopped VCGR Container"

Check that indeed no java process is running:

  anywhere>ps auxww | grep java  

Delete the old system state files by running the clean script:


Tearing Down Windows Containers

Connect to the windows maching using remote desktop. Don't forget to logoff and not just close the remote desktop connection when you are done.

In a command window, run the uninstall-container script with the following parameters:

  Genesis II>uninstall-container.bat GeniiNetFullContainer GeniiNetContainer

Check that no Genesis II service is up and running. Go to

  Start->All Programs->Administrative Tools->Services.  

Open up Cygwin and delete the old system state files by running the clean script:

  Documents and Settings>./

Tearing Down the Root Container

To tear down the root container, follow the Tearing Down Linux Containers instructions after tearing down all the other containers of the net.

Restarting a Container

If one of the containers on the net goes down, it can be restarted using the GeniiNetContainer-manage-script with the following the argument start or restart:

  GeniiNet/GeniiNetInstall>./GeniiNetContainer-manage-script start


  GeniiNet/GeniiNetInstall>./GeniiNetContainer-manage-script restart
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Page last modified on October 07, 2011, at 11:33 AM