iPlant Atmosphere Virtual Machines (VMs)

For this class we will make extensive use of VMs in iPlant's Atmosphere cloud computing environment. We have prepared a virtual machine “image” that has a variety of relevant software pre-installed. When you launch VMs in Atmosphere, use the CGS-IU-v1.2 image.

First-time setup

When you launch your VM, you need to run a setup script to put software locations in your PATH and to configure VNC. Anytime you launch a new VM or restart a suspended VM, run the following commands.

/usr/local/src/CGS-IU/first-time-setup.sh
source /usr/local/src/CGS-IU/0README

Your VM will then have software and VNC properly configured. You should not have to repeat these steps for any subsequent logins to the same machine.

VNC issues

It turns out that VNC was not working correctly on the base image upon which we built our class' image. For now, if you want access to graphical interfaces to software on your VM, you have a couple of options.

  • You can enable X11 port forwarding and run the GUI on your local system.
  • You can follow the instructions below to fix the VNC issues.

We are working on a new version of our class image with a working installation of VNC, so hopefully this will not be a problem for us much longer!

To fix VNC on your system, first run the following commands.

sudo apt-get install xfce4
sudo apt-get autoremove libpathplan4
sudo apt-get upgrade # This step could take a while

Then, create a file with the name ~/.vnc/xstartup with containing the following lines:

xstartup
#!/bin/sh
 
unset SESSION_MANAGER
unset DBUS_SESSION_BUS_ADDRESS
 
xsetroot -solid grey
xterm -geometry 140x40+100-100 -ls -title "$VNCDESKTOP Desktop" &
 
startxfce4 &
xrandr --size 1920x1080

Note: The xrandr command sets the default size of the VNC window. The displayed values are for a large screen. Run xrandr on the commandline to see size options. You can change the size dynamically. The xterm command launches a terminal window of the specified size and location within your VNC display. You can set the values to your liking, or drop the command. You can also add other commands to be run at start-up (the file xstartup is aptly named).

Finally, run these command to activate your desktop.

chmod a+x ~/.vnc/xstartup
vncserver -kill :1
vncserver :1

You should now be able to connect to your VM with VNCviewer as explained in the iPlant documentation (with address <CURRENT-IP>:1 and your iPlant username and password; be alert that after suspend/resume of your VM, your VM's IP will likely have changed, and thus you will need to change the address given to VNCviewer accordingly).

cgss15/orientation/vms.txt · Last modified: 2015/02/27 11:59 by standage
 
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