Getting help with BCE

Using BCE

You now have a machine that has all the software installed as part of BCE, including IPython, useful Python packages, R, RStudio, and useful R packages.

You can get a terminal window that allows you to type commands in a UNIX-style shell by clicking on the icon of the black box with the $ symbol on the top panel. You can start applications by typing them in the terminal or by clicking on their menu entry. For example:

  • Typing ipython notebook or clicking Applications > Programming > IPython Notebook
  • Typing rstudio or clicking Applications > Programming > RStudio
  • Typing R or clicking Applications > Programming > R

More information can be found in our screencasts of tutorials on various topics.

Stopping and restarting the VM on your laptop

To stop the VM, simply click the red power button in the upper right.

You can restart the VM at any time by opening VirtualBox and clicking on the tab for the VM and clicking “Start” as you did above.

Using shared folders to move files between the VM and your laptop

One useful thing will be to share folders between the VM and the host machine so that you can access the files on your computer from the VM. Do the following:

  • On the VirtualBox Taskbar go to Devices > Shared Folder Settings and click on the icon of a folder with a “+” on the right side.
  • Select a folder to share, e.g. your home directory on your computer by clicking on the down arrow by Folder Path and choosing Other and navigating to the folder of interest. For our purposes here, assume we click on “Documents”.
  • Click Auto-mount and Make permanent and then click Ok twice.
  • Reboot the machine by clicking on the red power button on the upper right and choosing Restart.
  • Once the VM is running again, click on the Shared folder on the desktop. You should see the folder sf_Documents (or whatever the folder name you selected was, in place of “Documents”). You can drag and drop files into and out of the folder.
  • Alternatively, from the Terminal, you can also see the directory by doing cd ~/Desktop/Shared/sf_Documents and then ls will show you the files.
  • Be careful. Unless you selected Read only at the same time as Make permanent, any changes to the shared folder on the VM affects the folder in the real world, namely your computer.

Changing the memory (RAM) and number of CPUs of your VirtualBox VM

Before starting the VM, click on the Settings icon in the VirtualBox Manager window task bar. Select System. To increase memory, click on Motherboard and adjust the Base Memory slider. To increase the number of virtual CPUs to be more than the default of one, click on Processor and adjust the Processor(s) slider. In general you would not want to select more processors than the host machine has cores.

At the moment, you cannot increase the amount of disk space associated with the VM beyond 16 Gb, but you can of course use Shared Folders to access the disk on the host machine.

Adding tools for parallel computation

Please run our script on your running VM. This provides standard parallel packages for Python and R as well as providing MPI for multi-node computation.

Note that these tools are available automatically on the BCE CfnCluster AMI.

If you have started a virtual cluster via Starcluster (deprecated), please also run our script on your running (master) VM to add parallel software to the worker nodes. Note at present only BCE-spring-2015 supports use with Starcluster.