RAVE:MacPro

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RAVE logo R Analysis and Visualization of iEEG

RAVE


Using RAVE on the BeauchampLab MacPro at Penn

Updated Sept 2021 after server move to Pennovation

Click here to download the script. After download, double-click to unzip the file. This will create two files, one for launching pre-processing and one for launching RAVE. Drag the unzipped icons to your desktop or other convenient location. Double click on an icon to run. This will open a "Terminal" window, necessary to connect to the MacPro. The first time a script is run, you must right-click on it to open a context menu, then select "Open", then "Open" again to bypass the security warnings. Then, answer the question

 Are you sure you want to continue connecting (yes/no/[fingerprint])? 

with "yes". You will be prompted for the server password and a browser window will open showing the RAVE GUI.

The BeauchampLab MacPro has a 3.2 GHz 16-Core Intel Xeon W CPU and 786 GB 2933 MHz DDR4 RAM. The MacPro also has a direct fiber channel connection to the RAID where the iEEG data is stored. In combination, this allow for much faster performance than on a user's local machine. RAVE runs on the MacPro and the RAVE GUI is displayed in a web browser on the local machine. To run RAVE in this mode:

  1. Connect to the institutional network VPN (if outside of campus).
  2. Start a RAVE session on the MacPro.
  3. Connect to the MacPro RAVE session with a web browser on your local machine.

Shutting down a RAVE Client

Closing the browser window on your local machine will NOT terminate RAVE running on the MacPro. You must click on the "Terminal" window (opened above). Click on the red circle in the top left of the window to close it. Select "Terminate" to terminate running processes. This will shut down the RAVE server and disconnect the RAVE client, graying out the web browser window containing the RAVE GUI, which can be safely closed.

Troubleshooting

  1. if you have previously connected to the server with ssh, you may need to clear the ssh cache with
 ssh-keygen -R serverIP

before you execute the script for the first time.

  1. If the browser window shows an error, such as "Host not found", wait a few seconds and then refresh the window. You may wish to copy the script to the desktop or to the /Applications folders.

Older instructions (also a template for other client/server configurations)

Setup a RAVE instance on the server (only required once).

ScreenShare with the server. e.g.

 vnc://serverIP

On the server, run RStudio/Session/new session

 rave::start_rave(host = 'serverIP', launch.browser=FALSE, port = 1111)

where 1111 is a port number.

Access the RAVE instance from your local machine

VPN into the same network as the server if necessary (most universities have firewalls that will block incoming web browser connections). Start a Chrome browser on your local machine, enter this into address bar:

 http://serverIP:1111

where 1111 is the port number used above for your RAVE instance. You will the RAVE GUI in Chrome on your local (client) machine, connected to RAVE on the remote server.

Troubleshooting

If no data appear on the "Select Data" screen in RAVE, close RAVE, go to RStudio Console and run

 rave::rave_options()

change Raw subject data path to the appropriate path, e.g.

 [...]/data/rave_data/ent_data

change RAVE subject data path to

 [...]/data/rave_data/raw

Make sure to click "Set Directory". Sometime it may be necessary to clear variables and restart the session.

 rm(list=ls(all.names = TRUE))

 rstudioapi::restartSession()

Return to Other Notes.