Computer Help

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[edit] Creating a new wiki user account

Encourage new lab members to start to learn things from the wiki and make improvements and contributions, especially to pay-forward any training you are doing with them that isn't currently well documented. Ask anyone who already has a wiki account to click on the View allspecial pages link on the wiki tools sidebar, and choose Create new user account.

[edit] Connecting to a Linux box from your PC

You may want to do this if you are running especially intensive processes (e.g,. loading many dt6 files, tracking fibers from a large sphere on many subjects, running batch scripts on a fast machine without wanting to take the time to view things through a GUI).

  • e.g., through teal.stanford.edu


VMware
If you have already installed the Linux virtual machine of FSL package on your PC for anatomical preprocessing, you can use it to access remote Linux servers with excellent graphics quality (significantly better than Cygwin). Start FSL_vm on VMware, open a terminal and SSH into a remote Linux machine (e.g., by running: "ssh -Y username@teal.stanford.edu"). Start matlab (e.g., matlabr2008&), and run your code. You will have full graphical access to Matlab on the Linux server.

Cygwin
Another way to access remote Linux servers is installing Cygwin.

  1. Download the setup.exe file and doubleclick on the icon. It will take you through the installation steps.
  2. Accept the defaults for the first few screens (e.g., install from the internet, install for all users, unix/binary text file type, direct connection).
  3. On the screen, "Select Packages", make sure to include X11. See the figure below for a picture of what this might look like. Scroll down until you see "X11" and expand the category (click on the + sign indicated by the RED ARROW). You will see a list of individual packages (e.g., WindowMaker, etc) with the word "Skip" next to them. Click on the circular arrow (indicated by the GREEN ARROW) until it says "Install" rather than "Default", and you should see the word "Skip" replaced by a series of checked boxes.
  4. On the same screen, "Select Packages", make sure to check the box for OpenSSH. You will find this package under the category Net, and can check the box in a similar way as described in the previous step.
  5. The package should finish downloaded in about ten minutes.


File:CygwinX11.jpeg



To connect to a linux box through Cygwin (e.g., teal), follow these steps:

  1. Open a Cygwin command-line terminal window
  2. Start X11 on your Windows computer by typing: "startx". A new "xterm" window should open.
  3. From the xterm terminal window, SSH into the remote Linux machine (e.g., by running: "ssh -X teal.stanford.edu"). Of course, you need an account on the remote Linux machine.
  4. Change to the directory where you keep a copy of VISTASOFT ("cd cvs/VISTASOFT")
  5. Update CVS, if you haven't in a long time ("cvs update -d")
  6. Start Matlab: "matlab -nojvm" (no java scripts/interfaces for greater efficiency)
  7. Run your script -- you can also copy and paste it in. The trick with pasting into Cygwin is that you cannot use Ctrl+v, instead you have to click in the Cygwin window with the middle button on your mouse, or by pressing down on the scroll wheel if you don't have a three-button mouse (or, failing those, left+right mouse buttons together)

[edit] Connecting to a Linux box from your Mac

  1. Open an xterm window (X11, NOT terminal)
  2. Ssh into the machine: ssh -Y user@teal.stanford.edu
  3. Start MATLAB: 'matlab -nojvm'


Alternatively, you can connect via samba and mount the server as a disk (similar to "Tools --> Map Network Drive" on the PC)

  1. In Finder: Go --> Connect to server
  2. Enter address: smb://sns2.stanford.edu, press Connect
  3. Press authenticate: enter user name and password
  4. Server should show up on your desktop as a disk

[edit] Remote Computing

If you're working offsite you should install stanford's VPN software. Stanford has a very informative page that will take you through how to set everything up for your OS.

  • Note that you will need a Stanford login to use the VPN service.

[edit] Connecting to a lab computer (VPN)

  1. Start the VPN connection to SU.
  2. Open an XTERM
  3. Login to a computer
 $ ssh -XY username@azure.stanford.edu

The "-XY" will forward the X-windows to your machine so that you can see graphics on your screen from the remote computer.

[edit] Connecting to a lab computer (no VPN)

If you don't have a stanford login you won't be able to use the stanford vpn service. To get around this you must first login to White then you can login to another machine.

  • Note that White is NOT to be used for any computations or programs (i.e. no matlab on white).
  1. Open an XTERM
  2. SSH to white
  3. SSH to another machine
 $ ssh -XY username@white.sanford.edu
 $ ssh -XY username@azure.stanford.edu

[edit] Library access

To gain access to Stanford resources such as library and PubMed you need to set up a proxy server through your browser.

  • See this page for more details and instructions for your OS and browser.
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