The SVN repository described below is no longer supported

This page only exists for reference

Checking out and updating Continuity 6.4 from Windows XP and Linux / Mac

Please note: Currently the Continuity source code is only available for collaborators and is ONLY available for academic use.
If you need access to our internal cluster, please see: Cluster Account

Windows

Checking Out Continuity

  1. Download pageant and PuTTYgen from: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

  2. If you have not already done so, download and install TortoiseSVN and restart your computer

  3. Run PuTTYgen, and click generate, after making sure that “SSH-2 DSA” is selected at the bottom. When its done, copy everything in the box under “Public key for pasting into Open SSH authorized key file:” into a text file. Save this text file as publickey.txt or something like that. Click “Save private key” and save as privatekey.ppk or something like that. See How to Generate Key for more information.

  4. Send your public key to Dr. McCulloch (amcculloch@ucsd.edu) requesting to have access to the Continuity SVN repository and explain why you need access to it.

  5. Wait until you received an e-mail stating that access has been granted. This is not an automated process, this can take some time.
  6. Run Pageant (downloaded in step 1). Right click pagent in the Windows tray (bottom right of your screen) It looks like a computer with a black “secret agent” hat on top of it. Click “Add key…” and select to the privatekey.ppk file you saved in step 3.

  7. Make some folder you want to stick Continuity in. I usually call mine ContinuityDev

  8. Go into that folder and right click anywhere. You should see “SVN Checkout” in the context menu. Click it.
  9. In the “Checkout” menu that pops up, enter: 
    svn+ssh://cmrg@nbcr-223.ucsd.edu/cmrg/continuity/trunk/

     

    and make sure “Checkout directory:” is the directory you want all the files to go into (C:\Documents and Settings\fred\Desktop\ContinuityDev my case)

  10. Click OK. If it asks you for your password then you don’t have pageant running with your private key. Do step 8 again. Then click “OK” with a blank password. If it still asks for your password, double check to make sure your private key is in pageant by right-clicking pageant in the tray, and clicking “View Keys” If your key is in that list, then make sure Wilfred has granted you access to the repository.
  11. If all goes well with step 11, you should see hundreds of files being listed as they are downloaded. Wait 5 to 30 minutes depending upon the speed of your internet connection.
  12. You need to make sure that you define the environmental variable CONTINUITYPATH to point where you have installed Continuity and CONTPYTHON to point to the which Python on your system you are using.
  13. You can then start Continuity and finish the setup. First, it will copy a large number of files into place which can take a significant amount of time.
  14. Lastly, when you restart Continuity after the previous step, you should be able to click on the ‘Configure Continuity’ button on the splash screen to finalize setting up Continuity.

Instructions for Updating Continuity 6.4 on Windows XP

  1. Make sure pageant is running in the windows tray and has your key loaded. If not, see step 7 in the instructions above.

  2. Right click on your continuity root folder (for me this is C:\Documents and Settings\fred\Desktop\ContinuityDev). Click “SVN Update”

  3. After running Continuity, make sure to click the link on the splash (i.e. “loading”) window that says “Update Server Binaries” the first time.

Linux / Mac

Checking Out Continuity

  1. If you have not already done so, download and install Subversion (svn)

  2. From the shell type 
    ssh-keygen -t dsa

     

  3. Send your public key to Jeff Van Dorn (jvandorn@ucsd.edu), copying Dr. McCulloch (amcculloch@ucsd.edu) on the email, requesting to have access to the Continuity SVN repository.

  4. Wait until you received an e-mail stating that access has been granted. This is not an automated process, this can take some time.
  5. Make a directory to place Continuity, and cd to the directory. I called mine cont_dev, but you can substitute that with whatever you like: 
    mkdir cont_dev
cd cont_dev

    Then check out Continuity from that directory like this (make sure to include the “.” at the end of the line as shown): 

    svn co svn+ssh://cmrg@nbcr-223.ucsd.edu/cmrg/continuity/trunk/ .

     

  6. If all goes well with step 5, you should see hundreds of files being listed as they are downloaded. Wait 5 to 30 minutes depending upon the speed of your internet connection.
  7. Then you just need to do some setup/configuring commands 
    ./updatemgl
sh setup
source mglinit
autoconf
./configure

     

  8. Lastly, the first time you start Continuity you need to move some files into place and you need to include the –update-binaries command to do that: 
    ./continuity --update-binaries

     

Instructions for Updating Continuity 6.4 on Linux

  1. cd to cont_dev (or whatever your directory is called)
  2. Type 
    svn update

     

  3. After running Continuity, make sure to click the link on the splash (i.e. “loading”) window that says “Update Server Binaries” the first time.

Old NBCR notes on generating SSH public/private pair:

For Linux/Mac

[tester ~]$ ssh-keygen -t dsa Generating public/private dsa key pair. Enter file in which to save the key (/home/tester/.ssh/id_dsa): Enter passphrase (empty for no passphrase): ********** Enter same passphrase again: ********** Your identification has been saved in /home/tester/.ssh/id_dsa. Your public key has been saved in /home/tester/.ssh/id_dsa.pub. The key fingerprint is: fa:7a:29:2a:4a:a7:ef:13:45:e9:35:10:a4:32:ba:16

Note: In place of “**********” enter your own password.

You can then send your “id_dsa.pub” file. Do NOT send the “id_dsa” file.

Once your public key is placed on the server you can simply SSH to that server like normal. If your private key is in a non-standard location you can specify It’s location using the “-i” parameter in SSH.

ssh -i /path/to/private_key -l username server.name.here

The password it prompts you for is simply the password you set earlier.

For Windows

Cygwin

The commands above should also work for Cygwin on Windows. This tool is available at: http://www.cygwin.com/

PuTTY

Alternatively the Puttey Key Generator, known as PuTTYgen, can be used to generate a keypair. This is available at http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

To generate the keypair

  • Run the PuTTYgen. Select the option towards the bottom that says “SSH-2 DSA”. Click “Generate”. Copy the contents of the larger textbox where it says “Key” and save it using Notepad instead of Wordpad. Then send this file to the administrator. Enter your passphrase twice. Then “Save public key” and “Save private key”. This will save the keypair to your computer. When saving your private key, make sure that it is in the “.ppk” format.

To authenticate you will need PuTTY, also available at the link above.

Use a pregenerated keypair

  • If you have already generated a key, say from a different machine, and you want to reuse it, you may just use PuTTYGen to load the private key, and then use the “Save Private Key” to convert it into a PPK format (PuTTY format).

Run PuTTY

  • Specify the hostname. In the menu to the left, under the section SSH, select “Auth”. Click “Browse” to load your private key file. Now click “Open”. It should now prompt you for a username and password. The password being the one you entered earlier when generating the keypair.

Autologin using Pagent

  • Start Pagent, and Add Key with the appropriate passphrase Start Putty, and in the Connection Data, enter your username as the autologin username. Save the session information. Double click the session title to autologin using Putty and Pagent.

Use of ssh-agent

eval ssh-agent ssh-add #enter passphrase #now you can ssh to other hosts without having to enter passphrase again and again ssh-add -l # to see which identity file is being used ssh-add -D # to clear all identities loaded

Use of customized config file with ssh

Custom settings are enabled via ~/.ssh/config file. Create this file and set its permissions to rw by owner:

touch ~/.ssh/config chmod 600 ~/.ssh/config vi ~/.ssh/config

Edit the file according to your specifications, for example:

Host *ucsd.edu

  • User username1 Port 22

    ForwardX11 yes IdentityFile ~/.ssh/id_dsa.ucsd

Host *nbcr.net

  • User username2 Port 23

    ForwardX11Trusted yes IdentityFile ~/.ssh/id_dsa.nbcr