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Andy Adler: Research Group

This page contains general information for students in Andy Adler's research group.

Group Meetings

Group meetings take place on Tuesdays at 12:00.

SVN Access

I have implemented a subversion software and document repository for the research group. You should be able to access it from both inside and outside SCE using your SCE username and password.

For windows access:

  1. Install Tortoise SVN (
  2. Reboot after install
  3. Right Click on "TortoiseSVN -> Settings -> General -> "Subversion configuration file" -> Edit"
  4. Add the following text to the file (in the section [tunnels]). Save and Quit.
      adler01ssh=$ADLER01SSH tortoiseplink -P ##
    (Replace ## with the correct port number (ask)
    You may also put your password like this:
      adler01ssh=$ADLER01SSH tortoiseplink -P ## -pw ##YOURPASSWD##
    Note that this is less secure. Anyone who can access your computer can now get your password.
  5. To Check out a project (PROJ):
    Right click in an empty folder to select SVN Checkout
    In URL of repositorywrite
    (Replace USERNAME with your username, and PROJ with the project name)
  6. There are currently two PROJECTS:
      proj for software and documents
      data for recorded data

For unix access, use:

  1. Edit the file $HOME/.subversion/config
  2. Add the following text to the file (in the section [tunnels]). Save and Quit.
      adler01ssh=$ADLER01SSH ssh -p ##
    (Replace ## with the correct port number (ask)
  3. To Check out a project (PROJ):
    svn checkout svn+adler01ssh://
    Check out the projects "data" and "proj". You may also checkout "testproj", as a place to try various experiments with SVN.

Setup SSH agent in windows

The use of the ssh agent means that you don't have to type in your password all the time with CVS. Its a little complicated to setup, but these instructions should help:
  1. Run Puttygen.exe
  2. Generate a SSH v.2 key (this will also work for other keys, but the instruction are for this one)
  3. Enter your passphrase (suggestion, your SCE unix password)
  4. Save private key (suggestion: to My Documents/putty-private-key)
  5. Select public key; type CTRL-C to copy
  6. Use Putty.exe to log into (at the port ## given)
  7. Type these commands
       mkdir .ssh
       chmod go-rwx .ssh
       cat > .ssh/authorized_keys
    EDIT −> PASTE the public key
       ^D  ( TYPE CTRL D)
       chmod go-rwx .ssh/authorized_keys
  8. Download and save Pageant.exe to C:\Documents and Settings\YOURNAME\Start Menu\Programs\Startup
  9. Run Pageant.exe
  10. Click Add Key
  11. Select private key (My Documents/putty-private-key)
  12. Close
Now, pagent will popup once at startup, and afterwards you shouldn't need type the password each time.

Setup SSH agent in unix

  1. To generate the key type:
       ssh-keygen -b 2048 -t DSA -C EMAILADDRESS
    The key will be in $HOME/.ssh/
  2. Copy the key to the server
       scp -P ## $HOME/.ssh/
       ssh -p ##
       mkdir .ssh
       chmod go-rwx .ssh
       cat $HOME/ >> $HOME/.ssh/authorized_keys
       chmod go-rwx .ssh/authorized_keys
Subsequently, you can load the key into the agent using ssh-add. ssh should no longer ask for passwords.

Running Matlab on adler-server

  • Install Cygwin. Make sure you install the xorg-server and xinit packages.
  • Set a shortcut to C:\cygwin\bin\startxwin.exe
  • Install Putty
  • Make sure the Forward X11 button is clicked
  • Log into the server with putty
  • Open Matlab

Getting high quality figures into latex

In general, you can't put jpg or png figures into papers. The quality is too low for publication and the journal won't accept them. Instead, use the vector drawing format inherent in exporting to pdf. Then use pdfcrop (avail in miktex in windows and in all linux distributions)
  1. Export the document to pdf
    − Openoffce -> print to pdf
    − Matlab: print -dpdf filename.pdf
    − Other software, install a pdf printer such as PDFCreator
  2. Use pdfcrop
    pdfcrop filename.pdf filename.pdf
  3. in latex put
    \includegraphics[width= 0.80 \textwidth]{ figures/filename.pdf }
    \caption{ \label{fig:Whatever_label_you_want}
     Caption text
  1. Access to adler-server
    − Choose a VNC server session (ie. #)
    − On the server, run
    rm -f /tmp/.X#-lock ; rm -f /tmp/.X11-unix/X# ; vncserver :# -geometry 1600x1000 -depth 24

    − From a unix machine, run, first
    ssh USERNAME@adler-server -p #### -L590#:localhost:590#
    Next run
    vncviewer localhost:590#

Last Updated: $Date: 2016-10-20 04:36:39 -0400 (Thu, 20 Oct 2016) $