Installing Cygwin

MSWin users will need the Cygwin development environment in order to get a local copy of NEURON's Subversion repository and / or compile NEURON from source code.

  1. Go to and download setup.exe
    To avoid cluttering up my desktop, I made a special directory on my hard drive called c:\installed\cygwin and put cygwin.exe in there.
  2. Run setup.exe as yourself (not as Administrator).
    • Select "Install from Internet".
    • Specify the Root Install Directory to be c:\cygwin
    • Install for "All Users" and set the "Default Text File Type" to be Unix / binary.
    • Specify your preferred Local Package Directory (I chose c:\installed\cygwin). This is where the cygwin installer is going to put a folder that has a long, ugly name. You're not going to want to see this folder on your desktop.
    • Choose a download site that is nearby. ftp sites will probably do faster downloads than http. I chose
    • Select Packages. Accept the defaults except for the following:
      • Archive--get zip and unzip
      • Devel--change to Install
      • Editors--get what you're familiar with. I chose vim.
      • Net--accept the Default selections, but check to make sure openssl is selected.
        openssh doesn't seem to be necessary.
      • Shells--get rxvt: VT102 terminal emulator for both X and Windows

      In each of these cases, be sure to get the "Bin" (binary), not the "Src" (source).

    • Cygwin Setup may select additional packages to "meet dependencies"; accept the selections.
    • At the last step in installation, the installer asks if you want to
      "Create icon on Desktop" or "Add icon to Start Menu".
      You will not be using these icons, so uncheck the boxes, then click the Finish button.

Configuring Cygwin

Set up an rxvt shortcut

This will be very handy for quickly creating several shell terminals.


  1. Open Windows Explorer, go to c:\cygwin\bin, and create a shortcut to rxvt.exe
    Move this shortcut to your desktop.
  2. Right click on the shortcut icon, select Properties, and change its "Target" string to
        c:\cygwin\bin\rxvt.exe -fg black -bg white -sl 1000 -e bash
    (that "sl" is lower case "SL", not an s followed by the number 1).
    This will give you an rxvt terminal with black text on white background, which runs under the bash shell, and has 1000 lines of scrollable output.
  3. Click on "Apply", then "OK" to close the properties window.

Set up your home directory and bash shell environment

  1. Double click on the rxvt.exe shortcut to open a bash shell window.
    In this window, type
    cd /

    That should produce the following output:

    Cygwin.bat  Cygwin.ico  bin  cygdrive  etc  lib  proc  sbin  srv  tmp  usr  var
  2. Type the following commands:
    /bin/mkdir home
    cd home
    /bin/mkdir yourname

    where "yourname" will be the name of your "home" directory under Cygwin.
    There must be no spaces in whatever you choose for "yourname".

  3. Next,
    cd yourname

    and use a text editor to create a file called .bashrc that has these contents:

    export PATH=/usr/bin:$PATH
    export HOME=/home/yourname
    export PATH=$HOME/bin:$PATH

    Save the file and close the rxvt window.

  4. Test this by opening Cygwin's rxvt window (rxvt.exe shortcut on desktop!) and executing this command:

    It should return


    Close the rxvt window.