Skip to content

Latest commit

 

History

History
73 lines (46 loc) · 4.57 KB

cygwin.md

File metadata and controls

73 lines (46 loc) · 4.57 KB
Raw

Instructions to run Cytosim on Cygwin

Cytosim runs on Windows, using Cygwin, but this is not supported directly by us. This method requires the simulataneous use of of two programs in parallel: Cygwin, a Unix-like enviroment where Cytosim will be installed and called; and X11, a graphical environment that will be used by Cytosim to display graphics while it is running.

32 or 64 bit systems

Cygwin has two versions, 32 bits and 64 bits, you must use the one that is compatible with your system. Follow these step to find out if your Windows is 32 bits or 64 bits:

  1. Click the Start(Windows icon) button; right-clicking Computer; click Properties
  2. Under System, you can view the system type


Installation

Run the Cygwin installer with default settings until you get to the package selection screen. To compile and run Cytosim, several packages must be explicitely selected:

  • gcc (GNU compiler suite including C++)
  • make (GNU make)
  • libBLAS (Basic Linear Algebra Subprograms)
  • libLAPACK (Linear Algebra PACKage)
  • OpenGL (Open Graphics Library)
  • GLEW (OpenGL Extension Wrangler Library)
  • GLUT (OpenGL Utility Toolkit)
  • X11 (X Window System)
  • Xt, Xmu, Xi (X11 packages)
  • GIT (version control system)
  • python3 (python interpreter for cygwin)

Search for the keywords provided in the search box. The packages are organized into groups that can be opened with the '+' button. Open the groups that have either "Devel" or "Lib" and select the package matching item description and mentionning "devel" or "lib" on it's name. To select items for installation click the weird icon to the left of "Skip" or "Default" until it reads "Install" instead. In some version of Cygwin, you should click on a button and select the version you want (we recommend the lastest ones without the (test) indicator) After all packages are selected press 'Next' to install Cygwin.

Tip: In the view drop-down menu select "Category" which will reorganize packages to show them by category. You may then chose to install all the developer tools for Cygwin, which is overkill and will take ~20-30 minutes, but may be easier than finding out the tools listed above.

Compilation

Once you open Cygwin, download Cytosim using the command:

git clone https://gitlab.com/f.nedelec/cytosim.git cytosim

Compile from within the Cygwin terminal, which will use the toolchain (gcc and make) provided by cygwin. The MACHINE should be automatically selected (in case of trouble, set MACHINE:=cygwin in makefile.inc). You may disable PNG support by setting HAS_PNG:=0. The procedure is the same as on other platforms (enter make). If you experience trouble, please let us know.

If an error occur, look at the last messages to find out which library is missing. You can add them back to Cygwin by exiting it and running the setup.exe again. Then search for the missing library and install. This will only update Cygwin with the missing package, there is no need to select all other packages again.

The X Window System (X11)

Finally, all graphical tools included in cytosim (in particular 'play') will use the X Window System also known as X11 to open a window, and this will work only if a X11 server is running on your local computer. Two X11 implementations can be installed with Cygwin:

Cygwin/X

Xming

We got things to work with the free 2007 version of Xming. Xming can be installed while Cygwin installation is running. Once Xming is installed run XLaunch to start the X11 window server, and direct your application to this server by setting the DISPLAY environment variable.

This will instruct 'play' to send X11 queries to the default X11 server on the local machine. This command should be run once every time a new cygwin terminal is opened, otherwise 'play' will fail with a message "failed to open display".

Tip: To debug X11, it may be useful to run standard program such as xclok. This way you can test if the X11 server is operational.

Starting

Cytosim will only work within Cygwin, and not directly under Windows. This means that it cannot be started from the Windows command line, and you can close the Windows/MS-DOS command prompt.

Cytosim should be started from the Cygwin terminal window:

cd cytosim
export DISPLAY=:0
bin/play live

Author: Daniel Cortes, Julio Belmonte and Francois Nedelec, last updated 4.04.2020