A blog about free research software, alternative to commercial paid software.

One way to help people is to share your knowledge with those who could benefit from it. As a researcher , constant effort to solve scientific problems have exposed me to various scientific resources that can be accessed free of charge. Especially these knowledge is useful to labs and institution unable to access expensive software or novice users due to lack of expertise. In this blog, I have provided a comprehensive list of freely available softwares, alternative to commercial software. I shall share with you all that I have learned, as I make the changes or learn something new, I shall document them. Hope this blog will help those finding the way………….

Research software and books

Jan 6, 2011

Cygwin for scientific computing on windows

Microsoft Windows is run by more than 95% of personal computers. Even taking Apple's Mac OS into account, Microsoft Windows is still present on more than 80% of computers. In the free software section, I have included softwares for linux as well as windows. Now some programs are exclusively linux based. Is it possible to run linux based application on windows.


Cygwin is free software that provides a linux-like environment and software tool set to users of any modern version of MS-Windows for x86 CPUs (NT/2000/XP/Vista/7) . Cygwin consists of a Unix system call emulation library, cygwin1.dll, together with a vast set of GNU and other free software applications organized into a large number of optional packages.

Cygwin is not a means for running GNU/Linux or other Unix binary executables under MS-Windows. In order to run such research programs using cygwin, the software must be compiled from its sources. All the components needed for this task can easily be ported to MS-Windows using Cygwin.

Getting started:

1. Download and run the Cygwin installer (setup.exe).
Website to download: http://cygwin.com/index.html

Save the link (setup.exe) to your desktop, then double-click on the saved icon to begin installation.

2. A window titled Cygwin Net Release Setup Program appears. Click Next to get started.

3. Choose A Download Source: Accept the default ("Install from Internet") and click Next.

Choosing the default "Install from Internet" causes the files you will choose in a later step to be downloaded first and then validated and installed. The other choices allow you to perform this procedure in two steps.

4. Select Root Install Directory: Accept the defaults ("C:/cygwin", All Users) and click Next.

5. Select Local Package Directory: Accept the default or change it to any temporary directory of your choice, but make a note of it.

6. Select Your Internet Connection: The default should be correct for most users. Change it only if you encounter problems.

7. Choose A Download Site: Select a nearby mirror site from which to download the Cygwin packages.

At this time, the installer downloads a list of available packages from the site you have chosen. Normally, this takes only a few seconds; if there is a lengthy pause, you may wish to start over and choose a different mirror site.

8. Select Packages: If you wish to do a full installation, click on the rotating selector next to "All" (at the top of the Category list) so that the indicator to its right changes from "Default" to "Install".Click Next and skip ahead to step 10.

9. If you wish to do a custom installation, click the View button so that the indicator to its right changes from "Category" to "Full".

To select a package for installation, click on its rotating selector (in the New column) to cycle through the available choices until a version number appears. In most cases, you should choose the highest version number from those that are available. When you have completed your selections,

10. Click next. The downloading process begins once the packages have been selected. The installer indicates its progress.

Once all selected package files have been downloaded and checked, they are unpacked into the Cygwin root install directory.

11. Create Icons: Unless these icons already exist from a previous Cygwin installation, make sure the boxes are checked and click Finish.

Using Cygwin

Pathnames of files are often confusing to new Cygwin users. A pathname is simply a set of directions for locating file. An absolute pathname begins at a fixed location (the root of the file system). The confusion arises because native Windows programs use c:\ as their root, and Cygwin programs use c:\cygwin.

If you need to use a Cygwin program to read or write a file located outside of c:\cygwin, you can use a pathname beginning with /cygdrive/c/ for this purpose.

The installation directory (by default, c:\cygwin) is the root of the Unix-like file system, which contains bin, etc, home, tmp, and usr directories as would be found on a GNU/Linux or other Unix system. Within home will be one or more subdirectories, each allocated to a Windows user.

To begin, click on the Cygwin desktop icon,

or choose the Cygwin entry from your start menu, to open a Cygwin terminal window. Initially, the current (working) directory is /home/user, where user is your Windows login name.

Test Cygwin and installed packages:

Type the following commands:

$ ls -l     (list files in current directory)
$ cygcheck -c     (list installed packages in alphabetic order)
$ cd c:     (change to C-directory) 

Test the C compiler: 

$ gcc --version     (compiler version)
$ gcc --help     (for a list of options)

Test the C++ compiler:

$ g++ --version     (compiler version)
$ g++ --help     (for a list of options)


 Test the Fortran compiler:

$ g77 --version     (compiler version)
$ g77 --help     (for a list of options)

Test Python:
$ python