How to install intel compiler to work on cygwin at the command line: 

This is what I got from the following post on google: 

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All necessary paths and environment variables are set if you put the Microsoft linker path in ICL.CFG, and open the Intel 
compiler command line window on the Start menu. Then you can run cygwin.bat so that bash inherits the ICL paths, 
without breaking ICL. You will sometimes get the bash warning about finding Windows style paths in the environment, 
but those are necessary for ICL and Microsoft link. Needless to say, the Windows environment variable forgetfulness
 point will be reached sooner with this setup.

After I run cygwin.bat, and try to run icl, it says:

link: invalid option -- o
Try `ling --help' for more information.

I verified that icl compiles without any problems before I run cygwin.bat

What am I missing?



This would indicate that you ignored my advice about icl.cfg, and so you are getting the wrong link.exe.  It should have said "link" not "ling."
For a VC9 installation, /windows/C/Program Files/Intel/Compiler/11.1/026/bin/ia32/icl.cfg:
-Qlocation,link,"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin"
-Qprec-div -Qprec-sqrt -Qansi_alias
----------------------------------------------------------





So here is what you do: 
edit /cygdrive/c/IntelInstall/Compiler/11.1/026/bin/ia32/icl.cfg

add: 
-Qlocation,link,"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin"
-Qprec-div -Qprec-sqrt -Qansi_alias


Then run the intel compiler command window. Go to C:\Cygwin and run Cygwin.bat. 
you are now running cygwin with the correct paths.  Type "export" at the command line, and figure out which variables have been set that relate to the intel compiler and visual studio environment. Build a file containing specific export commands and source it from your .bashrc. intel.sh is an example of such file on a Windows XP 32 build. 



Compiling ISSM using Matlab compatible  compilers. 

At: http://www.mathworks.com/support/compilers/R2011b/win64.html#n2 
you will find a list of Matlab supported compilers. 


We'll try the compile with the Microsoft Windows SDK 7.1: http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=8279



MPICH2: 
to run in parallel.  First install MPICH2 from www.mpich.org/downloads. Make 
sure the install directory in C:\Program Files\MPICH2, otherwise, ISSM will 
not be able to figure out where the mpi libraries are installed on your windows platform.

Then fire up smpd in a command line under Administrator privileges: 
smpd -install

Then: 
mpiexe.exe -remove
mpiexe.exe -register (type enter for username, for password, type your windows password, do not chose anything else!)
mpiexe.exe -validate (should return SUCCESS)

Then you are ready to run parallel.

To do: how do we document this? Create webpage for all of this. + get a fortran compiler giong!
