== Setup Model Compiler on Linux/Mac ==

[[TableOfContents(3)]]

=== Description ===
 * To compile Ionic, Constitutive, Active Tension, and Material Coordinate Models on your computer please follow these instructions to install a fortran compiler if you do not have one and link it to Continuity.
 * You can choose between 2 compilers, g95 and the Intel Fortran Compiler. g95 is free but not as fast as the Intel Fortran Compiler. You can get a trial version of the Intel Fortran Compiler but after 30 days you must purchase it to continue using it.

=== Install g95 ===
 1. Make sure you have the latest release of Continuity.
 1. If you are running Linux and have sudo priviledges, try running <{{{sudo apt-get install g95}}}>. Otherwise go to [http://www.g95.org/dl.shtml] to download and install the compiler.
 1. Find the path to the g95 compiler executable. For example mine is <{{{/home/aguthals/Documents/g95-install/bin/i686-unknown-linux-gnu-g95}}}>. The executable should be in a folder named g95-install/bin.
 1. Now bind the {{{g95}}} command to this executable. If you do not have root privileges, go to the next step. Otherwise go to your /bin directory and run:
  1. <{{{ln -s <PATH TO g95 executable> g95}}}>. For example, I would run <{{{ln -s /home/aguthals/Documents/g95-install/bin/i686-unknown-linux-gnu-g95 g95}}}>.
 1. If you do not have root privileges:
  1. cd to the directory containing the g95 executable and rename the file to g95. For example, I would run <{{{mv i686-unknown-linux-gnu-g95 g95}}}>.
  1. Modify your startup script (.bashrc in your home directory for bash users) in your home directory. Insert the following line: <{{{export PATH=<PATH TO g95 executable directory>:$PATH}}}>. For example, I would insert <{{{export PATH=/home/aguthals/Documents/g95-install/bin:$PATH}}}>.
  1. Restart the terminal.
 1. cd to Continuity's home directory and run:
  1. {{{./setup}}} (if running continuity for the first time)
  1. {{{source mglinit}}}
  1. {{{autoconf}}}
  1. {{{./configure --with-g95}}}
  1. After you running ./configure --with-95, you should see something more or less like this:
    {{{
  Shell:                      /bin/sh
  C compiler:                 gcc
  C++ compiler:               /usr/bin/g++
  C compiler flags:           -c  -DG95 -O2 -finline-functions
  Fortran compiler:           /bin/g95
  F90C compiler:
  Fortran compiler flags:     -c -r8 -fno-second-underscore -ffixed-line-length-132 -cpp -DPYTHON -DLINUX -DHAVE_LAPACK -DG95 -O3 -ftree-vectorize
  Fortran libraries:
  Linker:                     /bin/g95
  Linker flags:               -shared
  Libs:
  MPICC:             
  MPILD:              
  MPILDFLAGS:                
  MPICCFLAGS:                
  Install path:               /opt/continuity
  Host binary type:           linux32
  OBJEXT:                     o
  LIBEXT:                     a
  SWIG:                       /usr/local/bin/swig
    }}}
 1. You can now compile model equations within the various model editors. After editing an equation, go to the {{{Compile}}} tab and select your current server from the drop-down menu. If it is not there type in "localhost (current server)", then click {{{Compile}}}.

=== Install Intel Fortran Compiler ===
 1. Make sure you have the latest release of Continuity.
 1. Go to [http://www.intel.com/cd/software/products/asmo-na/eng/278834.htm] to download and install the compiler.
 1. Find the path to a shell script named something like "ifortvars.sh" (or .csh for cshell users) in the fortran compiler's bin directory. For example mine is <{{{/opt/intel/Compiler/11.1/038/bin/ia32/ifortvars_ia32.sh}}}>. The script will be in the same folder as {{{ifort}}} (the compiler executable).
 1. Find the path to the fortran compiler's lib directory, for example mine is <{{{/opt/intel/Compiler/11.1/038/lib/ia32}}}>. The folder will contain numerous libraries such as {{{libifcore.so}}}.
 1. In your startup script (.bashrc in your home directory for bash users), insert the following lines: <{{{export IFC_LIB_PATH="<PATH TO lib>"}}}> and <{{{source <PATH to ifortvars>}}}>. For example, I would insert <{{{source /opt/intel/Compiler/11.1/038/bin/ia32/ifortvars_ia32.sh}}}> and <{{{export IFC_LIB_PATH="/opt/intel/Compiler/11.1/038/lib/ia32"}}}>.
 1. Restart the terminal.
 1. cd to Continuity's home directory and run:
  1. {{{./setup}}} (if running continuity for the first time)
  1. {{{source mglinit}}}
  1. {{{autoconf}}}
  1. {{{./configure}}}
 1. You can now compile model equations within the various model editors. After editing an equation, go to the {{{Compile}}} tab and select your current server from the drop-down menu. If it is not there type in "localhost (current server)", then click {{{Compile}}}.
=== Using g95 on the Mac ===
 * Note: This work around is '''only''' for running g95 on the MacOS.  Not Linux.
 * If you try to compile on the Mac with g95 you may get an error like this:
    {{{
ld: in /Applications/cont5609/continuity/pcty/MglToolsLib/lib/python2.5/config, can't map file, errno=22
make[2]: *** [BMOrtho_incompmodule.so] Error 1
make[1]: *** [BMOrtho_incomp] Error 2
make: *** [bmdynamic] Error 2
}}}
   Here's a work around:
   1. Make sure that the python2.5 framework is installed.  In particular you need this file:
      /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/config/libpython2.5.a
      If you don't have this file, you should be able to find python2.5 from the python.org website.
   2. Open the <continuity>/src/Options.mk file and change this line
      LDFLAGS   = -dynamic -bundle -bundle_loader /Applications/cont5609/continuity/pcty/!MglToolsLib/lib/python2.5/config
   to this line:
      LDFLAGS   = -dynamic -bundle -bundle_loader /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/config/libpython2.5.a