FrontPage

Contents of CM Wiki

• User Documentation
• Developer Documentation

User Documentation

• Introductory links (mainly) for new users
  • Getting Started
  • CMISS Examples and CMISS (cm) Tutorials
  • Cm New User Notes.
  • Creating Dot Com Files.
  • CMISS Manual Table of Contents.
  • Sparse Matrix Notes.
  • What Is The Difference Between Classes Vs Regions In CMISS
  • CMISS back-end commands
• Recording and discussing bugs and ideas for future features
  • Tracker
  • How to Find Out Which Source Changes Broke an Example
  • Summary Notes on Failed cm Tests
• A collection of general how-tos for cm
  • Change Memory Allocation Parameters
  • Time Varying Boundary Conditions For Advection Diffusion Equation Problems
  • Mesh Export Cmgui 2 Cm
  • Exporting signals from cellML in cm to Unemap
  • cm-debug version: reading .irgrid files
  • Testing your new version of cmiss before submitting
  • Run the cm-debug-clear-malloc test
  • Exporting exelem and exnode file from Grid-based FEM
  • Updating a tricubic slave mesh with host mesh fitting
  • How to generate a rapid prototype of your mesh
  • Using LoadLeveler to run cm on the IBM p595 (hpc.bioeng)
  • Using HPCx
  • Using CARP
  • [Using TETGEN]?
  • [Using GMSH]?
  • HPC tips
• Group specific how-tos (e.g. bioelectric, mechanics) collections of links
  • Bidomain for notes on development of Bidomain part of cm.
  • fem solve versus fem solve restart
  • Finite Elasticity for notes of mechanics development within cm.
  • Coupled Electro Mechanics for notes on solving coupled electromechanics.
  • Write out material points positions If you would like to know the coordinates of material points in the mesh.
• Useful bits of code for use alongside cm (perl etc)
  • Perl script to create a thick-walled cylinder node file createMesh.com
  • Perl script to convert exelem to ipelem files: http://www.cmiss.org/cm/wiki/ex2ipelem/view
  • Perl script to convert bilinear mesh in 2d coord system to a trilinear mesh in a 3d coord system of known uniform thickness convert2d23d
  • Link to all perl modules available within cm for your use:

    http://cmiss.bioeng.auckland.ac.nz/help/PerlUtilities/index.html

• Useful other links
  • Data resources
• Can't find what you are looking for?
  • Try the frontend, cmgui, wiki

Developer Documentation

CMISS Viewer

• Development Guidelines
  • Programmers Style Guides
    • Fortran style guide
    • C style guide
    • Latex style guide
    • Source documentation format
  • Install cm on a laptop for development
  • Editing cm source
  • cm build speed enhancements through use of local hard drive
• Compiler Issues
  • Using the Cross compilers for win32 and glibc21 from linux.
  • Notes on Compiling a local version of CMISS on a Mandrake 10 Linux system
  • Notes on compiling a local version of cmiss on a Xeon machine
  • Notes on compiling a local version of cmiss on IA-32 using the Intel compilers
  • Notes on compiling a local version of cmiss on a ia64 machine with MKL library's
  • MP CMISS with the intel compilers
  • Development Branches and Merging Changes
  • Notes on EngsciLab CMISS.
• General code information
  • List of modules in cm
  • CMISS File Extensions
  • A summary of cm field parameters including comments on versions and scale factors.
  • Itemised cm code errors
    • Enters/Exits errors
    • Argument mismatch errors
    • Array dimension errors
    • General errors
    • Common block errors
    • All FTNCHEK errors in CMISS
• Everything CVS
  • Configuring your CVS environment variables
  • Introduction to CVS, see also the CVS manual
  • Configuring the automatic CVS update
  • Setting Up for CMISS CVS Access
  • Change CVS Root
    • If you have an old version with the old CVS_ROOT in CVS/Root then use script to change them all so you can e.g. properly cvs diff.

• Examples
  • Overview of test examples
  • CMISS Examples (Examples tested each night.)
  • Complete list of test examples (Above examples plus more.)
  • View Failed test examples
• Useful Other Links
  • Debugging CMISS
    • Using Totalview
  • Profiling Code to estimate time spent in individual routines, to help make your code more efficent.
  • Collector to present new ideas.
  • The Strategy for Introducing Distributed Memory Multiprocessing to CMISS has now been changed to start afresh with openCMISS rather than evolve from cm.
  • Using HPCx
  • Using NGS
  • OMP code notes