FrontPage

<h1>Contents of CM Wiki</h1>

<ul>

<li><a name="user" href="#user">User Documentation</a></li> <li><a name="user" href="#developer">Developer Documentation</a></li>

</ul>

User Documentation <a name="user"></a>

• Introductory links (mainly) for new users
  • Getting Started
  • "CMISS Examples":http://cmiss.bioeng.auckland.ac.nz/development/examples

and CMISS (cm) Tutorials

• Cm New User Notes.
• Creating Dot Com Files.
• "CMISS Manual Table of Contents":CMISSManualTOC.
• Sparse Matrix Notes.
• What Is The Difference Between Classes Vs Regions In CMISS
• "CMISS back-end commands":http://cmiss.bioeng.auckland.ac.nz/development/help/cm/commands/index.html

• Recording and discussing bugs and ideas for future features

  • "Tracker":https://tracker.bioeng.auckland.ac.nz/buglist.cgi?query_format=specific&bug_status=__open__&product=CMISS-cm
  • 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
  • <a href="https://cms.bioeng.auckland.ac.nz/intranet/itgroup/support/loadlevellertool">Using LoadLeveler</a> 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":/cmgui/wiki

Developer Documentation<a name="developer"></a>

<p> <a href="http://cmiss.bioeng.auckland.ac.nz/cgi-bin/cmiss-lookup.cgi">CMISS Viewer</a></p>

• 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
  • <A HREF="http://www.physiome.org.nz/lung/mp-cmiss-with-the-intel-compilers-1/mp-cmiss-with-the-intel-compilers">MP CMISS with the intel compilers</A>

  • Development Branches and Merging Changes
  • Notes on EngsciLab CMISS.

• General code information

  • "List of modules in cm":http://cmiss.bioeng.auckland.ac.nz/development/help/cm/modules-list.html
  • CMISS File Extensions
  • A summary of "cm field parameters":http:/openCMISS/wiki/CmFieldParameters including comments on versions and scale factors.
  • Itemised cm code errors
    • "Enters/Exits errors":http://cmiss.bioeng.auckland.ac.nz/development/help/errors/findenterexit.html
    • "Argument mismatch errors":http://cmiss.bioeng.auckland.ac.nz/development/help/errors/argument_usage_mismatch/argument_usage_mismatch.html
    • "Array dimension errors":http://cmiss.bioeng.auckland.ac.nz/development/help/errors/dimension_error.html
    • "General errors":http://cmiss.bioeng.auckland.ac.nz/development/help/errors/general_error/general_error.html
    • "Common block errors":http://cmiss.bioeng.auckland.ac.nz/development/help/errors/common-errors.html
    • "All FTNCHEK errors in CMISS":http://cmiss.bioeng.auckland.ac.nz/development/help/errors/checkcmiss.txt

• Everything CVS

  • Configuring your CVS environment variables

  • Introduction to CVS, see also <a href="http://ximbiot.com/cvs/manual/">the CVS manual</a>

  • Configuring the automatic CVS update

  • Setting Up for CMISS CVS Access

  • "Change CVS Root":http://www.cmiss.org/Members/taus007/Change%20CVS%20Root/view

    • 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":http://cmiss.bioeng.auckland.ac.nz/development/examples (Examples tested each night.)
  • "Complete list of test examples":http://cmiss.bioeng.auckland.ac.nz/development/examples/list_all.html (Above examples plus more.)
  • "View Failed test examples":http://cmiss.bioeng.auckland.ac.nz/development/examples/notify_all_mail.html

• Useful Other Links

  • Debugging CMISS

    • Using Totalview

  • Profiling Code to estimate time spent in individual routines, to help make your code more efficent.

  • "Collector":CMISSfeatures 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