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<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]
* [fem solve versus fem solve restart]
* "CMISS back-end commands":http://cmiss.bioeng.auckland.ac.nz/development/help/cm/commands/index.html
* **A Collection of How-Tos within 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 I found out about using the WIKI]
* [How to generate a rapid prototype of your mesh]
* **Group Specific (i.e. bioelectric, mechanic) collections of links**
* [Bidomain] for notes on development of Bidomain part of cm.
* [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.
* **Recording and discussing bugs and ideas for future features**
* "Tracker":../tracker
* [How to Find Out Which Source Changes Broke an Example]
* [Summary Notes on Failed cm Tests]
* **Code Repository**
* 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]
* **Perl Repository for cm stuff**
* Link to all perl modules available within cm for your use:
http://cmiss.bioeng.auckland.ac.nz/help/PerlUtilities/index.html
* **Useful Other Links**
* <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]
* [HPC tips]
* [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]
* [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]
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