Contents of CM Wiki

User Documentation * **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] * 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":/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":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 the CVS manual * 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]