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
- 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
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
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
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>
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
Introduction to CVS, see also <a href="http://ximbiot.com/cvs/manual/">the CVS manual</a>
Configuring the automatic CVS update
"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**
- "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
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.