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Building OpenCMISS examples (Unix/terminal)

With the new CMake-based build system, building OpenCMISS applications and examples has become much easier. Any installed OpenCMISS suite has a OPENCMISS_INSTALL_ROOT directory, which contains all the information needed to build and link applications against the installed libraries.

Building existing PMR examples

Building examples obtained from the PMR (Physiome Model Repository) is very simple.

  1. Download/clone the examples source code to a location of your choice
  2. Create a build folder inside and enter it
  3. Invoke cmake -DOPENCMISS_INSTALL_DIR=<OPENCMISS_INSTALL_ROOT> ..
  4. Invoke make install

Now you should have a binary ./run in your example source that can be executed.

For convenience, you can also define the OPENCMISS_INSTALL_DIR variable in your local environment. The examples will use that if found, simplifying the build process even more!

Caution

Not all models found at the PMR there are CMake-based. Moreoever, many examples using Iron need to be executed using your MPI binary in order to run in parallel. Please refer to the model’s own documentation in each case.

Building all examples

Caution

This feature is for the transition phase from the SVN global examples repo to separate PMR examples only

Among the build system targets is also a examples target. Invoke that to have the build system create a folder <OPENCMISS_ROOT>/examples for you, which contains all the examples from the GitHub main examples repository. All of them will be attempted to build.

Also see the Troubleshooting section for common issues.

Creating new OpenCMISS applications

With the new CMake-based build system, building OpenCMISS applications and examples has become much easier. Any installed OpenCMISS suite has a OPENCMISS_INSTALL_ROOT directory, which also contains a CMake package config file.

Hence, any (CMake-powered) application using OpenCMISS just need to add the OpenCMISS installation directory to their CMAKE_PREFIX_PATH and can import OpenCMISS build targets via find_package(OpenCMISS). The config file provides the following CMake link targets:

opencmiss:An interface target to add as link library to any example library or executable. Wraps the :cmake:iron and :cmake:zinc build targets (if installed).
iron:The iron library. Only available if OC_USE_IRON is set.
zinc:The zinc library. Only available if OC_USE_ZINC is set.

Note

The OPENCMISS_INSTALL_DIR variable used for the PMR examples does nothing but set the CMAKE_PREFIX_PATH variable. For unexperienced users this is more intuitive and it also allows to specify the environment variable of the same name (using CMAKE_PREFIX_PATH in the environment has wider consequences!)