OpenCMISS Build System

Basic instructions for building the OpenCMISS computational library.

The build system is 99% done so this documentation is interim, more detailed documentation will follow.

1. Install Linux OS or VM etc.

2. Check compiler version. The GCC 13 compilers have a compiler bug (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=103931) that means they may not compile the OpenCMISS source. Ensure that you have a compiler that works.

   For example:

   • Install GCC 14.

     • On Ubuntu

       sudo apt install gcc-14 g++-14 gfortran-14
       sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-14 140
       sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-14 140
       sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-14 140
       gcc -v
       g++ -v
       gfortran -v

   • Install Intel oneAPI. Following the instructions to install the Intel oneAPI base

   toolkit (https://www.intel.com/content/www/us/en/developer/tools/oneapi/base-toolkit.html) and HPC toolkit (https://www.intel.com/content/www/us/en/developer/tools/oneapi/hpc-toolkit.html).

3. Install necessary pre-requisite packages are installed.

   • For Ubuntu

     sudo apt install git cmake gfortran pkg-config bison flex libmpich-dev liblapack-dev libblas-dev python3-dev python3-numpy swig doxygen graphviz

   • For Fedora

     sudo git dnf install cmake gcc-gfortran pkgconf bison flex mpich-devel lapack-devel blas-devel python3-devel python3-numpy swig doxygen graphviz

4. Create a directory for OpenCMISS and change directory into it e.g.,

   mkdir ~/OpenCMISS
   cd ~/OpenCMISS

5. Clone the build system.

   git clone https://github.com/OpenCMISS/build_system.git

6. Create some sub-directories.

   mkdir setup
   mkdir src
   cd src
   mkdir dependencies

7. There is a small bug in the git repository handling. Until I get a chance to fix the bug the git commands are disabled and we will just get the repositories manually. It only has to be done once. This will eventually change.

   git clone https://github.com/OpenCMISS/libOpenCMISS.git
   cd dependencies
   git clone https://github.com/OpenCMISS-Dependencies2/FieldML-API.git
   cd FieldML-API
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/GKlib.git
   cd GKlib
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/hdf5.git
   cd hdf5
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/hypre.git
   cd hypre
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/lapack.git
   cd lapack
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/libcellml.git
   cd libcellml
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/libxml2.git
   cd libxml2
   git fetch --all --tags --prune
   git checkout tags/v2.9.11 -b opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/METIS.git
   cd METIS
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/mumps.git
   cd mumps
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/ParMETIS.git
   cd ParMETIS
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/petsc.git
   cd petsc
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/scalapack.git
   cd scalapack
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/scotch.git
   cd scotch
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/slepc.git
   cd slepc
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/superlu.git
   cd superlu
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/superlu_dist.git
   cd superlu_dist
   git checkout opencmiss_develop
   cd ..
   git clone https://github.com/OpenCMISS-Dependencies2/zlib.git
   cd zlib
   git checkout opencmiss_develop
   cd ../../..

8. Create the build system files.

   • GNU/mpich configuration.

     cd setup
     cmake -DOpenCMISS_ROOT=~/OpenCMISS -DOpenCMISS_TOOLCHAIN=gnu -DOpenCMISS_MPI=mpich ../build_system/.
     make create_configuration

   • Intel configuration.

     cd setup cmake -DOpenCMISS_ROOT=~/OpenCMISS -DOpenCMISS_TOOLCHAIN=intel -DOpenCMISS_MPI=intel ../build_system/. make create_configuration

9. Check the variables are OK, e.g., in the Variables directory of the directory below are the variables that control this configuration of OpenCMISS. Edit if required or just use the current defaults

   • GNU/mpich configuration

     cd ~/OpenCMISS/build/configs/x86_64-linux/gnu-C14.2-gnu-F14.2/mpi-mpich-system/Release

   • Intel configuraiton

     cd ~/OpenCMISS/build/configs/x86_64-linux/intel-C2025.0-intel-F2025.0/mpi-intel-system/Release

10. Build OpenCMISS.

    make

11. Once OpenCMISS has been successfully build and installed, any updates to the OpenCMISS code in the ~/OpenCMISS/src/libOpenCMISS directory can be compiled and installed by

    • GNU/mpich configuration

      cd ~/OpenCMISS/build/x86_64-linux/gnu-C14.2-gnu-F14.2/mpi-mpich-system/OpenCMISS/Release
      make install

• Intel configuration

  cd ~/OpenCMISS/build/x86_64-linux/intel-C2025.0-intel-F2025.0/mpi-intel-system/OpenCMISS/Release
  make install