OpenCMISS FAQ

Building OpenCMISS

~/hpc/opt/OpenCMISS/cercmissprd01
mkdir main
cd main/
git clone https://github.com/OpenCMISS/setup.git
mkdir setup-build
cd setup-build
cmake -DOPENCMISS_ROOT=../ -DOPENCMISS_PERFORM_INITIAL_BUILD=false -DOPENCMISS_CONFIG_BUILD_TYPE=Debug ../setup
make
cd ../build/manage/release/
pluma OpenCMISSInstallationConfig.cmake
# set(IRON_BRANCH devel)
# set(IRON_DEVEL git@github.com:PrasadBabarendaGamage/iron)
# option(OPENCMISS_USE_ARCHITECTURE_PATH "Use architecture path to enable multiple configs in the same installation." YES)
# option(OPENCMISS_DEVEL_ALL "Download/checkout development branches of all components of the OpenCMISS build." YES)
cmake -DOPENCMISS_MPI=mpich -DOPENCMISS_MPI_USE_SYSTEM=NO -DOPENCMISS_TOOLCHAIN=gnu -DOPENCMISS_BUILD_TYPE=debug .
make create_config
pluma configs/x86_64_linux/gnu-C5.4-gnu-F5.4/mpich_release/OpenCMISSLocalConfig.cmake
# set(OC_SYSTEM_LIBXML2 OFF)
# set(OC_PYTHON_BINDINGS_USE_VIRTUALENV YES)
# set(OC_USE_ZINC OFF)
# set(IRON_WITH_Python_BINDINGS YES)
make build_config
cd /home/psam012/hpc/opt/OpenCMISS/cercmissprd01/main/install/x86_64_linux/gnu-C5.4-gnu-F5.4/mpich_release/python/Release
python setup.py install --force
source /home/psam012/hpc/opt/OpenCMISS/cercmissprd01/main/install/x86_64_linux/gnu-C5.4-gnu-F5.4/mpich_release/virtual_environments/oclibs_venv_py27_release/bin/activate

Using python bindings on hpc3

# To use it, open a terminal and log in​to​ the hpc3 machine:
ssh hpc3 # or
ssh upi@hpc3​

# Make sure you are running the bash shell
bash

# Setup environmental variables for OpenCMISS
source /people/cmiss/develop_opencmiss.sh

# Tell python where the OpenCMISS libraries are located
source /people/cmiss/opencmiss/install/x86_64_linux/gnu-C4.4-gnu-F4.4/openmpi_release/virtual_environments/bin/activate

# Go to the directory where the Laplace example is located (if needed, download from the OpenCMISS-examples repo)
cd python/example/location/

# Run the OpenCMISS example.
python LaplaceExample.py

Debugging OpenCMISS examples

Set diagnostics on and off before/after the line of interest.

Use Totalview.

Hydrostatic pressure export

Element constant hydrostatic pressure fields are stored in the exelem files.