Biological Dynamic Modeller - Based on Cortex 3D (Cx3D)
##Introduction:
The brain is an extremely complex system, consisting of approximately 100 billion neurons that are connected to one another. The way these neurons are structured allows for very efficient and robust function. For example, human face recognition outperforms any currently available machine algorithm. One way to better understand this complex structure is to elucidate how it arises during development. The improvements in computing technology in the last few years have made it possible to use large-scale computer simulations to investigate such developmental processes. However, the appropriate software that can fully exploit the potentials of the state-of-the-art hardware remains to be implemented.
A currently available software solution to simulate neural development is Cx3D, https://www.ini.uzh.ch/~amw/seco/cx3d/. However, this software is Java-based, and not ideal for high-performance computing (HPC). In order to adapt Cx3D to support HPC, a software that has similar functionalities as Cx3D but is coded in C++ is needed.
Check out code from this repository:
git clone https://github.com/BioDynaMo/biodynamo.git
cd biodynamo
Create build directory
mkdir build && cd build
Build
cmake ..
make
This commands build a shared library for BioDynaMo together with a test executable. Furthermore, dependencies (GMP, gtest, ...) are automatically downloaded and built as well. They are defined in CMake as ExternalProjects
Run Tests
make check
In contrast to make test, the target check will show the test ouput on failure
Our CMake build script uses a few options to influence the build process. They can be set as follows:
cmake -Doption=value ..
The value for binary options is on or off.
If you change the value of these switches, you might have to delete CMakeCache.txt beforehand.
| Option | Default Value | Description |
|---|---|---|
test |
on |
build the test executable; precondition for e.g. valgrind and coverage |
valgrind |
on |
enable memory leak checks |
coverage |
off |
creates a make target to generate a html report indicating which parts of the code are tested by automatic tests |
The build type can be specified using the -DCMAKE_BUILD_TYPE= command line parameter. Possible values are Debug|Release|RelWithDebInfo|MinSizeRel
make test executes all tests
make check executes all tests and shows test output on failure
make clean will clean all targets, also the external projects
make bdmclean will only clean the biodynamo and runBiodynamoTests targets
make testbdmclean will only clean the runBiodynamoTests target
make doc will generate the Doxygen documentation in directory build/doc. It contains a html and latex version.
You can view the html version by opening build/doc/html/index.html in your browser.
make coverage will execute the test target and generate a coverage report in build/coverage. Make sure that gcov
and lcov are installed and configure cmake with cmake -Dcoverage=on ..
Reference files for the simulation outcome are stored as Json in directory test/resources/
In rare cases it might be necessary to update these files:
./runBiodynamoTests --update-references
The reference files are then overwritten with the simulation result of the current execution. No assertions will be performed! Therefore, handle this option with care!
After each run, simulation test execution time are stored together with the latest_commit id in the corresponding csv file in test/resources/
Memory leak tests are run using the tool valgrind. To reduce the execution time, simulation result assertions are turned off by adding the --disable-assertions option.