Mini-Aevol : A mini-application based on the Aevol simulator
A reduced version (from a model and implementation point of view) of Aevol.
DO NOT USE IT TO SIMULATE BIOLOGICAL RESULTS ! See http://www.aevol.fr for that !
It must be used only to test HPC optimization of the code (parallel, vector, porting to new architecture...).
Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
Prerequisites
You will need a unix base system. Sorry for Windows users, maybe try with Cygwin
You will also need to install zlib (and its headers):
- On Debian, Ubuntu, Mint, ... (apt):
zlib1g-dev - On Arch (pacman):
zlib - On Fedora (dnf, rpm):
zlib-devel
To use cuda implementation, you will need to install the cuda-toolkit:
- On all distributions:
cuda
Compilation
The compilation is straightforward
mkdir build
cd build
cmake ..
make
It will produced the executable micro_aevol_cpu.
If CUDA toolkit is available on your system, you can build the software with GPU support
cmake .. -DUSE_CUDA=on
make
It will produced the executable micro_aevol_gpu.
Running a simulation
A help is given to explain the different parameters when using option -H or --help.
Basically, you must create a directory to store the simulation files (backup/checkpointing and stats files) and then run the simulation
mkdir simulation_example_1
cd simulation_example_1
PATH/TO/micro_aevol_cpu
You can also resume a simulation from a backup/checkpointing file (for example, resuming from the generation 1000):
cd simulation_example_1
PATH/TO/micro_aevol_cpu -r 1000
Model and Implementation
These slides give a short presentation of the model and the purpose of this project can
Authors
- Jonathan Rouzaud-Cornabas - Initial work
- Laurent Turpin
For the authors of Aevol software, see http://www.aevol.fr
License
This project is licensed under the GPLv2 License