https://github.com/patriciobcs/mini-aevol
Parallel implementation of a reduced version of the Aevol simulator
https://github.com/patriciobcs/mini-aevol
aevol cuda simulation
Last synced: about 1 month ago
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Parallel implementation of a reduced version of the Aevol simulator
- Host: GitHub
- URL: https://github.com/patriciobcs/mini-aevol
- Owner: patriciobcs
- Created: 2022-11-14T23:21:48.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-12-05T13:49:32.000Z (over 3 years ago)
- Last Synced: 2025-03-13T11:18:22.639Z (over 1 year ago)
- Topics: aevol, cuda, simulation
- Language: Jupyter Notebook
- Homepage: https://gitlab.inria.fr/lturpin/micro-aevol2/
- Size: 5.88 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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 [aevol.fr](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](http://www.cygwin.com/)
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
```sh
mkdir build
cd build
cmake ..
ninja
```
It will produced the executable `micro_aevol_cpu`.
If CUDA toolkit is available on your system, you can build the software with GPU support
```sh
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
```sh
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):
```sh
cd simulation_example_1
PATH/TO/micro_aevol_cpu -r 1000
```
## Model and Implementation
These [slides](/presentation/slides.pdf) 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 [aevol.fr](http://www.aevol.fr)
## License
This project is licensed under the GPLv2 License