Installation and Usage

Work In Progres

There are two forms to use DuneCopasi. The first and easiest one is using a Docker Container where the software is boundled such that no installation other than docker is required. On the second one, the compilation of the source code is compulsory.

Containerized Usage

In this mode, there is no need to fullfil specific requirements other than those for docker installation.

Install Docker

First, get and install Docker following the docker installation instructions.

Pull Container

Then, you may get the latest stable DuneCopasi container by pulling it from the GitLab registry

docker pull registry.dune-project.org/copasi/dune-copasi/dune-copasi:latest

Run DuneCopasi

Finally, run the dune_copasi_md executable from the container

# TODO

Manual Installation

Locally building and installing DuneCopasi requires to first obtain the dependencies, then compile the dependent dune modules and finally installing on a final directory.

Dependencies

The following list of software is required to install and use DuneCopasi:

info

Notice that some required dune modules are forks of original reopsitories and are placed under the COPASI namespace on the DUNE GitLab.

Software	Version/Branch
CMake	>= 3.1
C++ compiler	>= C++17
libTIFF	>= 3.6.1
muParser	>= 2.2.5
dune-common	== 2.7
dune-geometry	== 2.7
dune-grid	== 2.7
dune-uggrid	== 2.7
dune-istl	== 2.7
dune-localfunctions	== 2.7
dune-functions	== 2.7
COPASI/dune-logging	support/dune-copasi-latest
COPASI/dune-typetree	support/dune-copasi-latest
COPASI/dune-pdelab	support/dune-copasi-latest
COPASI/dune-multidomaingrid	support/dune-copasi-latest

Installation

The first four can be obtained by your prefered package manager in unix-like operating systems. e.g.

Debian/Ubuntu

apt update

apt install cmake gcc g++ libtiff-dev libmuparser-dev git

macOS

# Apple Command Line Tools and Brew assumed to be available

brew update

brew install cmake gcc libtiff muparser git

The required DUNE modules (including DuneCopasi) can be obtained via internet by using git. For smooth installation, is better place all the dune modules within the same directory.

# prepare a folder to download and build dune modules

mkdir ~/dune-modules && cd ~/dune-modules

# fetch dependencies & dune-copasi in ~/dune-modules folder

git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-common

git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-geometry

git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-grid

git clone -b releases/2.7 https://gitlab.dune-project.org/staging/dune-uggrid

git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-istl

git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-localfunctions

git clone -b releases/2.7 https://gitlab.dune-project.org/staging/dune-functions

git clone -b support/dune-copasi-latest --recursive https://gitlab.dune-project.org/copasi/dune-logging

git clone -b support/dune-copasi-latest https://gitlab.dune-project.org/copasi/dune-typetree

git clone -b support/dune-copasi-latest https://gitlab.dune-project.org/copasi/dune-pdelab

git clone -b support/dune-copasi-latest https://gitlab.dune-project.org/copasi/dune-multidomaingrid

git clone -b latest https://gitlab.dune-project.org/copasi/dune-copasi

Then build and install the DUNE modules with the dunecontrol script:

# configure and build dune modules

./dune-common/bin/dunecontrol make all

# install dune-copasi (this operation may requiere sudo)

./dune-common/bin/dunecontrol bexec make install

# remove source and build files

cd .. && rm -r ~/dune-modules

For further info on dune module installation process, please check out the dune-project web page.

Custom installation path

If you don't want to install the DUNE modules system-wide, you can set the CMAKE_INSTALL_PREFIX to a custom directory. See CMake documentation here.

Run DuneCopasi

In case you installed DuneCopasi system-wide, you should be able to call the program dune_copasi_md from your command line accompained with a configuration file. Otherwise, the executable will be under bin/ folder on the installed directory.

# TODO

To find out the appropiated contents on the configuration file, check out the Parameter Tree documentation.