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NEOS

pipeline status coverage report

Get Neos

To use last development state of Neos, please clone the master branch.

To get sources please use these commands:

  git clone git@gitlab.inria.fr:memphis/neos.git
  cd neos
  git submodule init
  git submodule update

My first code with Neos

Neos is available as a Docker Container.

  • On your Operating System, install Docker Desktop.

  • Launch Docker Desktop

  • In a Terminal Shell get Neos Docker Image:

$ docker pull registry.gitlab.inria.fr/memphis/neos
  • Create a working directory (for example, the directory will be in your home dir, in a subfolder called Neos):
$ mkdir -p ~/Neos/first_example
  • Get into Neos, bind your working directory with a similar one in Docker:
$ docker run -v~/Neos/first_example:/builds/first_example -it registry.gitlab.inria.fr/memphis/neos /bin/bash
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

gitlab@8cc432b5546a:/builds$ ls
neos first_example
  • Go in your working directory, copy template files
gitlab@8cc432b5546a:/builds$ cd first_example
gitlab@8cc432b5546a:/builds/first_example$
gitlab@8cc432b5546a:/builds/first_example$ cp ../neos/first_example/* .
gitlab@8cc432b5546a:/builds/first_example$ ls
CMakeLists.txt  levelsept.cpp
  • Compile your code in CMake way:
gitlab@8cc432b5546a:/builds/first_example$ mkdir build && cd build
gitlab@8cc432b5546a:/builds/first_example$ cmake .. && make
...
  • Run it
gitlab@8cc432b5546a:/builds/first_example$ ./levelset
...

Build and install

Neos requires to have some library dependencies:

  • Lapacke or Eigen3 (Eigen is enable by default)
  • MPI (optional)
  • PetsC (optional: for laplacian)
  • Bitpit (optional but strongly recommended for CORE and GEOMETRY features) (http://optimad.github.io/bitpit/)
  • mpi4py and pybind11 pip modules (optional: for Python bindings)

The main options to configure Neos build are:

  • BUILD_CORE: Enable levelset, transport...
  • BUILD_GEOMETRY: Enable somme standard geometries
  • BUILD_MATH:
    • BUILD_INTERPOLATOR: Enable distance weighted, Polynomial and RBF interpolation.
    • BUILD_LAPLACIAN: Enable laplacian

Installation example

# install bitpit
cd $HOME
git clone https://github.com/optimad/bitpit.git
cd bitpit
export BITPIT_ROOT=$PWD
mkdir build && cd build
cmake .. -DPETSC_DIR=/usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/ -DPETSC_ARCH='' -DBUILD_DOCUMENTATION=ON -DBUILD_EXAMPLES=ON -DENABLE_MPI=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$BITPIT_ROOT

cd $HOME
git clone --recursive git@gitlab.inria.fr:memphis/neos.git
cd neos
mkdir build ; cd build
export CMK=" -DCMAKE_BUILD_TYPE=Debug -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$PWD../install"
export CMK2=" -DBUILD_CORE=ON -DBUILD_GEOMETRY=ON -DBUILD_LAPLACIAN=ON -DENABLE_MPI=ON -DGEN_PYTHON=ON -DBUILD_EXAMPLES=ON -DBUILD_TESTS=ON"
export CMK3=" -DPETSC_DIR=/usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/ -DPETSC_ARCH=''"
cmake ..  $CMK $CMK1 $CMK2 $CMK3 -DBUILD_DOCUMENTATION=ON
make -j4

examples/time-poisson

To customize examples

with your preferred editor, edit ../examples/time-poisson.cpp

make
examples/time-poisson

To install Python module

cd python
pip  install --user --upgrade ./pyneos
# or
pip3 install --user --upgrade ./pyneos

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