Installation¶
Install MIIND package with pip¶
To install with pip:
$ python -m pip install miind
MIIND is available on Windows, MacOS, and Linux for python versions >=3.6.
Standalone package¶
Additional python libraries which need to be installed using pip or conda:
numpy
matplotlib
shapely
descartes
scipy
Standalone Docker¶
Pull MIIND from DockerHub:
$ docker pull hughosborne/miind:latest
CUDA is currently disabled for the MIIND Docker image.
Building Python MIIND From Source¶
Build and Install Python MIIND Locally:
$ python setup.py install
Python MIIND depends on:
Boost
GSL
Freeglut
OpenGL
FFTW
PugiXML
Python3-Dev (Python.h)
Python MIIND optionally depends on:
CUDA Toolkit
OpenMP
MPI
ROOT
setup.py defines the cmake options for building MIIND in the variable cmake_args. When using setup.py to build MIIND, these options should be changed if a different configuration is required to the default (ENABLE_OPENMP, ENABLE_CUDA, ENABLE_TESTING). Note that platform specific versions of cmake_args are defined later in the script.
cmake_args = (
[
'-DCMAKE_BUILD_TYPE=Release',
'-DENABLE_OPENMP:BOOL=ON',
'-DENABLE_MPI:BOOL=OFF',
'-DENABLE_TESTING:BOOL=ON',
'-DENABLE_CUDA:BOOL=ON',
'-DENABLE_ROOT:BOOL=OFF',
'-DCMAKE_CUDA_FLAGS=--generate-code=arch=compute_30,code=[compute_30,sm_30]'
]
)
For example, to build MIIND with CUDA disabled and ROOT enabled.
cmake_args = (
[
'-DCMAKE_BUILD_TYPE=Release',
'-DENABLE_OPENMP:BOOL=ON',
'-DENABLE_MPI:BOOL=OFF',
'-DENABLE_TESTING:BOOL=ON',
'-DENABLE_CUDA:BOOL=OFF',
'-DENABLE_ROOT:BOOL=ON'
]
)
On Windows, vcpkg is used for building Python MIIND therefore only CUDA drivers and Ninja are required in addition to cmake and a compiler.
Building Standalone MIIND From Source¶
Standalone MIIND can also be built in the tranditional way (create a build directory and run cmake then install).
Create a build directory in the MIIND root directory:
$ mkdir build
Change directory:
$ cd build
Run ccmake to set the required cmake options and generate a cmake file:
$ cmake ..
Once generated, call make install (with admin permissions if required):
$ make install
Additional python libraries which need to be installed using pip or conda:
numpy
matplotlib
shapely
descartes
scipy
Set the following environment variables:
OMP_NUM_THREADS (See OpenMP documentation)
Add <MIIND_Installation_Directory>/share/miind/python to PATH
Add <MIIND_Installation_Directory>/share/miind/python to PYTHONPATH