Installation - malcolmw/PyVoroTomo GitHub Wiki
Table of Contents
Dependencies
PyVoroTomo depends on a few external packages:
| Package | Version |
|---|---|
| cython | >= 0.29.14 |
| h5py | >= 2.10.0 |
| KDEpy | >= 1.0.3 |
| mpi4py | == 3.0.3 |
| numpy | >= 1.18.1 |
| pandas | >= 1.0.3 |
| pykonal | >= 0.2.3 |
| pytables | >= 3.6.1 |
| scipy | >= 1.4.1 |
A - Installing on a cluster
A1 - Create base environment
bash-4.4$ conda create --name=pyvorotomo python=3.8
bash-4.4$ conda activate pyvorotomo
A2 - Install mpi4py
mpi4py comes with its own implementation of OpenMPI when installed using conda, but you want to use the system-wide installation of MPI that should be available on your cluster. To link mpi4py with the MPI implementation available on your system, you need to use pip, but first you need to initialize your environment to make the mpicc wrapper available:
(pyvorotomo) bash-4.4$ source /path/to/system/mpi/setup.sh
(pyvorotomo) bash-4.4$ export MPICC=$(which mpicc)
Note: On discovery.usc.edu I also executed
(pyvorotomo) bash-4.4$ export CC=$(which mpicc)
Now you can install mpi4py using pip:
(pyvorotomo) bash-4.4$ pip install mpi4py
A3 - Install other dependencies available through conda
(pyvorotomo) bash-4.4$ conda install cython h5py numpy pandas pytables scipy
A4 - Install KDEpy using pip
(pyvorotomo) bash-4.4$ pip install KDEpy
A5 - Install PyKonal
(pyvorotomo) bash-4.4$ git clone [email protected]:malcolmw/pykonal.git
(pyvorotomo) bash-4.4$ cd pykonal
(pyvorotomo) bash-4.4$ pip install .
A6 - Install PyVoroTomo
(pyvorotomo) bash-4.4$ git clone [email protected]:malcolmw/PyVoroTomo.git
(pyvorotomo) bash-4.4$ cd PyVoroTomo
(pyvorotomo) bash-4.4$ pip install .
B - Installing on a desktop or laptop
B1 - Create base environment with dependencies
bash-4.4$ conda create --name=pyvorotomo python=3.8 cython h5py mpi4py numpy pandas pytables scipy
bash-4.4$ conda activate pyvorotomo
(pyvorotomo) bash-4.4$ pip install KDEpy
B2 - Install PyKonal
(pyvorotomo) bash-4.4$ git clone [email protected]:malcolmw/pykonal.git
(pyvorotomo) bash-4.4$ cd pykonal
(pyvorotomo) bash-4.4$ pip install .
B3 - Install PyVoroTomo
(pyvorotomo) bash-4.4$ git clone [email protected]:malcolmw/PyVoroTomo.git
(pyvorotomo) bash-4.4$ cd PyVoroTomo
(pyvorotomo) bash-4.4$ pip install .