Installation

Table of Contents

1. Dependencies
2. Installing on a cluster
3. Installing on a desktop/laptop

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 .