pyGPCCA requires Python >= 3.6 to run. If any problems arise, please consult the Troubleshooting section.
pyGPCCA is available as a conda package and can be installed as:
conda install -c conda-forge pygpcca
This is the recommended way of installing, since this package also includes PETSc/SLEPc libraries. We use PETSc/SLEPc internally to speed up the computation of the leading Schur vectors. These are optional dependencies - if they’re not present, we compute a full Schur decomposition instead and sort it using the method introduced by Brandts (2002). Note that this scales cubically in sample number, making it essential to use PETSc/SLEPc for large sample numbers. PETSc/SLEPc implement iterative methods to only compute the leading Schur vectors, which is computationally much less expensive.
In order to install pyGPCCA from The Python Package Index, run:
pip install pygpcca # or with libraries utilizing PETSc/SLEPc pip install pygpcca[slepc]
If you want to use the development version of pyGPCCA from GitHub, run:
pip install git+https://github.com/msmdev/pygpcca
During the installation of
slepc4py, the following error(s) might appear:
ERROR: Failed building wheel for <package name>
However, this should be fine if in the end, it also outputs:
Successfully installed <package name>
To quickly verify that the packages have been installed, you can run:
python3 -c "import petsc4py; import slepc4py; print(petsc4py.__version__, slepc4py.__version__)"
Below are an alternative steps for installing PETSc/SLEPc, in case any problems arise, especially when installing from PyPI:
# install dependencies sudo apt-get update -y sudo apt-get install gcc gfortran libopenmpi-dev libblas-dev liblapack-dev petsc-dev slepc-dev -y # install a message passing interface for Python pip install --user mpi4py # install petsc and and petsc4py pip install --user petsc pip install --user petsc4py # install slepc and slepc4py pip install --user slepc pip install --user slepc4py
The most robust way is to follow the PETSc installation guide and the SLEPc installation guide or to take a look at our continuous integration steps for macOS.
The installation steps can be roughly outlined as:
# install dependencies brew install gcc open-mpi openblas lapack arpack # follow the PETSc installation steps # follow the SLEPc installation steps # install petsc4py pip install --user petsc4py # install slepc4py pip install --user petsc4py