Installation Tutorial for Linux

June 26, 2023 ยท View on GitHub

The following is a more detailed description of the installation process of BanditPAM for Linux machines.

Prerequisites

Please ensure the following dependencies are installed:

  • A package manager like yum or apt
  • A C++ compiler; we recommend LLVM's clang: via the LLVM installation instructions
  • CMake: via the CMake installation instructions
  • OpenMP: via sudo apt install libomp-dev or sudo yum install libomp-dev
  • Armadillo: via the Armadillo installation instructions
  • CARMA: via the instructions in its guide
  • Python3: if not installed, we recommend installing Python3 via Anaconda, which is CPython compiled with clang
  • pip for your Python3 installation: this should be completed if installing via Anaconda above
  • The necessary python packages: via python -m pip install -r requirements.txt

(NOT RECOMMENDED): Instead of LLVM's clang, you can also use another C++ compiler and point your CC environment variable to it. Please ensure this is the same compiler used to compile your Python installation if using CPython. If you open a python REPL it will show the compiler used during the language installation:

>> python
Python 3.7.9 (default, Mar  1 2021, 13:32:26)
[Clang 11.0.0 (clang-1100.0.33.17)] :: Intel Corporation on darwin
Type "help", "copyright", "credits" or "license" for more information.
Intel(R) Distribution for Python is brought to you by Intel Corporation.
Please check out: https://software.intel.com/en-us/python-distribution

Do not attempt to compile the BanditPAM extension with gcc if your Python used clang, and vice versa.

BanditPAM Installation

BanditPAM can then be installed via one of the following ways:

  1. Running python -m pip install banditpam, OR
  2. Running python -m pip install . in the home directory (/BanditPAM)

Known Issues

The following is a list of issues seen when installing BanditPAM on Linux. To report a bug, please file an issue at https://github.com/motiwari/BanditPAM/

  • Beware that installing libarmadillo-dev using apt or yum may provide an outdated version of armadillo, especially if you are running an older version of Linux. In this case, you may need to download the latest stable version of armadillo and compile it from source