HPC/Applications/python

In recent years, Python-based software distributions with a broad sope and an integrated package manager became popular. The suites typically contain:

• A Python interpreter.
• The Conda/pip package management systems.
• A wide-ranging set of Python-native packages, extensions, and add-on executables, often including:
  • Idle – Python Integrated DeveLopment Environment
  • iPython and juPyter – Interactive computation system
  • Cython – Compiler for a superset of Python and C/C++
• Supporting binaries and all libraries used by the above, e.g.:
  • BLAS/LAPACK – Linear algebra libraries
  • Tcl – Interpreter for the Tool Command Language
  • MPI – Runtime environment for parallel applications using Message Passing Interface, providing the mpirun or mpiexec commands, plus related binaries and libraries.

The inclusion of libraries and supporting binaries can interfere with other software modules installed on an HPC system like Carbon. This is because HPC software typically leverages conventional Unix environment variables like PATH, LD_LIBRARY_PATH, and PYTHONPATH, to become accessible to users. These environment variables are interpreted in a priority-based manner which can easily lead to parts of one module overshadowing parts from another.

Caveat: Avoid loading modules at the same time for both a Python suite with an included MPI and a separate MPI implementation, especially in your dot-files.

A Python suite with an included MPI runtime makes parallel computing easily accessible under Python, but this means a "mere python module" can clash with other MPI implementations used on Carbon. Loading a module for a Python suite that contains MPI and a separate MPI module at the same time can be done but then requires more detail for the MPI launcher in job scripts. Without that, non-obvious failures will result for either bundled parallel applications within the Python suite or (worse) unrelated compiled applications on Carbon.

Interpreter-only releases from the Python Software Foundation

Module nomenclature

python/pyMajor.pyMinor/compilerName-compMajor.compMinor/pyMajor.pyMinor.pyPatch-moduleBuild

Contains

• The Python interpreter only, from the python.org sources.

Python interpreters and packages as bundled with the OS

Module nomenclature

python-osname/pyMajor.pyMinor/compilerName-compMajor.compMinor/pyMajor.pyMinor.pyPatch

Contains

• The Python interpreter that comes with the operating system, which is required for many system internals and for system-provided add-on packages (installed via rpm or yum).

These module normally do not need to be loaded. They are included here for visibility in the module system, and as a prerequisite for (usually older) modules which provide Python packages outside of Conda or Pip. Such packages are usually tied to the version of the Python interpreter under which they were installed.

Suites with vendor-distributed package set

Module nomenclature

python-distributor/pyMajor.pyMinor/distMajor/distributor_defined_version[…]-moduleBuild

Contains

• Python software suite with the package selection as distributed by the vendor.

Suites with customized package set

Module nomenclature

python-env-distributor/pyMajor.pyMinor/distMajor/pyVersion[…]-moduleBuild

A default selection of packages deemed useful for jobs on Carbon.

python-env-distributor-purpose/pyMajor.pyMinor/distMajor/pyVersion[…]-moduleBuild

Same, with alternative package selections. (TBD)

Contains

• Python software suite with the package selection customized for Carbon.

This is usually implemented as a Conda "environment" derived from a vendor-distributed Conda suite.