HPC/Applications/python

Python on Carbon can be accessed through several routes. Each route gives access to certain packages for import, and sometimes to supporting software. To choose a particular Python implementation, use the command module load modulename.

The routes are shown below, along with their module naming convention.

Caution: Python add-on packages that were installed under one route (or module) usually are not accessible through another module.

Standard distributions

Module nomenclature

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

Contains

A Python interpreter and the standard packages, as distributed from python.org.

OS-provided bundles

Module nomenclature

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

Contains

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

Examples

python-centos/2.4/gcc-4.1/2.4.3

python-centos/2.6/gcc-4.4/2.6.6

python-centos/2.7/gcc-4.8/2.7.5

Recommend module name form

(none)

These modules 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 provided Python independently (instead of by package manager), and which 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.

Examples

python-intel/2.7/2018/2.7.14-2018.1.023-1

python-intel/3.5/2017/3.5.3-2017.3.052-1

python-intel/3.6/2018/3.6.3-2018.1.023-1

python-anaconda/2.7/4/2.7.11-4.0.0-2

Recommend module name form

python-intel/2.7

python-intel/3.6

python-anaconda/2.7

python-anaconda/3.5

Python-based software suites with a broad sope became popular in recent years. They 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++
• All libraries and supporting binaries required 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, including the mpirun or mpiexec launch commands.

The last item can be problematic because libraries and supporting binaries included in a Python suite can interfere with other software modules on Carbon. For access by users, HPC software typically leverages conventional Unix environment variables like PATH, LD_LIBRARY_PATH, and PYTHONPATH. These environment variables are interpreted front-to-back, which implies priorities and can easily lead to resources from one module overshadowing those from another when they use the same name.

In particular, 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.

Caution: 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 (.bashrc, .modules-el*).

Various workarounds for MPI clashes exist:

• Altering the module load order.
• Launching the non-python MPI variant with qualified paths like $FOO_HOME/bin/mpirun.
• If MPI is not needed on the Python side, use a custom virtual environment that has MPI excluded (described in the next section).

Please contact [email protected] for help to choose an approach.

Suites with customized package set

Module nomenclature

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

Python with 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 virtual environment with a package selection customized for Carbon.

The virtual environments are derived from one of the vendor-distributed Conda suites described in the previous section.