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Searching aditional Python/Perl/R packages

Created by Potthoff, Sebastian, last modified on 27. Oct 2020

Additional packages for Python, Perl or R are installed in various ways:

  • As and extension of the default Python installation
  • As a separate module
  • As a bundle of extension which can also be loaded as a module

You can search for those packages by

  • Looking at the output of module help \<MODULENAME>
  • Searching for the package via module keyword \<PACKAGENAME>

More information and details are provided below.

Extension of the default installation(s)

Example: The Python installation provided in the foss or intel toolchain comes with a default set of additional Python packages. These can be seen, e.g. when using the module help Python command (only available if also the Python module can be loaded, i.e. after loading e.g. the foss toolchain), listed under \"Included Extensions\":

module help Python

---------------------- Module Specific Help for "Python/3.7.2" ------------------------------

Description
===========
Python is a programming language that lets you work more quickly and integrate your systems
 more effectively.


More information
================
 - Homepage: http://python.org/


Included extensions
===================
alabaster-0.7.12, asn1crypto-0.24.0, atomicwrites-1.3.0, attrs-19.1.0,
Babel-2.6.0, bcrypt-3.1.6, bitstring-3.1.5, blist-1.3.6, certifi-2019.3.9,
cffi-1.12.2, chardet-3.0.4, Click-7.0, cryptography-2.6.1, Cython-0.29.6,
deap-1.2.2, decorator-4.3.2, docopt-0.6.2, docutils-0.14, ecdsa-0.13,
future-0.17.1, idna-2.8, imagesize-1.1.0, ipaddress-1.0.22, Jinja2-2.10,
joblib-0.13.2, liac-arff-2.4.0, MarkupSafe-1.1.1, mock-2.0.0, more-
itertools-6.0.0, netaddr-0.7.19, netifaces-0.10.9, nose-1.3.7, packaging-19.0,
paramiko-2.4.2, pathlib2-2.3.3, paycheck-1.0.2, pbr-5.1.3, pip-19.0.3,
pluggy-0.9.0, psutil-5.6.1, py-1.8.0, py_expression_eval-0.3.6, pyasn1-0.4.5,
pycparser-2.19, pycrypto-2.6.1, Pygments-2.3.1, PyNaCl-1.3.0, pyparsing-2.3.1,
pytest-4.3.1, python-dateutil-2.8.0, pytz-2018.9, requests-2.21.0,
scandir-1.10.0, setuptools-40.8.0, setuptools_scm-3.2.0, six-1.12.0,
snowballstemmer-1.2.1, Sphinx-1.8.5, sphinxcontrib-websupport-1.1.0,
tabulate-0.8.3, ujson-1.35, urllib3-1.24.1, virtualenv-16.4.3, wheel-0.33.1,
xlrd-1.2.0

A separate module

Some packages are simply installed as a separate module which can be loaded via the module load command, e.g.

module load PLYfile/0.7

A bundle of extensions provided as a single module

There are a number of modules, which do not just add one extension to the environment but bundle a number of different packages. A good example is the TensorFlow module. Using module help on it reveals a list of extensions:

module help TensorFlow/2.0.0-Python-3.7.2

---------------------------- Module Specific Help for "TensorFlow/2.0.0-Python-3.7.2" ------------------

Description
===========
An open-source software library for Machine Intelligence


More information
================
 - Homepage: https://www.tensorflow.org/


Included extensions
===================
absl-py-0.8.1, astor-0.8.0, cachetools-3.1.1, cloudpickle-1.1.1,
decorator-4.4.1, gast-0.2.2, google-auth-1.7.1, google-auth-oauthlib-0.4.1,
google-pasta-0.1.8, grpcio-1.25.0, Keras-Applications-1.0.8, Keras-
Preprocessing-1.1.0, Markdown-3.1.1, oauthlib-3.1.0, opt-einsum-3.1.0,
protobuf-3.10.0, pyasn1-0.4.8, pyasn1-modules-0.2.7, requests-oauthlib-1.3.0,
rsa-4.0, setuptools-41.3.0, tensorboard-2.0.1, TensorFlow-2.0.0, tensorflow-
estimator-2.0.1, tensorflow-probability-0.8.0, termcolor-1.1.0,
Werkzeug-0.16.0, wrapt-1.11.2

Searching via module keyword

Another way to search for extension is using the module keyword command, e.g the output of module keyword Babel would give you the following output, hinting at the Python module:

module keyword

------------------------------------------------------------------------------------------------------------------------

The following modules match your search criteria: "Babel"
------------------------------------------------------------------------------------------------------------------------

  Python: Python/2.7.15, Python/3.7.2
    Python is a programming language that lets you work more quickly and integrate your systems more effectively.

------------------------------------------------------------------------------------------------------------------------

To learn more about a package execute:

   $ module spider Foo

where "Foo" is the name of a module.

To find detailed information about a particular package you
must specify the version if there is more than one version:

   $ module spider Foo/11.1

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