Available software

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Revision as of 09:18, 8 February 2018 by Phillips (talk | contribs) (2018-02-08 - Elaborated the explanation at the beginning of the "List of modules" table.)
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A current list of the software available on Compute Canada national systems is below. This list changes frequently as new software is added. You can request the installation or updating of a particular program or library by contacting Technical support.

Notes

Except for basic system programs, you access most software by loading a module. See Using modules for more on how to use the Lmod module system. Note that some prerequisite modules are loaded by default.

Here are a few things to know about the available software:

  • Most Python modules are not installed as (Lmod) modules. They are instead provided as binary wheels, stored on the Compute Canada systems under /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/. One such package is Tensorflow. For instructions on how to install Python packages, see the Python page.
  • Similarly, most R or Perl packages are not installed either. We recommend installing them in your personal or group file space. See the R and Perl pages for instructions on how to do so.
  • Note that Docker is not available on Compute Canada clusters but Singularity is available by loading the module singularity. Docker containers can be converted to Singularity as discussed here.
  • Some of the software packages listed below are not immediately usable because they require you to have a license. You may need to be granted access to them by us. Attempting to load the module for one of these will give you instructions on what to do to obtain access.
  • While the vast majority of the software packages below are accessible on all Compute Canada servers, a few are only available at one site or another due to licensing restrictions.
    • The chemistry programs ADF, AMBER, and Gaussian are only available at Graham and so do not appear on the list below.
  • Many packages related to the operating system, such as Autotools, Make, Git, and others, are not installed as modules but are part of the default environment. These are not listed below.

List of modules

The table below lists software for which an environment module has been installed on Compute Canada systems. In simple cases, the module name listed in the Module column can be used with the module load command to configure your environment. In more complicated cases, some prerequisite modules may also need to be loaded. Click on the corresponding [Expand] link in the Description column for a list of prerequisites and brief notes about the software. If more extensive Compute Canada documentation about a package is available, there will be a link in the Documentation column. Click the double arrows in the column heading to sort in ascending or descending order for a given column. In particular, sorting by software type might be of interest. The Type column shows the software tagged as: ai (artificial intelligence), bio (biology, bioinformatics), chem (chemistry), geo (earth sciences), io (input/output), math (mathematics), mpi (MPI), phys (physics and engineering), tools (languages and libraries), vis (visualization).

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In computing, a module is a unit of software that is designed to be independent, interchangeable, and contains everything necessary to provide the desired functionality. [1] The term "module" may sometimes have a more specific meaning depending on the context. This page describes a few types of modules and suggests links to further documentation content.

Disambiguation

Lmod modules

Also called "environment modules", Lmod modules are used to alter your (shell) environment so as to enable you to use a particular software package, or to use a non-default version of certain common software packages such as compilers. See Using modules.

Python modules

In Python, a module is a file of code (usually Python code) which can be loaded with the import ... or from ... import ... statements to provide functionality. A Python package is a collection of Python modules; the terms "package" and "module" are frequently interchanged in casual use. [2]

Certain frequently used Python modules such as Numpy can be imported if you first load the scipy-stack Lmod module at the shell level. See SciPy stack for details.

We maintain a large collection of Python "wheels." These are modules which are pre-compiled to be compatible with the Standard software environments. Before importing modules from our wheels, you should create a virtual environment.

Python modules which are not in the scipy-stack Lmod module or in our wheels collection can be installed from the internet as described in the Installing packages section.

Other related topics

The main Available software page is a good starting point. Other related pages are:

Footnotes

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Software on legacy systems

Software installed on legacy regional systems is listed on these pages:

  1. ↑ Wikipedia, "Modular programming"
  2. ↑ Tutorialspoint.com, "What is the difference between a python module and a python package?"
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