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Tabulate non-CVMFS software
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(Tabulate non-CVMFS software) |
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* Note that [https://www.docker.com/ Docker] is not available on Compute Canada clusters but [[Singularity]] is available by loading the module <tt>singularity</tt>. Docker containers can be converted to Singularity as discussed [http://singularity.lbl.gov/docs-docker here]. | * Note that [https://www.docker.com/ Docker] is not available on Compute Canada clusters but [[Singularity]] is available by loading the module <tt>singularity</tt>. Docker containers can be converted to Singularity as discussed [http://singularity.lbl.gov/docs-docker 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. | * 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. | * 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. See [[#Site-specific software]] 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. | * 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. | ||
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==List of modules== <!--T:4--> | ==List of globally-installed modules== <!--T:4--> | ||
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 <tt>module load</tt> 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]]). | 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 <tt>module load</tt> 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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<translate> | <translate> | ||
== Site-specific software == | |||
Most application software is installed in CVMFS, a distributed file system which makes central management of the many packages easier. | |||
Certain packages, however, are not installed in CVMFS but are installed only at some sites, or are installed separately at each site. | |||
This is usually due to license restrictions on the package in question. | |||
Such packages are listed in the following table. | |||
{| class="wikitable" | |||
|+ style="text-align: left;" |List of software installed locally | |||
|- | |||
! scope="col" |Module !! scope="col" | Type !! scope="col" | Documentation !! scope="col" | Machines !! scope="col" | Description | |||
|- | |||
| adf || chem || [[ADF]] || graham || Amsterdam Density Functional Modeling Suite, computational chemistry software | |||
|- | |||
| dirac/16.0 ||rowspan="2"| phys ||rowspan="2"| ||rowspan="2"| cedar ||rowspan="2"| The DIRAC program computes molecular properties using relativistic quantum chemical methods. Homepage: http://diracprogram.org | |||
|- | |||
| dirac/17.0 | |||
|- | |||
| galaxy/17.09 || bio || || cedar || Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Any group on Cedar can have one Galaxy instance. The Galaxy instance will be run under a shared account which will be created by admins. Please contact support@computecanada.ca to set up Galaxy for you. Homepage: https://usegalaxy.org/ | |||
|- | |||
| gaussian/g03.d01 ||rowspan="5"| chem ||rowspan="5"| [[Gaussian]] ||rowspan="5"| cedar & graham ||rowspan="5"| Gaussian is a general purpose computational chemistry software package. Homepage: http://gaussian.com/ | |||
|- | |||
| gaussian/g09.b01 | |||
|- | |||
| gaussian/g09.e01 | |||
|- | |||
| gaussian/g09.a03 | |||
|- | |||
| gaussian/g09.b01 | |||
|- | |||
| gbrowse/2.56 || bio || [[GBrowse]] || cedar || GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Homepage: http://gmod.org/wiki/GBrowse | |||
|- | |||
| sas/9.4 || math|| || cedar || SAS is a software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics. SAS on cedar is licensed software and it belongs to users from the Alberta School of Business who are eligible to run SAS. Homepage: https://www.sas.com/en_ca/home.html | |||
|- | |||
| x2go/4.0.1.22 || vis || || cedar || X2Go is an open source remote desktop software for Linux that uses the NX technology protocol. On cedar we support only ICEVM window manager Homepage: https://wiki.x2go.org/doku.php | |||
|} | |||
==Software on legacy systems== <!--T:5--> | ==Software on legacy systems== <!--T:5--> | ||