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Linux Standard Software

Introduction

On Linux workstations in Stronghold, scientific software is managed using a module system. In particular, there are "software modules" and "environment modules". Both of these are accessible using the Linux command line. In general, we prefer environment modules, because they provide software package collections that are known to work well together.

Software Modules

Software modules on a given workstation can be accessed using the Linux command line. In particular, open the Terminal application and type module avail. This will show a long list of software packages that is organized by category (see example below).

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ category: languages ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/3.2.3               java/9.0.4            stata/mp-14-20151007
R/dev                 julia/0.4.3           stata/mp-14-20151116
anaconda/2-2.4.0      julia/0.4.6           stata/se-14-20151116
anaconda/2-2.7.0      julia/0.5.0           stata-addons/v1
anaconda/2.3.0        mathematica/11.0.0    stata-addons/v2
anaconda/3-2.4.0      matlab/R2017a         stata-addons/v3
anaconda/3-3.5.0      mro/3.3.1             stata-ado/20160907
anaconda/4.3.0        nodejs/0.12.9         stata-mp/19Dec2017
java/8u162            scala/2.11.11         texlive/2018

Loading a Software Module

In order to use a module, you can simply load if from the command line using the module load command. For example we can load the julia language module by simply typing module load julia from the command line. The software module can now be launched as it normally would be. In the case of Julia, we would simply launch the interpreter by running julia from the command line. Note that this will load the version of Julia that has been designated as the default; as of this writing, that is Julia 0.4.6. However, there is a newer version, which we could load by running module load julia/0.5.0. In this case, we would load version 0.5.0 of Julia.

Environment Modules

The environment modules are configured only for the RHEL 7 system and are not compatible with the migrated RHEL 9 environment. To activate conda environments, see the instructions here.

Environment modules are essentially a collection of software. For example, a given lab might have a collection of software packages that they use frequently. This collection of packages can be wrapped up in an "environment". Technically speaking, these environments are Conda environments, and we simply store them in the module database as if they were standard software.

We can view the available environment modules by simply running module avail conda. This will show the list of available environment modules (see example below).

Each of these environment modules contains a huge list of packages. For example, consider the conda/datasci_v2 environment module. In order to view the available software in this particular module, run conda list --name=datasci_v2to produce a huge list of output that resembles the truncated list below.

Loading Environment Modules

Much like software modules, we can load environment modules with the module load command. In particular, we give the full name of the module. For example we could load the conda/datasci_v2 module by running module load conda/datasci_v2.

Default Environment Modules to load

The conda/cbc_generic module provides R, Python, and Rstudio. In general, a user may start with the conda/cbc_generic module by

If a user needs to access Julia, the user may load the conda/bcbi_v0.3.1 by

Conda Environments

The conda environments are configured only for the RHEL 9 system and are not compatible with the older RHEL 7 system. Instead, follow these instructions.

Environment modules are essentially a collection of software. For example, a given lab might have a collection of software packages that they use frequently. This collection of packages can be wrapped up in an "environment". On Stronghold, we provide these environments as "Conda" environments.

Using Conda

You need to run these two commands to use conda environments

List Conda environments

To view all the available environments, run

Here's an example output

Each of these environment contains a huge list of packages. For example, consider the ccvtest_env environment module. In order to view the available software in this particular module, run conda list --name=ccvtest_env to produce a huge list of output that resembles the truncated list below.

Activating Conda environments

To activate the required environment, run the command conda activate <env-name> . For example, to activate the ccvtest_env environment

To deactivate this environment, run

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