Pre-installed Modules

Most software available on Cheaha is installed as modules, managed by the Lmod system. This document will provide a basic rundown of using Lmod commands to customize a software environment. module is the main command used to interface with module files in Lmod.

As of the most recent update of this page there are 4,445 active modules installed on Cheaha. The most commonly used general research software modules are listed in the table below. Read on to learn more about searching for and loading modules. If you can't find what you need in our modules, learn more about getting software installed. If you need further assistance, please contact Support.

Name	Description
Anaconda3	Software that can install the Python language, Python packages, and other research software. Learn more about using Anaconda at our Anaconda on Cheaha page. You may be interested in our OpenOnDemand Jupyter Notebook interactive app.
CUDA, cuDNN	Libraries for developing and using deep learning and AI models with NVidia GPUs. Commonly used with TensorFlow and PyTorch. See our GPU page for more information.
Mathematica	Mathematical CAS and numerical computing software. Try our Open OnDemand HPC Desktop interactive app.
Matlab	Matlab language and development environment. We recommend using our Open OnDemand Matlab interactive app.
R, Rstudio	R language and RStudio IDE. We recommend using our Open OnDemand RStudio interactive app.
SAS	Statistical analysis software. Try our Open OnDemand HPC Desktop interactive app.
Singularity	Software container engine. See our Containers page for more information.
Stata	Statistical analysis software. Try our Open OnDemand HPC Desktop interactive app.

Listing and Searching Modules

To begin, all module commands are run from the terminal. To know what software is installed on Cheaha, use the avail command.

module avail

If you need to know what software is already loaded in your environment, run:

module list

If there is specific software you want to search for, you can use the spider subcommand, and provide a string or regular expression to match against. All modules containing the string (case-insensitive) or matching the regular expression will be returned along with their installed versions.

# list modules containing string
module spider <string>

# list modules matching a regular expression
module -r spider <regex>

Loading Modules

To load modules, run:

module load module1 module2 ...

Note

If you only specify a module name without an accompanying version tag, the most recently installed version will be loaded into the workspace. If your scripts depend on specific versions of software being used, explicitly load the module version you need.

To unload packages, run:

module unload package1 package2 ...

If you want to revert to the default modules, you can use:

module reset

Saving Modules using Collections

To save time in typing in long list of modules everytime you work on a project, you can save the desired list of modules using module collection. To acheive this, load the desired modules and save them to a collection using a module collection name, as shown below.

module load module_1 module_2 ...

module save collection_name

Here, the collection_name can be something relevant to your project and easy to remember.

To load the desired modules using the saved collection use,

module restore collection_name

To delete a collection use the below command,

module disable collection_name

To list the save list of module collection use,

module savelist

Warning

Using module save command without a collection name saves the desired modules in the name default to the location $HOME/.lmod.d/default, and causes issue in launching Open On Demand (OOD) HPC desktop job. The user gets a VNC error such as, Unable to contact settings server and/or Unable to load a failsafe session. To address this issue, it is recommended to follow the instructions outlined in the FAQ entry.

Best Practice for Loading Modules

To reduce unexpected behavior and/or to get rid of Lmod errors,

1. Avoid using module load in $HOME/.bashrc. Instead, create a bash script with the module load commands and source it each time to load the modules needed in a shell/sbatch script. Here is an example of loading module in a bash script named module_test.sh and compilation,

   #!/bin/bash
   module reset
   module load Bowtie/1.1.2-foss-2016a
   module load SAMtools/1.3.1-foss-2016a
   module load TopHat/2.1.1-foss-2016a
   module -t list
   

   $ chmod +x module_test.sh
   $ source ./module_test.sh
   
   Resetting modules to system default
   
   # Currently Loaded Modules
   shared
   slurm/18.08.9
   rc-base
   DefaultModules
   GCCcore/4.9.3
   binutils/2.25-GCCcore-4.9.3
   GCC/4.9.3-2.25
   numactl/2.0.11-GCC-4.9.3-2.25
   hwloc/1.11.2-GCC-4.9.3-2.25
   OpenMPI/1.10.2-GCC-4.9.3-2.25
   OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0
   gompi/2016a
   FFTW/3.3.4-gompi-2016a
   ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0
   foss/2016a
   Bowtie/1.1.2-foss-2016a
   ncurses/6.0-foss-2016a
   zlib/1.2.8-foss-2016a
   SAMtools/1.3.1-foss-2016a
   bzip2/1.0.6-foss-2016a
   Boost/1.61.0-foss-2016a
   TopHat/2.1.1-foss-2016a
   

2. Before loading modules in a shell/bash/sbatch script, use a clean shell by using module reset at the beginning to restore to default system settings. Using module reset before loading modules separates what software is loaded in the working shell from the software loaded in the script shell. Be aware that forked processes (like scripts) and Slurm commands inherit the environment variables of the working shell, including loaded modules. Here is an example that shows module conflict between cuda11.8 and cuda11.4 versions that may lead to unexpected behavior or an erroneous output.

# Working shell where you may try testing module load and your run script
$ module load cuda11.4/toolkit

$ module -t list

#Currently Loaded Modules
shared
slurm/18.08.9
rc-base
DefaultModules
cuda11.4/toolkit/11.4.2

# bash script you are passing in a sbatch script
#!/bin/bash
module load cuda11.8/toolkit
module -t list

# Not using `module reset` at the beginning of the bash script could cause CUDA conflict issues.
$ source ./module_test2.sh

#Currently Loaded Modules
shared
slurm/18.08.9
rc-base
DefaultModules
cuda11.4/toolkit/11.4.2
cuda11.8/toolkit/11.8.0

Note

The best practice would be to avoid using module reset in the Environment Setup of Open OnDemand jobs as the OOD session, by default, resets the module at the beginning of every session. It is observed to cause unexpected behavior if module reset is used in the Rstudio server OOD sessions.

Licensed and Commercial Software Restrictions

The following software have license restrictions that may preclude some researchers or collaborators depending on their departmental or group affiliations. In the table, "affiliated" means employed by, or a student of, unless otherwise noted. External collaborators are not considered affiliated with UAB for the purposes of software licensing and access, unless otherwise noted. These software packages may be commercial paid software. If you believe you should have access to software that you do not have access to, please contact Support.

Software	Restricted to...	License Holder
Amber	Lab Specific	Lab PI
Ansys	School of Engineering affiliated people	School of Engineering
Gurobi	Named individual	Individuals
LS-Dyna	School of Engineering affiliated people	School of Engineering
Matlab	UAB affiliated people	UAB Campus
Mathematica	UAB affiliated people	UAB Campus
SAS	UAB affiliated people	UAB Campus
Stata	UAB affiliated people	UAB Campus

Use of these software packages without authorization may be a violation of the UAB IT Acceptable Use Policy.

Security Issues

IGV

Danger

Versions of IGV prior to 2.11.9 use a compromised version of log4j. Those versions are affected by a serious remote code execution issue. Please transition your software to use versions of IGV >= 2.11.9.

GSEA

Danger

Versions of GSEA prior to 4.2.3 use a compromised version of log4j. Those versions are affected by a serious remote code execution issue. Please transition your software to use versions of GSEA >= 4.2.3.