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Modules and Applications

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.

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

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 Restrictions License Holder
Ansys School of Engineering affiliated School of Engineering
Gurobi One individual user per license Individuals
LS-Dyna School of Engineering affiliated School of Engineering
MATLAB UAB affiliated UAB Campus
Parabricks 2 GPUs for researchers using RC systems Research Computing
SAS UAB affiliated UAB Campus
Stata UAB affiliated 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.