Software Modules on Carina
Carina has several software packages available via module load on the command line.
To see a complete list of the available modules, use ml avail in a terminal.
Each package with more than one version has a default version marked with (D) (for example, python/3.14.3 (D)). To load a non-default version, specify the version in your module load command, like ml python/3.13.12.
To see which modules are currently loaded in your environment, use ‘ml list’.
Environment & Package Management Utilities
You can’t install software on Carina, but you can create a Conda environment on Carina where you have the power to install the exact versions of every package your project requires. The benefits of using Conda include:
- The environment can run anywhere without touching the underlying system
- Anyone can spin up an exact copy of the environment from a simple requirements file
- Projects are organized and isolated
Conda can be considered the underlying technology, but there are different snake-themed wrappers for it. We offer two that are especially good for HPC systems, Anaconda and Micromamba.
Anaconda
Anaconda lets you install Python and scientific libraries in your own user space. Channels like conda-forge have optimized versions of libraries and applications ready to be included in your environment.
Command Line Examples:
Load the Anaconda module using module load/ml
module load anaconda3 or ml anaconda3
Create a new isolated environment named ‘my-project’ with a specific Python version
conda create --name my-project python=3.11 pandas
Activate the environment to use its packages
conda activate my-project
Run a Python script using the environment’s interpreter
python run_analysis.py
List packages in the current environment
conda list
Deactivate the environment when finished
conda deactivate
Micromamba
Micromamba is a fast, lightweight, C++ reimplementation of the conda package manager. It provides the same core functionality for creating environments and installing packages but is significantly faster and has a much smaller footprint.
Command Line Examples:
Load the Micromamba module using module load/ml
module load micromamba or ml micromamba
Create a new environment named ‘my-env’ from the popular conda-forge channel
micromamba create --name my-env -c conda-forge numpy scipy
Activate the new environment
micromamba activate my-env
Install an additional package
micromamba install matplotlib
List packages in the current environment
micromamba list
Deactivate environment
micromamba deactivate
Software for Computation & Analysis
MATLAB
MATLAB (Matrix Laboratory) is a high-performance language and interactive environment for numerical computation, visualization, and programming. It is widely used in engineering, science, and finance for tasks like matrix manipulation, algorithm development, data analysis, and creating models. It is a commercial product known for its extensive set of specialized “toolboxes.”
MATLAB is also available via Carina OnDemand.
Command Line Examples:
Load the MATLAB module with module load/ml
module load matlab or ml matlab
Run a script and pipe the output to a log file
matlab -nodisplay -batch "run('myscript.m')" > output.log
Run a MATLAB script (‘myscript.m’) in non-graphical “batch” mode
matlab -nodisplay -r "run('myscript.m'); exit;"
-r: Run the specified MATLAB command and then exit
R
R is a free, open-source programming language and software environment for statistical computing and graphics. It is a dominant tool in academia and data science for statistical analysis, data visualization, and machine learning.
R Studio is also available via Carina OnDemand.
Command Line Examples:
Load the R module with module load
module load R or ml R (note the capital R)
Start the R interactive console
R
Run an R script (‘analysis.R’) non-interactively from the command line
Rscript analysis.R
Run a script and save the output and messages to a log file
Rscript analysis.R > analysis.log 2>&1
SAS
SAS (Statistical Analysis System) is a commercial software suite used for advanced analytics, business intelligence, data management, and predictive analytics.
SAS is also available on the Carina Desktop.
Command Line Examples:
Load the SAS module with module load/ml
module load sas or ml sas
Run a SAS program (‘my_job.sas’) in batch mode
sas my_job.sas -nodms -log my_job.log -print my_job.lst
-log: specifies the file to write the execution log to
-print: specifies the file to write procedure output to
Copy Utility
rclone
rclone is a powerful command-line program to manage files on cloud storage. It supports over 40 backends, including Google Drive, Amazon S3, Dropbox, and OneDrive.
Tutorial for connecting Carina and Medicine Box
GPU Support
CUDA
CUDA (Compute Unified Device Architecture) is a parallel computing platform developed by NVIDIA that allows developers to use GPUs for general-purpose processing.
Command Line Examples:
Load CUDA with module load/ml
module load cuda or ml cuda