Software Available on NMTHPC

Software Available on NMTHPC#

NMTHPC provides a wide range of scientific and research software. This page explains how to find and use available software.

Environment Modules System#

NMTHPC uses the Environment Modules system to manage software. Modules allow you to easily load and switch between different software packages and versions.

Basic Module Commands#

List available modules:

$ module avail

or

$ module spider

Search for specific software:

$ module avail python

or

$ module spider python

Load a module:

$ module load python/3.12.5-xondaab

List currently loaded modules:

$ module list

Unload a module:

$ module unload python/3.12.5-xondaab

Unload all modules:

$ module purge

Display module information:

$ module show python/3.12.5-xondaab

or

$ module spider python/3.12.5-xondaab

Get help with modules:

$ module help

Module Loading Best Practices#

  1. Load modules in your job scripts: Always load required modules in your SLURM scripts

  2. Specify versions: Use specific versions for reproducibility (e.g., python/3.12.5-xondaab not just python)

  3. Check dependencies: Some modules automatically load dependencies

  4. Clean environment: Use module purge before loading modules to avoid conflicts

Software Categories#

Compilers#

GCC (GNU Compiler Collection):

$ module load gcc/14.2.0-y5jrcb6

Intel Compilers:

$ module load intel-oneapi-compilers/2024.0.2-j5ujkki

Programming Languages#

Python:

$ module load python/3.12.5-xondaab

See Python and Jupyter Notebooks for detailed information.

R:

$ module load r/4.4.1-gcc-11.5.0-araotop

See R for detailed information.

Parallel Computing Libraries#

OpenMPI:

$ module load openmpi/4.1.6-52xkn4g

Note - this version of openmpi currently uses the version of gcc (11.5.0) that was provided with the system (Rocky 9).

Intel MPI:

$ module load intel-mpi/2021.6

GPU Computing#

Mathematical and Scientific Libraries#

BLAS/LAPACK (Linear algebra):

$ module load openblas/0.3.28-x5wjuis

HDF5 (Hierarchical data format):

$ module load hdf5/1.14.5-onz4pba

Scientific Applications#

VASP (Vienna Ab initio Simulation Package):

$ vasp/6.4.3-gcc-11.5.0-zraz3n2

See VASP for computational chemistry examples.

Python Package Management#

Using Anaconda/Miniconda#

Anaconda is recommended for managing Python environments:

$ module load anaconda
$ conda create -n myenv python=3.12.5
$ conda activate myenv
$ conda install numpy scipy matplotlib

See Anaconda for instructions.

R Package Installation#

Install R packages in your home directory:

$ module load r/4.4.1
$ R
> install.packages("ggplot2", repos="https://cloud.r-project.org")

See R for more details. Note: we recommend installing R using conda environments.

Compiling Your Own Software#

You can compile software in your home directory:

$ module load gcc/14.2.0-y5jrcb6
$ ./configure --prefix=$HOME/software/myapp
$ make
$ make install

Tips:

  • Install to $HOME/software or similar directory

  • Load required modules before compiling

  • Add installation directory to PATH in your ~/.bashrc

Requesting New Software#

If you need software that’s not currently installed:

  1. Check if containers are an option

  2. Try installing in your home directory

  3. Contact HPC support at hpc@nmthpc.atlassian.net with:

    • Software name and version

    • Website or download link

    • Brief description of your use case

    • Whether it requires a license

We’ll evaluate requests for system-wide installation.

Module Files in Your Job Scripts#

Always load required modules in your SLURM scripts:

#!/bin/bash
#SBATCH --job-name=my_job
#SBATCH --ntasks=4
#SBATCH --time=01:00:00

# Load required modules
module purge
module load gcc/11.2.0
module load openmpi/4.1.4
module load python/3.11

# Run your application
python my_script.py

Software Versions#

Note

Software versions listed on this page are examples. Use module avail to see currently installed versions on NMTHPC.

License-Restricted Software#

Some software requires licenses:

  • MATLAB: Check license availability

  • VASP: Requires proof of license

  • Intel Compilers: Site license available

  • Other commercial software: Contact HPC support

If you have a license for commercial software, contact HPC support to inquire about installation.

Frequently Asked Questions#

Why isn’t my module loading?#

  • Check spelling: module avail packagename

  • Module conflicts: Try module purge first

  • Dependencies: Some modules require others to be loaded first

How do I see which version of software is loaded?#

$ module list
$ which python
$ python --version

Can I use multiple versions of the same software?#

Not simultaneously, but you can switch:

$ module unload python/3.10
$ module load python/3.11

How do I make modules load automatically?#

Add to your ~/.bashrc:

module load python/3.11

Warning

Be cautious about loading modules automatically in .bashrc. This can cause issues with job scripts that need different module environments.

Additional Resources#

Questions?#

For questions about available software or module usage, contact hpc@nmthpc.atlassian.net.