Overview
This page provides an overview of available software on the XLence cluster and explains how to access them.
What are Environment Modules?
Most scientific software on the cluster is managed through Environment Modules (Lmod).
What is a Module?
A module is a configuration file that sets up your environment to use a specific software package. When you load a module, it:
- Adds software binaries to your PATH
- Sets environment variables (e.g., GROMACS_ROOT)
- Configures library paths
- Ensures compatibility between different software versions
Why Use Modules?
Version Management:
- Multiple versions of the same software can coexist
- Switch between versions easily: module load gromacs/2025.0
- No conflicts between incompatible software
Clean Environment: - Your environment only includes what you need - Avoid conflicts between different packages - Easy to reproduce your computational environment
Simple Commands:
# List available modules
module avail
# Load a software package
module load software/version
# See what's loaded
module list
# Remove a module
module unload software/version
# Get help
module help software/version
Available Software
Structural Bioinformatics
Tools for protein structure prediction, molecular dynamics simulations, and molecular modeling.
| Software | Module | Description |
|---|---|---|
| Amber | amber/26 |
Molecular dynamics with GPU acceleration |
| GAMESS | gamess/VERSION |
Quantum chemistry calculations |
| Gaussian | gaussian/16-c02 |
Computational chemistry |
| GROMACS | gromacs/2025.0 |
Molecular dynamics simulations |
| MOE | moe/2024 |
Molecular Operating Environment |
| NAMD | namd/3.0 |
Single-node molecular dynamics |
| NAMD Multi-node | namd-multinode/3.0 |
Multi-node capable MD |
| PLUMED | plumed/2.10.1 |
Free energy calculations |
| Rosetta | rosetta/3.15 |
Protein structure prediction and design |
| RoseTTAFold | rosettafold/2.0 |
Deep learning structure prediction |
| Schrödinger Suite | schrodinger/2025-3 |
Integrated modeling platform |
| VMD | vmd/2.0 |
Molecular visualization |
NGS Data Analysis
Next-Generation Sequencing pipeline tools and bioinformatics analysis.
| Software | Module | Description |
|---|---|---|
| BLAST | blast/2.17.0 |
Sequence similarity search |
| Biostar | biostar/VERSION |
Bioinformatics workflows |
| CellRanger | cellranger/VERSION |
Single-cell RNA-seq analysis |
| SpaceRanger | spaceranger/VERSION |
Spatial transcriptomics |
Proteomics
Mass spectrometry and protein sequence analysis tools.
| Software | Module | Description |
|---|---|---|
| InterProScan | interproscan/VERSION |
Protein sequence classification |
| MaxQuant | maxquant/VERSION |
Quantitative proteomics |
Python and Data Science
| Software | Module | Description |
|---|---|---|
| Miniforge3 | miniforge3/20250911 |
Conda environment with scientific packages |
Software Without Modules
Some software is installed system-wide and available without loading a module.
Programming Languages and Compilers
Python 3:
python3 --version
# Python 3.12 (system)
For scientific Python packages, use module load miniforge3.
R and RStudio:
R --version
# R version 4.x
R is installed system-wide with common packages. For additional packages, contact administrators.
Compilers:
- gcc, g++, gfortran (GNU Compiler Collection 12.x)
- clang, clang++ (LLVM 18.x)
Development Tools
- Git: Version control (
git --version) - Make: Build automation
- CMake: Cross-platform build system
- Autotools: Configure scripts
System Utilities
- tmux: Terminal multiplexer for persistent sessions
- htop: Interactive process viewer
- rsync: Efficient file transfer
Module Commands Quick Reference
Basic Commands
# List all available modules
module avail
# Search for a module
module avail blast
# Load a module
module load gromacs/2025.0
# Load multiple modules
module load miniforge3 rosetta/3.15
# See loaded modules
module list
# Unload a module
module unload gromacs
# Unload all modules
module purge
Getting Information
# Show module help
module help gromacs/2025.0
# Show what a module does (without loading)
module show gromacs/2025.0
# List versions of a software
module avail gromacs
In Job Scripts
Always load modules inside your Slurm job scripts:
#!/bin/bash
#SBATCH --job-name=my_job
# Start with clean environment
module purge
# Load required software
module load gromacs/2025.0
# Run computation
gmx_mpi mdrun -s simulation.tpr
Why? This ensures the correct software version is loaded when your job runs on a compute node.
Software Not Listed?
Python Packages
Many Python packages can be installed in your home directory:
module load miniforge3
pip install --user package_name
R Packages
Install R packages in your home directory:
R
> install.packages("package_name")
Request New Software
If you need software that is not installed, contact the administrators:
Requirements: 1. Software name and version 2. Purpose and use case 3. License information (if commercial) 4. Dependencies or special requirements
Contact: - Uliano Guerrini: uliano.guerrini@unimi.it - Omar Ben Mariem: omar.benmariem@unimi.it
Best Practices
1. Use Modules for Reproducibility
Always specify versions in your job scripts:
module load gromacs/2025.0 # Good
module load gromacs # Avoid (version might change)
2. Document Your Environment
Save your loaded modules:
module list > my_environment.txt
This helps reproduce your analysis later.
3. Avoid Mixing Incompatible Software
Some software packages conflict. If you encounter issues:
module purge # Start fresh
module load only_what_you_need
4. Check Module Help
Before using new software:
module help software/version
This shows important usage notes and dependencies.
Support
For questions about software or modules:
- Uliano Guerrini: uliano.guerrini@unimi.it
- Omar Ben Mariem: omar.benmariem@unimi.it
Last Updated: October 2025