Software on ALICE

Software on ALICE

We provide a range of scientific software for users on ALICE. The lmod module system facilitates easy management of versions and dependencies like any HPC system. The software is organized in several software stacks with default ALICE.

Software stack

ALICE/default

EESSI

ALICE/Legacy

SBGrid

Software stack

ALICE/default

EESSI

ALICE/Legacy

SBGrid

Scientific software packages and dependancies additional to OS software tooling

The general software stack on ALICE. Most versatile, optimised for avx2. a single software stack that works on all CPUs on ALICE (e.g., Intel Skylake, AMD Zen2, Zen3, Zen4). Easy to run jobs on nodes with different hardware, but not fully optimized for the latest architecture.
New software can be requested via helpdesk@alice.leidenuniv.nl

a shared optimized distributed stack of scientific software installations, available on many HPC systems (Snellius, LUMI, …)
https://www.eessi.io/

 

At the heart of SBGrid is our curated software collection: 500+ ready-to-run applications for X-ray crystallography, cryo-EM, NMR, tomography, computational chemistry, molecular visualization, and more. https://sbgrid.org/

Accessible to

all

all

 

group Steffen Brünle

Use

module load ALICE

module load EESSI

 

module load SBGrid

  • Note only one software stack can be active. Loading one swaps the module files.


Following the maintenance of ALICE in May 2024, we have moved to a single software stack that works on all CPUs on ALICE (e.g., Intel Skylake, AMD Zen II, Zen III, Zen IV). This makes it easier for you to run your jobs on different nodes, but it also means that we cannot build the software with full optimization for the underlying CPU architecture. However, for many workloads on ALICE this is not an issue. For users, who need optimized modules, we are planning a separate stack in the future or you can always build your software yourself in your user environment.

New software is added upon request to the ALICE Helpdesk.
To get an overview of installed software run:

module ov

In order to access the scientific software stack on ALICE, run the following command and add it to your Slurm batch file:

module load ALICE/default

For the time being, the old modules are still available. However, they may or may not work. You can access them by loading the following module:

module load ALICE/legacy

You can find information on how to use the module system here: Using available software - Environment Modules

See also: About ALICE for an hardware overview and Partitions on ALICE for a information on the partitions.

Recently added software

Here, you can find a list of recently added software to our software stack. It usually excludes dependencies and focuses on the main software package that was installed.

The list has been started on 8 Aug 2023 which means that software installed prior to this date is not shown here. For a complete list, run module avail, but the output will be extensive.

You can get a description of the module with module whatis <module_name>

We are testing to maintain this list as a method to communicate to you when new software is available on ALICE.

When added

Module

 

When added

Module

 

3 Mar 2026

 

/zfsstore/shared/singularity_images/h/halfpipe-1.3.2.sif

21 Feb 2026

olmocr/0.4.25

https://github.com/allenai/olmocr

11 Jul 2025

dcm2niix/1.0.20250506-GCCcore-13.3.0

 

Jun 26, 2025

BLAST+/2.16.0-gompi-2024a

 

May 26, 2025

snakemake/8.4.2-foss-2023a

 

26 Mar 2025

FSL/6.0.6.17-CUDA-12.4.0

 

2 Apr 2025

GROMACS/2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2

 

11 Mar 2025

Alphafold/cc7_3-20250304, Alphafold/cc8_3-20250304

 

24 Jan 2025

Java/21.0.2

 

20 Jan 2025

IQ-TREE/2.3.6-gompi-2023a

 

18 Dec 2024

AMUSE/2024.4.0 and AMUSE/2024.6.0

 

15 Nov 2024

PyTorch/2.1.2-foss-2023a-CUDA-12.1.1