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We provide a range of software for users on ALICE. The software is organized in modules. Because nodes on ALICE feature Intel Skylake CPUs as well as AMD EPYC Zen II and III CPUs and because we build software optimized for the CPU architecture, we maintain two module trees for users. One tree is for the Intel and one for the AMD nodes.

New software is added upon request by users send to the ALICE Helpdesk. While we usually install new software in both module trees, the module tree for AMD is newer than the tree for our Intel nodes, which means that some software might not be available in the AMD tree. If you are missing software in the AMD module tree, just send an e-mail to the ALICE Helpdesk.

Switching between both trees is easily done using module load ALICE/Intel or module load ALICE/AMD. Alternatively, you can use module load ALICE to automatically load the correct tree for the CPU architecture of the node, e.g., in Slurm batch scripts.

Because we build software for the CPU architecture, it is possible that you need to compile or set up environments twice if you want to use nodes with both type of CPUs on ALICE.

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

Description

Intel software stack

AMD software stack

2024-02-23

Stacks/2.66-foss-2022a

software pipeline for building loci from short-read sequences

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2024-02-16

Pandoc/3.1.2

Converting files from one markup format to another

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2024-02-15

cuDNN/8.9.7.29

NVidia cuDNN toolkit

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2024-02-15

CUDA/12.3.2

NVidia CUDA toolkit

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(tick)

2024-01-12

JAGS/4.3.2-foss-2022b

Just Another Gibbs Sampler

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2023-12-08

MATLAB/2023b

MATLAB

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2023-12-08

SageMath 10.2

SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more

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2023-11-13

tesseract/5.3.0-GCCcore-11.3.0

Optical character recognition engine

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(tick)

2023-10-25

FragPipe/20.0-Java-11

Java interface for the analysis of mass spectrometry-based proteomics data

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2023-10-06

torchvision/0.13.1-foss-2022a-CUDA-11.7.0

Datasets, Transforms and Models specific to Computer Vision

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2023-08-21

breseq/0.38.1-foss-2022a

Computational pipeline for the analysis of short-read re-sequencing data

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2023-08-09

mpi4py/3.1.4-GCC-11.3.0

MPI support for Python 3.10.4 based on OpenMPI

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2023-08-09

htop/3.2.1

Process viewer for Linux (alternative to top)

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2023-08-08

impi/2021.8.0-intel-compilers-2023.0.0

Intel MPI Library, compatible with MPICH ABI

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2023-08-07

intel-compilers/2023.0.0

Intel C, C++ & Fortran compilers (classic and oneAPI)

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