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Resources software - All software

Name Version Description Topic Availability Target user
2decomp_fft 1.5.847

Library for 2D pencil decomposition and distributed Fast Fourier Transform

Maths Libraries GALILEO100, MARCONI all
Abaqus 2017 (MARCONI) 2016 (G100)

Finite Element Analyzer 

Engineering GALILEO100, MARCONI restricted
ABINIT 8.10.2

A Density Functional Theory (DFT) package, using pseudopotentials and a planewave basis.

Chemistry, Physics MARCONI all
Adf 2018.105 (MARCONI) 2019.104 (G100)

Amsterdam Density Functional: DFT calculations

Chemistry, Physics GALILEO100, MARCONI academic
ADIOS2 1.13.1 (LEONARDO), 2.5.0 (G100)

ADIOS2 is an adaptable, scalable, and unified framework to aid scientific applications when data transfer volumes exceed the capabilities of traditional file I/O.

Data Libraries, Production Environment GALILEO100, LEONARDO all
ADMesh 0.98.2

CLI and C library for processing triangulated solid meshes

Physics MARCONI all
Alphafold 2.2.0

AI system that predicts a protein's 3D structure from its amino acid sequence.

Bioinformatics GALILEO100 restricted
Amber 16 (MARCONI), 22 (M100), 2020 (G100)

Molecular Dynamics on Biomolecules

Chemistry, Life Science, Physics GALILEO100, MARCONI, MARCONI100 academic
Amgx 2.2.0

A GPU accelerated core solver library to speed up computationally intense linear solvers

Maths Libraries, Production Environment MARCONI100 all
Anaconda 2022.05 (LEONARDO), 2019.10 (MARCONI), 2020.11 (M100), 2021.5 (G100)

Python distribution for scientific computing.

Production Environment GALILEO100, LEONARDO, MARCONI, MARCONI100 academic
Annovar 2016Feb01 (MARCONI), 2019Oct24 (G100)

A software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

Bioinformatics GALILEO100, MARCONI all
ANSA 22.1.0 (G100)

ANSA is an advanced multidisciplinary CAE pre-processing tool that provides all the necessary functionality for full-model build up, from CAD data to ready-to-run solver input file, in a single integrated environment.

Engineering GALILEO100 all
Ansys 192 (MARCONI) 212,221,193,195,202 (G100)

General purpose software for mechanical engineering

Engineering GALILEO100, MARCONI restricted
Apbs 3.0.0(G100)

APBS solves the equations of continuum electrostatics for large biomolecular assemblages.

Life Science GALILEO100 all
Armadillo 9.200.4

Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use

Maths Libraries MARCONI all
Ataqv 1.0.0

Ataqv is a toolkit for measuring and comparing ATAC-seq resultsand to make it easier to spot differences that might be caused by library prep or sequencing.

Bioinformatics MARCONI all
Autodock-gpu 4.2.6

The AutoDock Suite is a growing collection of methods for computational docking and virtual screening, for use in structure-based drug discovery and exploration of the basic mechanisms of biomolecular structure and function.

Life Science MARCONI100 all
Bazaar 2.7.0

Bazaar is a version control system that helps you track project history over time and to collaborate easily with others

Production Environment MARCONI all
Bazel 5.2.0

Bazel is a free software tool that allows for the automation of building and testing of software.

Deep Learning MARCONI100 all
BBMap 37.87

This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded.

Bioinformatics MARCONI all
Bcftools 1.13 (G100), 1.2 (MARCONI)

BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF

Bioinformatics GALILEO100, MARCONI all
Beagle 4.1

 Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

Bioinformatics MARCONI all
Bedtools 2.30.0(G100) 2.26(Bedtools2Marconi)

A toolset for genome arithmetic.

Bioinformatics GALILEO100, MARCONI all
Bigdft 1.8.1

A DFT massively parallel electronic structure code (GPL license) using a wavelet basis set.

Chemistry MARCONI all
Binutils 2.34

A collection of binary tools for creating and managing binary programs, object files, libraries, profile data, and assembly source code.

Production Environment MARCONI100 all
BLAS 3.8.0

Basic Linear Algebra Subprograms

Maths Libraries, Physics MARCONI, MARCONI100 academic
BLAST+ 2.12.0

Basic Local Alignment Search Tool

Bioinformatics GALILEO100 all
Blat 36

Blat is an alignmet tool for proteic and genomic sequences

Bioinformatics MARCONI all
Boost 1.80.0 (LEONARDO), 1.78.0 (MARCONI), 1.76.0 (M100), 1.77.0 (G100)

Boost provides free peer-reviewed portable C++ source libraries.

Bowtie 1.1.2 (MARCONI) 1.3.0 (G100)

Bowtie is an ultrafast, memory-efficient short read aligner.

Bioinformatics GALILEO100, MARCONI all
Bowtie2 2.4.4 (G100) 2.2.9 (Marconi)

Fast and sensitive read alignment

Bioinformatics GALILEO100, MARCONI all
Bwa 0.7.12 (G100) 0.7.15 (MARCONI)

Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.

Bioinformatics GALILEO100, MARCONI all
Cactus 2.1.1

Cactus is a reference-free whole-genome multiple alignment program

Bioinformatics GALILEO100 all
Cdo 2.0.0(M100) 1.9.10 (G100) 1.9.7 (Marconi)

CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

Engineering GALILEO100, MARCONI, MARCONI100 all
Cfitsio 3.420 (MARCONI) 3.490 (M100) 4.0.0 (G100)

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

Astronomy, Data Libraries GALILEO100, MARCONI, MARCONI100 all

Computational Geometry Algorithms Library

Maths Libraries MARCONI all
Chimera 1.12 (MARCONI) 1.15 (G100)

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures

Bioinformatics, Chemistry, Physics, Visualisation GALILEO100, MARCONI all
ChromHMM 1.14

ChromHMM is software for learning and characterizing chromatin states.

Bioinformatics MARCONI all
Cineca-ai 2.1.0 (M100) 2.02 (G100)

The bulk of the package is based on OpenCE dedicated to AI which includes (for example) Tensorflow, Pytorch, XGBoost, and other related packages and dependencies.

Deep Learning GALILEO100, MARCONI100 all
Cirq 0.7.0

Cirq is a Python library for writing, manipulating, and optimizing quantum circuits and running them against quantum computers and simulators.

Maths Libraries, Production Environment MARCONI100 all
CMake 3.24.2 (M100) 3.23.3 (MARCONI) 3.21.4 (G100)

CMake build system

Production Environment GALILEO100, MARCONI, MARCONI100 all
Converge 3.0.25

Computational fluid dynamics software

Engineering GALILEO100 restricted
CP2K 6.1 (MARCONI) 9.1(M100) 9.1 (G100)

Atomistic and molecular simulations of solid state, liquid, molecular and biological systems

Chemistry, Physics GALILEO100, MARCONI, MARCONI100 all
CPMD 4.3 (G100, M100, MARCONI)

Plane wave and  pseudopotential implementation of Density Functional Theory

Chemistry, Life Science, Physics GALILEO100, MARCONI, MARCONI100 all
Crystal14 1.0.4

Crystal14 is an ab initio code that uses a Gaussian-type basis set: both pseudopotential and all-electron strategies are permitted

Physics MARCONI restricted
CRYSTAL17 1.0.1 (MARCONI) 1.0.2 (G100)

Solid state chemistry and physics

Chemistry, Physics GALILEO100, MARCONI restricted
Ctiffind 4.1.14

CTFFIND is a program for finding CTFs of electron micrographs.

Life Science MARCONI100 all
CubeGUI 4.4

CubeGUI is a performance report explorer for Scalasca and Score-P

Production Environment MARCONI all
CubeLib 4.4

The Cube 4.x series and the associated Cube4 data format is provided for Cube files produced with the Score-P performance instrumentation and measurement infrastructure, the Scalasca version 2.x trace analyzer and other compatible tools.

Maths Libraries MARCONI all
CUDA 11.5.0 (G100) 11.3 (M100)

CUDA Toolkit

Production Environment GALILEO100, MARCONI100 all
Cudnn 8.0.4

NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks

Deep Learning MARCONI100 all
Cufflinks 2.2.1

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

Bioinformatics GALILEO100 academic
Curl 7.79.0

cURL is an open source command line tool and library for transferring data with URL syntax.

Production Environment GALILEO100 all
Cython 0.27.3 (MARCONI), 0.29.24 (G100)

Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex)

Production Environment MARCONI all
Dakota 6.8 (G100 - MARCONI)

The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ.

Engineering GALILEO100, MARCONI all
Dali 0.27.0 (M100)

DALI (R), the NVIDIA (R) Data Loading Library

Deep Learning MARCONI100 all
Deal.II 9.0.1 (MARCONI)

Deal.II is a A C++ software library supporting the creation of finite element codes and an open community of users and developers.

Maths Libraries MARCONI all
DeePMD 2.0 (M100) 2018 (MARCONI)

DeePMD-kit, a package written in Python/C++ that has been designed to minimize the effort required to build deep learning based representation of potential energy and force field and to perform molecular dynamics.

Chemistry, Deep Learning, Life Science, Physics MARCONI100 all
Deeptools 2.0

Tools for exploring deep sequencing data

Bioinformatics MARCONI all
Detectron2 0.2.1

Detectron2 is Facebook AI Research's next generation software system that implements state-of-the-art object detection algorithms.

Deep Learning MARCONI100 all
Dfast 1.2.12

DFAST is a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the INSDC

Bioinformatics GALILEO100 all
Dirac 21.1

The DIRAC program computes molecular properties using relativistic quantum chemical methods. 

Chemistry, Physics GALILEO100 all
Dlib 19.20

Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems.

Deep Learning MARCONI100 all
DL_POLY 4.08

General purpose classical molecular dynamics (MD) simulation software 

Chemistry, Life Science, Physics MARCONI academic
Dssp 3.1.4

Calculates DSSP (dictionary of protein secondary structure) entries from PDB entries

Chemistry, Life Science MARCONI100 all
Dwgsim 0.1.14

Genome simulation 

Bioinformatics GALILEO100 all
EcCodes 2.13.0 (MARCONI) 2.21.0 (G100)

EcCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages.

Production Environment GALILEO100, MARCONI all
ELPA 2017.11.001 (MARCONI), 2020.11.001(M100), 2021.05 (G100)

Eigenvalue SoLvers for Petaflop-Applications (ELPA)

Chemistry, Physics, Production Environment GALILEO100, MARCONI, MARCONI100 all
Elsi 2.5.0

 ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields.

Maths Libraries MARCONI100 all
Emacs 28.1 (M100), 27.2 (G100)

An extensible, customizable, free/libre text editor — and more.

Production Environment GALILEO100, MARCONI100 all
Epic-Kitchens 100

EPIC-KITCHEN-100 dataset

Deep Learning MARCONI100 all
Ericscript 0.5.5

EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data.

Bioinformatics MARCONI all
Essl 6.2.1 (M100)

Engineering and Scientific Subroutine Library

Maths Libraries MARCONI100 all
Extrae 3.7.0 (MARCONI) 3.8.0 (M100)

Instrumentation framework to generate execution traces of the most used parallel runtimes

Production Environment MARCONI, MARCONI100 all
Fastqc 0.11.9 (M100, G100) 0.11.2 (MARCONI)

 A quality control tool for high throughput sequencing data

Bioinformatics GALILEO100, MARCONI, MARCONI100 all
FFmpeg 4.1.4 (MARCONI) 4.1.4 (M100)

Collection of libraries and tools to process multimedia contents

Deep Learning, Production Environment MARCONI, MARCONI100 all
FFTW 3.3.10 (G100) 3.3.8 (MARCONI) 3.3.8 (M100)

Fastest Fourier Transform in the West

Maths Libraries GALILEO100, MARCONI, MARCONI100 all
Flux 2018

Flux 2D/3D features a big number of functionalities dedicated to electromagnetism

Engineering MARCONI restricted
Freebayes 1.3.4 (G100) 1.1.0 (MARCONI)

Freebayes, a haplotype-based variant detector

Bioinformatics GALILEO100, MARCONI all

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Bioinformatics, Life Science GALILEO100 academic
FusionCatcher 0.99.6a

Finder of somatic fusion-genes in RNA-seq data.

Bioinformatics MARCONI all
Gamess 2018R3

The General Atomic and Molecular Electronic Structure System (GAMESS)
is a general ab initio quantum chemistry package.  

Chemistry MARCONI restricted
GATK 4.0(MARCONI) 4.2.0 (G100)

GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data.

Bioinformatics, Life Science GALILEO100, MARCONI academic
Gaussian G16 B.01(MARCONI), C.01(G100)

Ab-initio and semi-empirical quantum chemistry package

Chemistry GALILEO100, MARCONI restricted
Gcta 1.94.1

Software package to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait and for other analyses of data from genome-wide association studies (GWASs)

Bioinformatics GALILEO100 academic
Gdl 1.0.0-rc.3

GDL is a free/libre/open source incremental compiler compatible with IDL (Interactive Data Language) and to some extent with PV-WAVE

Astronomy MARCONI100 all
Get-homologues-est 20210828

A package for pan-genome analysis

Bioinformatics GALILEO100 all
Git 2.17 (MARCONI) 2.27 (M100) 2.31.1 (G100)

Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

Production Environment GALILEO100, MARCONI, MARCONI100 all

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. GMP has a rich set of functions, and the functions have a regular interface.

Maths Libraries MARCONI all
Gmplib 6.2.0

The GNU Multiple Precision Arithmetic Library

Maths Libraries MARCONI100 all
gmt 6.2.0

GMT is an open source collection of command-line tools for manipulating geographic and Cartesian data sets and producing PostScript illustrations.

Production Environment GALILEO100 all
GNU 8.3.0 (MARCONI), 10.2.0 (G100), 10.3.0 (M100)

GNU Compiler Collection

Production Environment GALILEO100, MARCONI, MARCONI100 all
Gnuplot 5.0 (MARCONI) 5.2.8 (G100) 5.2.6 (M100)

A command-driven plotting program.

Visualisation GALILEO100, MARCONI, MARCONI100 all
Go 1.17.3

Go is an open source programming language supported by Google

Deep Learning MARCONI100 all
Grace 5.99

Grace is a WYSIWYG 2D plotting tool

Visualisation MARCONI, MARCONI100 all
GrADS 2.2.1 (MARCONI) 2.2.2 (G100)

Grid Analysis and Display System - manipulation of earth science data.

Engineering, Production Environment GALILEO100, MARCONI all
GROMACS 2020.6 (MARCONI), 2022 (M100), 2021.3 (G100)

GROningen Machine for Chemical Simulations - Molecular Dynamics on Parallel Computers

Chemistry, Life Science, Physics GALILEO100, MARCONI, MARCONI100 all
Gsl 2.5 (MARCONI), 2.6 (M100), 2.7 (G100)

GNU Scientific Library: numerical library for C and C++

Maths Libraries, Production Environment GALILEO100, MARCONI, MARCONI100 all
GTS 0.7.6

GNU Triangulated Surface Library

Maths Libraries MARCONI all
Gurobi 9.1.2

The Gurobi Optimizer a solver available for your LP, QP, QCP, and MIP (MILP, MIQP, and MIQCP) problems.

Engineering GALILEO100 all
Habitat 0.1.6

A platform for research in embodied artificial intelligence

Deep Learning MARCONI100 all
Hdf5 1.12.0 (M100) 1.10.7 (G100) 1.12.2 (MARCONI)

HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.

Maths Libraries GALILEO100, MARCONI, MARCONI100 all
Healpix 3.50(Marconi), 3.70 (M100)

Hierarchical Equal Area isoLatitude Pixelation of a sphere.

Maths Libraries MARCONI, MARCONI100 academic
HISAT2 2.0.4 (MARCONI) 2.2.1 (G100)

Graph-based alignment of next generation sequencing reads to a population of genomes

Bioinformatics GALILEO100, MARCONI all
Horovod 0.20.0

Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and Apache MXNet. The goal of Horovod is to make distributed deep learning fast and easy to use.

Deep Learning MARCONI100 all
Hpc-sdk 2021

The NVIDIA HPC SDK is a comprehensive suite of C, C++, and Fortran compilers, libraries, and tools for GPU-accelerating HPC applications.

Production Environment MARCONI100 all
Hwloc 1.11.3

The hwloc software package provides a portable abstraction of the hierarchical topology of modern architectures

Production Environment MARCONI all
Hyperworks 2019.1

Altair Hyperworks is the most comprehensive, open architecture CAE simulation platform in the industry, offering the best technologies to design and optimize high performance, weight efficient and innovative products.

Engineering GALILEO100 restricted
IDL 8.5 (G100, MARCONI)

Interactive Data language

Astronomy, Physics GALILEO100, MARCONI restricted
Illumina genome Bos taurus bt8

Ready-To-Use Reference Sequences and Annotations

Biodata GALILEO100 all
Illumina genome Homo sapiens hg19 hg38

Ready-To-Use Reference Sequences and Annotations

Biodata GALILEO100, MARCONI all
Illumina_genome_Mus_musculus mm10

Ready-To-Use Reference Sequences and Annotations

Life Science GALILEO100 academic
ImageNet 2012

ImageNet ILSVRC 2012 dataset

Deep Learning MARCONI100 all
Intel pe-xe-2020--binary (MARCONI) oneapi-2021--binary (G100)

Intel compilers

Production Environment GALILEO100, MARCONI all
Intelmpi 2020--binary (MARCONI) oneapi-2022--binary, intel-oneapi-mpi/2021.4.0 (G100)

Intel MPI compilers

Production Environment GALILEO100, MARCONI all
Jaxlib 0.1.55

Jaxlib with CUDA support

Deep Learning MARCONI100 all
JDK 1.8.0_111

Development environment for building applications, applets, and components using the Java programming language.

Production Environment MARCONI all
Jellyfish 2.3.0

A fast multi-threaded k-mer counter

Bioinformatics GALILEO100 all
JRE 1.8.0_111 (MARCONI, G100)

Java Runtime Enviroment

Production Environment GALILEO100, MARCONI all
Jsoncpp 1.9.3

 Json  is a lightweight data-interchange format. It can represent numbers, strings, ordered sequences of values, and collections of name/value pairs.

Production Environment MARCONI, MARCONI100 all
Jupyter 1.0.0 (M100)

The Jupyter notebook is a web-based notebook environment for interactive computing.

Deep Learning MARCONI100 all
Kinetics 700

Kinetics700 dataset

Deep Learning MARCONI100 all
Kraken 2

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences.

Bioinformatics GALILEO100 all
LAMMPS 23jun2022 (G100) 29sep2021 (M100) 12dec2018 (MARCONI)

Molecular Dynamics Simulator (classical dynamics)

Chemistry, Life Science, Physics GALILEO100, MARCONI, MARCONI100 academic
LAPACK 3.9.0 (M100) 3.8 (G100, MARCONI)

Linear Algebra PACKage: Fortran library for solving linear equations, eigenvalue problems, and singular value problems.

Maths Libraries GALILEO100, MARCONI, MARCONI100 academic
Lftp 4.9.1

LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).

Production Environment MARCONI all
Libgridxc 0.9.6

 A library based on SiestaXC

Chemistry, Physics MARCONI100 all
Libidn2 2.0.4

Libidn2 is an implementation of the IDNA2008 + TR46 specifications (RFC 5890, RFC 5891, RFC 5892, RFC 5893, TR 46)

Data Libraries MARCONI all
Libpsml 1.1.8

 A library to handle PSML, the pseudopotential markup language

Chemistry, Physics MARCONI100 all
Libxc 4.3.4 (MARCONI) 5.1.4 (M100) 5.1.5 (G100)

Libxc is a library of exchange-correlation functionals for density-functional theory.

Maths Libraries GALILEO100, MARCONI, MARCONI100 all
Llvm 10.0.1

The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.

Production Environment MARCONI100 all
Llvmlite 0.34.0 (M100)

A lightweight LLVM python binding for writing JIT compilers.

Deep Learning MARCONI100 all
Ls-dyna r12.1.0

General-purpose, implicit and explicit FEM software

Engineering GALILEO100 restricted
Macs 2.1.0

Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq)

Bioinformatics MARCONI all
MAGMA 2.5.3--cuda--10.2 (M100)

A dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current "Multicore+GPU" systems.

Maths Libraries, Production Environment MARCONI100 all
Matheval 1.1.11--intelmpi--2018--binary

GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.

Maths Libraries MARCONI all
Matlab r2020b (G100) r2019b (MARCONI)

MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming.

Engineering GALILEO100, MARCONI restricted
METIS 5.1.0

METIS is a software package for graph partitioning that implements various multilevel algorithms

Physics GALILEO100 all
MKL oneapi-2021 (MARCONI) oneapi-2021-binary (G100)

The Intel Math Kernel Library

Maths Libraries GALILEO100, MARCONI all
MOLCAS 8.2 (MARCONI), 8.4 (G100)

Quantum Chemistry Program

Chemistry, Physics GALILEO100, MARCONI academic

MOLGW is a Gaussian-type orbital code for finite systems. It implements a self-consistent mean-field calculation, followed by a many-body perturbtation theory post-treatment.

Chemistry GALILEO100, MARCONI all
Molpro 2010.1(MARCONI), 2021.2.1 (G100)

Quantum Chemistry Package. Ab-initio molecular electronic stucture with full electron-correlation

Chemistry, Physics GALILEO100, MARCONI academic
MOPAC 2016 (MARCONI, G100)

Semi-empirical software package.

Chemistry GALILEO100, MARCONI academic
Mpfr 4.1.0(MARCONI), 4.0.2 (M100)

A C library for multiple-precision floating-point computations

Maths Libraries MARCONI, MARCONI100 all
Mpi4py 3.0.0--python--3.6.4 (Marconi)

MPI for Python

Production Environment MARCONI all
MPlayer 1.4

Movie player.

Visualisation GALILEO100, MARCONI all
MUMPS 5.1.2

MUMPS: a MUltifrontal Massively Parallel sparse direct Solver

Maths Libraries MARCONI all
Mvapich2 2.3.1--intel--pe-xe-2018--binary (Marconi) 2.3.4 (M100)

BSD-licensed implementation of the MPI standard

Production Environment MARCONI, MARCONI100 all
NAG mark27--binary

Numerical Algorithms Group (NAG) libraries

Maths Libraries MARCONI all
NAMD 2.14 (G100, M100) 2.12 (MARCONI)

Scalable molecular dynamics for biomolecular modeling

Chemistry, Life Science GALILEO100, MARCONI, MARCONI100 academic
Nastran 2021.1

A multidisciplinary structural analysis application used by engineers to perform static, dynamic, and thermal analysis.

Engineering GALILEO100 restricted
Nbo 6.0

A discovery tool for chemical insights from complex wavefunctions. 

Chemistry MARCONI restricted
Nccl 2.8.3--cuda--11.3

 The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.

Production Environment MARCONI100 all
NcFTP 3.2.6

A set of FREE application programs implementing the File Transfer Protocol (FTP)

Production Environment GALILEO100, MARCONI all
NCL 6.6.2--intel--pe-xe-2018--binary

NCL is a free interpreted language designed specifically for scientific data processing and visualization.

Visualisation MARCONI all
NCO 4.9.3-oneapi--2021.2.0-ifort (G100) 4.8.1 (MARCONI)

NetCDF Operators

Data Libraries GALILEO100, MARCONI all
Ncview 2.1.7 (M100) 2.1.8 (G100)

Ncview is a X Windows visual browser for netCDF data format files.

Physics, Visualisation GALILEO100, MARCONI100 all
Nest 3.3

NEST is a simulator for spiking neural network models focusing on the dynamics, size and structure of neural systems.

Bioinformatics GALILEO100 all
NetCDF 4.9.0 (MARCONI) 4.7.3 (M100) 4.7.4 (G100)

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Maths Libraries GALILEO100, MARCONI, MARCONI100 all
NetCDF-cxx4 4.3.0

C++ interface of NetCDF, a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Maths Libraries MARCONI all
NetCDFF 4.9.0 (MARCONI), 4.5.2 (M100), 4.5.3 (G100)

Fortran interface of NetCDF, a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Maths Libraries GALILEO100, MARCONI, MARCONI100 all
Neuron 7.6.7

NEURON simulation environment

Life Science MARCONI all
Ninja 1.10.1

Ninja is a small build system with a focus on speed.

Deep Learning MARCONI100 all
Nni 1.8

NNI (Neural Network Intelligence) is a lightweight but powerful toolkit to help users automate Feature Engineering, Neural Architecture Search, Hyperparameter Tuning and Model Compression.

Deep Learning MARCONI100 all
NucleoATAC 0.2.1

NucleoATAC is a python package for calling nucleosome positions and occupancy using ATAC-Seq data.

Bioinformatics MARCONI all
NumPy 1.14.0-python3.6 (MARCONI) 1.19.4--python3.8.2 (M100)

NumPy for scientific computing with Python

Maths Libraries MARCONI, MARCONI100 all
Nwchem 6.6 (MARCONI) 7.0.2 (G100)

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

Chemistry MARCONI all
Octave 5.1.0(MARCONI), 6.2.0 (M100)

GNU Octave is a high-level language, primarily intended for numerical computations.

Maths Libraries MARCONI, MARCONI100 all
Openblas 0.3.9--gnu--8.4.0,0.3.17 (M100) 0.3.12 (G100)

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

Maths Libraries GALILEO100, MARCONI100 all
Opencv 4.3.0--gnu--8.4.0 (M100) 3.2.0 (MARCONI)

 OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.

Deep Learning, Visualisation MARCONI, MARCONI100 all
OpenFOAM 9.0 (G100) 8.0 (MARCONI)

Open Field Operation and Manipulation: CFD Toolbox 

Engineering, Physics GALILEO100, MARCONI all
Openfoam+ v2012 (Marconi) v2206 (G100)

OpenFOAM is a free, open source CFD software. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics

Production Environment MARCONI, MARCONI100 all
Openmolcas 21.10

OpenMolcas is a quantum chemistry software package developed by scientists

Chemistry GALILEO100 all
OpenMPI 4.0.3 (M100) 4.1.1 (G100), 4.1.1 (MARCONI)


Production Environment GALILEO100, MARCONI, MARCONI100 all
ORCA 5.0.3 (G100) 4.2.1(Marconi)

Ab initio quantum chemistry program package

Chemistry, Engineering, Physics GALILEO100 all
P4est 2.0--intelmpi--2018--binary (MARCONI) 2.3--intelmpi--2021--binary (G100)

The p4est software library enables the dynamic management of a collection of adaptive octrees, conveniently called a forest of octrees.

Maths Libraries GALILEO100, MARCONI all
Papi 5.7.1 Engineering MARCONI all
Parafoam 5.8.1--spectrum_mpi--10.3.1--binary

 Paraview readers for OpenFOAM (ESI)

Physics, Visualisation MARCONI100 all
ParMETIS 4.0.3

An MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.

Maths Libraries GALILEO100, MARCONI, MARCONI100 all
Pcrystal14 1.0.4

A program for the ab initio investigation of crystalline solids

Chemistry MARCONI restricted
Perturbo 1.0.3

PERTURBO is an open source software to compute from first principles the scattering processes between charge carriers (electrons and holes) and phonons, defects, and photons in solid state materials, including metals, semiconductors, oxides, and insulators.

Chemistry GALILEO100 restricted
PETSc 3.16.0 (MARCONI), 3.13.1(M100) 3.15.2 (G100)

Suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations

Maths Libraries GALILEO100, MARCONI, MARCONI100 all
Petsc4foam dev--spectrum_mpi--10.4.0--binary

Exploration and testing of linear solvers, matrix operations

Maths Libraries MARCONI100 all
PGI 19.10 (M100) 16.5 (MARCONI)

PGI's full suite of parallelizing F77, F95, HPF, C and C++ compilers and development tools. Includes the OpenMP parallel debugger/profiler.

Production Environment MARCONI, MARCONI100 all
Picard 2.25.7 (G100), 2.7.1 (Marconi)

Utilities for manipulating SAM files

Bioinformatics GALILEO100, MARCONI all
PLASMA 2.8.0--intel--pe-xe-2018--binary

PLASMA is a software package for solving problems in dense linear algebra

Maths Libraries MARCONI all
PLINK 1.90

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Bioinformatics GALILEO100 academic
PLUMED 2.5.0 (MARCONI), 2.8.0 (M100), 2.7.2 (G100)

PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines.

Chemistry, Physics GALILEO100, MARCONI, MARCONI100 all
PnetCDF 1.11--intelmpi--2018--binary (MARCONI) 1.12 (G100, M100)

A high-performance parallel I/O library for accessing Unidata's NetCDF

Production Environment GALILEO100, MARCONI, MARCONI100 all
Popt 1.16

Library for parsing arguments

Production Environment MARCONI all
Protobuf 3.11.1 (M100) 3.2.0 (MARCONI)

Protocol Buffers - Google's data interchange format

Deep Learning MARCONI, MARCONI100 all
Pulser 0.1--python--3.8.2


Quantum Computing MARCONI100 all
Py-Spy 0.3.3

py-spy is a sampling profiler for Python programs

Deep Learning MARCONI100 all
PyFrag 2007.02

Explorations and analyses of potential energy surfaces with the ADFpackage

Chemistry MARCONI all
Python 3.8.2 (M100) 3.8.6 (G100) 3.9.4 (MARCONI)

Python programming language

Production Environment GALILEO100, MARCONI, MARCONI100 all
Pytorch 1.7 (M100) 1.1.0--python--3.6.4 (MARCONI)

PyTorch is an open source machine learning library

Deep Learning, Maths Libraries MARCONI, MARCONI100 all
Q-Chem 5.1 (MARCONI), 5.4.2 (G100)

Ab initio quantum chemistry package

Chemistry GALILEO100, MARCONI all
QE 6.8 (MARCONI), 7.1 (M100), 7.1 (G100)

QE is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale based on density-functional theory, plane waves, and pseudopotentials.

Chemistry, Physics GALILEO100, MARCONI, MARCONI100 all
Qiskit 0.23.2

Qiskit is an open-source SDK for working with quantum computers at the level of circuits, algorithms, and application modules.

Physics, Quantum Computing MARCONI100 all
Qsimcirq 0.7.1

Quantum circuit simulators qsim and qsimh. These simulators were used for cross entropy benchmarking in 1.

Physics, Quantum Computing MARCONI100 all
Qt 5.9.0--gnu--6.1.0 (MARCONI), 6.1--gnu--8.4.0(M100)

Cross-platform application and GUI framework

Maths Libraries, Production Environment MARCONI, MARCONI100 all
Quantum-suite 0.1

Quantum-suite is a module that contains the most important sdk for quantum computing available today.

Quantum Computing GALILEO100 all
Qutip 4.5.0

QuTiP is open-source software for simulating the dynamics of open quantum systems.

Physics, Quantum Computing MARCONI100 all
R 4.2.0 (G100) 3.6.1 (Marconi) 4.0.1 (M100)

Statistical computing and graphics

Bioinformatics, Engineering, Life Science, Maths Libraries GALILEO100, MARCONI, MARCONI100 all
Ray 1.2.0

Ray provides a simple, universal API for building distributed applications.

Deep Learning MARCONI100 all
Relion 3.1.2

RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)

Life Science MARCONI100 all
ROOT 6.08.06

A modular scientific software framework

Production Environment MARCONI all
Rsem 1.3.0 (Marconi)

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data

Bioinformatics MARCONI all
Salmon 1.5.1

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Bioinformatics GALILEO100 all
Sambamba 0.6.6

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files.

Bioinformatics MARCONI all
Samtools 1.3.1(Marconi)1.13(G100)

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Bioinformatics GALILEO100, MARCONI all
ScaLAPACK 2.0.2 (MARCONI), 2.1.0--spectrum_mpi--10.3.1--binary(M100), 2.1.0 (G100)

ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machine

Maths Libraries GALILEO100, MARCONI, MARCONI100 all
Scalasca 2.4

Profiler for parallel scientific and engineering applications

Production Environment MARCONI all
Scilab 5.5.2

Open source software for numerical computation

Engineering GALILEO100 all
SciPy 1.5.1 (M100) 1.2.2 (MARCONI)

SciPy (pronounced “Sigh Pie”) is open-source software for mathematics, science, and engineering.

Deep Learning, Maths Libraries, Quantum Computing MARCONI, MARCONI100 all
SCons 2.5.1

Open Source software construction tool, a next-generation build tool.

Production Environment MARCONI all
Scorep 4.0

The Score-P is a highly scalable tool suite for profiling, event tracing, and online analysis of HPC applications.

Production Environment MARCONI all
Selfie 30nov2017

Self and Light proFIling Engine - a very light profiling tools for Linux commands and HPC codes

Production Environment MARCONI all
Seqtk 1.2-r94 (Marconi)

A tool for processing sequences in FASTA or FASTQ format.

Bioinformatics MARCONI all
Seqtk 1.3 (G100)

Seqtk is a fast and lightweight tool

Life Science GALILEO100 academic
SIESTA 4.1-b4(MARCONI, M100), rel-max (M100), 4.1.5 (G100)

Electronic structure calculations and ab-initio molecular dynamics of molecules and solid

Chemistry, Physics GALILEO100, MARCONI, MARCONI100 academic
Singularity 3.7.0 (M100) 3.6.1 (Marconi)


Containarization tool for HPC

Production Environment MARCONI, MARCONI100 all
Slate 2021.05.02

The Software for Linear Algebra Targeting Exascale (SLATE) provides fundamental dense linear algebra capabilities to the high-performance computing (HPC) community.

Maths Libraries MARCONI100 all
SLEPc 3.8.2_complex--intelmpi--2018--binary

SLEPc is a software library for the solution of large sparse eigenproblems on parallel computers.

Maths Libraries MARCONI all
Snpeff 4.3k

SnpEff is a toolthat annotates and predicts the effects of variants on genes (such as amino acid changes).

Bioinformatics MARCONI all
Spack 0.14.2

A flexible package manager supporting multiple versions, configurations, platforms and compilers. 

Production Environment GALILEO100, MARCONI100 all
Spectrum MPI 10.4.0--binary

Accelerating High-performance application parallelization.

Production Environment MARCONI100 all
Sra 3.0.0(Galileo100) 2.8.1 (Marconi)

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archive and download them locally

Bioinformatics, Life Science GALILEO100, MARCONI all
Stacks 2.59

Software pipeline for building loci from short-read sequences

Life Science GALILEO100 all
Star 2.7.9a (G100) 2.5.2a(Marconi)

Spliced Transcripts Alignment to a Reference

Bioinformatics GALILEO100, MARCONI all
STAR-CCM 16.04.012-r8 (MARCONI) 16.06.008 (G100)

STAR-CCM+ delivers the entire engineering simulation process in a single integrated software environment.

Engineering GALILEO100, MARCONI restricted
Stata 14

Stata is a complete, integrated software package that provides data manipulation, visualization, statistics, and automated reporting.

Physics MARCONI restricted
Stringtie 2.1.6(G100) 1.3.1 (Marconi)

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

Bioinformatics GALILEO100, MARCONI all
SU2 6.0.0

SU2 is an open-source collection of software tools written in C++ and Python for the analysis of partial differential equations (PDEs) and PDE-constrained optimization problems on unstructured meshes with state-of-the-art numerical methods.

Engineering MARCONI all
Szip 2.1.1--gnu--8.4.0 (M100) 2.1.1 (Marconi)

Szip is an implementation of the extended-Rice lossless compression algorithm. 

Maths Libraries MARCONI, MARCONI100 all
Tabix 0.2.6

Generic indexer for TAB-delimited genome position files.

Bioinformatics GALILEO100 all
Tecio 2018r2

TecIO is the library supplied with Tecplot 360 that enables third-party applications to output solution data directly to Tecplot binary-formatted files.

Engineering, Visualisation MARCONI100 all
Tecplot 2018r2 (Marconi), 2021r2 (G100)

Tecplot 360 EX is a CFD post-processor.

Engineering GALILEO100, MARCONI all
TensorFlow 2.3.0 (M100) 1.10.0 (MARCONI)

TensorFlow is an open-source library of software for dataflow and differential programing for various tasks.

Deep Learning MARCONI, MARCONI100 all
Tophat 2.1.1 (G100) 2.0.12 (Marconi)

A spliced read mapper for RNA-Seq

Bioinformatics GALILEO100 all
TotalView 2018.10, 2020.2.6 (Marconi), 2020.2.6 (G100)

Faster fault isolation, improved memory optimization, and dynamic visualization for your high-scale HPC apps

Production Environment GALILEO100, MARCONI all
Trilinos 12.12.1

The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.

Engineering MARCONI all
Trimmomatic 0.39

A flexible read trimming tool for Illumina NGS data

Bioinformatics, Life Science GALILEO100, MARCONI, MARCONI100 all
Usearch 11.0.667

USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST

Bioinformatics GALILEO100 academic
Valgrind 3.16.1(Marconi), 3.17.0(M100, G100)

Valgrind is an instrumentation framework for building dynamic analysis tools

Production Environment MARCONI, MARCONI100 all
Varscan 2.4.2 (G100, Marconi)

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments.

Bioinformatics, Life Science GALILEO100, MARCONI all
VASP 5.4.4, 6.3.2 (MARCONI, M100, G100)

Vienna Ab initio Simulation Package: atomic scale materials modelling

Chemistry, Physics GALILEO100, MARCONI, MARCONI100 restricted
Vcftools 0.1.16

VCFtools is a program package designed for working with VCF files.

Bioinformatics GALILEO100 all
Vep 104

Variant Effect Predictor

Bioinformatics GALILEO100 all
Visit 3.1.3

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool

Visualisation MARCONI all
VMD 1.9.3(Marconi) 1.9.4(M100, G100)

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Chemistry, Visualisation GALILEO100, MARCONI all
VTune 2018 (Marconi), oneapi-2022 (G100)

Intel VTune Amplifier performance analysis toolkit

Production Environment GALILEO100, MARCONI all
Wannier90 3.0.0(Marconi) 3.1.0(G100)

Wannier90 is an open-source code (released under GPLv2) for generating maximally-localized Wannier functions and using them to compute advanced electronic properties of materials with high efficiency and accuracy.

Physics GALILEO100, MARCONI all
Wanniertools 2.5.1(M100),2.1.5(G100)

WannierTools is a software for investigation of novel topological materials.

Chemistry GALILEO100, MARCONI100 all
WMLCE 1.7.0

IBM Watson Machin Learning and Deep Learning Framework

Deep Learning MARCONI100 all
WSMP 19.06.27--intelmpi--2018--binary

Watson Sparse Matrix Package (WSMP) is a collection of algorithms for efficiently solving large sparse systems of linear equations.

Maths Libraries MARCONI restricted
WxWidget 3.1.5

WxWidgets is a free and open source cross-platform C++ framework for writing advanced GUI applications using&nbsp

Visualisation MARCONI100 all
XL 16.1.1--binary

IBM XL High performance compiler

Production Environment MARCONI100 all
Xmlf90 1.5.4--gnu--8.4.0

A suite of light-weight libraries to work with XML in Fortran.

Production Environment MARCONI100 all
Xmvb 3.0

Xiamen Valence Bond (XMVB) is a valence bond (VB) theory based quantum chemistry program for performing electronic structure calculations

Chemistry, Physics GALILEO100 academic
Yambo 5.0. (G100) 5.1.1 (M100) 5.0(MARCONI)

Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.

Chemistry, Physics GALILEO100, MARCONI, MARCONI100 all
YAML 0.2.2

LibYAML is a YAML parser and emitter library

Data Libraries MARCONI all
Zlib 1.2.11--intel--pe-xe-2018--binary(Marconi)

Zlib is a free, general-purpose, legally unencumbered lossless data-compression library for use on virtually any computer hardware and operating system.

Data Libraries MARCONI all