Available Software on HPC Alma 9

Abseil

20230125.2-GCCcore-12.2.0

Google’s C++ library providing foundational components for modern C++ code.

Armadillo

11.4.3-foss-2022b

C++ linear algebra library with MATLAB-like syntax.

Arpack-ng

3.8.0-foss-2022b

A library for solving large-scale eigenvalue problems (sparse matrices).

ATK

2.38.0-GCCcore-12.2.0 ,2.46.0-GCCcore-12.2.0

 Framework for creating accessible applications in GNOME.

Autoconf

2.71-GCCcore-11.3.0 - 2.72-GCCcore-13.3.0

Tool for generating automatic configuration scripts in software projects.

Autotools

1.16.5-GCCcore-11.3.0 - 1.16.5-GCCcore-13.3.0

Suite of tools (Autoconf, Automake, Libtool) for compiling and packaging software.

Binutils  

2.38 - 2.42

Collection of binary tools (e.g., ld, as, objdump) for handling object files.

Bison

3.8.2   

Parser generator (YACC replacement) for converting grammar rules into code.

BLIS

0.9.0

High-performance BLAS (Basic Linear Algebra Subprograms) library.

Boost

1.81-1.82

Extensive C++ library collection for tasks like multithreading, algorithms, and data structures.

Brotli

1.0.9

Google’s compression algorithm/library for efficient data compression.

Brunsli

0.1-GCCcore-12.2.0

Lossless JPEG repacking library (improves compression).

bzip2

1.0.8

Compression library and tool for lossless data compression.

cairo

1.17.4-GCCcore-12.2.0, 1.17.8-GCCcore, 12.3.0 , 1.18.0-GCCcore-13.3.0

2D graphics library supporting vector and raster output (used in GTK, browsers).

CASTEP

25.1.1-intel-2024a, 25.1.1-foss-2023b

First-principles quantum mechanics code for materials modeling.

Catch2

2.13.9

Modern C++ testing framework (header-only, simple syntax).

cffi

1.15.1

Foreign function interface (FFI) for Python to call C code.

CFITSIO

4.2.0 - 4.3.1

Library for reading/writing FITS files (astronomy data format).

CGAL

5.6-GCCcore-12.3.0

Computational Geometry Algorithms Library (C++ templates for geometric operations).

CMake 

3.24.3 -  3.29.3

Cross-platform build system generator (replaces Makefiles).

crytography

41.0.1, 41.0.5

Python library for secure cryptographic operations (e.g., encryption, hashing).

cURL

7.86.0 - 8.7.1

Command-line tool and library for transferring data with URLs (supports HTTP, FTP, etc.).

Cython

3.0.10-GCCcore-13.2.0

Python-to-C compiler for writing C extensions in Python-like syntax.

DB

18.1.40

Embedded database library for key-value storage.

DBus

1.15.2 - 1.15.4

Message bus system for inter-process communication (IPC) in Linux.

double-conversion

3.3.0

Library for precise binary-decimal number conversion (used in V8, LLVM).

Doxygen

1.9.5 - 1.11.0

Documentation generator for C++, C, Java, etc. (extracts comments into docs).

Easybuild

4.9.1, 5.0.0

Framework for automating software builds on HPC systems.

Eigen

3.4.0

C++ template library for linear algebra (matrices, vectors, numerical solvers).

expat

2.4.8 - 2.6.2

Stream-oriented XML parser library written in C.

FFmpg

6.0-GCCcore-12.3.0 

Multimedia framework for handling audio/video (encoding, decoding, streaming).

ffnvcodec

12.0.16.0

NVIDIA’s hardware-accelerated video codec SDK (for FFmpeg).

FFTW

3.3.10

Fastest Fourier Transform in the West (C library for FFT computations).

FLAC

1.4.2

Free Lossless Audio Codec for compressed audio without quality loss.

flex

2.6.4

Fast lexical analyzer generator (lexical tokenizer, often used with Bison).

FlexiBLAS

3.2.1 - 3.4.4

A flexible BLAS (Basic Linear Algebra Subprograms) wrapper that allows runtime switching between different BLAS implementations.

flit

3.9.0

A simple Python packaging tool for pure-Python modules (alternative to setuptools).

fontconfig

2.14.1 - 2.15.0

A library for configuring and customizing font access in Linux/Unix systems (used by GUI apps).

fonttools

4.53.1

A Python library for manipulating fonts (e.g., OpenType, TrueType) programmatically.

foss

2022b -  2024a

Free and Open Source Software tools

freeglut

3.4.0

 An open-source alternative to GLUT (OpenGL Utility Toolkit) for creating OpenGL windows and handling input.

freetype

2.12.1

A widely used library for rendering fonts (supports multiple font formats like TTF, OTF).

friBidi

1.0.12 ,1.0.15

A library for handling bidirectional text (e.g., Arabic, Hebrew mixed with left-to-right languages).

GCC

12.2.0 - 13.2.0

A suite of compilers for C, C++, Fortran, Ada, and other languages.

GCCcore

GDAL

Gdk-Pixbuf

GEOS

gettext

gfbf

Ghostscript

giflib

git

GL2PS

GLib

GLPK

GMP

gnuplot

GObject-Introspection

gompi

googletest

gperf

graphite2

groff

GSL

GTK3

gzip

HarfBuzz

hatchling

HDF

HDF5

help2man

hwloc

hypothesis

ICU

iimpi

ImageMagick

Imath

imkl-FFTW

imkl

impi

intel-compilers

INTEL

2023.0, 2024.0

intltool

JasPer

Java

jbigkit

jq

 json-c

PYTHON

3.9.0, 3.11.1

ARGTABLE

2.13

ANSI C library for parsing GNU style command line options with a minimum of fuss

ASTRON

2014

IDL Astronomy Users Library

BEAGLE

r1090

A high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs)

BOOST

1.52.0

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

CANTERA

2.2.0(also 2.2.1)

Open-source collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes

CGIS

4.1

CLASS

Nov2011

CUDA

4.2.9(also 4.0.17, 7.0.28, 7.5.18)

a parallel computing platform and programming model to exploit the power of graphics processing unit (GPU)

EIGEN

3.8.2

C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

GDAL

1.9.2

is a translator library for raster geospatial data formats

GSL

1.15 (1.15 (also 1.15INTEL, 1.5_ICC, 2.3)

GNU Scientific Library (GSL) is a numerical library for C and C++ programmers

HDF5

1.8.10 (also 1.8.10INTEL, 1.8.16, 1.8.8_ICC)

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data

IGRAPH

0.7.1

Collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++

LAPACK

3.4.1

Linear Algebra PACKage

LIBTOOL

2.4.2

Generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

LUAJIT

2.0

A Just-In-Time Compiler for Lua.

MPFIT

1.3

A MINPACK-1 Least Squares Fitting Library in C

MPICH

3.0.4 (also 3.0.4_ICC)

A high performance and widely portable implementation of MPI standard.

MVAPICH2

2.0 (also 2.1rc1, 2.2)

MPI-3 over OpenFabrics-IB, OpenFabrics-iWARP, PSM, uDAPL and TCP/IP

NETCDF

4.2.1.1 (also 4.1.3, 4.4.0 and fortran 4.4.3)

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.

OPENBLAS

0.2.15

Optimized BLAS library based on GotoBLAS2 1.13 BSD version

OPENMPI

1.8.3(also 4.0.1, 1.8.4rc1, 1.8.3_ICC,1.6.5,1.6.3_ICC,1.4.5)

Open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry

PAPI

5.4.0(also 5.0.1)

The Performance API (PAPI) project specifies a standard application programming interface (API) for accessing hardware performance counters available on most modern microprocessors.

PROJ4

4.8.0

Cartographic Projections library

QT4

4.8.5

Cross-platform application development framework for desktop, embedded and mobile

ANSYS

2019R3

CFD simulation package for internal combustion engines

MATLAB

R2019b

Lenguaje de alto nivel y un entorno interactivo para el cálculo numérico, la visualización y la programación. VERSION EN PARALELO.

SAGE

5.3 (also 6.4.1)

Open source alternative to MATLAB

R

2.15.1 (also 3.2.3, 3.2.1)

Free software environment for statistical computing and graphics. VERSION EN PARALELO

ROOT

5.34.01 (also 5.34.17)

An object oriented framework for large scale data analysis developed at CERN. VERSION EN PARALELO: PROOF

CMS SW

Software setup for the CMS collaboration at CERN

SIESTA

3.1 (also 4.0)

A method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

CPMD

3.15.1

Car-Parrinello Molecular Dynamics: An ab initio Electronic Structure and Molecular Dynamics Program

DL_POLY

2.20

a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory

LAMMPS

22Feb13

a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

VASP

5.4.4_INTEL

5.3_INTEL

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

EXTRAE

2.3

is a dynamic instrumentation package to trace programs compiled and run with the shared memory model (like OpenMP and pthreads), the message passing (MPI) programming model or both programming models (different MPI processes using OpenMP or pthreads within each MPI process)

MPIBLAST

1.6.0

open-source, parallel implementation of NCBI BLAST. BLAST finds regions of similarity between biological sequences.

GPU-BLAST

1.1

an accelerated GPU version of the popular NCBI-BLAST.

BLAT

35:: The BLAST-Like Alignment Tool

MrBayes

3.2.1

a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models

BEAST

1.7.5

cross-platform program for Bayesian MCMC analysis of molecular sequences. Uses BEAGLE.

MIRA

3.4.0.1

whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).

BEDTOOLS

2.17.0

allow one to address common genomics tasks such as finding feature overlaps and computing coverage.

BEST

2.3.1

a phylogenetics program to estimate the joint posterior distribution of gene trees and species tree using multilocus molecular data that accounts for deep coalescence but not for other issues such as horizontal transfer or gene duplication

BIOPERL

1.6.1

a community effort to produce Perl code which is useful in biology.

NETLOGO

5.3(also 5.2.1)

PAML

4.6

package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

PARTITIONFINDER

1.0.1

Free open source programs for selecting best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments.

PICARD_TOOLS

1.79

Java-based command-line utilities that manipulate SAM (Sequence Alignment/Map) files, and a Java API (SAM-JDK) for creating new programs that r&w SAM files

PINDEL

0.2.4d

detects breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data.

BOWTIE

2.0.2

an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour.

PROTTEST

3.2

bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand.

PhyML

20120412

estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences.

BWA

0.6.2

for aligning sequencing reads against a large reference genome (e.g. human genome).

PhyloBayes

3.3e

is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction

RAxML

7.3.1

implements the popular RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. It uses a radically new MPI parallelization approach that yields improved parallel efficiency, in particular on partitioned multi-gene or whole-genome datasets.

FASTQC

0.10.1

A quality control tool for high throughput sequence data.

SAMTOOLS

0.1.18 (also 1.3 and 1.5)

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

GATK

2.2-8

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data.

SOAPdenovo

1.05

novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads.

HMMER

3.0 (also 2.3.2-MPI-0.92, GPU-0.92)

is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs)

TOPHAT

2.0.6

is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie and then analyzes the mapping results to identify splice junctions between exons.

TRINITY_RNA_SEQ

r2012-06-08

implements a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

INTERPROSCAN

5-RC4

allows you to scan your sequence for matches against the InterPro collection of protein signature databases.

JMODELTEST

2.1.1

a tool to carry out statistical selection of best-fit models of nucleotide substitution