Table of Software on ARC Systems

SOFTWARE

DESCRIPTION

INFER

TINKERCLIFFS

CASCADES

DRAGONSTOOTH

HUCKLEBERRY

guppyGPU

SOFTWAREDESCRIPTION

4.5.2

julia

Julia technical computing language

1.6.1-foss-2020b
1.6.1-fosscuda-2020b

1.6.1-foss-2020b
1.6.1-gomkl-2020b
1.6.2-foss-2020b

0.5.2
0.6.2
0.7.0
1.0.1
1.2.0

0.7.0
1.0.1
1.2.0

matlab

MATLAB Technical Computing

R2021a

R2021a

R2015a
R2016b
R2017b
R2018a
R2020a

R2017b
R2018a
R2020a

ABAQUS

Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit
dynamics FEA.

2018

ABINIT

ABINIT is a package whose main program allows one to find the total energy,
charge density and electronic structure of systems made of electrons and nuclei (molecules
and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a
planewave or wavelet basis.

8.10.3-intel-2019b

ABySS

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

2.1.5-gompi-2020a

ANSYS

ANSYS simulation software enables organizations to confidently predict
how their products will operate in the real world. We believe that every product is
a promise of something greater.

19.5
20.1
20.2
21.1
21.2

APR

Apache Portable Runtime (APR) libraries.

1.7.0-GCCcore-10.2.0

APR-util

Apache Portable Runtime (APR) util libraries.

1.6.1-GCCcore-10.2.0

ATK


ATK provides the set of accessibility interfaces that are implemented by other
toolkits and applications. Using the ATK interfaces, accessibility tools have
full access to view and control running applications.

2.36.0-GCCcore-10.2.0
2.36.0-GCCcore-9.3.0

AUGUSTUS

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

3.4.0-foss-2020b

AccelerateCFD_CE

Community Edition of AccelerateCFD platform for creating reduced order models from high fidelity CFD

20210615-foss-2020a

Anaconda3

Anaconda python distribution, python version 3.5

2020.07
2020.11

4.2.0

2019.03
2020.07

AtomPAW

AtomPAW is a Projector-Augmented Wave Dataset Generator that
can be used both as a standalone program and a library.

4.1.0.5-intel-2019b

Autoconf


Autoconf is an extensible package of M4 macros that produce shell scripts
to automatically configure software source code packages. These scripts can
adapt the packages to many kinds of UNIX-like systems without manual user
intervention. Autoconf creates a configuration script for a package from a
template file that lists the operating system features that the package can
use, in the form of M4 macro calls.

2.69-GCCcore-10.2.0
2.69-GCCcore-8.3.0
2.69-GCCcore-9.3.0

Automake

Automake: GNU Standards-compliant Makefile generator

1.16.1-GCCcore-8.3.0
1.16.1-GCCcore-9.3.0
1.16.2-GCCcore-10.2.0

Autotools


This bundle collect the standard GNU build tools: Autoconf, Automake
and libtool

20180311-GCCcore-8.3.0
20180311-GCCcore-9.3.0
20200321-GCCcore-10.2.0

BCFtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence
variants

1.10.2-GCC-9.3.0
1.11-GCC-10.2.0

BEDTools

BEDTools: a powerful toolset for genome arithmetic.
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and
computing coverage.
The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.

2.29.2-GCC-9.3.0

BLAST+

Basic Local Alignment Search Tool, or BLAST, is an algorithm
for comparing primary biological sequence information, such as the amino-acid
sequences of different proteins or the nucleotides of DNA sequences.

2.10.1-gompi-2020a
2.11.0-gompi-2020b

BUSCO

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

5.0.0-foss-2020b

BamTools

BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.

2.5.1-GCC-10.2.0
2.5.1-GCC-9.3.0

Bazel

Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google’s software.

3.7.2-GCCcore-10.2.0

Biopython

Biopython is a set of freely available tools for biological
computation written in Python by an international team of developers. It is
a distributed collaborative effort to develop Python libraries and
applications which address the needs of current and future work in
bioinformatics.

1.75-intel-2019b-Python-3.7.4
1.78-foss-2020a-Python-3.8.2
1.78-foss-2020b

Bison


Bison is a general-purpose parser generator that converts an annotated
context-free grammar into a deterministic LR or generalized LR (GLR) parser
employing LALR(1) parser tables.

3.0.4
3.0.5
3.3.2
3.3.2-GCCcore-8.3.0
3.5.3
3.5.3-GCCcore-9.3.0
3.5.3-intel-2019b
3.7.1
3.7.1-GCCcore-10.2.0

Boost

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

1.71.0-iimpi-2019b
1.72.0-gompi-2020a
1.74.0-GCC-10.2.0

Bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

2.4.1-GCC-9.3.0

CGAL

The Computational Geometry Algorithms Library is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry.

4.14.3-gompi-2020a-Python-3.8.2

4.9

4.9

CMake


CMake, the cross-platform, open-source build system. CMake is a family of
tools designed to build, test and package software.

3.15.3-GCCcore-8.3.0
3.16.4-GCCcore-9.3.0
3.16.4-intel-2019b
3.18.4-GCCcore-10.2.0

CP2K

CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular
simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different
methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and
classical pair and many-body potentials.

6.1-foss-2020a

DB

Berkeley DB enables the development of custom data management
solutions, without the overhead traditionally associated with such custom
projects.

18.1.40-GCCcore-10.2.0

DBus


D-Bus is a message bus system, a simple way for applications to talk
to one another. In addition to interprocess communication, D-Bus helps
coordinate process lifecycle; it makes it simple and reliable to code
a “single instance” application or daemon, and to launch applications
and daemons on demand when their services are needed.

1.13.12-GCCcore-8.3.0
1.13.12-GCCcore-9.3.0
1.13.18-GCCcore-10.2.0

Dalton

The Dalton suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites. Any published work arising from use of one of the Dalton programs must acknowledge that by a proper reference. The following list of capabilities of the Dalton programs should give you some indication of whether or not the Dalton suite is able to meet your requirements..

2020-iomkl-2019b
2020-iomkl-2019b-nompi

DendroPy

A Python library for phylogenetics and phylogenetic computing:
reading, writing, simulation, processing and manipulation of phylogenetic trees
(phylogenies) and characters.

4.5.2-GCCcore-10.2.0

Doxygen


Doxygen is a documentation system for C++, C, Java, Objective-C, Python,
IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some
extent D.

1.8.16-GCCcore-8.3.0
1.8.17-GCCcore-9.3.0
1.8.20-GCCcore-10.2.0

ELPA

Eigenvalue SoLvers for Petaflop-Applications .

2019.11.001-intel-2019b

EasyBuild

EasyBuild is a software build and installation framework
written in Python that allows you to install software in a structured,
repeatable and robust way.

4.2.2
4.3.2
4.3.3
4.3.4
4.4.0

Eigen

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

3.3.7
3.3.7-GCCcore-9.3.0
3.3.8-GCCcore-10.2.0

FDS

Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows,
with an emphasis on smoke and heat transport from fires.

6.7.1-intel-2019b
6.7.4-intel-2019b
6.7.5-intel-2019b

FFTW

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT

3.3.8-gompi-2020a
3.3.8-gompi-2020b
3.3.8-intel-2019b

FFmpeg

A complete, cross-platform solution to record, convert and stream audio and video.

4.2.1-GCCcore-8.3.0
4.2.2-GCCcore-9.3.0
4.3.1-GCCcore-10.2.0

FLAC

FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning
that audio is compressed in FLAC without any loss in quality.

1.3.3-GCCcore-10.2.0

FriBidi


The Free Implementation of the Unicode Bidirectional Algorithm.

1.0.10-GCCcore-10.2.0
1.0.5-GCCcore-8.3.0
1.0.9-GCCcore-9.3.0

GCC

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
as well as libraries for these languages (libstdc++, libgcj,…).

10.2.0
8.3.0
9.3.0

GCCcore

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
as well as libraries for these languages (libstdc++, libgcj,…).

10.2.0
8.2.0
8.3.0
9.3.0

GDAL

GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
data translation and processing.

3.0.4-foss-2020a-Python-3.8.2

GEOS

GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)

3.8.1-GCC-9.3.0-Python-3.8.2

GLPK

The GLPK (GNU Linear Programming Kit) package is intended for
solving large-scale linear programming (LP),
mixed integer programming (MIP), and other related problems.
It is a set of routines written in ANSI C
and organized in the form of a callable library.

4.65-GCCcore-10.2.0
4.65-GCCcore-8.3.0
4.65-GCCcore-9.3.0

GLib

GLib is one of the base libraries of the GTK+ project

2.62.0-GCCcore-8.3.0
2.64.1-GCCcore-9.3.0
2.66.1-GCCcore-10.2.0

GMP


GMP is a free library for arbitrary precision arithmetic, operating on signed
integers, rational numbers, and floating point numbers.

6.1.2-GCCcore-8.3.0
6.2.0-GCCcore-10.2.0
6.2.0-GCCcore-9.3.0
6.2.0-intel-2019b

GMT

GMT is an open source collection of about 80 command-line tools for manipulating
geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting,
etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps
to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another
40 more specialized and discipline-specific tools.

5.4.5-foss-2020a

GObject-Introspection

GObject introspection is a middleware layer between C libraries
(using GObject) and language bindings. The C library can be scanned at
compile time and generate a metadata file, in addition to the actual
native C library. Then at runtime, language bindings can read this
metadata and automatically provide bindings to call into the C library.

1.63.1-GCCcore-8.3.0-Python-3.7.4
1.64.0-GCCcore-9.3.0-Python-3.8.2
1.66.1-GCCcore-10.2.0

GROMACS


GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
Newtonian equations of motion for systems with hundreds to millions of
particles.

This is a CPU only build, containing both MPI and threadMPI builds
for both single and double precision.
It also contains the gmxapi extension for the single precision MPI build.

2020.1-foss-2020a-Python-3.8.2
2020.3-foss-2020a-Python-3.8.2

GSL

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
The library provides a wide range of mathematical routines such as random number generators, special functions
and least-squares fitting.

2.6-GCC-10.2.0
2.6-GCC-9.3.0
2.6-iccifort-2019.5.281

GTK+

GTK+ is the primary library used to construct user interfaces in GNOME. It
provides all the user interface controls, or widgets, used in a common
graphical application. Its object-oriented API allows you to construct
user interfaces without dealing with the low-level details of drawing and
device interaction.

3.24.17-GCCcore-9.3.0
3.24.23-GCCcore-10.2.0

Gdk-Pixbuf


The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation.
It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it
was distributed as part of GTK+ 2 but it was split off into a separate package
in preparation for the change to GTK+ 3.

2.40.0-GCCcore-10.2.0
2.40.0-GCCcore-9.3.0

Ghostscript

Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to
different targets. It used to be part of the cups printing stack, but is no longer used for that.

9.52-GCCcore-9.3.0
9.52-intel-2019b
9.53.3-GCCcore-10.2.0

GlobalArrays

Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model

5.7.2-intel-2019b
5.7.2-iomkl-2019b

Go

Go is an open source programming language that makes it easy to build
simple, reliable, and efficient software.

1.14

Guile

Guile is a programming language, designed to help programmers create flexible applications that
can be extended by users or other programmers with plug-ins, modules, or scripts.

1.8.8-GCCcore-9.3.0

HDF5

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.

1.10.2-intel-2019b
1.10.2-iomkl-2019b
1.10.5-iimpi-2019b
1.10.6-gompi-2020a
1.10.6-intel-2019b
1.10.7-gompi-2020b
1.12.0-gompi-2020a

HMMER

HMMER 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). Compared to BLAST, FASTA, and other sequence
alignment and database search tools based on older scoring methodology,
HMMER aims to be significantly more accurate and more able to detect remote
homologs because of the strength of its underlying mathematical models. In the
past, this strength came at significant computational expense, but in the new
HMMER3 project, HMMER is now essentially as fast as BLAST.

3.3.2-gompi-2020b

HMMER2

HMMER is used for searching sequence databases for sequence homologs,
and for making sequence alignments.

2.3.2-GCC-8.3.0

HPL

HPL is a software package that solves a (random) dense linear system in double precision (64 bits

2.3-foss-2020a
2.3-intel-2019b

HTSlib

A C library for reading/writing high-throughput sequencing data.
This package includes the utilities bgzip and tabix

1.10.2-GCC-9.3.0
1.11-GCC-10.2.0

HarfBuzz

HarfBuzz is an OpenType text shaping engine.

2.6.4-GCCcore-8.3.0
2.6.4-GCCcore-9.3.0
2.6.7-GCCcore-10.2.0

Hypre

Hypre is a library for solving large, sparse linear systems of equations on massively
parallel computers. The problems of interest arise in the simulation codes being developed at LLNL
and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.

2.18.2-intel-2019b

ICU

ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization
support for software applications.

64.2-GCCcore-8.3.0
66.1-GCCcore-9.3.0
66.1-intel-2019b
67.1-GCCcore-10.2.0

ImageMagick

ImageMagick

7.0.10-1-GCCcore-9.3.0
7.0.10-1-intel-2019b
7.0.10-35-GCCcore-10.2.0

6.8.9
7.0.10

JasPer


The JasPer Project is an open-source initiative to provide a free
software-based reference implementation of the codec specified in
the JPEG-2000 Part-1 standard.

2.0.14-GCCcore-8.3.0
2.0.14-GCCcore-9.3.0
2.0.24-GCCcore-10.2.0

Java

Java Platform, Standard Edition (Java SE) lets you develop and deploy
Java applications on desktops and servers.

11.0.2

Jellyfish

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

2.3.0-GCC-9.3.0

JsonCpp

JsonCpp is a C++ library that allows manipulating JSON values,
including serialization and deserialization to and from strings. It can also preserve existing comment in
unserialization/serialization steps, making it a convenient format to store user input files.

1.9.4-GCCcore-10.2.0

Julia

Julia is a high-level, high-performance dynamic programming language for numerical computing

1.4.2-linux-x86_64
1.5.1-linux-x86_64

LAME

LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.

3.100-GCCcore-10.2.0
3.100-GCCcore-8.3.0
3.100-GCCcore-9.3.0

LAMMPS

LAMMPS is a classical molecular dynamics code, and an acronym
for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
potentials for solid-state materials (metals, semiconductors) and soft matter
(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be
used to model atoms or, more generically, as a parallel particle simulator at
the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
parallel using message-passing techniques and a spatial-decomposition of the
simulation domain. The code is designed to be easy to modify or extend with new
functionality.

3Mar2020-foss-2020a-Python-3.8.2-kokkos

LLVM

The LLVM Core libraries provide a modern source- and target-independent
optimizer, along with code generation support for many popular CPUs
(as well as some less common ones!) These libraries are built around a well
specified code representation known as the LLVM intermediate representation
(“LLVM IR”). The LLVM Core libraries are well documented, and it is
particularly easy to invent your own language (or port an existing compiler

11.0.0-GCCcore-10.2.0
9.0.0-GCCcore-8.3.0
9.0.1-GCCcore-9.3.0

LMDB

LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance
of a pure in-memory database while retaining the persistence of standard disk-based databases.

0.9.24-GCCcore-10.2.0
0.9.24-GCCcore-9.3.0

LibTIFF

tiff: Library and tools for reading and writing TIFF data files

4.0.10-GCCcore-8.3.0
4.1.0-GCCcore-10.2.0
4.1.0-GCCcore-8.3.0
4.1.0-GCCcore-9.3.0

Libint

Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body
matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.

1.1.6-foss-2020a
2.6.0-GCC-10.2.0-lmax-6-cp2k

LittleCMS

Little CMS intends to be an OPEN SOURCE small-footprint color management engine,
with special focus on accuracy and performance.

2.11-GCCcore-10.2.0
2.9-GCCcore-8.3.0
2.9-GCCcore-9.3.0

Lua

Lua is a powerful, fast, lightweight, embeddable scripting language.
Lua combines simple procedural syntax with powerful data description constructs based
on associative arrays and extensible semantics. Lua is dynamically typed,
runs by interpreting bytecode for a register-based virtual machine,
and has automatic memory management with incremental garbage collection,
making it ideal for configuration, scripting, and rapid prototyping.

5.1.5-GCCcore-8.3.0

M4


GNU M4 is an implementation of the traditional Unix macro processor. It is
mostly SVR4 compatible although it has some extensions (for example, handling
more than 9 positional parameters to macros). GNU M4 also has built-in
functions for including files, running shell commands, doing arithmetic, etc.

1.4.17
1.4.18
1.4.18-GCCcore-10.2.0
1.4.18-GCCcore-8.2.0
1.4.18-GCCcore-8.3.0
1.4.18-GCCcore-9.3.0

MATLAB

MATLAB is a high-level language and interactive environment
that enables you to perform computationally intensive tasks faster than with
traditional programming languages such as C, C++, and Fortran.

2019b

METIS


METIS is a set of serial programs for partitioning graphs, partitioning
finite element meshes, and producing fill reducing orderings for sparse
matrices. The algorithms implemented in METIS are based on the multilevel
recursive-bisection, multilevel k-way, and multi-constraint partitioning
schemes.

5.1.0-GCCcore-10.2.0
5.1.0-GCCcore-8.3.0
5.1.0-GCCcore-9.3.0

MPFR


The MPFR library is a C library for multiple-precision floating-point
computations with correct rounding.

4.0.2-GCCcore-8.3.0
4.0.2-GCCcore-9.3.0
4.1.0-GCCcore-10.2.0

MUMPS

A parallel sparse direct solver

5.2.1-foss-2020a-metis
5.2.1-intel-2019b-metis

Mako

A super-fast templating language that borrows the best ideas from the existing templating languages

1.1.0-GCCcore-8.3.0
1.1.2-GCCcore-9.3.0
1.1.3-GCCcore-10.2.0

MariaDB-connector-c

MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases.

3.1.7-GCCcore-9.3.0
3.1.7-intel-2019b

Mathematica

Mathematica is a computational software program used in many scientific, engineering, mathematical
and computing fields.

12.0.0

Mesa

Mesa is an open-source implementation of the OpenGL specification -
a system for rendering interactive 3D graphics.

19.1.7-GCCcore-8.3.0
19.2.1-GCCcore-8.3.0
20.0.2-GCCcore-9.3.0
20.2.1-GCCcore-10.2.0

Meson

Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.

0.51.2-GCCcore-8.3.0-Python-3.7.4
0.53.2-GCCcore-9.3.0-Python-3.8.2
0.53.2-intel-2019b-Python-3.7.4
0.55.1-GCCcore-9.3.0-Python-3.8.2
0.55.3-GCCcore-10.2.0

MetaEuk

MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic
metagenomic contigs.

4-GCC-10.2.0

Miniconda3

Miniconda is a free minimal installer for conda. It is a small,
bootstrap version of Anaconda that includes only conda, Python, the packages they
depend on, and a small number of other useful packages.

4.7.10

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of
large biomolecular systems.

2.13-foss-2020a-mpi

NASM

NASM: General-purpose x86 assembler

2.14.02-GCCcore-8.3.0
2.14.02-GCCcore-9.3.0
2.15.05-GCCcore-10.2.0

NLopt

NLopt is a free/open-source library for nonlinear optimization,
providing a common interface for a number of different free optimization routines
available online as well as original implementations of various other algorithms.

2.6.1-GCCcore-8.3.0
2.6.1-GCCcore-9.3.0
2.6.2-GCCcore-10.2.0

NSPR

Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level
and libc-like functions.

4.21-GCCcore-8.3.0
4.25-GCCcore-9.3.0

NSS

Network Security Services (NSS) is a set of libraries designed to support cross-platform development
of security-enabled client and server applications.

3.45-GCCcore-8.3.0
3.51-GCCcore-9.3.0

NVHPC

C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)

20.7
21.2

Nastran

NASTRANDESCRIPTION

2021

Ninja

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

1.10.0-GCCcore-9.3.0
1.10.0-intel-2019b
1.10.1-GCCcore-10.2.0
1.9.0-GCCcore-8.3.0

OpenBLAS

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

0.3.12-GCC-10.2.0
0.3.9-GCC-9.3.0

OpenFOAM

Open source CFD package

v2006-foss-2020a

2.4.0
3.0.1
v1806
v1906

OpenMM

OpenMM is a toolkit for molecular simulation.

7.4.1-intel-2019b-Python-3.7.4

OpenMPI

The Open MPI Project is an open source MPI-3 implementation.

3.1.4-iccifort-2019.5.281
4.0.3-GCC-9.3.0
4.0.3-iccifort-2019.5.281
4.0.5-GCC-10.2.0

OpenMolcas

OpenMolcas is a quantum chemistry software package

18.09-intel-2019b-Python-3.7.4
19.11-intel-2019b-Python-3.7.4

OpenSSL

The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured,
and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1)
protocols as well as a full-strength general purpose cryptography library.

1.1.1e-GCCcore-9.3.0
1.1.1e-intel-2019b

PCRE


The PCRE library is a set of functions that implement regular expression
pattern matching using the same syntax and semantics as Perl 5.

8.43-GCCcore-8.3.0
8.44-GCCcore-10.2.0
8.44-GCCcore-9.3.0

PCRE2


The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax
and semantics as Perl 5.

10.33-GCCcore-8.3.0
10.34-GCCcore-9.3.0
10.34-intel-2019b
10.35-GCCcore-10.2.0

PETSc

PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
scalable (parallel) solution of scientific applications modeled by partial differential equations.

3.12.4-intel-2019b

PLUMED

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. Free energy calculations can be
performed as a function of many order parameters with a particular focus on biological problems, using
state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.

2.5.1-foss-2020a
2.6.0-foss-2020a-Python-3.8.2

PMIx

Process Management for Exascale Environments
PMI Exascale (PMIx) represents an attempt to
provide an extended version of the PMI standard specifically designed
to support clusters up to and including exascale sizes. The overall
objective of the project is not to branch the existing pseudo-standard
definitions - in fact, PMIx fully supports both of the existing PMI-1
and PMI-2 APIs - but rather to (a) augment and extend those APIs to
eliminate some current restrictions that impact scalability, and (b

3.1.5-GCCcore-10.2.0
3.1.5-GCCcore-8.3.0

PROJ

Program proj is a standard Unix filter function which converts
geographic longitude and latitude coordinates into cartesian coordinates

7.0.0-GCCcore-9.3.0

Pango

Pango is a library for laying out and rendering of text, with an emphasis on internationalization.
Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the
context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.

1.44.7-GCCcore-8.3.0
1.44.7-GCCcore-9.3.0
1.47.0-GCCcore-10.2.0

ParaView

ParaView Scientific Visualization

5.8.0-foss-2020a-Python-3.8.2-mpi

5.6.0

Patran

PATRANDESCRIPTION

2021

Perl

Larry Wall’s Practical Extraction and Report Language

5.30.0-GCCcore-8.3.0
5.30.2-GCCcore-9.3.0
5.32.0-GCCcore-10.2.0

Pillow

Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors.
PIL is the Python Imaging Library by Fredrik Lundh and Contributors.

6.2.1-GCCcore-8.3.0
7.0.0-GCCcore-9.3.0-Python-3.8.2
8.0.1-GCCcore-10.2.0

PyCharm

PyCharm Community Edition: Python IDE for Professional Developers

2019.3.1

PyTorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration.
PyTorch is a deep learning framework that puts Python first.

1.4.0-foss-2020a-Python-3.8.2
1.6.0-foss-2020a-Python-3.8.2
1.6.0-gomkl-2020a-Python-3.8.2
1.7.1-foss-2020b

PyYAML

PyYAML is a YAML parser and emitter for the Python programming language.

5.1.2-GCCcore-8.3.0
5.3-GCCcore-9.3.0
5.3.1-GCCcore-10.2.0

Pysam

Pysam is a python module for reading and manipulating Samfiles.
It’s a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

0.16.0.1-GCC-9.3.0

Python

Python is a programming language that lets you work more quickly and integrate your systems
more effectively.

2.7.16-GCCcore-8.3.0
2.7.18-GCCcore-10.2.0
2.7.18-GCCcore-9.3.0
3.7.4-GCCcore-8.3.0
3.8.2-GCCcore-9.3.0
3.8.6-GCCcore-10.2.0

QIIME2

QIIME is an open-source bioinformatics pipeline for performing microbiome analysis
from raw DNA sequencing data.

2020.6

Qt5

Qt is a comprehensive cross-platform C++ application framework.

5.13.1-GCCcore-8.3.0
5.14.1-GCCcore-9.3.0

QuantumESPRESSO

Quantum ESPRESSO is an integrated suite of computer codes
for electronic-structure calculations and materials modeling at the nanoscale.
It is based on density-functional theory, plane waves, and pseudopotentials
(both norm-conserving and ultrasoft).

6.5-intel-2019b

R

R For Statistical Computing

4.0.2-foss-2020a
4.0.3-foss-2020b

3.2.0
3.2.2
3.3.1
3.4.0
3.4.1
3.4.3
3.4.4
3.5.0
3.5.1
3.5.2
3.5.3
3.6.0
3.6.1
3.6.2

3.2.0
3.2.2
3.3.1
3.4.0
3.4.1
3.4.4
3.5.3
3.6.0
3.6.1
3.6.2

3.6.0

Ruby

Ruby is a dynamic, open source programming language with
a focus on simplicity and productivity. It has an elegant syntax that is
natural to read and easy to write.

2.7.2-GCCcore-9.3.0

SAMtools

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

1.11-GCC-10.2.0

SCOTCH

Software package and libraries for sequential and parallel graph partitioning,
static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.

6.0.9-gompi-2020a
6.0.9-iimpi-2019b

SCons

SCons is a software construction tool.

4.0.1-GCCcore-10.2.0

SEPP

SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic
placement of short reads into reference alignments and trees.

4.4.0-foss-2020b

SLEPc

SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution
of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for
either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a
partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.

3.12.2-intel-2019b

SQLite

SQLite: SQL Database Engine in a C Library

3.29.0-GCCcore-8.3.0
3.31.1-GCCcore-9.3.0
3.31.1-intel-2019b
3.33.0-GCCcore-10.2.0

SWIG

SWIG is a software development tool that connects programs written in C and C++ with
a variety of high-level programming languages.

4.0.1-GCCcore-8.3.0
4.0.1-GCCcore-9.3.0

ScaFaCoS

ScaFaCoS is a library of scalable fast coulomb solvers.

1.0.1-foss-2020a

ScaLAPACK

The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
redesigned for distributed memory MIMD parallel computers.

2.1.0-gompi-2020a
2.1.0-gompi-2020b

SciPy-bundle

Bundle of Python packages for scientific software

2019.10-intel-2019b-Python-3.7.4
2020.03-foss-2020a-Python-3.8.2
2020.03-gomkl-2020a-Python-3.8.2
2020.11-foss-2020b

Serf

The serf library is a high performance C-based HTTP client library
built upon the Apache Portable Runtime (APR) library

1.3.9-GCCcore-10.2.0

SoX

SoX is the Swiss Army Knife of sound processing utilities. It can convert audio files
to other popular audio file types and also apply sound effects and filters during the conversion.

14.4.2-GCC-10.2.0

SpaceRanger

Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output
and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices,
perform clustering and gene expression analysis, and place spots in spatial context on the slide image.

1.2.2-GCC-9.3.0

Subversion

Subversion is an open source version control system.

1.14.0-GCCcore-10.2.0

SuiteSparse

SuiteSparse is a collection of libraries manipulate sparse matrices.

5.6.0-intel-2019b-METIS-5.1.0
5.8.1-foss-2020b-METIS-5.1.0

Szip


Szip compression software, providing lossless compression of scientific data

2.1.1-GCCcore-10.2.0
2.1.1-GCCcore-8.3.0
2.1.1-GCCcore-9.3.0

TINKER

The TINKER molecular modeling software is a complete and general package for molecular mechanics
and dynamics, with some special features for biopolymers.

8.8.1-foss-2020a

Tcl


Tcl (Tool Command Language) is a very powerful but easy to learn dynamic
programming language, suitable for a very wide range of uses, including web
and desktop applications, networking, administration, testing and many more.

8.6.10-GCCcore-10.2.0
8.6.10-GCCcore-9.3.0
8.6.10-intel-2019b
8.6.9-GCCcore-8.3.0

TensorFlow

An open-source software library for Machine Intelligence

2.4.1-foss-2020b

Tk

Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for
building a graphical user interface (GUI) in many different programming languages.

8.6.10-GCCcore-10.2.0
8.6.10-GCCcore-9.3.0
8.6.10-intel-2019b

Tkinter

Tkinter module, built with the Python buildsystem

3.8.2-GCCcore-9.3.0
3.8.6-GCCcore-10.2.0

TopHat

TopHat is a fast splice junction mapper for RNA-Seq reads.

2.1.2-iimpi-2019b

UCX

Unified Communication X
An open-source production grade communication framework for data centric
and high-performance applications

1.8.0-GCCcore-8.3.0
1.8.0-GCCcore-9.3.0
1.9.0-GCCcore-10.2.0

UDUNITS

UDUNITS supports conversion of unit specifications between formatted and binary forms,
arithmetic manipulation of units, and conversion of values between compatible scales of measurement.

2.2.26-GCCcore-10.2.0
2.2.26-GCCcore-8.3.0
2.2.26-GCCcore-9.3.0

UnZip

UnZip is an extraction utility for archives compressed
in .zip format (also called “zipfiles”). Although highly compatible both
with PKWARE’s PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP’s
own Zip program, our primary objectives have been portability and
non-MSDOS functionality.

6.0-GCCcore-10.2.0

VASP

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.

5.4.4-intel-2019b

VTK

The Visualization Toolkit (VTK) is an open-source, freely available software system for
3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several
interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization
algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques
such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

8.2.0-foss-2020a-Python-3.8.2

Valgrind

Valgrind: Debugging and profiling tools

3.16.1-gompi-2020a
3.16.1-iimpi-2019b

Voro++

Voro++ is a software library for carrying out three-dimensional computations of the Voronoi
tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations,
computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that
rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used
to analyze a system of particles.

0.4.6-GCCcore-9.3.0

WRF

The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale
numerical weather prediction system designed to serve both operational forecasting and atmospheric
research needs.

4.1.3-intel-2019b-dmpar

Wannier90

A tool for obtaining maximally-localised Wannier functions

2.0.1.1-intel-2019b-abinit

X11

The X Window System (X11) is a windowing system for bitmap displays

20190717-GCCcore-8.3.0
20200222-GCCcore-9.3.0
20200222-intel-2019b
20201008-GCCcore-10.2.0

XML-LibXML

Perl binding for libxml2

2.0205-GCCcore-9.3.0

XZ

xz: XZ utilities

5.2.4-GCCcore-8.3.0
5.2.5-GCCcore-10.2.0
5.2.5-GCCcore-8.3.0
5.2.5-GCCcore-9.3.0
5.2.5-intel-2019b

Xvfb

Xvfb is an X server that can run on machines with no display hardware and no physical input devices.
It emulates a dumb framebuffer using virtual memory.

1.20.9-GCCcore-10.2.0

Yasm

Yasm: Complete rewrite of the NASM assembler with BSD license

1.3.0-GCCcore-10.2.0
1.3.0-GCCcore-8.3.0
1.3.0-GCCcore-9.3.0

Zip

Zip is a compression and file packaging/archive utility.
Although highly compatible both with PKWARE’s PKZIP and PKUNZIP
utilities for MS-DOS and with Info-ZIP’s own UnZip, our primary objectives
have been portability and other-than-MSDOS functionality

3.0-GCCcore-10.2.0

amd-uprof

AMD μProf for performance analysis

3.4.475

archspec

A library for detecting, labeling, and reasoning about microarchitectures

0.1.0-GCCcore-9.3.0-Python-3.8.2

aspect-2.2.0

AspectDESCRIPTION

intel-2019b

aspect-2.3.0

AspectDESCRIPTION

gcc-9.3.0
intel-2019b

at-spi2-atk

AT-SPI 2 toolkit bridge

2.34.2-GCCcore-9.3.0
2.38.0-GCCcore-10.2.0

at-spi2-core


Assistive Technology Service Provider Interface.

2.36.0-GCCcore-9.3.0
2.38.0-GCCcore-10.2.0

bcl2fastq2

bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

2.20.0-GCC-9.3.0

binutils

binutils: GNU binary utilities

2.30
2.31.1
2.32
2.32-GCCcore-8.3.0
2.34
2.34-GCCcore-9.3.0
2.34-intel-2019b
2.35
2.35-GCCcore-10.2.0

bokeh

Statistical and novel interactive HTML plots for Python

2.0.2-foss-2020a-Python-3.8.2
2.2.3-foss-2020b-Python-3.8.6

boost-1.58.0

BOOSTDESCRIPTION

intel-2019b

bzip2


bzip2 is a freely available, patent free, high-quality data compressor. It
typically compresses files to within 10% to 15% of the best available
techniques (the PPM family of statistical compressors), whilst being around
twice as fast at compression and six times faster at decompression.

1.0.8-GCCcore-10.2.0
1.0.8-GCCcore-8.3.0
1.0.8-GCCcore-9.3.0

cURL


libcurl is a free and easy-to-use client-side URL transfer library,
supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP,
LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP.
libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP
form based upload, proxies, cookies, user+password authentication (Basic,
Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling
and more.

7.66.0-GCCcore-8.3.0
7.69.1-GCCcore-9.3.0
7.72.0-GCCcore-10.2.0

cairo

Cairo is a 2D graphics library with support for multiple output devices.
Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers,
PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB

1.16.0-GCCcore-10.2.0
1.16.0-GCCcore-8.3.0
1.16.0-GCCcore-9.3.0

canu

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing

1.9-GCCcore-8.3.0-Java-11

dask

Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance
at scale for the tools you love.

2.18.1-foss-2020a-Python-3.8.2
2021.2.0-foss-2020b-Python-3.8.6

dealii-9.2.0

SOFTWAREDESCRIPTION

intel-2019b

dealii-9.3.1

DEALIIDESCRIPTION

gcc-9.3.0

double-conversion

Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.

3.1.4-GCCcore-8.3.0
3.1.5-GCCcore-10.2.0
3.1.5-GCCcore-9.3.0

dxa

DXA Dislocation Analysis

1.3.6-foss-2020b

ea-utils

EA-utils are command line tools for processing biological sequencing data.

1.04.807-intel-2019b

1.04.807

1.04.807

expat


Expat is an XML parser library written in C. It is a stream-oriented parser
in which an application registers handlers for things the parser might find
in the XML document (like start tags

2.2.7-GCCcore-8.3.0
2.2.9-GCCcore-10.2.0
2.2.9-GCCcore-9.3.0
2.2.9-intel-2019b

flatbuffers

FlatBuffers: Memory Efficient Serialization Library

1.12.0-GCCcore-10.2.0

flatbuffers-python

Python Flatbuffers runtime library.

1.12-GCCcore-10.2.0

flex

Github Repository

2.6.4
2.6.4-GCCcore-10.2.0
2.6.4-GCCcore-8.3.0
2.6.4-GCCcore-9.3.0

2.6.4

fontconfig


Fontconfig is a library designed to provide system-wide font configuration,
customization and application access.

2.13.1-GCCcore-8.3.0
2.13.92-GCCcore-10.2.0
2.13.92-GCCcore-9.3.0
2.13.92-intel-2019b

foss

GNU Compiler Collection (GCC) based compiler toolchain, including
OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

2020a
2020b

freetype


FreeType 2 is a software font engine that is designed to be small, efficient,
highly customizable, and portable while capable of producing high-quality
output (glyph images). It can be used in graphics libraries, display servers,
font conversion tools, text image generation tools, and many other products
as well.

2.10.1-GCCcore-8.3.0
2.10.1-GCCcore-9.3.0
2.10.3-GCCcore-10.2.0

gaussian

Gaussian is a computer program for computational quantum chemistry
that includes various methods for electronic structure calculations.

09.e01

gc


The Boehm-Demers-Weiser conservative garbage collector can be used as a
garbage collecting replacement for C malloc or C++ new.

7.6.12-GCCcore-9.3.0

gettext

GNU ‘gettext’ is an important step for the GNU Translation Project, as it is an asset on which we may
build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools
and documentation

0.19.8.1
0.20.1
0.20.1-GCCcore-8.3.0
0.20.1-GCCcore-9.3.0
0.21
0.21-GCCcore-10.2.0

gflags

Google command line flags

2.2.2-GCCcore-9.3.0

2.1.2

giflib

giflib is a library for reading and writing gif images.
It is API and ABI compatible with libungif which was in wide use while
the LZW compression algorithm was patented.

5.2.1-GCCcore-10.2.0

git

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.

2.28.0-GCCcore-10.2.0-nodocs

glm-0.9.8.5

SOFTWAREDESCRIPTION

intel-2019b

glog

Google Logging Library

0.4.0-GCCcore-9.3.0

0.3.5

gmsh

3D finite element grid generator with a build-in CAD engine and post-processor

4.5.6-intel-2019b-Python-2.7.16

2.12.0

2.12.0

gnuplot

GNU Plot

5.2.8-GCCcore-8.3.0

5.0.0

5.0.0

gomkl

GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL

2020a
2020b

gompi

GNU Compiler Collection (GCC) based compiler toolchain,
including OpenMPI for MPI support.

2020a
2020b

gperf


GNU gperf is a perfect hash function generator. For a given list of strings,
it produces a hash function and hash table, in form of C or C++ code, for
looking up a value depending on the input string. The hash function is
perfect, which means that the hash table has no collisions, and the hash
table lookup needs a single string comparison only.

3.1-GCCcore-10.2.0
3.1-GCCcore-8.3.0
3.1-GCCcore-9.3.0

gperftools


gperftools is a collection of a high-performance multi-threaded malloc(

2.8-GCCcore-10.2.0

guppyCPU

SOFTWAREDESCRIPTION

Anaconda3-2020.07

gzip

gzip (GNU zip) is a popular data compression program as a replacement for compress

1.10-GCCcore-10.2.0
1.10-GCCcore-9.3.0

h5py

HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
amounts of data.

2.10.0-foss-2020a-Python-3.8.2

help2man


help2man produces simple manual pages from the ‘–help’ and ‘–version’
output of other commands.

1.47.12-GCCcore-9.3.0
1.47.16-GCCcore-10.2.0
1.47.4
1.47.7-GCCcore-8.2.0
1.47.8-GCCcore-8.3.0

hwloc


The Portable Hardware Locality (hwloc) software package provides a portable
abstraction (across OS, versions, architectures, …) of the hierarchical
topology of modern architectures, including NUMA memory nodes, sockets, shared
caches, cores and simultaneous multithreading. It also gathers various system
attributes such as cache and memory information as well as the locality of I/O
devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily
aims at helping applications with gathering information about modern computing
hardware so as to exploit it accordingly and efficiently.

1.11.12-GCCcore-8.3.0
2.2.0-GCCcore-10.2.0
2.2.0-GCCcore-8.3.0
2.2.0-GCCcore-9.3.0

hypothesis

Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized
by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets
you find more bugs in your code with less work.

4.44.2-GCCcore-8.3.0-Python-3.7.4
5.41.2-GCCcore-10.2.0
5.41.5-GCCcore-10.2.0
5.6.0-GCCcore-9.3.0-Python-3.8.2

iccifort

Intel C, C++ & Fortran compilers

2019.5.281

iimpi

Intel C/C++ and Fortran compilers, alongside Intel MPI.

2019b

imkl

Intel Math Kernel Library is a library of highly optimized,
extensively threaded math routines for science, engineering, and financial
applications that require maximum performance. Core math functions include
BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.

2019.5.281-gompi-2020a
2019.5.281-iimpi-2019b
2019.5.281-iompi-2019b
2020.4.304-gompi-2020b

impi

Intel MPI Library, compatible with MPICH ABI

2018.5.288-iccifort-2019.5.281

intel

Intel Compilers (C, C++, Fortran)

2019b

15.3
17.0
18.2
19.4

13.1
15.3
16.1
18.2

intltool

intltool is a set of tools to centralize translation of
many different file formats using GNU gettext-compatible PO files.

0.51.0-GCCcore-10.2.0
0.51.0-GCCcore-8.3.0
0.51.0-GCCcore-9.3.0

iomkl

Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL &
OpenMPI.

2019b

iompi

Intel C/C++ and Fortran compilers, alongside Open MPI.

2019b

kaldi

Kaldi is a toolkit for speech recognition

20210429-foss-2020b

kim-api

Open Knowledgebase of Interatomic Models.

KIM is an API and OpenKIM is a collection of interatomic models (potentials) for
atomistic simulations. This is a library that can be used by simulation programs
to get access to the models in the OpenKIM database.

This EasyBuild only installs the API, the models can be installed with the
package openkim-models, or the user can install them manually by running
kim-api-collections-management install user MODELNAME
or
kim-api-collections-management install user OpenKIM
to install them all.

2.1.3-foss-2020a

libGLU

The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.

9.0.1-GCCcore-10.2.0
9.0.1-GCCcore-8.3.0
9.0.1-GCCcore-9.3.0

libarchive


Multi-format archive and compression library

3.4.3-GCCcore-10.2.0

libcerf


libcerf is a self-contained numeric library that provides an efficient and
accurate implementation of complex error functions, along with Dawson,
Faddeeva, and Voigt functions.

1.13-GCCcore-8.3.0

libdrm

Direct Rendering Manager runtime library.

2.4.100-GCCcore-9.3.0
2.4.102-GCCcore-10.2.0
2.4.99-GCCcore-8.3.0

libepoxy

Epoxy is a library for handling OpenGL function pointer management for you

1.5.4-GCCcore-10.2.0
1.5.4-GCCcore-9.3.0

libevent


The libevent API provides a mechanism to execute a callback function when
a specific event occurs on a file descriptor or after a timeout has been
reached. Furthermore, libevent also support callbacks due to signals or
regular timeouts.

2.1.11-GCCcore-8.3.0
2.1.11-GCCcore-9.3.0
2.1.12-GCCcore-10.2.0

libfabric


Libfabric is a core component of OFI. It is the library that defines and exports
the user-space API of OFI, and is typically the only software that applications
deal with directly. It works in conjunction with provider libraries, which are
often integrated directly into libfabric.

1.11.0-GCCcore-10.2.0
1.11.0-GCCcore-8.3.0

libffi


The libffi library provides a portable, high level programming interface to
various calling conventions. This allows a programmer to call any function
specified by a call interface description at run-time.

3.2.1-GCCcore-8.3.0
3.3-GCCcore-10.2.0
3.3-GCCcore-9.3.0
3.3-intel-2019b

libgd

GD is an open source code library for the dynamic creation of images by programmers.

2.2.5-GCCcore-8.3.0

libgeotiff

Library for reading and writing coordinate system information from/to GeoTIFF files

1.5.1-GCCcore-9.3.0

libglvnd

libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.

1.2.0-GCCcore-8.3.0
1.2.0-GCCcore-9.3.0
1.3.2-GCCcore-10.2.0

libiconv

Libiconv converts from one character encoding to another through Unicode conversion

1.16-GCCcore-10.2.0

libjpeg-turbo

libjpeg-turbo is a JPEG image codec that uses SIMD instructions to accelerate baseline JPEG compression and decompression on x86, x86-64, ARM, and PowerPC systems.

2.0.3-GCCcore-8.3.0
2.0.4-GCCcore-9.3.0
2.0.4-intel-2019b
2.0.5-GCCcore-10.2.0

1.5.1

1.5.1

libmatheval

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

1.1.11-GCCcore-9.3.0

libogg

Ogg is a multimedia container format, and the native file and stream format for the Xiph.org
multimedia codecs.

1.3.4-GCCcore-10.2.0

libpciaccess

Generic PCI access library.

0.14-GCCcore-8.3.0
0.16-GCCcore-10.2.0
0.16-GCCcore-8.3.0
0.16-GCCcore-9.3.0
0.16-intel-2019b

libpng

libpng is the official PNG reference library

1.6.37-GCCcore-10.2.0
1.6.37-GCCcore-8.3.0
1.6.37-GCCcore-9.3.0

libreadline


The GNU Readline library provides a set of functions for use by applications
that allow users to edit command lines as they are typed in. Both Emacs and
vi editing modes are available. The Readline library includes additional
functions to maintain a list of previously-entered command lines, to recall
and perhaps reedit those lines, and perform csh-like history expansion on
previous commands.

8.0-GCCcore-10.2.0
8.0-GCCcore-8.3.0
8.0-GCCcore-9.3.0

libsndfile

Libsndfile is a C library for reading and writing files containing sampled sound
(such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.

1.0.28-GCCcore-10.2.0
1.0.28-GCCcore-8.3.0
1.0.28-GCCcore-9.3.0

libtool


GNU libtool is a generic library support script. Libtool hides the complexity
of using shared libraries behind a consistent, portable interface.

2.4.6-GCCcore-10.2.0
2.4.6-GCCcore-8.3.0
2.4.6-GCCcore-9.3.0

libunistring


This library provides functions for manipulating Unicode strings and for
manipulating C strings according to the Unicode standard.

0.9.10-GCCcore-9.3.0

libunwind

The primary goal of libunwind is to define a portable and efficient C programming interface
(API) to determine the call-chain of a program. The API additionally provides the means to manipulate the
preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain
(non-local goto). The API supports both local (same-process) and remote (across-process) operation.
As such, the API is useful in a number of applications

1.3.1-GCCcore-8.3.0
1.3.1-GCCcore-9.3.0
1.4.0-GCCcore-10.2.0

libvorbis

Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed
audio format

1.3.7-GCCcore-10.2.0

libxc

Library of exchange-correlation functionals for density-functional theory

3.0.1-intel-2019b
4.2.3-intel-2019b
4.3.4-GCC-9.3.0
4.3.4-iccifort-2019.5.281

4.3.4

libxml2


Libxml2 is the XML C parser and toolchain developed for the Gnome project
(but usable outside of the Gnome platform).

2.9.10-GCCcore-10.2.0
2.9.10-GCCcore-8.3.0
2.9.10-GCCcore-9.3.0
2.9.10-intel-2019b
2.9.9-GCCcore-8.3.0

libxsmm

LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications
targeting Intel Architecture (x86).

1.10-GCC-9.3.0

libyaml

LibYAML is a YAML parser and emitter written in C.

0.2.2-GCCcore-8.3.0
0.2.2-GCCcore-9.3.0
0.2.5-GCCcore-10.2.0

lpsolve

Mixed Integer Linear Programming (MILP) solver

5.5.2.11-GCC-10.2.0

ls-dyna

LS-DYNA general-purpose finite element simulation software.

10.2.0-intel-2019b
13.0.0-intel-2019b
R12.0.0

8.0.0

ls-prepost

LS-PrePost

4.8

lz4

LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core.
It features an extremely fast decoder, with speed in multiple GB/s per core.

1.9.2-GCCcore-10.2.0
1.9.2-GCCcore-9.3.0

matplotlib

matplotlib is a python 2D plotting library which produces publication quality figures in a variety of
hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python
and ipython shell, web application servers, and six graphical user interface toolkits.

3.2.1-foss-2020a-Python-3.8.2
3.3.3-foss-2020b

metis-5.1.0

METISDESCRIPTION

gcc-8.3.0
gcc-9.3.0
intel-2019b

minimap2

Minimap2 is a fast sequence mapping and alignment
program that can find overlaps between long noisy reads, or map long
reads or their assemblies to a reference genome optionally with detailed
alignment (i.e. CIGAR). At present, it works efficiently with query
sequences from a few kilobases to ~100 megabases in length at an error
rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited
test data sets, minimap2 is over 20 times faster than most other
long-read aligners. It will replace BWA-MEM for long reads and contig
alignment.

2.17-GCCcore-9.3.0

molmod

MolMod is a Python library with many compoments that are useful to write molecular modeling programs.

1.4.5-foss-2020a-Python-3.8.2

mpi4py

MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
the Python programming language, allowing any Python program to exploit multiple processors.

3.0.2-gompi-2020a-timed-pingpong
3.0.2-iimpi-2019b-timed-pingpong

nanopolish

Software package for signal-level analysis of Oxford Nanopore sequencing data.

0.13.2-foss-2020a-Python-3.8.2

ncurses


The Ncurses (new curses) library is a free software emulation of curses in
System V Release 4.0, and more. It uses Terminfo format, supports pads and
color and multiple highlights and forms characters and function-key mapping,
and has all the other SYSV-curses enhancements over BSD Curses.

6.0
6.1
6.1-GCCcore-8.3.0
6.2
6.2-GCCcore-10.2.0
6.2-GCCcore-9.3.0
6.2-intel-2019b

netCDF

NetCDF (network Common Data Form) is a set of software libraries
and machine-independent data formats that support the creation, access, and sharing of array-oriented
scientific data.

4.6.1-intel-2019b
4.7.1-iimpi-2019b
4.7.4-gompi-2020a
4.7.4-gompi-2020b

netCDF-Fortran

NetCDF (network Common Data Form) is a set of software libraries
and machine-independent data formats that support the creation, access, and sharing of array-oriented
scientific data.

4.4.4-intel-2019b
4.5.2-iimpi-2019b

nettle

Nettle is a cryptographic library that is designed to fit easily
in more or less any context: In crypto toolkits for object-oriented
languages (C++, Python, Pike, …), in applications like LSH or GNUPG,
or even in kernel space.

3.5.1-GCCcore-8.3.0
3.6-GCCcore-10.2.0

networkx

NetworkX is a Python package for the creation, manipulation,
and study of the structure, dynamics, and functions of complex networks.

2.4-foss-2020a-Python-3.8.2

nodejs

Node.js is a platform built on Chrome’s JavaScript runtime
for easily building fast, scalable network applications. Node.js uses an
event-driven, non-blocking I/O model that makes it lightweight and efficient,
perfect for data-intensive real-time applications that run across distributed devices.

12.16.1-GCCcore-9.3.0
12.19.0-GCCcore-10.2.0

nsync

nsync is a C library that exports various synchronization primitives, such as mutexes

1.24.0-GCCcore-10.2.0

numactl


The numactl program allows you to run your application program on specific
cpu’s and memory nodes. It does this by supplying a NUMA memory policy to
the operating system before running your program. The libnuma library provides
convenient ways for you to add NUMA memory policies into your own program.

2.0.12-GCCcore-8.3.0
2.0.13-GCCcore-10.2.0
2.0.13-GCCcore-8.3.0
2.0.13-GCCcore-9.3.0

p4est

Parallel adaptive mesh refinement on forests of octrees

2.2-intel-2019b
gcc-8.3.0

1.1

1.1

p4est-2.2

P4ESTDESCRIPTION

gcc-9.3.0
intel-2019b

parallel

GNU Parallel

20190922-GCCcore-8.3.0
20200522-GCCcore-9.3.0

20170622
20180222

20180222

parmetis-4.0.3

PARMETIS4.0.3DESCRIPTION

gcc-8.3.0
gcc-9.3.0
intel-2019b

picard

Picard: A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats

2.21.6-Java-11

1.138

pixman


Pixman is a low-level software library for pixel manipulation, providing
features such as image compositing and trapezoid rasterization. Important
users of pixman are the cairo graphics library and the X server.

0.38.4-GCCcore-8.3.0
0.38.4-GCCcore-9.3.0
0.40.0-GCCcore-10.2.0

pkg-config


pkg-config is a helper tool used when compiling applications and libraries.
It helps you insert the correct compiler options on the command line so an
application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0
for instance, rather than hard-coding values on where to find glib (or other
libraries).

0.29.2-GCCcore-10.2.0
0.29.2-GCCcore-8.3.0
0.29.2-GCCcore-9.3.0

pkgconfig

pkgconfig is a Python module to interface with the pkg-config command line tool

1.5.1-GCCcore-10.2.0-python
1.5.1-GCCcore-9.3.0-Python-3.8.2

prodigal

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm

2.6.3-GCCcore-10.2.0

protobuf

Google Protocol Buffers

3.10.0-GCCcore-8.3.0
3.10.0-GCCcore-9.3.0
3.14.0-GCCcore-10.2.0

protobuf-python

Python Protocol Buffers runtime library.

3.10.0-foss-2020a-Python-3.8.2
3.10.0-gomkl-2020a-Python-3.8.2
3.10.0-intel-2019b-Python-3.7.4
3.14.0-GCCcore-10.2.0

pybind11

pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa,
mainly to create Python bindings of existing C++ code.

2.4.3-GCCcore-8.3.0-Python-3.7.4
2.4.3-GCCcore-9.3.0-Python-3.8.2
2.6.0-GCCcore-10.2.0

rclone


Rclone is a command line program to sync files and directories to and from
a variety of online storage services

1.42-amd64
1.42-foss-2020a-amd64

re2c

re2c is a free and open-source lexer generator for C and C++. Its main goal is generating
fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using
traditional table-driven approach, re2c encodes the generated finite state automata directly in the form
of conditional jumps and comparisons.

1.2.1-GCCcore-8.3.0
1.3-GCCcore-9.3.0

scikit-build

Scikit-Build, or skbuild, is an improved build system generator
for CPython C/C++/Fortran/Cython extensions.

0.10.0-foss-2020a-Python-3.8.2

snappy

Snappy is a compression/decompression library. It does not aim
for maximum compression, or compatibility with any other compression library;
instead, it aims for very high speeds and reasonable compression.

1.1.7-GCCcore-8.3.0
1.1.8-GCCcore-10.2.0
1.1.8-GCCcore-9.3.0

sparsehash

An extremely memory-efficient hash_map implementation

2.0.3-GCCcore-9.3.0

2.0.2

2.0.2

starccm+

Engineering simulation software

12.04.011
15.04.010

12.04.011
13.04.011
14.06.013
15.02.007
15.04.010

11.2.10
12.04.011
13.04.011
14.06.013

tbb

Intel Threading Building Blocks

2020.1-GCCcore-9.3.0

4.3.5

4.3.5

tcsh

Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh).
It is a command language interpreter usable both as an interactive login shell and a shell script command
processor. It includes a command-line editor, programmable word completion, spelling correction, a history
mechanism, job control and a C-like syntax.

6.22.02-GCCcore-8.3.0

time

The `time’ command runs another program, then displays information about the resources used by that
program, collected by the system while the program was running.

1.9-GCCcore-8.3.0

tpl-4.4.18

SOFTWAREDESCRIPTION

GCC-9.3.0
intel-2019b

trilinos-12.18.1

TRILINOS12.18.1DESCRIPTION

gcc-8.3.0
gcc-9.3.0
intel-2019b

typing-extensions

Typing Extensions – Backported and Experimental Type Hints for Python

3.7.4.3-GCCcore-10.2.0

utf8proc

utf8proc is a small, clean C library that provides Unicode normalization, case-folding,
and other operations for data in the UTF-8 encoding.

2.5.0-GCCcore-10.2.0

util-linux

Set of Linux utilities

2.34-GCCcore-8.3.0
2.35-GCCcore-9.3.0
2.35-intel-2019b
2.36-GCCcore-10.2.0

x264

x264

20190925-GCCcore-8.3.0
20191217-GCCcore-9.3.0
20201026-GCCcore-10.2.0

1.0
7.5.2020

1.0

x265


x265 is a free software library and application for encoding video streams
into the H.265 AVC compression format, and is released under the terms of
the GNU GPL.

3.2-GCCcore-8.3.0
3.3-GCCcore-10.2.0
3.3-GCCcore-9.3.0

xorg-macros

X.org macros utilities.

1.19.2-GCCcore-10.2.0
1.19.2-GCCcore-8.3.0
1.19.2-GCCcore-9.3.0

yaff

Yaff stands for ‘Yet another force field’. It is a pythonic force-field code.

1.6.0-foss-2020a-Python-3.8.2

zlib

zlib

1.2.11
1.2.11-GCCcore-10.2.0
1.2.11-GCCcore-8.2.0
1.2.11-GCCcore-8.3.0
1.2.11-GCCcore-9.3.0

1.2.11
1.2.8

1.2.8

zstd

Zstandard is a real-time compression algorithm, providing high compression ratios.
It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder.
It also offers a special mode for small data, called dictionary compression, and can create dictionaries
from any sample set.

1.4.4-GCCcore-9.3.0
1.4.5-GCCcore-10.2.0

Anaconda

Anaconda python distribution with TensorFlow 1.7 and Pytorch

2.3.0
2020.07
5.1.0
5.2.0

5.2.0

Anaconda-boost

BOOST template libraries

1.58.0

Anaconda2

Anaconda python distribution, python version 2.7

4.2.0

2019.03

CLAPACK

LAPACK linear algebra routines in C

3.1.1.1

3.1.1.1

JAGS

Just Another Gibbs Sampler (JAGS)

4.3.0

4.3.0

LBPM

Lattice Boltzmann simulator

4.9.2018

R-gpu

GPU packages for R

3.5.0

R-parallel

Parallel packages for R

3.3.1
3.5.0
3.5.1
3.5.2
3.5.3
3.6.0
3.6.1
3.6.2

3.4.1
3.4.4
3.5.3

RSEM

RSEM is a RNASeq utility

1.3.3

1.3.3

STAR

STAR 2.5

2.5.2b

2.5.2b

ViennaCL

Set of header files for GPU support

1.7.1

1.7.1

abaqus

Abaqus Research Edition

2018
6.14_4

2018
6.14_4

abinit

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

8.0.8

8.0.8

abyss

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

1.5.2
2.0.2

1.5.2

allpathslg

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

52488

52488

amber

APBS Molecular Dynamics Simulations Software Package

2015

ansys

Engineering simulation software

17.0
19.0
21.1

17.0

ansysEM

Electromagnetics simulation software

17.0

17.0

apbs-static

Adaptive Poisson Boltzmann Solver

1.4

1.4

atlas

ATLAS Tuned Linear Algebra (includes LAPACK)

3.11.34
3.11.36

3.10.2

autodocksuite

Automated molecule docking tool

4.2.6

4.2.6

automake

automake tools

1.15

1.15

bamtools

BAMTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.

2.4

2.4

bcftools

Bcftools

1.3.1

1.2

beagle-lib

BEAGLE-lib

2.1.2

2.1.2

bedtools

Bedtools is a fast, flexible toolset for genome arithmetic.

2.25.0

2.25.0

bison

GNU Software

3.5

boost

BOOST template libraries

1.58.0
1.69.0

1.58.0

boost-mpi

BOOST template libraries

1.58.0

1.58.0

bowtie

Short read aligner

1.1.2

1.1.1

bowtie2

Bowtie 2 Fast and Sensitive Read Alignment

2.2.9

2.2.5
2.2.9

bwa

Burrows-Wheeler Aligner

0.7.12

0.7.12

cddlib

CDD library for fundamental polyhedral computations

0.94h

0.94h

charm

Charm++

6.6.1

cmake

Cross Platform Makefile Generator

3.10.3
3.17.2
3.6.2
3.8.2

3.10.3
3.2.2
3.8.2

3.10.3
3.14.3

comsol

COMSOL

5.3a
5.4

cora

CORA (CORrelation and Analysis) provides an objective evaluation of time-history signal

3.6.1

3.6.1

cp2k

CP2K Open Source Molecular Dynamics

6.1.0

cplex

Optimization

12.6.2

12.6.2

cuda

NVIDIA CUDA Toolkit (C, C++, cuda-gdb, cuda-memcheck, gpu accel)

8.0.44
8.0.61
9.0.176
9.1.85
9.2.148

8.0.44

10.1.105
10.2.89

cudnn

cuDNN

GPU-accelerated library for deep neural networks

7.0
7.1

cufflinks

Transcriptome assembly and differential expression analysis for RNA-Seq.

2.2.1

2.2.1

cytoscape

Cytoscape - Network Data Integration, Analysis, and Visualization in a Box

3.6.1

dcw

Geography Database

1.1.1

1.1.1

diamond

Sequence Alignment Tool

0.6.13

discovar

new genome assembler

52488

52488

discovardenovo

new genome assembler

52488

52488

eigen

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

3.2.10
3.2.5

3.2.5
3.3.7

ensight

CSM and CFD Post processing

10

10

espresso

nanoscale material modeling

5.1.2

evolver

evolver

2.70

examl

Exascale Maximum Likelihood (ExaML)

3.0.11

3.0.11

extrae

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

3.5.1

3.5.1

fastp

An ultra-fast all-in-one FASTQ preprocessor

1.0.0

1.0.0

fastqc

FastQC - A quality control tool for high throughput sequence data.

0.11.3

0.11.3

fdk-aac

fdk-aac

1.0

1.0

fds

Fire Dynamics Simulator and Smokeview

6.7.1

ffmpeg

ffmpeg

2.5.4
4.2.3

2.5.4

fftw

Fastest Fourier Transform in the West

2.1.5
3.3.4
3.3.5
3.3.6
3.3.8

2.1.5
3.3.4

flann

FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces.

1.8.4

1.8.4

flint

Fast Library for Number Theory

2.5.2

2.5.2

gamit-globk

GPS measurement analysis software

10.6.150811

10.6.150811

gatb

Genome Assembly and Analysis Tool Box

1.0.6

1.0.6

gatk

The Genome Analysis Toolkit or GATK is a software package developed to analyze high-throughput sequencing data.

3.4.46

3.4.46

gcc

GNU Compiler Collection (C, C++, Fortran, Go)

4.7.2
5.2.0
6.1.0
6.4.0
7.3.0

4.7.2
5.1.0
5.2.0
6.1.0
7.3.0

6.4.0
7.3.0

gdal

Geospatial Data Abstraction Library

2.0.1

2.0.1

gdk

NVIDIA GPU Deployment Kit

340.29

geos

GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS).

3.4.2

3.4.2

glm

OpenGL Mathematics

0.9.4.3
0.9.8.5

0.9.4.3

gmap-gsnap

GMAP/GSNAP 2017-01-10

2017.01.10

2017.01.10

go

The Go programming language is an open source project to make programmers more productive.

1.12.7
1.13.5

1.12.7
1.13.5

1.12.9
1.13.5

graphviz

Graphviz is open source graph visualization software.

2.40.1

2.40.1

gromacs

GROMACS

5.1.2

gromacs.c9

GROMACS

2018
2018.1

gshhg

Geography Database

2.3.0

2.3.0

gsl

GNU Scientific Library

2.4

1.9
2.4

guile

GNU Ubiquitous Intelligent Language for Extensions

2.2.0

2.2.0

guppy-cpu

guppy-cpu

3.2.4

harminv

Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion — given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.

1.4.1

1.4.1

hdf5

Tool suite for managing very large and complex data collections

1.8.15
1.8.16
1.8.17

1.8.15
1.8.16

1.8.12
1.8.17

hisat2

HiSat2 Fast and Sensitive Read Alignment

2.1.0

2.1.0

hmmer

Sequence Homology Search

3.1b2

3.1b2

hpctoolkit

HPCToolkit

5.3.2

5.3.2

hpgl

High Performance Geostatistics Library

0.9.3

hpl

High-Performance Linpack

2.2

2.1

htk

Hidden Markov Model Toolkit (HTK)

3.4.0

3.4.1

hypre

Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers

2.10.0b

2.10.0b

igv

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

2.3.82

2.3.82

ioapi

Input/Output Applications Programming Interface

3.2

iperf

iPerf - The ultimate speed test tool for TCP, UDP and SCTP

3.1

2.0.9
3.1

jdk

Java Development Kit

1.11.0.9
1.8.0
1.8.0u172

1.6.0
1.7.0
1.8.0

8.0.5.31

lame

lame

3.99.5

3.99.5

lammps

Large-scale Atomic/Molecular Massively Parallel Simulator

11Aug17

11Aug17

lbpm

Lattice Boltzmann simulator

4.5.2019

3.17.2021
4.23.2019
4.5.2019
9.21.2020

libctl

A Guile-based library implementing flexible control files for scientific simulations.

4.0.1

libmsym

Molecular point group symmetry lib

2019Dec06

ls-dyna-mpp

LS-DYNA general-purpose finite element simulation software.

11.0.0

11.0.0

ls-dyna-smp

LS-DYNA general-purpose finite element simulation software.

11.0.0

11.0.0

lua

Lua Scripting Language

5.1.4.8

5.1.4.8

5.1.4.8

luaJIT

Lua Just-in-time compiler

2.0.4

2.0.4

mathematica

Mathematica Technical Computing

11.0.0
11.3.0
12.0.0

11.3.0
12.0.0

meep

Meep is a free finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems.

1.3

1.3

megan

MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data

6.11.6

metis

Multilevel Partitioning Algorithms

5.1.0

5.1.0

minia

genome assembler

2.0.7

2.0.7

mira

MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects

4.0.2

mkl

Intel MKL Library

11.2.3
18.2
19.4
2017.0

11.2.3
18.2

mpe2

MPI Parallel Environment

2.4.9b

2.4.9b

mpiP

mpiP: Lightweight, Scalable MPI Profiling

3.4.1

3.4.1

mpiblast

mpiBLAST: Open-Source Parallel BLAST

1.6.0

1.6.0

mrbayes

MrBayes is a program for Bayesian inference

3.2.5

3.2.5

mvapich2

OSU MPI

2.2
2.3.1
2.3rc1

2.2

mysql

MySQL: a very fast and reliable SQL database server

5.6.14

5.5.37
5.6.14

namd

NAMD Scalable Molecular Dynamics

2.10
2.12
2.13

2.10

namd-gpu

NAMD Scalable Molecular Dynamics

2.10

nasm

nasm

2.13

nastran

Multidisciplinary Structural Analysis

2014.1

2014.1

ncbi-blast+

BLAST sequence alignment

2.4.0

2.4.0

ncl

NCAR Command Language

6.4.0

6.4.0

nco

netCDF Operators

4.4.9

ncview

Ncview

2.1.7

netcdf

Network Common Data Form

4.1.3
4.3.3.1

4.3.3.1

4.3.3.1

netcdf-c

Network Common Data Form

4.4.0

4.4.0

netcdf-c-par

Network Common Data Form

4.4.0

4.4.0

netcdf-cxx

Network Common Data Form

4.2.1

netcdf-fortran

Network Common Data Form

4.4.3

4.4.3

nose

Nose is open-source testing software for python.

1.3.7

numpy

NumPy is the fundamental package for scientific computing in Python

1.10.1

openblas

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

0.2.20
0.3.6

0.2.14
0.2.20
0.3.6

0.2.20
0.3.6

opencv

opencv

2.4.11

2.4.11

openmpi

Open MPI

1.10.7
2.0.0
2.1.3
3.0.0
3.1.2
4.0.1

1.10.2

2.1.3
3.1.2
4.0.1
4.0.5

opensees

OpenSees Earthquake Engineering Simulation

2.5.0

p2fa

Penn Phonetics Lab Forced Aligner

1.003

1.003

p7zip

p7zip is a quick port of 7z

15.09

15.09

papi

Performance Application Programming Interface

5.4.1

5.4.1

parallel-netcdf

Parallel Network Common Data Form

1.6.0
1.7.0
1.8.1

1.6.0
1.7.0

parmetis

Multilevel Partitioning Algorithms

4.0.3

4.0.3

patran

FEA Modeling Solution

2014.1

2014.1

pcre2

Perl Compatible Regular Expressions

10.34

pdtoolkit

Program Database Toolkit (PDT)

3.20

3.20

perl

The Perl Programming Language

5.20.2

5.20.2

pgi

PGI Compilers (C, C++, Fortran)

17.5
18.1
18.4

17.5
18.1

18.5

phdf5

Tool suite for managing very large and complex data collections

1.8.15
1.8.16

1.8.15
1.8.16

pigz

Parallel implimentation of gzip

2.3.4
2.4

2.3.4
2.4

prinseq

PRINSEQ for sequence data manipulation

0.20.4

proj

RPROJ.4 (or proj) is a library for performing conversions between cartographic projections.

4.9.2
7.1.0

4.9.2

proovread

proovread

2.13.10

2.13.10

pv

pipe viewer

1.6.6

1.6.6

python

Python

2.7.10
2.7.12
2.7.13
2.7.2
2.7.9
3.5.0
3.5.2

2.7.10
2.7.13
3.5.0

qt

Qt GUI SDK

4.8.4
5.12.3

4.8.4
5.12.1

rstudio

Engineering simulation software

1.1.414
1.1.463

0.99.486
1.1.414

samtools

Samtools

1.10
1.3.1

1.2
1.3.1

scalapack

Scalable Linear Algebra PACKage

2.0.2

2.0.2

scipy

SciPy is open-source software for mathematics, science, and engineering.

0.16.1

scons

Open source software construction / build tool

2.3.4

seqtk

Toolkit for processing sequences in FASTA/Q formats

1.2

1.2

shrimp

SHRiMP - SHort Read Mapping Package

2.2.3

silo

Silo is a library for IO

4.10.2

4.10.2

singularity

Singularity is an open source container platform designed to be simple, fast, and secure.

3.3.0
3.5.1
3.7.3

3.3.0
3.5.1

3.3.0
3.5.1

sox

Sound eXchange (SoX)

14.4.2

14.4.2

spades

genome assembler

3.10.0
3.14.0

3.6.0

sqlite

SQLite is a relational database management system contained in a C library.

3.33.0

stata

Statistical software

14.0.0

14.0.0

swig

SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

3.0.11

szip

Szip compression software

2.1

2.1

2.1

tau

Tuning and Analysis Utilities

2.24.1

2.24.1

tcl

Tool command language

8.6.9

tcltk

Tool Command Language and Toolkit

8.6.9

8.6.9

tecplot

Scientific Visualization

17.1.0

15.2.0
17.1.0

tophat

TopHat A spliced read mapper for RNA-Seq

2.1

2.1

tpl

Collection of commonly used third party libraries

4.4.18

trilinos

Object-oriented software framework for multiphysics applications

11.12.1
12.12.1

11.12.1

trimmomatic

Trimmomatic: A flexible read trimming tool for Illumina NGS data

0.33

0.33

trinityrnaseq

RNA-Seq De novo Assembly Using Trinity

2.2.0

2.0.6

udunits

UDUNITS units package

2.2.25
2.2.26

2.2.25
2.2.26

2.2.26

valgrind

Valgrind Tool Suite

3.12.0

3.10.0

vasp

The Vienna Ab initio Simulation Package

5.4.1
5.4.4

5.4.1

vasp-wannier

The Vienna Ab initio Simulation Package

5.4.1

velvet

De Novo Genomic Assembler

1.2.08

vtk

Visualization ToolKit

7.0.0

vtune

Intel VTune Performance Profiler

17.0.2

wannier90

Wannier90

1.2
2.0.1

1.2
2.0.1

yasm

yasm

1.3

1.3

apache-ant

Apache Ant for building Java applications

1.9.2

lsopt

LS-OPT is a standalone package with an interface to LS-DYNA.

5.1.1

mpich

OSU MPI

3.1.4

petsc

Portable, Extensible Toolkit for Scientific Computation (PETSc)

3.5.2

singular

Computer algebra system for polynomial computations

4.0.3

nvhpc

NVidia HPC SDK (PGI Compilers, libraries, CUDA, NCCL, NVSHEM, debugger, profiler, HPC container maker, NGC)

20.9