Software Modules¶
All software available via the modules system on Midway2 are listed on this page. To load any particular software module shown below use the following syntax from the command line on Midway2:
[jbravo@midway2 ~]$ module load <modulename>
where <modulename>
is the name of the software module.
See the page Using software modules on Midway for more information.
- GUI
- JSON
- alignment
- array
- assembler
- astrophysics
- bioinformatics
- biology
- browser
- checkpointing
- chemistry
- climate
- cloud computing
- compilers
- compression
- computation
- computer architecture
- container
- copy
- crystallography
- data
- data analysis
- database
- debugging
- deep-learning
- development
- differential solvers
- differentiation
- disk
- docs
- documentation
- economics
- electronic structure
- evolution
- general programming
- genetics
- genetics and genomics
- genomics
- geoscience
- gis
- graphical interfaces
- graphics
- graphs
- high energy physics
- high performance computing
- image
- image analysis
- image processing
- image progressing
- imaging
- integration
- jpeg
- library
- linear algebra
- linguistics
- machine learning
- many-body perturbation theory
- materials
- materials science
- math library
- mathematics
- matrix computation
- media
- medical
- medicine
- messaging
- molecular dynamics
- molecular modeling
- molecular visualization
- multimedia
- network
- network library
- neural networks
- neuroscience
- numerical
- numerical analysis
- optimization
- parallel
- parser
- paste
- photonic
- physics
- postgres
- profiler
- profiling
- programming
- proteins
- python
- simulation
- slrum
- software
- statistics
- system
- systems research
- terminal
- testing
- text
- text editor
- typesetting
- usage
- utility
- version control
- video
- visualization
- workflow
GUI¶
Application | Version | Description |
---|---|---|
fltk | fltk/1.3.4 (default) | FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X |
xdiskusage | xdiskusage/1.51 (default) | Graphical display of disk usage |
JSON¶
Application | Version | Description |
---|---|---|
jq | jq/1.5 (default) | jq is a lightweight and flexible command-line JSON processer |
alignment¶
Application | Version | Description |
---|---|---|
muscle | muscle/3.8.31 (default) | MUSCLE is one of the best-performing multiple alignment programs |
array¶
Application | Version | Description |
---|---|---|
swarm | swarm/latest (default) | Swarm reads a list of command lines then submits all command scripts to the cluster as a Slurm job array |
assembler¶
Application | Version | Description |
---|---|---|
glew | glew/1.9, glew/2.0.0 (default) | The OpenGL Extension Wrangler Library |
nasm | nasm/2.13.01+gcc-6.2 (default) | The Netwide Assembler |
yasm | yasm/1.3.0 (default) | The Yasm Modular Assembler Project |
astrophysics¶
Application | Version | Description |
---|---|---|
Fermi Science Tools | fermi-fssc/v10r0p5 (default) | suite of tools for the analysis of both LAT and GBM data |
snid | snid/5.0 (default) | Supernova Identification software |
bioinformatics¶
Application | Version | Description |
---|---|---|
MACS | MACS/1.4 (default) | Model-based Analysis for ChIP-Seq |
MEME | MEME/4.11 (default) | Motif-based sequence analysis tools. |
RSEM | RSEM/1.3 (default) | Accurate quantification of gene and isoform expression from RNA-Seq data. |
blast | blast/2.9.0 (default) | BLAST+: command-line tools for Basic Local Alignment Search |
bowtie | bowtie/1.1.2, bowtie/1.2.1.1 (default) | DNA sequence alignment software |
bwa | bwa/0.7.15 (default) | Burrow-Wheeler Aligner for pairwise alignment between DNA sequences. |
clark | clark/1.2.3.1 (default) | Fast, accurate and versatile sequence classification system |
gatk | gatk/3.7 (default) | Genome Analysis Toolkit: variant siscovery in high-throughput sequencing data |
gcta | gcta/1.91.2, gcta/1.92.2 (default) | Software for genome-wide complex trait analysis. |
Integrative Genomics Viewer Tools | igv/2.4.11 (default) | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. |
Integrative Genomics Viewer Tools | igvtools/2.3.98 (default) | Accompanying CLI tools for IGV |
picard | picard/2.18.15, picard/2.18.2, picard/2.21.8 (default) | A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. |
tophat | tophat/2.1 (default) | splice junction mapper for RNA-Seq reads |
biology¶
Application | Version | Description |
---|---|---|
bcftools | bcftools/1.4.1, bcftools/1.9 (default) | BCFtools are meant as a faster replacement for most of the perl vcftools commands; originally distributed with samtools. |
bcl2fastq2 | bcl2fastq2/2.20 (default) | Sequencing software used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis. |
BEAGLE | beagle/trunk (default) | library for core calculations with phylogenetics packages |
BEAST | beast/1.8, beast/2.3 (default), beast/2.6.2 | Bayesian analysis of molecular sequences |
blast | blast/2.9.0 (default) | BLAST+: command-line tools for Basic Local Alignment Search |
bowtie | bowtie/1.1.2, bowtie/1.2.1.1 (default) | DNA sequence alignment software |
bowtie2 | bowtie2/2.2.9 (default) | DNA sequence alignment software |
breseq | breseq/0.32.0 (default) | Computational pipeline for identfying mutations in short-read DNA re-sequencing data for haploid microbial genomes. |
cellranger | cellranger/2.1.1 (default), cellranger/3.0.0 | An analysis pipeline for processing Chromium single-cell RNA-sequences. Capable of converting BCL files from Illumina sequencing systems to FASTQ file formats. |
cufflinks | cufflinks/2.2 (default) | Transcriptome assembly and differential expression analysis for RNA-Seq. |
ea-utils | ea-utils/current (default) | Command-line tools for processing biological sequencing data |
fastqc | fastqc/0.11.5 (default) | A quality control tool for high throughput sequence data. |
fasttree | fasttree/2.1.8 (default) | FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. |
fastx_toolkit | fastx_toolkit/0.0 (default) | A collection of command-line tools for FASTA sequence files preprocessing |
fsl | fsl/5.0.11, fsl/5.0.9, fsl/6.0.0, fsl/6.0.1 (default), fsl/6.0.3, fsl/6.0.4 | FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
hmmer | hmmer/3.1b2 (default) | HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. |
htslib | htslib/1.4.1 (default) | C library for high-throughput sequencing data formats; originally distributed with samtools. |
Integrative Genomics Viewer Tools | igv/2.4.11 (default) | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. |
Integrative Genomics Viewer Tools | igvtools/2.3.98 (default) | Accompanying CLI tools for IGV |
mafft | mafft/7.310 (default) | Multiple alignment program for amino acid or nucleotide sequences |
mothur | mothur/1.36 (default) | Bioinformatics tool for microbial ecology community |
motioncor2 | motioncor2/latest (default) | This program corrects anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. |
motioncorr | motioncorr/2.1 (default) | This program corrects whole frame image motion recordded with dose fractionated image stack. |
muscle | muscle/3.8.31 (default) | MUSCLE is one of the best-performing multiple alignment programs |
openbabel | openbabel/2.3 (default), openbabel/2.4 | toolbox for using chemical data |
openbabel | openbabel_nopy/2.3 (default) | toolbox for using chemical data |
Rosetta | rosetta/2017.08.59291 (default) | The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. |
samtools | samtools/1.2, samtools/1.4.1, samtools/1.9 (default) | Tools written in C using htslib for manipulating next-generation sequencing data. |
tophat | tophat/2.1 (default) | splice junction mapper for RNA-Seq reads |
treePL | treepl/git (default) | phylogenetic penalized likelihood program |
vmd | vmd/1.9.2 (default), vmd/1.9.3, vmd/1.9.4 | molecular visualization program |
browser¶
Application | Version | Description |
---|---|---|
firefox | firefox/67.0 (default), firefox/esr | web browser |
checkpointing¶
Application | Version | Description |
---|---|---|
dmtcp | dmtcp/2.5 (default) | Distributed MultiThreaded CheckPointing |
chemistry¶
Application | Version | Description |
---|---|---|
amber | amber/16, amber/16+intelmpi-2018.2.199+intel-18.0, amber/18, amber/18+intelmpi-2017.up4+intel-17.0, amber/20+intelmpi-2017.up4+intel-17.0 (default) | suite of biomolecular simulation programs |
Atomic Simulation Environment (ASE) | ase/3.16 (default) | ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. |
avogadro | avogadro/1.2.0 (default) | Molecule editor and visualization tool |
BerkeleyGW | berkeleygw/1.2.0+intelmpi-5.1+intel-16.0 (default), berkeleygw/1.2.0+openmpi-2.0+intel-16.0 | software package for the evaluation of quasiparticle properties and optical responses of materials and molecules |
crux | crux/3.2, crux/3.2.3 (default) | Analysis tools for interpreting protein mass spectrometry data |
DeePMD | deepmd/0.12.4 (default) | Package for building deep learning based models of interatomic potential energy and force field |
mkl/2017 | dftbplus/18.1+intelmpi-2017.up4+intel-17.0 (default) | Density Functional based Tight Binding (DFTB) method |
Quantum ESPRESSO | espresso/6.0+intelmpi-5.1+intel-16.0 (default), espresso/6.0-west-2.0+intelmpi-5.1+intel-16.0, espresso/6.1+intelmpi-5.1+intel-16.0, espresso/6.1-west-3.1.0+intelmpi-2017.up4+intel-17.0, espresso/6.1-west-3.1.0+intelmpi-2018.2.199+intel-18.0, espresso/6.2.1+intelmpi-2018.2.199+intel-18.0, espresso/6.4+intelmpi-2018.2.199+intel-18.0, espresso/6.4-elpa-2017.11+intelmpi-2018.2.199+intel-18.0, espresso/6.4-environ-1.1+intelmpi-2018.2.199+intel-18.0 | Suite of codes for electronic-structure calculations and nanoscale materials modeling |
Gaussian | gaussian/09RevA.02, gaussian/09RevB.01 (default), gaussian/09RevD.01, gaussian/16RevA.03 | electronic structure and quantum chemistry |
i-pi | i-pi/2.2.0 (default) | A Universal Force Engine for Advanced Molecular Dynamics |
Jmol | jmol/14.29 (default) | molecular viewer and editor |
NWChem | nwchem/6.6+intelmpi-5.1+intel-16.0 (default) | Software toolkit for computational chemistry |
openbabel | openbabel/2.3 (default), openbabel/2.4 | toolbox for using chemical data |
openbabel | openbabel_nopy/2.3 (default) | toolbox for using chemical data |
Orca | orca/3.0 (default), orca/4.0, orca/4.1 | Quantum Chemistry Electronic Structure Package |
ovito | ovito/3.0 (default) | Scientific visualization and analysis software for atomistic and particle simulation data |
Pathways Program in Molecular Engineering Env settings | ppme/1.0 (default) | Setup environment to find required software and utilities for the Pathways Program in Molecular Engineering |
pyscf | pyscf/1.2.1 (default), pyscf/1.6.1+python-3.5.2+intel-16.0 | Python Module for Quantum Chemistry |
tinker | tinker/8.6 (default), tinker/8.6+intel-18.0 | Software Tools for Molecular Design |
wannier90 | wannier90/3.0 (default) | Maximally localized Wannier functions. |
XCrySDen | xcrysden/1.6 (default) | A crystalline and molecular structure visualisation program |
climate¶
Application | Version | Description |
---|---|---|
Climate Data Operators (CDO) | cdo/1.6, cdo/1.9 (default) | Analysis of climate and NWP model data. |
cloud computing¶
Application | Version | Description |
---|---|---|
cloud | cloud/1.0 (default) | RCC Cloud Connector |
compilers¶
Application | Version | Description |
---|---|---|
ant | ant/1.8.4 (default), ant/1.9.7 | Java library and command-line tool for building Java applications |
berkeley_upc | berkeley_upc/2.26 (default) | An extension of the C programming language designed for high performance computing on large-scale parallel machines |
clang | clang/3.8.0, clang/3.9 (default), clang/7.1.0+gcc-6.1 | C compiler from LLVM project |
GNU Compiler Collection (GCC) | gcc/10.1.0, gcc/4.4.7, gcc/6.1 (default), gcc/6.2, gcc/6.3.0, gcc/7.2.0, gcc/8.2.0, gcc/9.1.0, gcc/9.2.0 | C/C++/Fortran compiler suite |
Intel Parallel Studio | intel/12.1, intel/15.0, intel/16.0 (default), intel/17.0, intel/18.0, intel/18.0.5, intel/19.0.1, intel/19.0.4, intel/19.1.1 | C/C++/Fortran compiler suite, including Intel Threaded-Building-Blocks |
java | java/1.7, java/1.8 (default), java/11.0.1 | programming language |
julia | julia/0.4, julia/0.5, julia/0.5+intel-16.0, julia/0.6, julia/0.6.2, julia/1.0.1, julia/1.1.0, julia/1.1.1, julia/1.4.2 (default) | The Julia dynamic programming language for technical computing. |
m4 | m4/1.4.18 (default) | Implementation of the traditional Unix macro processor. |
PGI Compiler Suite | pgi/2016, pgi/2017 (default) | C/C++/Fortran compiler suite |
racket | racket/6.7 (default) | full-spectrum programming language |
compression¶
Application | Version | Description |
---|---|---|
lzo | lzo/2.10 (default) | LZO is a portable lossless data compression library written in ANSI C. |
computation¶
Application | Version | Description |
---|---|---|
octave | octave/4.0 (default) | High-level interpreted language for numerical computations |
computer architecture¶
Application | Version | Description |
---|---|---|
gem5 | gem5/2015-09-03 (default) | Modular platform for computer-system architecture research, encompassing system-level architecture as well as processor microarchitecture. |
container¶
Application | Version | Description |
---|---|---|
singularity | singularity/3.0.1, singularity/3.4.0 (default) | Application container |
copy¶
Application | Version | Description |
---|---|---|
xclip | xclip/latest+gcc-6.2 (default) | xclip provides an interface to X selections from the command line |
xsel | xsel/latest+gcc-6.2 (default) | XSel is a command-line program for getting and setting the contents of the X selection |
crystallography¶
Application | Version | Description |
---|---|---|
Precognition | precognition/5.2.2 (default) | Software for processing single crystal diffraction images and yields experimentally-observed structure factor amplitudes. |
data¶
Application | Version | Description |
---|---|---|
redis | cassandra/3.11.3 (default) | A key-value cache and store server |
cfitsio | cfitsio/3, cfitsio/3+gcc-6.2 (default), cfitsio/3.450 | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. |
curl | curl/7.50 (default) | tool and library for transferring data over the internet |
ferret | ferret/6.9 (default) | An interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data set |
cfitsio | flask/git (default) | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. |
HDF5 | hdf5/1.10.0-patch1+intelmpi-5.1+intel-16.0, hdf5/1.12.0+openmpi-4.0+pgi-2017, hdf5/1.12.0+pgi-2017, hdf5/1.8, hdf5/1.8.15, hdf5/1.8.16+intelmpi-5.1+intel-16.0, hdf5/1.8.16+openmpi-1.10+intel-16.0, hdf5/1.8.16+openmpi-2.0+intel-16.0, hdf5/1.8.16+openmpi-2.0.1, hdf5/1.8.16+openmpi-2.0.2+gcc-6.2, hdf5/1.8.17 (default), hdf5/1.8.17+intel-16.0, hdf5/1.8.20+intelmpi-5.1+intel-16.0 | data model, library, and file format for storing and managing data |
HDF5 | hdf5_hl/1.8.17 (default), hdf5_hl/1.8.17+intel-16.0 | data model, library, and file format for storing and managing data |
lzo | lzo/2.10 (default) | LZO is a portable lossless data compression library written in ANSI C. |
mysql-workbench | mysql_workbench/6.3 (default) | mysql GUI client |
netcdf | netcdf/3.6.3+intel-12.1, netcdf/4.2+intel-12.1, netcdf/4.3, netcdf/4.4.1 (default), netcdf/4.4.1+intel-16.0, netcdf/4.4.1.1+intelmpi-5.1+intel-16.0, netcdf/4.4.1.1-c-fortran+intelmpi-5.1+intel-16.0, netcdf/4.7.4-c-cxx-fortran+intelmpi-5.1+intel-16.0 | software library for self-describing, machine-independent data formats |
netcdf-cxx | netcdf-cxx/4.2+intelmpi-5.1+intel-16.0 (default) | C++ bindings for netcdf |
netcdf-fortran | netcdf-fortran/4.4.4 (default), netcdf-fortran/4.4.4+intel-16.0, netcdf-fortran/4.4.4+intelmpi-5.1+intel-16.0 | Fortran bindings for Netcdf |
netcdf-java | netcdf-java/4.6.8+intelmpi-5.1+intel-16.0 (default) | NetCDF-Java Library is a Java interface to NetCDF files, as well as to many other types of scientific data formats. |
nosqlbooster4mongo | nosqlbooster4mongo/4.7.4 (default) | nosqlbooster4mongo |
openbabel | openbabel/2.3 (default), openbabel/2.4 | toolbox for using chemical data |
openbabel | openbabel_nopy/2.3 (default) | toolbox for using chemical data |
openrefine | openrefine/3.0 (default) | openrefine |
pnetcdf | pnetcdf/1.11.0 (default) | High-performance parallel I/O library for accessing files in format compatibility with Unidata’s NetCDF. |
redis | redis/3.2, redis/4.0.11 (default) | A key-value cache and store server |
spark | spark/2.0.2, spark/2.1 (default), spark/2.2, spark/2.2.1, spark/2.2_mkl, spark/2.3.0, spark/2.3.2, spark/2.4.3 | Apache Spark is a fast and general engine for large-scale data processing. |
sra_toolkit | sra_toolkit/2.6, sra_toolkit/2.8 (default) | a collection of tools and libraries for using data in the INSDC Sequence Read Archives |
tensorflow | tensorflow_c_gpu/1.8 (default) | tensorflow, C API, GPU |
treePL | treepl/git (default) | phylogenetic penalized likelihood program |
UnRAR | unrar/5.4 (default) | utility for extracting rar format archives |
Xerces-C++ XML Parser | xerces/2.8.0, xerces/3.1.4 (default) | validating XML parser written in C++ |
data analysis¶
Application | Version | Description |
---|---|---|
ROOT | ROOT/5.34.14, ROOT/6.06.08 (default), ROOT/6.10.02+gcc-6.2, ROOT/6.16.00, ROOT/6.22.02+gcc-10.1.0 | An object oriented framework for large scale data analysis |
CLUTO | cluto/2.1 (default) | clustering low- and high-dimensional datasets and for analysis of various clusters |
hmmer | hmmer/3.1b2 (default) | HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. |
jags | jags/4.2.0 (default) | JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo. |
sra_toolkit | sra_toolkit/2.6, sra_toolkit/2.8 (default) | a collection of tools and libraries for using data in the INSDC Sequence Read Archives |
Teem | teem/trunk (default) | scientific raster data visualization |
database¶
Application | Version | Description |
---|---|---|
leveldb | caffe/git (default) | LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values |
redis | cassandra/3.11.3 (default) | A key-value cache and store server |
HDF5 | hdf5/1.10.0-patch1+intelmpi-5.1+intel-16.0, hdf5/1.12.0+openmpi-4.0+pgi-2017, hdf5/1.12.0+pgi-2017, hdf5/1.8, hdf5/1.8.15, hdf5/1.8.16+intelmpi-5.1+intel-16.0, hdf5/1.8.16+openmpi-1.10+intel-16.0, hdf5/1.8.16+openmpi-2.0+intel-16.0, hdf5/1.8.16+openmpi-2.0.1, hdf5/1.8.16+openmpi-2.0.2+gcc-6.2, hdf5/1.8.17 (default), hdf5/1.8.17+intel-16.0, hdf5/1.8.20+intelmpi-5.1+intel-16.0 | data model, library, and file format for storing and managing data |
HDF5 | hdf5_hl/1.8.17 (default), hdf5_hl/1.8.17+intel-16.0 | data model, library, and file format for storing and managing data |
hmmer | hmmer/3.1b2 (default) | HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. |
leveldb | leveldb/git (default) | LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values |
lmdb | lmdb/git (default) | Lightning Memory-Mapped Database from Symas |
mysql | mysql/5.6 (default) | MySQL database server |
mysql-workbench | mysql_workbench/6.3 (default) | mysql GUI client |
nosqlbooster4mongo | nosqlbooster4mongo/4.7.4 (default) | nosqlbooster4mongo |
openrefine | openrefine/3.0 (default) | openrefine |
pnetcdf | pnetcdf/1.11.0 (default) | High-performance parallel I/O library for accessing files in format compatibility with Unidata’s NetCDF. |
redis | redis/3.2, redis/4.0.11 (default) | A key-value cache and store server |
debugging¶
Application | Version | Description |
---|---|---|
Allinea Performance Reports | PerformanceReports/7.0 (default) | profiler |
DDD | ddd/3.3+gcc-6.2 (default) | GNU DDD is a graphical front-end for command-line debuggers |
Allinea DDT | ddt/5.0, ddt/7.0 (default) | debugger |
ARM (former Allinea) forge (ddt, map) | forge/18.0.1 (default) | debugger and profiler |
GNU Debugger (GDB) | gdb/7.12+gcc-6.2 (default) | A command-line program for tracing and altering the execution of compiled programs for the purposes of debugging. |
Valgrind | valgrind/3.12+gcc-6.2 (default) | Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools. |
deep-learning¶
Application | Version | Description |
---|---|---|
artifice | artifice/0.0 (default) | Object detection for scientific images |
DeePMD | deepmd/0.12.4 (default) | Package for building deep learning based models of interatomic potential energy and force field |
JAX | jax/0.1.39 (default) | Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more |
development¶
Application | Version | Description |
---|---|---|
IntelPython2 | IntelPython2/2018.1.023 (default) | Intel distribution of python |
IntelPython3 | IntelPython3/2018.1.023 (default) | Intel distribution of python |
Allinea Performance Reports | PerformanceReports/7.0 (default) | profiler |
R | R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4, R/3.4.1, R/3.4.3, R/3.5.1, R/3.6.1 (default), R/3.6.3-no-openblas, R/4.0.0 | The R language and environment for statistical computing and graphics. |
UCLAPhonotacticLearner | UCLAPhonotacticLearner/latest (default) | A Maximum Entropy Model of Phonotactics and Phonotactic Learning |
ant | ant/1.8.4 (default), ant/1.9.7 | Java library and command-line tool for building Java applications |
Autoconf | autoconf/2.68 (default) | configures software source code packages |
Bash Automated Testing System (BATS) | bats/latest (default) | TAP compliant testing framework for bash |
berkeley_upc | berkeley_upc/2.26 (default) | An extension of the C programming language designed for high performance computing on large-scale parallel machines |
binutils | binutils/2.28+gcc-6.2 (default) | binutils |
Boost | boost/1.50, boost/1.51.0, boost/1.55, boost/1.61, boost/1.62.0, boost/1.62.0+intelmpi-5.1+intel-16.0, boost/1.62.0+openmpi-1.6, boost/1.63.0+gcc-6.2, boost/1.64.0, boost/1.66.0 (default), boost/1.68.0, boost/1.73.0-CXX14+gcc-10.1.0 | Portable C++ source libraries. |
check | check/0.10.0 (default) | Check is a unit testing framework for C |
clang | clang/3.8.0, clang/3.9 (default), clang/7.1.0+gcc-6.1 | C compiler from LLVM project |
cmake | cmake/3.11.0 (default), cmake/3.15, cmake/3.6.2 | Cross-platform build system. |
Nvidia CUDA Toolkit | cuda/10.0, cuda/10.1, cuda/6.5 (default), cuda/7.5, cuda/8.0, cuda/9.0, cuda/9.0a, cuda/9.1, cuda/9.2 | parallel computing platform and programming model |
DDD | ddd/3.3+gcc-6.2 (default) | GNU DDD is a graphical front-end for command-line debuggers |
Allinea DDT | ddt/5.0, ddt/7.0 (default) | debugger |
dos2unix | dos2unix/7.3.5 (default) | Dos2Unix / Unix2Dos - Text file format converters |
ARM (former Allinea) forge (ddt, map) | forge/18.0.1 (default) | debugger and profiler |
GNU Compiler Collection (GCC) | gcc/10.1.0, gcc/4.4.7, gcc/6.1 (default), gcc/6.2, gcc/6.3.0, gcc/7.2.0, gcc/8.2.0, gcc/9.1.0, gcc/9.2.0 | C/C++/Fortran compiler suite |
gcj | gcj/6.2+gcc-6.2 (default) | GNU implementation of java |
GNU Debugger (GDB) | gdb/7.12+gcc-6.2 (default) | A command-line program for tracing and altering the execution of compiled programs for the purposes of debugging. |
git-lfs | git-lfs/1.4 (default) | an open source git extension for versioning large files |
glew | glew/1.9, glew/2.0.0 (default) | The OpenGL Extension Wrangler Library |
gsl | gsl/1.16, gsl/2.2.1 (default), gsl/2.2.1+gcc-6.2, gsl/2.2.1+gcc-7.2.0, gsl/2.2.1+intel-12.1, gsl/2.2.1+intel-16.0, gsl/2.5 | The GNU scientific library |
haskell-stack | haskell-stack/1.1 (default) | cross-platform program for developing Haskell projects |
Intel Parallel Studio | intel/12.1, intel/15.0, intel/16.0 (default), intel/17.0, intel/18.0, intel/18.0.5, intel/19.0.1, intel/19.0.4, intel/19.1.1 | C/C++/Fortran compiler suite, including Intel Threaded-Building-Blocks |
java | java/1.7, java/1.8 (default), java/11.0.1 | programming language |
julia | julia/0.4, julia/0.5, julia/0.5+intel-16.0, julia/0.6, julia/0.6.2, julia/1.0.1, julia/1.1.0, julia/1.1.1, julia/1.4.2 (default) | The Julia dynamic programming language for technical computing. |
libedit | libedit/0.3 (default) | Non-GPL replacement for readline library. A spin-off from NetBSD code. Aim is for 100% readline API compatibility |
libevent | libevent/2.1.8 (default) | 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 |
libfabric | libfabric/1.7.0 (default) | Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications |
libffi | libffi/3.2 (default) | A portable foreign-function interface library |
libgmp | libgmp/4.3.1, libgmp/6.1 (default), libgmp/6.1.0+gcc-6.2 | The GNU multiple precision arithmetic library |
libmatio | libmatio/1.5 (default) | MATLAB MAT file I/O library |
libpng | libpng/1.2 (default), libpng/1.5 | Reference library for supporting the Portable Network Graphics (PNG) format. |
lua | lua/5.3.3 (default) | Lua is a powerful, efficient, lightweight, embeddable scripting language |
m4 | m4/1.4.18 (default) | Implementation of the traditional Unix macro processor. |
mathematica | mathematica/10.2, mathematica/11.2, mathematica/11.3, mathematica/12.0 (default) | symbolic mathematical software |
Matlab | matlab/2011b, matlab/2012b, matlab/2014b, matlab/2016a, matlab/2016b, matlab/2017b (default), matlab/2018b, matlab/2019b, matlab/2020b | high level language and interactive environment for numerical computation, visualization, and programming |
Metis | metis/5.1 (default) | Serial Graph Partitioning and Fill-reducing Matrix Ordering |
Node.js | node/6.11.3 (default), node/8.4.0 | framework for building network applications |
php | php/7.0 (default) | general-purpose scripting language for web development |
Python | python/anaconda-2019.03, python/anaconda-2020.02 (default), python/cpython-3.7.0, python/cpython-3.8.5, python/intel-2020.up1 | A popular high-level, general purpose programming language with a large set of libraries and packages for many scientific and research tasks. |
Python | python_ucs4/2.7.12 (default), python_ucs4/2.7.13+gcc-6.2 | A popular high-level, general purpose programming language with a large set of libraries and packages for many scientific and research tasks. |
Qt | qt/4.8, qt/5.7 (default) | cross-platform application framework |
racket | racket/6.7 (default) | full-spectrum programming language |
ARM (former Allinea) performance reports | reports/18.0.1 (default) | profiler |
rstudio | rstudio/1.1.138, rstudio/1.1.383, rstudio/1.1.453, rstudio/1.1.9, rstudio/1.2.1335 (default) | Open source edition of RStudio, an integrated development environment (IDE) for R. |
scilab | scilab/5.5 (default) | environment for numerical computation |
scons | scons/2.5.1 (default), scons/3.0.0 | Open source software construction tool expanding on Make and autoconf/automake. |
Apache Serf | serf/1.3.9 (default) | High performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library |
SML/NJ | smlnj/110.79, smlnj/110.80 (default), smlnj/110.85 | compiler for the Standard ML ‘97 programming language |
subversion | subversion/1.9.4 (default) | Version control |
Valgrind | valgrind/3.12+gcc-6.2 (default) | Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools. |
yasm | yasm/1.3.0 (default) | The Yasm Modular Assembler Project |
differential solvers¶
Application | Version | Description |
---|---|---|
Hypre | hypre/2.17 (default) | A library of high performance preconditioners and solvers featuring multigrid methods for the solution of large, sparse linear systems of equations on massively parallel computers |
differentiation¶
Application | Version | Description |
---|---|---|
JAX | jax/0.1.39 (default) | Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more |
disk¶
Application | Version | Description |
---|---|---|
xdiskusage | xdiskusage/1.51 (default) | Graphical display of disk usage |
docs¶
Application | Version | Description |
---|---|---|
doxygen | doxygen/1.8 (default) | Doxygen is a JavaDoc like documentation system for C++, C, Java and IDL. |
flex | flex/2.6.1 (default), flex/2.6.4 | Fast lexical analyzer generator |
gettext | gettext/0.19.8 (default) | Set of tools that provides a framework to help other GNU packages produce multi-lingual messages |
texinfo | texinfo/4.13a, texinfo/6.3 (default) | GNU documentation system |
documentation¶
Application | Version | Description |
---|---|---|
TeX Live | texlive/2016, texlive/2017 (default) | TeX typesetting system, including extensions (etex, latex, pdflatex, etc.) |
economics¶
Application | Version | Description |
---|---|---|
dynare | dynare/4.5 (default) | Software platform for handling a wide class of economic models. |
electronic structure¶
Application | Version | Description |
---|---|---|
pyscf | pyscf/1.2.1 (default), pyscf/1.6.1+python-3.5.2+intel-16.0 | Python Module for Quantum Chemistry |
evolution¶
Application | Version | Description |
---|---|---|
SLiM | SLiM/2.4, SLiM/3.0 (default) | Selection on Linked Mutations (SLiM): A forward population genetic simulation for studying linkage effects, such as hitchhiking, background selection, and Hill-Robertson interference. |
breseq | breseq/0.32.0 (default) | Computational pipeline for identfying mutations in short-read DNA re-sequencing data for haploid microbial genomes. |
general programming¶
Application | Version | Description |
---|---|---|
R | R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4, R/3.4.1, R/3.4.3, R/3.5.1, R/3.6.1 (default), R/3.6.3-no-openblas, R/4.0.0 | The R language and environment for statistical computing and graphics. |
haskell-stack | haskell-stack/1.1 (default) | cross-platform program for developing Haskell projects |
IDL | idl/8.2 (default) | scientific programming language for visualization |
java | java/1.7, java/1.8 (default), java/11.0.1 | programming language |
julia | julia/0.4, julia/0.5, julia/0.5+intel-16.0, julia/0.6, julia/0.6.2, julia/1.0.1, julia/1.1.0, julia/1.1.1, julia/1.4.2 (default) | The Julia dynamic programming language for technical computing. |
libffi | libffi/3.2 (default) | A portable foreign-function interface library |
libgmp | libgmp/4.3.1, libgmp/6.1 (default), libgmp/6.1.0+gcc-6.2 | The GNU multiple precision arithmetic library |
libmatio | libmatio/1.5 (default) | MATLAB MAT file I/O library |
libpng | libpng/1.2 (default), libpng/1.5 | Reference library for supporting the Portable Network Graphics (PNG) format. |
Matlab | matlab/2011b, matlab/2012b, matlab/2014b, matlab/2016a, matlab/2016b, matlab/2017b (default), matlab/2018b, matlab/2019b, matlab/2020b | high level language and interactive environment for numerical computation, visualization, and programming |
Node.js | node/6.11.3 (default), node/8.4.0 | framework for building network applications |
php | php/7.0 (default) | general-purpose scripting language for web development |
Python | python/anaconda-2019.03, python/anaconda-2020.02 (default), python/cpython-3.7.0, python/cpython-3.8.5, python/intel-2020.up1 | A popular high-level, general purpose programming language with a large set of libraries and packages for many scientific and research tasks. |
Python | python_ucs4/2.7.12 (default), python_ucs4/2.7.13+gcc-6.2 | A popular high-level, general purpose programming language with a large set of libraries and packages for many scientific and research tasks. |
rstudio | rstudio/1.1.138, rstudio/1.1.383, rstudio/1.1.453, rstudio/1.1.9, rstudio/1.2.1335 (default) | Open source edition of RStudio, an integrated development environment (IDE) for R. |
SML/NJ | smlnj/110.79, smlnj/110.80 (default), smlnj/110.85 | compiler for the Standard ML ‘97 programming language |
stata | stata/14, stata/15, stata/16 (default) | General-purpose statistical software package developed by StataCorp. |
vtune | vtune/2017 (default), vtune/2018, vtune/2019, vtune/2020 | Intel Vtune Profiler developed by Intel Corp. |
genetics¶
Application | Version | Description |
---|---|---|
MACS | MACS/1.4 (default) | Model-based Analysis for ChIP-Seq |
MEME | MEME/4.11 (default) | Motif-based sequence analysis tools. |
RSEM | RSEM/1.3 (default) | Accurate quantification of gene and isoform expression from RNA-Seq data. |
SLiM | SLiM/2.4, SLiM/3.0 (default) | Selection on Linked Mutations (SLiM): A forward population genetic simulation for studying linkage effects, such as hitchhiking, background selection, and Hill-Robertson interference. |
bcftools | bcftools/1.4.1, bcftools/1.9 (default) | BCFtools are meant as a faster replacement for most of the perl vcftools commands; originally distributed with samtools. |
bcl2fastq2 | bcl2fastq2/2.20 (default) | Sequencing software used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis. |
blast | blast/2.9.0 (default) | BLAST+: command-line tools for Basic Local Alignment Search |
bowtie | bowtie/1.1.2, bowtie/1.2.1.1 (default) | DNA sequence alignment software |
bowtie2 | bowtie2/2.2.9 (default) | DNA sequence alignment software |
breseq | breseq/0.32.0 (default) | Computational pipeline for identfying mutations in short-read DNA re-sequencing data for haploid microbial genomes. |
bwa | bwa/0.7.15 (default) | Burrow-Wheeler Aligner for pairwise alignment between DNA sequences. |
cellranger | cellranger/2.1.1 (default), cellranger/3.0.0 | An analysis pipeline for processing Chromium single-cell RNA-sequences. Capable of converting BCL files from Illumina sequencing systems to FASTQ file formats. |
cufflinks | cufflinks/2.2 (default) | Transcriptome assembly and differential expression analysis for RNA-Seq. |
fastqc | fastqc/0.11.5 (default) | A quality control tool for high throughput sequence data. |
fastx_toolkit | fastx_toolkit/0.0 (default) | A collection of command-line tools for FASTA sequence files preprocessing |
gatk | gatk/3.7 (default) | Genome Analysis Toolkit: variant siscovery in high-throughput sequencing data |
gcta | gcta/1.91.2, gcta/1.92.2 (default) | Software for genome-wide complex trait analysis. |
gemma | gemma/0.98 (default) | Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS). |
htslib | htslib/1.4.1 (default) | C library for high-throughput sequencing data formats; originally distributed with samtools. |
picard | picard/2.18.15, picard/2.18.2, picard/2.21.8 (default) | A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. |
pplacer | pplacer/1.1.alpha19 (default) | genetics |
samtools | samtools/1.2, samtools/1.4.1, samtools/1.9 (default) | Tools written in C using htslib for manipulating next-generation sequencing data. |
sickle | sickle/1.33 (default) | A windowed adaptive trimming tool for FASTQ files using quality |
tophat | tophat/2.1 (default) | splice junction mapper for RNA-Seq reads |
trinity | trinity/2.2 (default) | a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data |
genetics and genomics¶
Application | Version | Description |
---|---|---|
bcl2fastq | bcl2fastq/2.19.1 (default), bcl2fastq/2.20 | Demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. |
BEAGLE | beagle/trunk (default) | library for core calculations with phylogenetics packages |
BEAST | beast/1.8, beast/2.3 (default), beast/2.6.2 | Bayesian analysis of molecular sequences |
plink | plink/1.07, plink/1.90, plink/1.90b6.9 (default) | 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. |
trinity | trinity/2.2 (default) | a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data |
vcftools | vcftools/0.1 (default) | VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. |
genomics¶
Application | Version | Description |
---|---|---|
HISAT | HISAT/2.1.0 (default) | Fast and sensitive alignment program for mapping next-generation sequencing reads to a population of human genomes |
MACS | MACS/1.4 (default) | Model-based Analysis for ChIP-Seq |
MEME | MEME/4.11 (default) | Motif-based sequence analysis tools. |
RSEM | RSEM/1.3 (default) | Accurate quantification of gene and isoform expression from RNA-Seq data. |
SLiM | SLiM/2.4, SLiM/3.0 (default) | Selection on Linked Mutations (SLiM): A forward population genetic simulation for studying linkage effects, such as hitchhiking, background selection, and Hill-Robertson interference. |
STAR | STAR/2.6.1b (default) | Spliced Transcripts Alignment to a Reference |
bcftools | bcftools/1.4.1, bcftools/1.9 (default) | BCFtools are meant as a faster replacement for most of the perl vcftools commands; originally distributed with samtools. |
bcl2fastq2 | bcl2fastq2/2.20 (default) | Sequencing software used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis. |
blast | blast/2.9.0 (default) | BLAST+: command-line tools for Basic Local Alignment Search |
bowtie | bowtie/1.1.2, bowtie/1.2.1.1 (default) | DNA sequence alignment software |
breseq | breseq/0.32.0 (default) | Computational pipeline for identfying mutations in short-read DNA re-sequencing data for haploid microbial genomes. |
bwa | bwa/0.7.15 (default) | Burrow-Wheeler Aligner for pairwise alignment between DNA sequences. |
canu | canu/2.1 (default) | Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). |
cellranger | cellranger/2.1.1 (default), cellranger/3.0.0 | An analysis pipeline for processing Chromium single-cell RNA-sequences. Capable of converting BCL files from Illumina sequencing systems to FASTQ file formats. |
fasta | fasta/36.3 (default) | protein and DNA sequence similarity searching and alignment programs |
gatk | gatk/3.7 (default) | Genome Analysis Toolkit: variant siscovery in high-throughput sequencing data |
gcta | gcta/1.91.2, gcta/1.92.2 (default) | Software for genome-wide complex trait analysis. |
gemma | gemma/0.98 (default) | Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS). |
htslib | htslib/1.4.1 (default) | C library for high-throughput sequencing data formats; originally distributed with samtools. |
Integrative Genomics Viewer Tools | igv/2.4.11 (default) | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. |
Integrative Genomics Viewer Tools | igvtools/2.3.98 (default) | Accompanying CLI tools for IGV |
interproscan | interproscan/5 (default) | Software package that allows sequences (protein and nucleic) to be scanned against InterPro’s signatures |
picard | picard/2.18.15, picard/2.18.2, picard/2.21.8 (default) | A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. |
redundans | redundans/0.13c (default) | Redundans takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly. |
samtools | samtools/1.2, samtools/1.4.1, samtools/1.9 (default) | Tools written in C using htslib for manipulating next-generation sequencing data. |
tophat | tophat/2.1 (default) | splice junction mapper for RNA-Seq reads |
geoscience¶
Application | Version | Description |
---|---|---|
Geometry Engine - Open Source (GEOS) | geos/3.6 (default), geos/3.7.0 | spatial predicates and functions for processing geometry |
UDUNITS | udunits/2.2 (default) | support package for units of physical quantities |
gis¶
Application | Version | Description |
---|---|---|
postgis | postgis/2.3, postgis/2.3.2+gcc-6.2 (default) | PostGIS is a spatial database extender for PostgreSQL object-relational database |
graphical interfaces¶
Application | Version | Description |
---|---|---|
Qt | qt/4.8, qt/5.7 (default) | cross-platform application framework |
graphics¶
Application | Version | Description |
---|---|---|
R | R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4, R/3.4.1, R/3.4.3, R/3.5.1, R/3.6.1 (default), R/3.6.3-no-openblas, R/4.0.0 | The R language and environment for statistical computing and graphics. |
Persistence of Vision Raytracer | povray/3.7 (default) | Ray tracing tool for creating three-dimensional graphics. |
rstudio | rstudio/1.1.138, rstudio/1.1.383, rstudio/1.1.453, rstudio/1.1.9, rstudio/1.2.1335 (default) | Open source edition of RStudio, an integrated development environment (IDE) for R. |
graphs¶
Application | Version | Description |
---|---|---|
mcl | mcl/14.137 (default) | Markov Cluster Algorithm |
high energy physics¶
Application | Version | Description |
---|---|---|
Class Library for High Energy Physics (CLHEP) | clhep/2.3 (default) | C++ mathematical library for high energy physics analysis |
Fermi Science Tools | fermi-fssc/v10r0p5 (default) | suite of tools for the analysis of both LAT and GBM data |
geant4 | geant4/10.01 (default), geant4/10.02.p03, geant4/10.03.p02 | a toolkit for the simulation of particles through matter |
high performance computing¶
Application | Version | Description |
---|---|---|
Intel MPI Library | intelmpi/2017.up4+intel-17.0, intelmpi/2018.2.199+intel-18.0, intelmpi/2018.4.274+intel-18.0.5, intelmpi/2019.up7+intel-19.1.1, intelmpi/4.0+intel-12.1, intelmpi/5.0+intel-15.0, intelmpi/5.1+intel-16.0 (default) | MPI library |
OpenMPI | openmpi/1.10+intel-16.0, openmpi/1.10+pgi-2016, openmpi/1.6, openmpi/1.6+intel-12.1, openmpi/1.8, openmpi/2.0+intel-16.0, openmpi/2.0.1 (default), openmpi/2.0.2, openmpi/2.0.2+gcc-6.2, openmpi/3.0.0, openmpi/3.0.0+gcc-10.1.0, openmpi/3.0.0+gcc-6.2, openmpi/3.0.0+gcc-7.2.0, openmpi/3.1.2, openmpi/4.0+pgi-2017 | A High Performance Message Passing Library |
image¶
Application | Version | Description |
---|---|---|
ImageMagick | ImageMagick/7.0.7-3 (default) | ImageMagick can create, edit, compose, or convert bitmap images. |
libjpeg-turbo | libjpeg-turbo/1.5.2+gcc-6.2 (default) | libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression |
libjpeg-turbo | libjpeg-turbo8/8d (default) | libjpeg-turbo8 from IJG |
image analysis¶
Application | Version | Description |
---|---|---|
artifice | artifice/0.0 (default) | Object detection for scientific images |
image processing¶
Application | Version | Description |
---|---|---|
afni | afni/16.2, afni/18.0 (default), afni/19.0 | AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data. |
Convert3D | c3d/1.1 (default) | A command-line tool for converting 3D images between common file formats |
cisTEM | cistem/1.0.0-beta (default) | cisTEM is a computational imaging system for transmission electron microscopy |
fsl | fsl/5.0.11, fsl/5.0.9, fsl/6.0.0, fsl/6.0.1 (default), fsl/6.0.3, fsl/6.0.4 | FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
image progressing¶
Application | Version | Description |
---|---|---|
spm | spm/12 (default) | SPM software for analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG and MEG). |
imaging¶
Application | Version | Description |
---|---|---|
dicom3tools | dicom3tools/1 (default) | command line utilities for creating, modifying, dumping, and validating files of DICOM attributes |
gate | gate/8.0 (default) | Simulations of Preclinical and Clinical Scans in Emission Tomography, Transmission Tomography and Radiation Therapy |
integration¶
Application | Version | Description |
---|---|---|
cuba | cuba/git (default) | library for multidimensional numerical integration |
jpeg¶
Application | Version | Description |
---|---|---|
libjpeg-turbo | libjpeg-turbo/1.5.2+gcc-6.2 (default) | libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression |
libjpeg-turbo | libjpeg-turbo8/8d (default) | libjpeg-turbo8 from IJG |
library¶
Application | Version | Description |
---|---|---|
SuperLU_dist | SuperLU_dist/5.4.0+intelmpi-5.1+intel-16.0 (default) | SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Distributed version. |
SuperLU_mt | SuperLU_mt/3.1 (default) | SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Multithreaded (OpenMP) version. |
SuperLU_seq | SuperLU_seq/5.2.1 (default) | SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Sequential version. |
atlas | atlas/3.10.3 (default) | Automatically Tuned Linear Algebra Software |
cfitsio | cfitsio/3, cfitsio/3+gcc-6.2 (default), cfitsio/3.450 | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. |
cfitsio | flask/git (default) | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. |
fltk | fltk/1.3.4 (default) | FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X |
gsl | gsl/1.16, gsl/2.2.1 (default), gsl/2.2.1+gcc-6.2, gsl/2.2.1+gcc-7.2.0, gsl/2.2.1+intel-12.1, gsl/2.2.1+intel-16.0, gsl/2.5 | The GNU scientific library |
lapack | lapack/3.6.1 (default) | Linear Algebra PACKage |
Simple DirectMedia Layer (SDL) | libsdl/1.2 (default) | A cross-platform development library designed to provide low level access to audio, keyboard, mouse, joystick, and graphics hardware via OpenGL and Direct3D |
Metis | metis/5.1 (default) | Serial Graph Partitioning and Fill-reducing Matrix Ordering |
parmetis | parmetis/4.0.3+intelmpi-5.1+intel-16.0 (default) | Parallel Graph Partitioning and Fill-reducing Matrix Ordering |
scalapack | scalapack/2.0.2+openmpi-2.0.1 (default) | Scalable Linear Algebra PACKage |
spfft | spfft/0.9.8+openmpi-3.0.0+gcc-10.1.0 (default) | SpFFT - A 3D FFT library for sparse frequency domain data written in C++ |
tiff | tiff/4.0.6 (default) | LibTIFF - TIFF Library and Utilities |
linear algebra¶
Application | Version | Description |
---|---|---|
SuiteSparse | SuiteSparse/4.5.5 (default), SuiteSparse/5.3.0+intel-18.0 | SuiteSparse is a suite of sparse matrix algorithms |
linguistics¶
Application | Version | Description |
---|---|---|
mecab | mecab/0.996 (default) | open source morphological analysis engine |
mecab-ipadic | mecab-ipadic/2.7.0 (default) | open source morphological analysis engine dictionary |
praat | praat/5.3.42 (default) | Praat: doing phonetics by computer |
machine learning¶
Application | Version | Description |
---|---|---|
darknet | darknet/latest (default) | Open Source Neural Networks in C |
mcl | mcl/14.137 (default) | Markov Cluster Algorithm |
many-body perturbation theory¶
Application | Version | Description |
---|---|---|
BerkeleyGW | berkeleygw/1.2.0+intelmpi-5.1+intel-16.0 (default), berkeleygw/1.2.0+openmpi-2.0+intel-16.0 | software package for the evaluation of quasiparticle properties and optical responses of materials and molecules |
materials¶
Application | Version | Description |
---|---|---|
Atomic Simulation Environment (ASE) | ase/3.16 (default) | ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. |
BerkeleyGW | berkeleygw/1.2.0+intelmpi-5.1+intel-16.0 (default), berkeleygw/1.2.0+openmpi-2.0+intel-16.0 | software package for the evaluation of quasiparticle properties and optical responses of materials and molecules |
Quantum ESPRESSO | espresso/6.0+intelmpi-5.1+intel-16.0 (default), espresso/6.0-west-2.0+intelmpi-5.1+intel-16.0, espresso/6.1+intelmpi-5.1+intel-16.0, espresso/6.1-west-3.1.0+intelmpi-2017.up4+intel-17.0, espresso/6.1-west-3.1.0+intelmpi-2018.2.199+intel-18.0, espresso/6.2.1+intelmpi-2018.2.199+intel-18.0, espresso/6.4+intelmpi-2018.2.199+intel-18.0, espresso/6.4-elpa-2017.11+intelmpi-2018.2.199+intel-18.0, espresso/6.4-environ-1.1+intelmpi-2018.2.199+intel-18.0 | Suite of codes for electronic-structure calculations and nanoscale materials modeling |
Jmol | jmol/14.29 (default) | molecular viewer and editor |
ovito | ovito/3.0 (default) | Scientific visualization and analysis software for atomistic and particle simulation data |
Pathways Program in Molecular Engineering Env settings | ppme/1.0 (default) | Setup environment to find required software and utilities for the Pathways Program in Molecular Engineering |
pyscf | pyscf/1.2.1 (default), pyscf/1.6.1+python-3.5.2+intel-16.0 | Python Module for Quantum Chemistry |
XCrySDen | xcrysden/1.6 (default) | A crystalline and molecular structure visualisation program |
materials science¶
Application | Version | Description |
---|---|---|
avogadro | avogadro/1.2.0 (default) | Molecule editor and visualization tool |
mkl/2017 | dftbplus/18.1+intelmpi-2017.up4+intel-17.0 (default) | Density Functional based Tight Binding (DFTB) method |
math library¶
Application | Version | Description |
---|---|---|
Eigenvalue SoLvers for Petaflop-Applications ELPA | elpa/2015.11.001+intelmpi-5.1+intel-16.0, elpa/2017.11.001+intelmpi-2018.2.199+intel-18.0 (default) | efficient eigenvalue solver for petaflop applications |
mathematics¶
Application | Version | Description |
---|---|---|
bertini | bertini/1.5.1 (default), bertini/1.5.1+openmpi-2.0.2+gcc-6.2 | a general-purpose solver, written in C, that was created for research about polynomial continuation |
macaulay2 | macaulay2/1.6 (default), macaulay2/1.8 | software system devoted to supporting research in algebraic geometry and commutative algebra |
mathematica | mathematica/10.2, mathematica/11.2, mathematica/11.3, mathematica/12.0 (default) | symbolic mathematical software |
matrix computation¶
Application | Version | Description |
---|---|---|
arpack | arpack/3.5.0 (default), arpack/3.7.0+intelmpi-2017.up4+intel-17.0 | Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. |
media¶
Application | Version | Description |
---|---|---|
blender | blender/2.78a (default) | Blender is the free and open source 3D creation suite |
ffmpeg | ffmpeg/3.2 (default), ffmpeg/3.3 | A complete, cross-platform solution to record, convert and stream audio and video. |
mplayer | mplayer/1.3.0 (default) | Movie player |
tiff | tiff/4.0.6 (default) | LibTIFF - TIFF Library and Utilities |
vpx | vpx/1.6 (default) | |
x264 | x264/0.148 (default) | x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. |
x265 | x265/2.1 (default) | x265 |
medical¶
Application | Version | Description |
---|---|---|
slicer | slicer/4.10.2, slicer/4.5.0 (default), slicer/4.8.1 | software platform for the analysis and visualization of medical images and research in image guided therapy |
medicine¶
Application | Version | Description |
---|---|---|
dicom3tools | dicom3tools/1 (default) | command line utilities for creating, modifying, dumping, and validating files of DICOM attributes |
messaging¶
Application | Version | Description |
---|---|---|
rabbitmq | rabbitmq/3.7.15 (default) | message broker |
molecular dynamics¶
Application | Version | Description |
---|---|---|
amber | amber/16, amber/16+intelmpi-2018.2.199+intel-18.0, amber/18, amber/18+intelmpi-2017.up4+intel-17.0, amber/20+intelmpi-2017.up4+intel-17.0 (default) | suite of biomolecular simulation programs |
Atomic Simulation Environment (ASE) | ase/3.16 (default) | ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. |
avogadro | avogadro/1.2.0 (default) | Molecule editor and visualization tool |
DeePMD | deepmd/0.12.4 (default) | Package for building deep learning based models of interatomic potential energy and force field |
Quantum ESPRESSO | espresso/6.0+intelmpi-5.1+intel-16.0 (default), espresso/6.0-west-2.0+intelmpi-5.1+intel-16.0, espresso/6.1+intelmpi-5.1+intel-16.0, espresso/6.1-west-3.1.0+intelmpi-2017.up4+intel-17.0, espresso/6.1-west-3.1.0+intelmpi-2018.2.199+intel-18.0, espresso/6.2.1+intelmpi-2018.2.199+intel-18.0, espresso/6.4+intelmpi-2018.2.199+intel-18.0, espresso/6.4-elpa-2017.11+intelmpi-2018.2.199+intel-18.0, espresso/6.4-environ-1.1+intelmpi-2018.2.199+intel-18.0 | Suite of codes for electronic-structure calculations and nanoscale materials modeling |
Gaussian | gaussian/09RevA.02, gaussian/09RevB.01 (default), gaussian/09RevD.01, gaussian/16RevA.03 | electronic structure and quantum chemistry |
HOOMD-blue | hoomd/2.3.0 (default) | HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs. |
i-pi | i-pi/2.2.0 (default) | A Universal Force Engine for Advanced Molecular Dynamics |
openbabel | openbabel/2.3 (default), openbabel/2.4 | toolbox for using chemical data |
openbabel | openbabel_nopy/2.3 (default) | toolbox for using chemical data |
Orca | orca/3.0 (default), orca/4.0, orca/4.1 | Quantum Chemistry Electronic Structure Package |
Pathways Program in Molecular Engineering Env settings | ppme/1.0 (default) | Setup environment to find required software and utilities for the Pathways Program in Molecular Engineering |
qbox | qbox/1.66.2+intelmpi-5.1+intel-16.0, qbox/1.66.3+intelmpi-2018.2.199+intel-18.0 (default), qbox/1.67.3+intelmpi-2018.2.199+intel-18.0, qbox/1.71.4+intelmpi-2018.2.199+intel-18.0 | scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism |
XCrySDen | xcrysden/1.6 (default) | A crystalline and molecular structure visualisation program |
molecular modeling¶
Application | Version | Description |
---|---|---|
tinker | tinker/8.6 (default), tinker/8.6+intel-18.0 | Software Tools for Molecular Design |
molecular visualization¶
Application | Version | Description |
---|---|---|
avogadro | avogadro/1.2.0 (default) | Molecule editor and visualization tool |
multimedia¶
Application | Version | Description |
---|---|---|
gstreamer | gstreamer/1.9.90 (default) | GStreamer is a library for constructing graphs of media-handling components |
network¶
Application | Version | Description |
---|---|---|
netcat | netcat/1.10 (default) | Computer networking utility for reading from and writing to network connections using TCP or UDP |
network library¶
Application | Version | Description |
---|---|---|
libfabric | libfabric/1.7.0 (default) | Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications |
neural networks¶
Application | Version | Description |
---|---|---|
darknet | darknet/latest (default) | Open Source Neural Networks in C |
neuroscience¶
Application | Version | Description |
---|---|---|
afni | afni/16.2, afni/18.0 (default), afni/19.0 | AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data. |
fsl | fsl/5.0.11, fsl/5.0.9, fsl/6.0.0, fsl/6.0.1 (default), fsl/6.0.3, fsl/6.0.4 | FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
spm | spm/12 (default) | SPM software for analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG and MEG). |
numerical¶
Application | Version | Description |
---|---|---|
cuba | cuba/git (default) | library for multidimensional numerical integration |
numerical analysis¶
Application | Version | Description |
---|---|---|
MINUIT2 | Minuit2/5.34 (default) | library for function minimization |
Armadillo | armadillo/7.5 (default), armadillo/7.6, armadillo/7.8 | C++ linear algebra software library |
arpack | arpack/3.5.0 (default), arpack/3.7.0+intelmpi-2017.up4+intel-17.0 | Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. |
artifice | artifice/0.0 (default) | Object detection for scientific images |
Class Library for High Energy Physics (CLHEP) | clhep/2.3 (default) | C++ mathematical library for high energy physics analysis |
eigen | eigen/3.2 (default), eigen/3.3 | C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. |
JAX | jax/0.1.39 (default) | Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more |
Intel Math Kernel Library (MKL) | mkl/10.3, mkl/11.2, mkl/11.3, mkl/2017 (default), mkl/2017.up4, mkl/2018.up2, mkl/2019.up1, mkl/2019.up4, mkl/2020.up1 | library of optimized numerical routines |
openblas | openblas/0.2.19 (default), openblas/0.3.1 | Optimized BLAS library based on GotoBLAS2 1.13 BSD version. . |
optimization¶
Application | Version | Description |
---|---|---|
PyGMO | PyGMO/current, PyGMO/current+gcc-6.2, PyGMO/current+intelmpi-5.1+intel-16.0 (default) | Python Parallel Global Multiobjective Optimizer |
parallel¶
Application | Version | Description |
---|---|---|
PyGMO | PyGMO/current, PyGMO/current+gcc-6.2, PyGMO/current+intelmpi-5.1+intel-16.0 (default) | Python Parallel Global Multiobjective Optimizer |
parser¶
Application | Version | Description |
---|---|---|
antlr | antlr/2.7.7 (default) | ANother Tool for Language Recognition |
jq | jq/1.5 (default) | jq is a lightweight and flexible command-line JSON processer |
paste¶
Application | Version | Description |
---|---|---|
xclip | xclip/latest+gcc-6.2 (default) | xclip provides an interface to X selections from the command line |
xsel | xsel/latest+gcc-6.2 (default) | XSel is a command-line program for getting and setting the contents of the X selection |
photonic¶
Application | Version | Description |
---|---|---|
lumerical | lumerical/2016a, lumerical/2017b, lumerical/2020a (default) | Photonic Component & Circuit Design Software |
physics¶
Application | Version | Description |
---|---|---|
harminv | harminv/1.4 (default) | A free program (and accompanying library) to solve the problem of harmonic inversion. |
meep | meep/1.16+intelmpi-5.1+intel-16.0 (default) | A finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems. |
ovito | ovito/3.0 (default) | Scientific visualization and analysis software for atomistic and particle simulation data |
postgres¶
Application | Version | Description |
---|---|---|
postgis | postgis/2.3, postgis/2.3.2+gcc-6.2 (default) | PostGIS is a spatial database extender for PostgreSQL object-relational database |
profiler¶
Application | Version | Description |
---|---|---|
oprofile | oprofile/1.2.0+gcc-7.2.0 (default) | profiler |
profiling¶
Application | Version | Description |
---|---|---|
ARM (former Allinea) forge (ddt, map) | forge/18.0.1 (default) | debugger and profiler |
ARM (former Allinea) performance reports | reports/18.0.1 (default) | profiler |
programming¶
Application | Version | Description |
---|---|---|
elixir | elixir/1.9.0 (default) | A dynamic, functional language designed for building scalable and maintainable applications. |
make | make/4.0 (default) | GNU Make utility |
proteins¶
Application | Version | Description |
---|---|---|
openbabel | openbabel/2.3 (default), openbabel/2.4 | toolbox for using chemical data |
openbabel | openbabel_nopy/2.3 (default) | toolbox for using chemical data |
python¶
Application | Version | Description |
---|---|---|
PyGMO | PyGMO/current, PyGMO/current+gcc-6.2, PyGMO/current+intelmpi-5.1+intel-16.0 (default) | Python Parallel Global Multiobjective Optimizer |
simulation¶
Application | Version | Description |
---|---|---|
comsol | comsol/53a, comsol/54, comsol/54trial, comsol/55, comsol/56 (default) | physics simulations |
gate | gate/8.0 (default) | Simulations of Preclinical and Clinical Scans in Emission Tomography, Transmission Tomography and Radiation Therapy |
geant4 | geant4/10.01 (default), geant4/10.02.p03, geant4/10.03.p02 | a toolkit for the simulation of particles through matter |
HOOMD-blue | hoomd/2.3.0 (default) | HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs. |
libctl | libctl/4.1.3 (default) | A Guile-based library implementing flexible control files for scientific simulations. |
lumerical | lumerical/2016a, lumerical/2017b, lumerical/2020a (default) | Photonic Component & Circuit Design Software |
meep | meep/1.16+intelmpi-5.1+intel-16.0 (default) | A finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems. |
wannier90 | wannier90/3.0 (default) | Maximally localized Wannier functions. |
slrum¶
Application | Version | Description |
---|---|---|
swarm | swarm/latest (default) | Swarm reads a list of command lines then submits all command scripts to the cluster as a Slurm job array |
software¶
Application | Version | Description |
---|---|---|
google_depot_tools | google_depot_tools/1.0 (default) | Google Tools for working with Chromium development |
statistics¶
Application | Version | Description |
---|---|---|
MultiNest | MultiNest/git (default) | Nested Sampling Monte Carlo library |
R | R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4, R/3.4.1, R/3.4.3, R/3.5.1, R/3.6.1 (default), R/3.6.3-no-openblas, R/4.0.0 | The R language and environment for statistical computing and graphics. |
BEAGLE | beagle/trunk (default) | library for core calculations with phylogenetics packages |
jags | jags/4.2.0 (default) | JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo. |
rstudio | rstudio/1.1.138, rstudio/1.1.383, rstudio/1.1.453, rstudio/1.1.9, rstudio/1.2.1335 (default) | Open source edition of RStudio, an integrated development environment (IDE) for R. |
sas | sas/9.4 (default) | business intelligence software |
stata | stata/14, stata/15, stata/16 (default) | General-purpose statistical software package developed by StataCorp. |
system¶
Application | Version | Description |
---|---|---|
proot | proot/current (default) | user-space implementation of chroot, mount –bind, and binfmt_misc |
systems research¶
Application | Version | Description |
---|---|---|
gem5 | gem5/2015-09-03 (default) | Modular platform for computer-system architecture research, encompassing system-level architecture as well as processor microarchitecture. |
terminal¶
Application | Version | Description |
---|---|---|
tmux | tmux/current (default) | tmux is a terminal multiplexer, it enables a number of terminals (or windows) to be accessed and controlled from a single terminal. |
testing¶
Application | Version | Description |
---|---|---|
check | check/0.10.0 (default) | Check is a unit testing framework for C |
text¶
Application | Version | Description |
---|---|---|
pandoc | pandoc/1.13 (default), pandoc/2.9.2.1 | Document converter supporting many markup formats |
tkdiff | tkdiff/4.2 (default) | graphical interface for diff |
xpdf | xpdf/3.04 (default) | pdf viewer and utilities |
text editor¶
Application | Version | Description |
---|---|---|
GNU Emacs | emacs/25, emacs/26 (default) | GNU Emacs text editor |
typesetting¶
Application | Version | Description |
---|---|---|
TeX Live | texlive/2016, texlive/2017 (default) | TeX typesetting system, including extensions (etex, latex, pdflatex, etc.) |
usage¶
Application | Version | Description |
---|---|---|
xdiskusage | xdiskusage/1.51 (default) | Graphical display of disk usage |
utility¶
Application | Version | Description |
---|---|---|
lftp | lftp/4.8.4 (default) | file transfer program for CLI |
version control¶
Application | Version | Description |
---|---|---|
git | git/2.10 (default) | distributed version control system |
git-lfs | git-lfs/1.4 (default) | an open source git extension for versioning large files |
Mercurial | mercurial/4.0 (default) | distributed version control system |
video¶
Application | Version | Description |
---|---|---|
blender | blender/2.78a (default) | Blender is the free and open source 3D creation suite |
ffmpeg | ffmpeg/3.2 (default), ffmpeg/3.3 | A complete, cross-platform solution to record, convert and stream audio and video. |
mplayer | mplayer/1.3.0 (default) | Movie player |
vpx | vpx/1.6 (default) | |
x264 | x264/0.148 (default) | x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. |
x265 | x265/2.1 (default) | x265 |
visualization¶
Application | Version | Description |
---|---|---|
MapRes | ResMap/1.1.4 (default) | ResMap (Resolution Map) is a Python (NumPy/SciPy) application with a Tkinter GUI and a command-line interface. It is a software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryoEM). |
ferret | ferret/6.9 (default) | An interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data set |
fv | fv/5.4 (default) | Fv is the easy to use graphical program for viewing and editing any FITS format image or table. |
Gephi | gephi/0.9 (default) | visualization and exploration of network data |
IDL | idl/8.2 (default) | scientific programming language for visualization |
opencv | opencv/2.4 (default), opencv/3.1 | Open Source Computer Vision library |
ovito | ovito/3.0 (default) | Scientific visualization and analysis software for atomistic and particle simulation data |
pgplot | pgplot/5.2 (default) | Fortran- or C-callable, device-independent graphics package for making simple scientific graphs |
Persistence of Vision Raytracer | povray/3.7 (default) | Ray tracing tool for creating three-dimensional graphics. |
Teem | teem/trunk (default) | scientific raster data visualization |
vmd | vmd/1.9.2 (default), vmd/1.9.3, vmd/1.9.4 | molecular visualization program |
vtk | vtk/7.0 (default), vtk/7.1+python-2.7.12 | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing, and visualization. |
XCrySDen | xcrysden/1.6 (default) | A crystalline and molecular structure visualisation program |
workflow¶
Application | Version | Description |
---|---|---|
AiiDA | aiida/1.0.0b3 (default), aiida/1.2.1 | Workflow tool for Computational Science |