This page lists the software that is centrally installed and supported at Pawsey.Pawsey supports a wide range of software packages from Physics to Bioinformatics, from Chemistry to Fluid Dynamics. Most packages are managed by and accessed through Modules. Different software may be installed on different machines depending on their intended purposes.
Note that you can also install packages in your own /group directory using Spack (external site). How to Install Software describes how to install software that you require which is not already available.
For some specific domains and applications (for instance bioinformatics), Containers technology can represent an optimal alternative to Modules for installing and maintaining software.
Select one of the following categories to see the list of packages.
GPU-enabled applications
Applications supporting GPU offloading are installed a second time with that feature enabled. Module name of GPU-enabled software is postfixed with amd-gfx90a.
Applications
Click here to expand...
Name | Domain | Description | GPU support | Comments |
|---|
AMBER | Molecular Dynamics | Biomolecular systems | Yes |
|
ANSYS Fluids | CFD | Fluid-dynamics CFD | No |
|
ANSYS Structures | CFD | Structural analysis CFD | No |
|
COMSOL | FEM Multiphys. | General purpose multiphysics | No | Installation on-demand |
CPMD | Ab-initio Molecular Dynamics | plane wave / pseudopotential implementation of Density Functional Theory (DFT) | No |
|
CP2K | Ab-initio Molecular Dynamics | mixed Gaussian and plane waves approaches GPW and GAPW for DFT | Yes |
|
Gromacs | Molecular Dynamics | Biomolecular systems | Yes |
|
LAMMPS | Molecular Dynamics | Condensed matter modelling | Yes |
|
NAMD | Molecular Dynamics | Biomolecular systems | Yes |
|
Nektar | CFD/FEM | Framework for efficient high-performance scalable solvers for partial differential equations (PDEs) using the spectral/hp element method | Yes |
|
NWchem | Quantum Chemistry | Electronic structure, molecular dynamics, hybrid methods. Capable of using both plane wave and Gaussian basis sets | No |
|
OpenFoam-org | CFD | OpenFoam Foundation variant of OpenFoam (openfoam.org). Spack recipe is openfoam-org | No | Containerised installation provided |
OpenFoam | CFD | OpenCFD variant of OpenFoam (openfoam.com). Spack recipe is openfoam | No | Containerised installation provided
|
Quantum Espresso | Quantum Chem./Materials Sci. | Suite of electronic-structure tools based on density-functional theory, plane waves, and pseudopotentials | No |
|
ROMS | Weather Forecast | https://www.myroms.org | No | Dependencies only, allowing users to build as desired |
VASP | Quantum Chem./Materials Sci. | DFT/plane-wave based for solid state | No |
|
WRF | Weather Forecast | https://github.com/wrf-model/WRF | No | Dependencies only, allowing users to build as desired |
Libraries
Click here to expand...
Name | Description | GPU support | Comments |
|---|
ADIOS | Fortran C/C++ I/O library | No |
|
AMD AOCL | Numerical libraries tuned for AMD EPYC | No |
|
| Blaspp | C++ API for the Basic Linear Algebra Subroutines | No |
|
Boost | C++ libraries | No | Multiple builds available |
Eigen | C++ linear algebra, numerical solvers | No |
|
FFTW | C/Fortran Fourier transform | See ROCm | Multiple versions available |
GSL | C/C++ numerical library | No |
|
HDF5 | Fortran/C/C++ I/O library | No | Multiple builds available |
| HPX | C++ standard library for parallelism and concurrency | No |
|
| Kokkos | C++ performance portability programming model | Yes | Multiple builds available |
Lapack | Fortran linear algebra, spack lists netlib-lapack | No | Provided through openblas and netlib, and cray-libsci modules |
Magma | C/C++ heterogeneous/hybrid linear algebra | Yes | Only available in phase-2 of Setonix |
NetCDF | I/O, C distribution is netcdf-c, C++ is netcdf-cxx4, Fortran is netcdf-fortran | No |
|
OpenBLAS | Linear algebra | See ROCm |
|
OpenCV | C/C++ computer vision | No |
|
PETSc | Data structures, routines for applications modeled by partial differential equations | No |
|
| Plasma | C/C++ linear algebra | No |
|
Plumed | Molecular dynamics plugin library | No |
|
Scalapack | Linear algebra, spacl lists netlib-scalapack | No | Provided through openblas and netlib, and cray-libsci modules |
Slate | Linear algebra |
|
|
Trilinos | C++ object-oriented software framework for the solution of large-scale, complex multi-physics engineering/scientific problems |
|
|
Programming languages
Click here to expand...
Name | Languages | Comments |
|---|
AMD AOCC | Fortran, C/C++ |
|
AMD ROCm/HIP | C++ |
|
GCC | Fortran, C/C++ |
|
GO | GO |
|
Java | Java |
|
LLVM | C/C++ |
|
Python | Python |
|
R | R |
|
Perl | Perl |
|
Ruby | Ruby |
|
Rust | Rust |
|
Click here to expand...
| Name | Description | Comments |
|---|
| Caliper | Instrumentation and performance profiling library |
|
| HPC Toolkit | Suite of tools for performance measurement and analysis |
|
| HPC Viewer | Visualisation for HPC Toolkit outputs |
|
| Hatchet | Post-processing of profiling data from various tools |
|
| ROCm | AMD GPU development framework. |
|
Domain-specific software
Astronomy
Click here to expand...
Name | Description | Comments |
|---|
Astropy | Python, astronomy focused package |
|
Casacore | Library, radio astronomy focused |
|
Emcee | Python, implementation of the affine-invariant ensemble sampler for Markov chain Monte Carlo (MCMC) |
|
Healpy | Python, package to handle pixelated data on the sphere |
|
Imfit | Program for fitting astronomical images (primarily of galaxies) in FITS format |
|
PyBDSF | Python, tool to decompose radio interferometry images into sources |
|
WCSTools | Programs & library, provides world coordinate systems (WCS) common astronomical image formats |
|
WSClean | Programs & library, radio interferometry astronomy |
|
Click here to expand...
Name | Description/Function | Available as Biocontainer | Comments |
|---|
bamtools | BAM file manipulation | Y |
|
BBtools (BBmap) | Suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data | Y |
|
BCFtools | BCF/VCF manipulation | Y |
|
Beast (with Beagle Lib) | Phylogenetics *Beagle Lib can use GPUs | No |
|
BEDtools2 | BED file manipulation | Y |
|
BLAST+ | Multiple sequence alignment | Y |
|
Bowtie2 | Align sequencing to reference genome | Y |
|
BWA | Align sequencing to reference genome | Y |
|
| BWA-MEM2 | Align sequencing to reference genome |
|
|
Canu | De novo assembly | Y |
|
Clustal Omega | Multiple sequence alignment | Y |
|
CutAdapt | Fastq read trimming (QC) | Y |
|
Diamond | Multiple sequence alignment | Y |
|
ExaBayes | Phylogenetics | No |
|
ExaML | Phylogenetics | No |
|
FastQC | Fastq file QC | Y |
|
GATK4 | Align sequencing to reference genome, perform recalibration | Y |
|
Maker | De novo genome annotation *large dep. tree, tricky to install | Y |
|
MrBayes | Phylogenetics | Y |
|
Mummer | Align sequencing to reference genome and de novo assembly | Y |
|
Sambamba | Bam file manipulation | Y |
|
SAMtools | BAM/SAM file manipulation | Y |
|
Spades | Single/multicellular genome assembly | Y |
|
STAR | RNA-seq aligner | Y |
|
Trimmomatic | Fastq read trimming (QC) | Y |
|
Trinity | De novo RNA-seq assembly | Y |
|
VCFtools | VCF file manipulation | Y |
|
Velvet | De novo genome assembly | Y |
|
Deep learning frameworks (GPU nodes only)
Click here to expand...
Name | Description | Container | Comments |
|---|
Caffe | Another framework | Y |
|
Keras | High-level framework, uses Tensorflow or Theano as back-end | NO |
|
Horovod | Multi-node extensions for Tensorflow, Pytorch, MXNet, Keras | Y |
|
MXNet | Popular framework | Y |
|
DeepMD | Framework for Molecular Dynamics | Y |
|
Pytorch | Popular framework | Y |
|
Tensorflow | Popular framework | Y |
|
Theano | Another framework | NO |
|
Non-HPC applications and utilities
Utilities
Click here to expand...
Name | Description | Comments |
|---|
Autoconf/Automake | build tool |
|
| AWS CLI | S3 client |
|
Cmake | build tool |
|
Emacs | editor |
|
FFmpeg | video editing |
|
gnuplot | visualisation |
|
Matlab | data analysis | Installation on-demand |
| MinIO CLI | S3 client |
|
Nano | editor |
|
Nextflow | workflow manager |
|
Parallel | workflow (scripting) |
|
| Pip | Python package installer |
|
| Rclone | S3 client |
|
| Reframe | regression tests |
|
| Setuptools | Python build system |
|
Singularity | container runtime |
|
| SHPC | containers as modules |
|
Vim | editor |
|
Visualisation
Click here to expand...
Name | Description | Comments |
|---|
Paraview | visualisation | Setonix remote visualisation only |
Visit | visualisation, spack install experimental, many features disabled | Setonix remote visualisation only |
VMD | molecular dynamics visualisation | Setonix remote visualisation only |
(Check Visualisation Documentation for more information.)
Python
Click here to expand...
Name | Description | Comments |
|---|
Cython | compiling Python code |
|
Dask | task distribution and scheduling |
|
| H5netcdf | I/O |
|
H5py | I/O |
|
IPython | enhanced console |
|
Matplotlib | visualisation |
|
MPI4py | MPI in Python |
|
| Netcdf4 | I/O |
|
Numba | compiling Python code / GPU offloading |
|
Numpy | optimised N-dimensional arrays |
|
Pandas | data analysis |
|
Plotly | visualisation |
|
Scikit-learn | machine learning |
|
Scipy | scientific computing |
|