Advanced Research Computing

Software

Hamilton has an array of software installed centrally as modules. These items can be accessed using the module command. We are happy to install additional applications and libraries on Hamilton, particularly if they will be of use for multiple people.

If you wish to install other software for your own use, please see the section below on installing software yourself.

Centrally installed software

Except where marked, all the items listed below are installed as modules and the module avail command will give up-to-date information about available versions.

Infrastructure

Items in italics are installed as system packages and are automatically available; there is no module for these.

List of infrastructure modules
Alphabetical list of modules, with brief desriptions. Some have a link to further information.
chkpt	Checkpoint and restart utilities
rclone	Rclone syncs your files to cloud storage
singularity	Run containers (e.g. from a Docker image)

Tools

List of modules containing tools for programmers
List of modules, with a brief description. Some items have links to further information.
advisor	Intel Advisor
autotools	GNU autoconf, automake, libtool
cmake	Software build tool
darshan	HPC I/O Characterization Tool
dyninst	Tools for binary instrumentation, analysis, and modification
elfutils	Read, create and modify ELF binary files
forge	ARM Forge (DDT)
inspector	Intel Inspector
itac	Intel Trace Analyzer and Collector
mpe2	MPI Performance Visualization
mpiP	A light-weight MPI profiler
pdt	Program Database Toolkit - source code analysis framework
tau	MPI Performance Visualization
valgrind	A system for debugging and profiling programs
vtune	Intel VTune Profiler

Compilers and programming languages

Note that perl is installed as a system package, not a module, and Jupyter can be installed by individual users. As well as the modules listed below, there are also system versions of gcc and python. For further information on compilers, see Compilers.

List of modules containing compilers and programming languages
List of compiler/language modules, with brief descriptions. Some items have links to further information.
aocc	AMD Optimising C/C++ Compiler
cuda	NVIDIA GPU programming platform
gcc	GNU compiler collection
intel	Intel compilers
java	Java (OpenJDK)
julia	Julia programming language
jupyter	Web-based interactive development environment (not a module)
llvm	LLVM Compiler Infrastructure
oneapi	Intel OneAPI compilers
perl	Perl 5 language interpreter
python	Python programming language (cpython)

Libraries

There are further pages on using MPI and numerical libraries on Hamilton.

advanpixmct	Matlab Multiprecision Computing Toolbox
antlr	Raster and vector geospatial data format translator
aocl	AMD MKL optimising GPU libraries (AOCL)
boost	Portable C++ source libraries
eigen	C++ template library for linear algebra
fftw	Fastest Fourier Transform in the West
gdal	Raster and vector geospatial data format translato
geos	C++ port of the Java Topology Suite (JTS)
glpk	GNU Linear Programming Kit
gmp	Arbitrary precision arithmetic library
hdf5	Hierarchical Data Format file library
intelmpi	Intel MPI library
jags	Just Another Gibbs Sampler
lemon	Library for Efficient Modeling and Optimization in Networks
likwid	'Like I Knew What I'm Doing' performance tools
mkl	Intel Math Kernel Library (BLAS/LAPACK)
mpfr	Multiple-precision floating-point library
mvapich2	MPICH-derived MPI optimised for InfiniBand
nag	NAG numeric library
netcdf	Network Common Data Form - file format
openblas	Optimised BLAS (based on GotoBLAS)
opencv	Open Source Computer Vision Library
openmpi	High Performance Message Passing Library
pmix	Process Management Interface (PMI) library
pvm	Parallel Virtual Machine
scotch	Graph and mesh partitioning, sparse matrix ordering
suitesparse	A suite of sparse matrix software
tbb	Intel Threading Building Blocks
vtk	Visualization Toolkit

Applications

As well as the items listed below, Hamilton has a substantial set of bioinformatics modules.

afni	Analysis of Functional Neuro Images
airss	Ab Initio Random Structure Searching
alphafold	Google Deepmind Alphafold
amber	Biomolecular simulation program
ansys	ANSYS Fluids - Computational Fluid Dynamics
ansysem	ANSYS Electronics and Electromagnetism suite
bisicles	Ice-sheet model
castep	Properties of materials from first principles
chimerax	Biocomputing, Visualisation and Informatics
connectome-wb	Mapping of neuroimaging data
crest	Automated exploration of low-energy molecular chemical space
csd	The Cambridge Structural Database
dynare	Economic modelling platform
ffmpeg	Record, convert and stream audio and video
fieldtrip	Matlab tools for analysis of MEG, EEG and iEEG brain activity data
freesurfer	Analysis and visualisation of neuroimaging data
fsl	Analysis tools for brain-imaging data
gaussian	Electronic structure modelling
grace	2D plotting tool
gromacs	Molecular dynamics package
gurobi	Gurobi Optimizer
jmol	Viewer for chemical structures in 3D
lsdyna	Crash simulation solver
mathematica	Mathematical and symbolic calculations
matlab	Programming and numeric computing platform
molden	Display Molecular Density from various Ab Initio packages
mran	Microsoft distribution of R
mricron	Visualisation and volume rendering tool for brain-imaging data
mrtools	Matlab tools for fMRI data analysis
mstudio	BIOVIA Materials Studio
multiwfn	Multifunctional Wavefunction Analyzer
nco	NetCDF Operators (NCO)
ncview	NetCDF visual browser
nektar	Open Source Spectral/HP Element Framework
occ	Open Computational Chemistry
openbabel	Chemical toolbox for many chemical data languages
openfoam	Open Source Computational Fluid Dynamics
orca	Ab initio quantum chemistry
paraview	Data analysis and visualization (GUI)
pism	Parallel Ice Sheet Model
povchem	Combining chemistry, ray tracing, and a little art
povray	Persistence of Vision Raytracer
proteinmpnn	Dauparas ProteinMPNN
r	Statistical computing and graphics (R)
relion	REgularised LIkelihood OptimisatioN
rfdiffusion	RosettaCommons RFdiffusion
rstudio	RStudio - IDE for R
spm	Statistical parametric mapping for neuro-imaging data
stata	Statistical analysis software
tecplot360	CFD tools and visualisation
topaz	CryoEM particle picking pipeline
vasp	The Vienna Ab initio Simulation Package
visit	Scalable, open source visualization
vmd	Visual Molecular Dynamics
xtb	Semiempirical Extended Tight-Binding Program

Installing applications and libraries yourself

You may also install software in your personal Hamilton directories, subject to any terms and conditions in the software licence.

Note that installations will not be able to use privileged access, e.g. using 'sudo', or place items in system directories.

In general, software can be downloaded either in a form where it is ready to run (binary or executable), or as 'source code' that needs to be compiled. In general, downloading the binary form is easiest; however, for compiled code this is normally only possible if the software was built for Hamilton's operating system (Rocky Linux 8). Software that can be compiled to use more than one compute node at a time, typically using MPI libraries, will need to be built from source on Hamilton.