Software support

A number of commercial and open-source applications are available on our systems, and new software can be installed with guidance from our experts.

We provide support to help researchers install the required software on our systems. This can be done centrally, allowing others to benefit from the same software, or within the researcher’s personal space.

Our systems have enabled researchers to access and run many software packages which otherwise may not have been possible.

Software options

Commerical software

Software licences must be checked to see how best to install it on our shared systems. If required, access can be limited to certain users, which can be specified in some licences. Usually licence managers can be used to monitor usage. Please contact us before purchasing software.

Open-source software

Open-source software is easily installed on ARCCA systems and our specialist knowledge can maximise its performance through central installations. We encourage the sharing of software across communities so we recommend contacting us to allow us to help run the software in a centralised way where possible.

Workflow tools

Workflow tools and web portals are becoming a common method to access specialist services.

Galaxy is an open source, web-based platform for data intensive biomedical research. Whether on the public server or through your own instance, you can perform, reproduce, and share complete analyses.

Webmo is used by the School of Chemistry to improve the accessibility and usability of computational chemistry software, as users can access and use their software from their web browser.

Gridchem is a distributed infrastructure for open scientific research that provides a collection of grid base resources to routinely run chemical physics applications. It aims to integrate the desktop environment into infrastructure for a specific community of users."

Originating as a scheduler for weather forecasting models for the Met Office, Rose (the Met Office led suite processor) and Cylc (a dependency-based queue scheduler) has developed into a general purpose workflow manager for a wide variety of functions. Incorporating time-based cycling, intelligent task scheduling, and dynamic parallelism, Rose/Cylc also allows the creation of sophisticated GUI-based front ends for increased ease of use.

Installed software releases

CompilerDescription
IntelPopular compiler suite (C, C++, Fortran) including OpenMP support and with the benefit of optimisations on Intel-based systems. Multiple versions installed.
GNU compilersWidely available compiler suite(C, C++, Fortran) including OpenMP support and benefits from being open-source and therefore widely tested and used by software developers.  Multiple versions installed.
ApplicationDescription
Intel Trace AnalyserProvides information to help understand and optimise application performance by quickly locating performance bottlenecks with MPI communication.
ipmIPM is a portable profiling infrastructure for parallel codes. It provides a low-overhead performance profile of the performance aspects and resource utilization in a parallel program.
tauTAU is a program and performance analysis tool framework being developed for the DOE Office of Science, ASC initiatives at LLNL, the ZeptoOS project at ANL, and the Los Alamos National Laboratory.
ApplicationDescription
COMSOLA multi-physics package to solve a variety of scientific problems.  Latest versions currently funded by research groups in School of Engineering.
Abaqus

A suite of software currently provided to solve dynamical events using the explicit package. Provided by the School of Engineering.

MatlabAn industry-standard programming language with associated extra tools to help solve problems.  Available for all users.
SPSSA popular statistics package.  Available for all users.
ApplicationDescription
BlastNCBI Blast - finds regions of similarity between biological sequences.
MolproMolpro is a complete system of ab-initioprograms for molecular electronic structure calculations.
siestasiesta performs electronic structure calculations and ab-initio molecular dynamic simulations
gromacsGromacs is a versatile package to perform molecular dynamics.
nwchemNWChem provides a quantum mechanical description of the electronic wavefunction / density.
VASPVASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.
wrfThe Weather Research & Forecasting Model.
Bowtie2Bowtie 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 to relatively long (e.g. mammalian) genomes, and contains a number of enhancements compared to its predecessor, bowtie.
PLINKPLINK 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. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

Get in touch

For more information please contact the team:

Advanced research computing