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
| Compiler | Description |
|---|---|
| Intel | Popular compiler suite (C, C++, Fortran) including OpenMP support and with the benefit of optimisations on Intel-based systems. Multiple versions installed. |
| GNU compilers | Widely 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. |
| Library | Description |
|---|---|
| FFTW | Fourier transforms are used in many applications and FFTW is one of the best open-source implementations. Multiple versions installed. |
| MPI | MPI is the de-facto standard to parallelise code across a network. Mutliple versions installed (Intel and OpenMPI variants). |
| GSL | GNU Scientific Library is an open-source library of popular scientific and mathematical functions (e.g. minimisation methods, root finding, curve fitting). Multiple versions installed. |
| HDF5 | A method of storing and managing data in a standardised fashion. Has many uses and is flexible enough to fit most requirements. Multiple versions installed. |
| netCDF | A method to store gridded data formats such as weather and climate data. Multiple versions installed. |
| SQLite | A method of accessing data via SQL without the need of an SQL server. |
| Application | Description |
|---|---|
| Intel Trace Analyser | Provides information to help understand and optimise application performance by quickly locating performance bottlenecks with MPI communication. |
| ipm | IPM 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. |
| tau | TAU 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. |
| Application | Description |
|---|---|
| COMSOL | A 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. |
| Matlab | An industry-standard programming language with associated extra tools to help solve problems. Available for all users. |
| SPSS | A popular statistics package. Available for all users. |
| Application | Description |
|---|---|
| Blast | NCBI Blast - finds regions of similarity between biological sequences. |
| Molpro | Molpro is a complete system of ab-initioprograms for molecular electronic structure calculations. |
| siesta | siesta performs electronic structure calculations and ab-initio molecular dynamic simulations |
| gromacs | Gromacs is a versatile package to perform molecular dynamics. |
| nwchem | NWChem provides a quantum mechanical description of the electronic wavefunction / density. |
| VASP | VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. |
| wrf | The Weather Research & Forecasting Model. |
| 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 to relatively long (e.g. mammalian) genomes, and contains a number of enhancements compared to its predecessor, bowtie. |
| PLINK | 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. 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: