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Software available on the HPC service
The applications, compilers, libraries and tools available on the HPC system are managed by the modules environment. A list of the available modules can be found in the tables below or by using the `module avail` command.
Request for new applications/libraries
If you would like a library or application installed centrally, please email the HPC team with the following information:
- the name of the library/application
- a link to the website of the library/application
- the reason you would like to have it installed
- any specific requirements, e.g. double precision, enabled features
- any additional information you may have in how to install the library/application
Outstanding requests
| Application Name | Version | Comments |
|---|---|---|
| GamessUS | 2012-R1 | Available under untested applications (module load untested) |
Applications
Installed
| Application | Version(s) | Description | Supported Hardware | License | Last Modified |
|---|---|---|---|---|---|
| IGV | 2.4.3 | The Integrative Genomics Viewer (IGV) is 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. | MIT License |
| |
| VMD | 1.9.2 | Molecular visualization program | UIUC Open Source License |
| |
| Amber | 16 | Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules; and a package of molecular simulation programs. | x86, GPU | Campus site license |
|
| Ansys | 15.07, 16.1, 16.2, 17.0 | Engineering simulation software | x86 | Campus site license |
|
| Patchelf | 0.8 | PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. | x86 |
| |
| NAMD | 2.12, 2.8 (plumed 1.3), 2.9 (plumed 2.3) | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems | x86 | Proprietary, freeware for noncommercial use |
|
| CP2K | 3.0 | CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems | x86 | Open source |
|
| Bowtie | 1.1.2 | Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint | x86 | Open Source |
|
| NWChem | 6.5 | NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality | x86 | Open Source |
|
| CASTEP | 8.0, 16.11 | A leading code for calculating the properties of materials from first principles. | UK Academic License |
| |
| COMSOL | 5.1 | Finite element analysis, solver and Simulation software / FEA Software package for various physics and engineering applications, especially coupled phenomena, or multiphysics. | x86 | Group license, FlexLM |
|
| CPLEX | 12.6.1, 12.7.0 | IBM® ILOG® CPLEX® Optimization Studio is an analytical decision support toolkit for rapid development and deployment of optimization models using mathematical and constraint programming. It combines an integrated development environment (IDE) with the powerful Optimization Programming Language (OPL) and high-performance ILOG CPLEX optimizer solvers. | x86 | Academic License |
|
| Crystal | Crystal09 | A computational tool for solid state chemistry and physics |
| ||
| Gaussian | Gaussian 16, Gaussian09 D.01 (with Linda) | A computational chemistry application for electronic structure modeling | Site license |
| |
| Gaussian | Gaussian 16, Gaussian09 D.01 (with Linda) | A computational chemistry application for electronic structure modeling | Site license |
| |
| Gromacs | 5.0.2, 2016.4 | A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. | GNU Lesser General Public License |
| |
| IDL | 8.5 | Interactive Data Language | x86 | Site licenses (Astrophysics) |
|
| Matlab | 2017b, 2016b, 2015b, 2014b | A high-level programming language and interactive development tool | University of Bath, Campus License |
| |
| OpenFOAM | 2.3.x-svn-06112014 | An application for Computational Fluid Dynamics | GNU General Public Licence |
| |
| PhyloBayes | 4.1b, 4.1c, mpi1.6j | x86 |
| ||
| Quantum Espresso | 5.1,5.2.0 | An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale | GNU General Public Licence |
| |
| R | 3.1.2, 3.3.0, 3.3.1 ,3.4.0, 3.4.3 | A programming language and software environment for statistical computing and graphics | Open-source |
| |
| Stata | 14 | A general-purpose statistical software package | x86 |
| |
| Tensorflow | 1.2.1(cpu), 1.3.0(gpu) | An open-source machine learning framework | x86,GPUs | Open-source |
|
| TRACE | 8.2, 9.0.411, 9.1.519 | The CFD solver TRACE is specifically aimed at simulation flow in turbo machinery | x86 |
| |
| VASP | 5.3.5, 5.4.1 (GPU) | Atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics | Group licenses |
|
Development
Tools
| Tools | Version(s) | Description | Supported Hardware | License | Last Modified |
|---|---|---|---|---|---|
| GaussView | GaussView 6 | A computational chemistry application for electronic structure modeling | Site license |
| |
| Mozilla Firefox | 45.8.0 | Web browser | x86 | Open-source |
|
| Allinea DDT/MAP | 4.2 | Application suite for profiling and debugging programs |
| ||
| HDF5 | 1.8.17 | HDF5 is a data model, library, and file format for storing and managing data. | BSD-style open source license |
| |
| netCDF | 4.3.1.1, 4.4.1 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data | x86 | Open Source |
|
| ParaView | 4.3.1 | ParaView is an open source multiple-platform application for interactive, scientific visualization | x86 | Open Source |
|
| Anaconda | Anaconda 2.3.0, Anaconda3 2.5.0 | Anaconda is a completely free Python distribution. It includes more than 300 of the most popular Python packages for science, math, engineering, and data analysis. | x86 | Open Source |
|
| Allinea Performance Reports | 5.0 | Application suite for doing performance analysis of programs |
| ||
| Valgrind | 3.10.0 | A suite of tools for debugging and profiling programs. | GNU General Public Licence |
|
Compilers
comments: links to compiler documentation by vendor
| Compiler | Version(s) | Description | Supported Hardware | License | Last Modified |
|---|---|---|---|---|---|
| Python | 2.7.8, 3.4.2 - (NumPy and SciPy supported), 2.6 (OS default) | A general-purpose high-level programming language |
| ||
| GNU Compiler | 4.8.2 | Suite of GNU C,C++ and Fortran compilers |
| ||
| Intel Compiler | 15 | Suite of Intel C,C++ and Fortran compilers |
|
Libraries
| Library | Version(s) | Description | Supported Hardware | License | Last Modified |
|---|---|---|---|---|---|
| OpenMPI | 1.8.4, 2.0.0 | A High Performance Message Passing Library | BSD License |
| |
| MXNet | MXNet is a deep learning framework designed for both efficiency and flexibility | x86 |
| ||
| OpenBLAS | 0.2.8 | An open source implementations of the Basic Linear Algebra Subprograms (BLAS) |
| ||
| LAPACK | 3.5.0 | LAPACK (Linear Algebra Package) is a standard software library for numerical linear algebra |
| ||
| BLAS | 1 | A specified set of low-level subroutines that perform common linear algebra operations. |
| ||
| Boost | 1.57.0 | A set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading etc. |
| ||
| FFTW | 3.3.4 | A software library for computing discrete Fourier transforms (DFTs) |
| ||
| Intel MKL | 11.2 | Intel Math Kernel Library (Intel MKL) is a library of optimized math routines for science, engineering, and financial applications. |
| ||
| Intel MPI | 5 | Intel Message Passing Interface library |
|
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