{"id":49,"date":"2020-06-02T17:54:02","date_gmt":"2020-06-02T16:54:02","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf4\/?page_id=49"},"modified":"2023-10-25T15:04:07","modified_gmt":"2023-10-25T14:04:07","slug":"applications","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/software\/applications\/","title":{"rendered":"Applications"},"content":{"rendered":"


\nSoftware that can be categorized as ‘Applications’, i.e., not compilers, tools etc. For a full list see the A-Z list<\/a>.<\/p>\n


\nInstructions shown only to logged-in-to-wordpress users<\/strong>
\nThe tables of apps for each category are now auto-generated. You should add two custom fields<\/em> to each software app page: RI_Summary<\/code> giving the summary description of the app, and RI_Cat<\/code> which can be a comma-separated list of one or more of: <\/p>\n
\r\n# Use the EasyBuild class<\/em> - do 'module avail' to see each class in its own grouping\r\n# (to see all supported classes: eb --show-default-moduleclasses)\r\nbio, cae, chem, compiler, data, devel, geo, lang, lib, math, mpi, numlib, system, toolchain, tools, vis\r\n<\/pre>\n
To add these custom fields you will need to click on ‘Screen Options’ (top-right when in the page editor) and tick ‘Custom Fields’ and then the boxes you need to fill in appear at the bottom of the page editor.<\/p>\n
For apps installed by us outside of EasyBuild (e.g. binapps such as Abaqus) then add it to the appropriate category above AND also ‘non-eb’.\n<\/p><\/div>\n
Available application categories: bio<\/a> chemistry<\/a> CAE\/CFD\/FEA<\/a> Compilers<\/a> Data files utils<\/a> Earth Sciences<\/a> Scripting languages<\/a> Mathematics<\/a> Physics<\/a> Machine-learning<\/a>  System Tools<\/a> GPU-capable<\/a> Programming<\/a> Tools<\/a> Visualization<\/a><\/p>\n
Bio-informatics<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
Anaconda Python<\/a><\/td>A scientific python distribution<\/td><\/tr><\/tbody><\/table>
Computational Chemistry and Molecular Dynamics<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
Amber<\/a><\/td>A general purpose molecular mechanics\/dynamics suite<\/td><\/tr>
CP2K<\/a><\/td>Atomistic and molecular simulations<\/td><\/tr>
DL_MESO<\/a><\/td>General purpose mesoscale simulation package. LBE and DPD.<\/td><\/tr>
Gaussian 09<\/a><\/td>Molecular Dynamics simulation package.<\/td><\/tr>
Gaussian16<\/a><\/td>Performs semi-empirical and ab-initio molecular orbital calculations<\/td><\/tr>
Gaussian16 Linda (multinode)<\/a><\/td>Multi-node version of Gaussian<\/td><\/tr>
GROMACS<\/a><\/td>Molecular Dynamics simulation package.<\/td><\/tr>
LAMMPS<\/a><\/td>Classical molecular dynamics code.<\/td><\/tr>
Molpro<\/a><\/td>Ab initio quantum chemistry<\/td><\/tr>
NAMD<\/a><\/td>Parallel molecular dynamics for biomolecular systems<\/td><\/tr>
NBO<\/a><\/td>Natural Bond Orbital program (Electron analysis)<\/td><\/tr>
ONETEP<\/a><\/td>Linear-scaling code for quantum-mechanical calculations based on density-functional theory.<\/td><\/tr>
OpenMolcas<\/a><\/td>Quantum chemistry software package using a multiconfigurational approach to the electronic structure.<\/td><\/tr>
ORCA<\/a><\/td>Ab initio, DFT and semiempirical SCF-MO package for quantum chemistry<\/td><\/tr>
Quantum Espresso<\/a><\/td>Electronic structure calculations using DFT<\/td><\/tr>
TURBOMOLE<\/a><\/td>Quantum chemistry \u2013 electronic structure calculations<\/td><\/tr>
VASP<\/a><\/td>The Vienna Ab initio Simulation Package<\/td><\/tr>
VMD<\/a><\/td>Molecular Graphics Visualisation Tool<\/td><\/tr><\/tbody><\/table>
Computer Aided Engineering (FEA and CFD)<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
Abaqus<\/a><\/td>Finite Element Analysis package<\/td><\/tr>
Code_Saturne<\/a><\/td>Highly scalable computational fluid dynamics solver<\/td><\/tr>
FEAT-WMT<\/a><\/td>Finite Element Weld Modelling Tool.<\/td><\/tr>
Fluent<\/a><\/td>A computational fluid dynamics package<\/td><\/tr>
OpenFOAM, RheoTool and swak4Foam<\/a><\/td>Fluid dynamics platform<\/td><\/tr>
StarCCM<\/a><\/td>A computation continuum mechanics application<\/td><\/tr><\/tbody><\/table>
Compilers for software development<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
FOSS (gcc) Toolchains<\/a><\/td>GCC toolchains (compiler, maths libraries, MPI)<\/td><\/tr>
Intel Toolchains<\/a><\/td>Intel Compiler toolchains (compiler, maths libraries, MPI)<\/td><\/tr>
PGI Compiler<\/a><\/td>C\/C++\/FORTRAN\/OpenACC compiler suite<\/td><\/tr><\/tbody><\/table>
Data-file reader\/writer libraries and tools<\/h2>
No apps documented in this category yet. Run module avail<\/code> to check if anything has been installed in this category.<\/p>
Misc software development libraries<\/h2>
No apps documented in this category yet. Run module avail<\/code> to check if anything has been installed in this category.<\/p>
Earth Sciences<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
WPS<\/a><\/td>WRF Prepocessing System<\/td><\/tr>
WRF<\/a><\/td>Weather Research and Forecasting<\/td><\/tr><\/tbody><\/table>
Scripting languages<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
Julia<\/a><\/td>Power mathematical programming and scripting language with native parallel capability<\/td><\/tr><\/tbody><\/table>
Low-level utility libraries<\/h2>
No apps documented in this category yet. Run module avail<\/code> to check if anything has been installed in this category.<\/p>
Mathematics, Data Structure and Meshing libraries<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
MATLAB<\/a><\/td>Numerical computation, visualization and programming<\/td><\/tr><\/tbody><\/table>
Message Passing Interface parallel software library and tools<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
FOSS (gcc) Toolchains<\/a><\/td>GCC toolchains (compiler, maths libraries, MPI)<\/td><\/tr>
Intel Toolchains<\/a><\/td>Intel Compiler toolchains (compiler, maths libraries, MPI)<\/td><\/tr>
PGI Compiler<\/a><\/td>C\/C++\/FORTRAN\/OpenACC compiler suite<\/td><\/tr><\/tbody><\/table>
Low-level maths routines<\/h2>
No apps documented in this category yet. Run module avail<\/code> to check if anything has been installed in this category.<\/p>
Physics<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
Serpent<\/a><\/td>Monte-carlo Nuclear reactor physics<\/td><\/tr><\/tbody><\/table>
Very low-level utility libraries and apps<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
Singularity<\/a><\/td>Container execution<\/td><\/tr><\/tbody><\/table>
Compiler + Maths libs + MPI bundles for convenience<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
FOSS (gcc) Toolchains<\/a><\/td>GCC toolchains (compiler, maths libraries, MPI)<\/td><\/tr>
Intel Toolchains<\/a><\/td>Intel Compiler toolchains (compiler, maths libraries, MPI)<\/td><\/tr><\/tbody><\/table>
Low-level utility libraries and apps<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
git & git-lfs<\/a><\/td>Free and open source distributed version control system<\/td><\/tr>
pigz and unpigz<\/a><\/td>Parallel gzip file compression\/decompression<\/td><\/tr>
XMGrace<\/a><\/td>2D interactive plotting tool<\/td><\/tr><\/tbody><\/table>
Visualization and graphics libraries and apps<\/h2><\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
VMD<\/a><\/td>Molecular Graphics Visualisation Tool<\/td><\/tr>
XMGrace<\/a><\/td>2D interactive plotting tool<\/td><\/tr><\/tbody><\/table>\n
Custom Applications<\/h2>\n
These applications (which also appear in the categories above) have been installed manually<\/em> by the RI Team. They may have restricted licenses that only users from specific groups, departments or faculties may access. Please check each application’s page for details.
\n<\/a>
PACKAGE<\/th>NOTES<\/th><\/tr><\/thead>
Abaqus<\/a><\/td>Finite Element Analysis package<\/td><\/tr>
FEAT-WMT<\/a><\/td>Finite Element Weld Modelling Tool.<\/td><\/tr>
Fluent<\/a><\/td>A computational fluid dynamics package<\/td><\/tr>
Gaussian 09<\/a><\/td>Molecular Dynamics simulation package.<\/td><\/tr>
NAMD<\/a><\/td>Parallel molecular dynamics for biomolecular systems<\/td><\/tr>
NBO<\/a><\/td>Natural Bond Orbital program (Electron analysis)<\/td><\/tr><\/tbody><\/table><\/p>\n","protected":false},"excerpt":{"rendered":"
Software that can be categorized as ‘Applications’, i.e., not compilers, tools etc. For a full list see the A-Z list. Instructions shown only to logged-in-to-wordpress users The tables of apps for each category are now auto-generated. You should add two custom fields to each software app page: RI_Summary giving the summary description of the app, and RI_Cat which can be a comma-separated list of one or more of: # Use the EasyBuild class – do.. Read more »<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":39,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-49","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/pages\/49","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/comments?post=49"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/pages\/49\/revisions"}],"predecessor-version":[{"id":1094,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/pages\/49\/revisions\/1094"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/pages\/39"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/wp-json\/wp\/v2\/media?parent=49"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}