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HOWTO Guides

Here is a set of guides to using applications on the Hartree Centre systems. These HOWTOs assume you are familiar with the application itself and focus on installation details and how to get it to run on the various computers available.

Application Howtoversionmodule nameDescription
Abaqus6.14abaqus/6.14Abaqus FEA (formerly ABAQUS) is a suite of software for finite element analysis and computer aided engineering, originally released in 1978. Abaqus is used in the automotive, aerospace, and industrial products industries. The product is popular with academic and research institutions due to the wide material modeling capability, and the program's ability to be customized. Abaqus also provides a good collection of multiphysics capabilities, such as coupled acoustic-structural, piezoelectric, and structural-pore capabilities, making it attractive for production-level simulations where multiple fields need to be coupled. Abaqus is a licensed product, part of the SIMULIA range from Dassault Systemes, see external link: http://www.3ds.com/products-services/simulia/portfolio/abaqus/overview/ .
Abinit8.0.8babinit/8.0.8bABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudo-potentials and a plane wave or wavelet basis. See external link: http://www.abinit.org/about/what-is-abinit
Amber12, 14amber/12, amber/14A suite of programs for molecular dynamics calculations, particularly on bio-molecules. Amber refers to two things: a set of molecular mechanical force fields for the simulation of bio-molecules (which are in the public domain, and are used in a variety of simulation programs) and a package of molecular simulation programs which includes source code and demos. The current version of the code is Amber version 11, which is distributed by UCSF. Amber is one of the most widely used program for bio-molecular studies, with an extensive user base. It is being used to for classical molecular dynamics simulations (NVT, NPT, etc), force field for bio-molecular simulations, combined Quantum Mechanics/Molecular Mechanics (QM/MM) implementation and more. Amber is licensed software, but AmberTools are free to use. See external link: http://ambermd.org .
ANSYS14.5, 15.0.7, 16.21, 17.2, 18.0ansys/14.5, ansys/15.0, ansys/16.2, ansys/17.2, ansys/18.0ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires. See external link: http://www.ansys.com/Products. This is a licensed product with restricted usage.
Astrar62astra/r62Astra is a parallel particle tracking code from DESY, see external link: http://tesla.desy.de/~meykopff
BMAD2016_0233bmad/2016_0233Bmad is an object oriented, open source, subroutine library for relativistic charged-particle dynamics simulations in high energy accelerators and storage rings. Bmad has been developed at Cornell University's Laboratory for Elementary Particle Physics and has been in use since the mid-1990s, see external link: http://www.lepp.cornell.edu/~dcs/bmad
CASTEP16.1.1castep/16.1.1CASTEP is a software package which uses density functional theory to provide a good atomic-level description of all manner of materials and molecules. CASTEP can give information about total energies, forces and stresses on an atomic system, as well as calculating optimum geometries, band structures, optical spectra, phonon spectra and much more. It can also perform molecular dynamics simulations. See external link: http://www.castep.org/ . An academic group license is required to use this code.
CFDEM2.4.0cfdem-gcc/2.4.0The CFD-DEM method is a synthesis of CFD and DEM to model coupled fluid-granular systems, see external link: https://en.wikipedia.org/wiki/CFD-DEM. The motion of the particles is resolved with DEM, and the CFD method is used to calculate the fluid flow. On our systems it couples LIGGGHTS and OpenFOAM. See external link: http://www.cfdem.com
ChemShell3.6.0chemshell/3.6.0a computational chemistry environment for standard quantum chemical or force field calculations, including hybrid QM/MM calculations. ChemShell includes interfaces to various QM and MM codes, and is designed to deal with the communication and data handling, whilst energy evaluations are undertaken by external codes. See external link: http://www.stfc.ac.uk/CSE/randd/ccg/software/36254.aspx .
CFX18.0, 18.1cfx/18.0, cfx/18.1ANSYS CFX is a high-performance computational fluid dynamics (CFD) software tool that delivers reliable and accurate solutions quickly and robustly across a wide range of CFD and multi-physics applications. See external link: http://www.ansys.com/en-GB/Products/Fluids/ANSYS-CFX .
cmake2.8.12, 3.3.2, 3.6.1cmake/2.8.12, cmake/3.3.2, cmake/3.6.1CMake is a cross platform, open source build system. CMake is a family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files. CMake generates native makefiles and work spaces that can be used in the compiler environment of your choice. See external link: http://www.cmake.org
CodeAster11.4code_aster/11.4A free and open source software package from EDF for civil and structural engineering, finite element analysis, and numerical simulation in structural mechanics which was originally developed as an in-house application by EDF. Code_Aster is mainly a solver for mechanics, based on the theory of Finite elements. This tool covers a large range of applications: 3D thermal analyses and mechanical analyses in linear and non-linear statics and dynamics, for machines, pressure vessels and civil engineering structures. Beyond the standard functionalities of a FEM software for solid mechanics, Code_Aster compiles specific research in various fields : fatigue, damage, fracture, contact, geomaterials, porous media, multi-physics coupling. It was released under GNU GPL in Oct'2001. See external link: http://www.code-aster.org/V2/UPLOAD/DOC/Presentation/plaquette_aster_en.pdf .
CodeSaturne4.0.4, 4.2.0code_saturne/4.0.4, code_saturne/4.2.0An open source CFD package from EDF, see external link: http://en.wikipedia.org/wiki/Code_Saturne . Its basic capabilities enable the handling of either incompressible or expandable flows with or without heat transfer and turbulence (mixing length, 2-equation models, v2f, Reynolds stress models, Large eddy simulation…). Dedicated modules are available for specific physics such as radiative heat transfer, combustion (gas, coal, heavy fuel oil, etc.), magneto-hydro dynamics, compressible flows, two phase flows (Euler-Lagrange approach with two-way coupling), extensions to specific applications (e.g. for atmospheric environment). This application is available under a GPL license.
CP2K3.0cp2k/3.0CP2K is a freely available (GPL-2) program, written in Fortran, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. CP2K provides state-of-the-art methods for efficient and accurate atomistic simulations, sources are freely available and actively improved. It is therefore easy to give the code a try, and to make modifications as needed. See external link: http://www.cp2k.org/ .
CPMD3.17.1cpmd/3.17.1CPMD, Car-Parrinello Molecular Dynamics, is a computational chemistry package. It provides many methods to compute the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wave function or density. It also has the capability to perform classical molecular dynamics and free energy simulations.
CRYSTAL14crystal/14CRYSTAL14 is a general purpose program for the study of crystalline solids. The program computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations (global, range-separated and double hybrids). The Bloch functions of the periodic systems are expanded as linear combinations of atom centred Gaussian functions. Powerful screening techniques are used to exploit real space locality. Restricted (closed Shell) and un-restricted (spin polarized) calculations can be performed with all electron and valence only basis sets with effective core pseudo-potentials. See external link: http://www.crystal.unito.it .
Delft3d12Jun13delft3d/12Jun13Delft3D is a flexible integrated modelling suite, which simulates two dimensional (in either the horizontal or a vertical plane) and three dimensional flow, sediment transport and morphology, waves, water quality and ecology and is capable of handling the interactions between these processes. The suite is designed for use by domain experts and non-experts alike, which may range from consultants and engineers or contractors, to regulators and government officials, all of whom are active in one or more of the stages of the design, implementation and management cycle. See external link: http://www.deltaressystems.com/hydro/product/621497/delft3d-suite .
DL_MESO2.6dlmeso/2.6A general purpose open source meso-scale simulation package developed by Michael Seaton for CCP5 under a grant provided by EPSRC. It is written in Fortran90 and C++ and supports both Lattice Boltzmann Equation (LBE) and Dissipative Particle Dynamics (DPD) methods. It is available under an individual academic license. See external link: http://www.stfc.ac.uk/cse/25522.aspx .
DL_CLASS1.9dlclassic/1.9DL_POLY Classic is available under a community BSD license.
DL_POLY4.07, 4.08dlpoly/4.07, dlpoly/4.08General purpose classical molecular dynamics application, see external link: http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/ . An individual academic license is required to use DL_POLY-4.
Dynamis3.1.0dynamis/3.1.0DYNAMIS (DYNAmics of MechanIcal Systems) is numerical finite element software for automated and efficient determination of static and dynamic response of mechanical systems.. It is used for systems of critical importance and safety, like for predicting the behaviour of automotive, aerospace, marine and civil engineering structures. Dynamis is licensed sofrware from DTech, see external link: http://www.dtech.gr .
ELK4.0.15elk/4.0.15ELK is an all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. It as written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably. The code is freely available under the GNU General Public License. See external link: http://elk.sourceforge.net/
Espresso5.3.0espresso/5.3.0Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. See external link: http://www.quantum-espresso.org
FDS-SMV6.2.0fds/6.2.0Fire Dynamics Simulator (FDS) is a large eddy simulation (LES) code from NIST for low speed flows, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualisation program used to display the output of FDS and CFAST simulations. See external link: https://pages.nist.gov/fds
Extrae3.4.3extrae-gcc/3.4.3Extrae is a package to generate Paraver trace files for a post-mortem analysis. Extrae is a tool that uses different interposition mechanisms to inject probes into the target application to gather information about the application performance. See external link: https://tools.bsc.es/extrae
FieldView16.1fieldview/16.1CFD post-processing application from IntelligentLight See external link: http://www.ilight.com/en/ .
Fluent14.5, 15.0, 16.2, 17.2, 18.0fluent/14.5, fluent/15.0, fluent/16.2, fluent/17.2, fluent/18.0widely used commercial CFD application, see external link: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+Fluent . This is a licensed product and you will need to ask to be added to the Fluent group.
FOAM-Extend3.2foam-extend-gcc/3.2The goal of the Extend-Project is to open the OpenFOAM CFD toolbox to community contributed extensions. See external link: http://www.extend-project.de
Genesis2.0genesis/2.0Genesis is a 3D time-dependent Free-Electron Laser code, simulating the interaction of an electron beam with a radiation field, coupled by the field of an undulator or wiggler. Its algorithm is based on the paraxial equation of the radiation field and enforces the right statistic in the longitudinal position despite the lower number of macro particles than the electrons to be simulated.
GETM and GOTM2.2.2getm/2.2.2GETM: General Estuarine Transport Model and GOTM: General Ocean Turbulence Model.
GPT3.34TBAOver the past years the General Particle Tracer (GPT) package has become a well established simulation tool for the design of accelerators and beam lines. GPT is based on full 3D particle tracking techniques, providing a solid basis for the study of 3D and non-linear effects of charged particles dynamics in electromagnetic fields. All built-in beam line components and external 2D/3D field-maps can be arbitrarily positioned and oriented to simulate a complicated setup-up and study the effects of misalignments. An embedded fifth order Runge-Kutta driver with adaptive stepsize control ensures accuracy while computation time is kept to a minimum. GPT provides various 2D and 3D space-charge models, including a sophisticated 3D particle-mesh method that scales O(N) in terms of CPU time. Because of its modern implementation, GPT can be easily extended by the user to perform highly specialized calculations for specific applications. Hierarchical data analysis, automatic parameter scans, built-in optimization and graphical output allow for fast and detailed interpretation of the simulation results. See external link: http://www.pulsar.nl/gpt/
GROMACS4.6.7, 5.0.4, 5.1.2, 5.1.4gromacs/4.6.7, gromacs/5.0.4, gromacs-mic/5.0.4 gromacs/5.1.2, gromacs/5.1.4GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package, primarily designed for biochemical molecules like proteins, lipids and nucleic acids. There is an ongoing development to extend GROMACS with interfaces both to Quantum Chemistry and bio-informatics and databases. GROMACS is open source software released under the GPL. Primarily designed for MD simulations of bio-chemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. See external link: http://www.gromacs.org/ .
GULP4.0gulp/4.0GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many. See external link: http://projects.ivec.org/gulp .
HYDRA-TH2.1hydra/2.1HYDRA is a thermo-dynamics code for nuclear reactor applications, see external link: http://www.casl.gov/docs/CASL-U-2013-0100-000.pdf
InterProScan5.26.64interproscan/5.26.64InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium. See external link: https://www.ebi.ac.uk/interpro/interproscan.html
KERAS and THEANO1.1.0, 0.8.2keras/1.1.0 theano/0.8.2Open source deep learning library. Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. It was developed with a focus on enabling fast experimentation. , see external link: https://keras.io/
KNIME3.1.2knime/3.1.2The KNIME Analytics Platform is the leading open solution for data driven innovation, helping you discover the potential hidden in your data, mine for fresh insights, or predict new futures. Our enterprise-grade, open source platform is fast to deploy, easy to scale and intuitive to learn. With more than 1,000 modules, hundreds of ready-to-run examples, a comprehensive range of integrated tools, and the widest choice of advanced algorithms available, KNIME Analytics Platform is the perfect toolbox for any data scientist. See external link: http://www.knime.org
LAMMPS10Feb15lammps/10Feb15LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator), a widely used classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS is distributed as an open source code under the terms of the GPL. LAMMPS is distributed by Sandia National Laboratories, a US Department of Energy laboratory. Funding for LAMMPS development has come primarily from DOE (OASCR, OBER, ASCI, LDRD, Genomes-to-Life). Available free under a GPL license, see external link: http://lammps.sandia.gov/ .
LIGGGHTS3.3.1liggghts/3.3.1LIGGGHTS is an Open Source Discrete Element Method Particle Simulation Software. LIGGGHTS stands for LAMMPS improved for general granular and granular heat transfer simulations. Thanks to physical and algorithmic analogies, LAMMPS offers basic functionalities for DEM simulations. LIGGGHTS aims to improve those capability with the goal to apply it to industrial applications. LIGGGHTS is currently used by a variety of research institutions world-wide. A number of Blue Chip companies in the fields of chemical, consumer goods, pharmaceutical, agricultural engineering, food production, steel production, mining, plastics production use LIGGGHTS for improvement of production processes. See external link: http://www.cfdem.com/liggghtsr-open-source-discrete-element-method-particle-simulation-code
LS-DYNA971-r4.2.1, r7.0.0ls-dyna/971-r4.2.1, ls-dyna/r7.0.0LS-DYNA is an advanced general purpose multi-physics simulation software package developed by the Livermore Software Technology Corporation (LSTC). While the package continues to contain more and more possibilities for the calculation of many complex, real world problems, its origins and core competency lie in highly non-linear transient dynamic finite element analysis (FEA) using explicit time integration. LS-DYNA is being used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. Licensed software from LLNL and LSTC, see external link: http://www.lstc.com/ .
MATLAB  MATLAB (MATrix LABoratory) is a multi-paradigm numerical computing environment and fourth-generation programming language. Developed by MathWorks, MATLAB allows matrixmanipulations, plotting of functions and data, implementation ofalgorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, and Fortran. Matlab is a licensed product from Mathworks external link: http://www.mathworks.co.uk .
MemoryScape3.4.0, 3.7.0memoryscape/3.4.0, memoryscape/3.7.0Advanced memory debugging and analysis capability to help identify and resolve difficult memory problems in C, C++ and Fortran. It provides a graphical, real time view into heap memory, memory usage, memory allocation bounds violations and memory leaks, without instrumentation. Its built in scripting language makes batch mode testing easy and efficient; incorporate the scripts into your nightly processing to verify that new development has introduced no new memory errors. This is a licensed product from Rogue Wave, external link: http://www.roguewave.com/products/memoryscape.aspx .
MUMPS4.10.0mumps/4.10.0MUMPS: MUltifrontal Massively Parallel sparse direct Solver, is a distributed multi-frontal solver (F90, MPI based) for the solution of large sparse systems of linear equations Ax=b using Gaussian elimination. The parallel version of MUMPS is installed. See external link: http://graal.ens-lyon.fr/MUMPS/ .
NAMD2.9namd/2.9NAMD is a parallel, object oriented molecular dynamics code designed for high performance simulation of large bio-molecular systems. Simulation preparation and analysis is integrated into the visualisation package VMD. See external link: http://www.ks.uiuc.edu/Research/namd . NAMD is available under a free to use non-commercial license from University of Illinois.
NWCHEM6.6nwchem/6.6Open source computational chemistry package under ECL-2.0 license, see external link: http://www.nwchem-sw.org/ . NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high performance parallel supercomputers to conventional workstation clusters.
Octave3.6.4octave/3.6.4GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. Octave is distributed under the terms of the GNU General Public License.
Octopus4.0.1octopus/4.0.1Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. Free under GPL, see external link: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page . Note that Libxc is distributed with Octopus.
OPAL1.1.9, 1.2.1opal/1.1.9, opal/1.2.1OPAL (Object Oriented Parallel Accelerator Library) is a tool for charged-particle optic calculations in large accelerator structures and beam lines including 3D space charge. OPAL is built from first principles as a parallel application, OPAL admits simulations of any scale: on the laptop and up to the largest High Performance Computing (HPC) clusters available today. Simulations, in particular HPC simulations, form the third pillar of science, complementing theory and experiment. OPAL includes various beam line element descriptions and methods for single particle optics, namely maps up to arbitrary order, symplectic integration schemes and lastly time integration. OPAL is based on IPPL (Independent Parallel Particle Layer) which adds parallel capabilities. Main functions inherited from IPPL are: structured rectangular grids, fields and parallel FFT and particles with the respective interpolation operators. Other features are, expression templates and massive parallelism (up to 8000 processors) which makes is possible to tackle the largest problems in the field. See external link: http://amas.web.psi.ch
OPC0.7.9opc/0.7.9optics code
OpenFOAM1.7.1, 2.1.1, 2.2.1, 2.3.0, 2.4.0, 4.0openfoam/1.7.1, openfoam/2.1.1, openfoam-gcc/2.1.1, openfoam-gcc/2.2.1, openfoam-gcc/2.3.0, openfoam-gcc/2.4.0, openfoam-gcc/4.0An open source CFD package, see external link: http://www.openfoam.com/ . OpenFOAM (Open Field Operation and Manipulation) CFD Toolbox is a free, open source CFD software package produced by a commercial company, OpenCFD Ltd. It has a large user base across most areas of engineering and science, from both commercial and academic organizations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. This application is available under a GPL license.
ParaView4.0.1, 4.3.1, 5.1.0paraview/4.0.1, paraview/4.3.1, paraview/5.1.0ParaView is an open source visualisation suite from KitWare based on VTK. See external link: http://www.paraview.org/ .
Pelegant27.0pelegant/25.0Elegant is a multi-purpose 3D particle tracking code through a linear accelerator. The beam line elements are described by transport elements up to 3rd order. Although it excludes space charge, Elegant has an analytical model for the coherent synchrotron radiation in a bending system and its interaction back on the beam. Elegant works in the SDDS environment, complemented with the SDDS tool set, to pre- and postprocess Elegant runs. See external link: http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/installationGuide_Pelegant.shtml
Puffin1.5.3, 1.8puffin-gcc/1.5.3, puffin/1.8A 3D un-averaged free electron laser simulation code from University of Strathlyde, see external link: https://accelconf.web.cern.ch/accelconf/FEL2012/papers/mopd12.pdf
PYWT0.4.0pywt/0.4.0PyWavelets, used for discrete wavelet transforms in Python
R3.0.1r/3.0.1GNU R is a free software environment for statistical computing and graphics, see external link: http://www.r-project.org/ .
Relion1.4 and vlionrelion/1.4 relion/vlionRELION (REgularised LIkelihood OptimisatioN) is a program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). It is developed in the group of Sjors Scheres at the MRC Laboratory of Molecular Biology. See external link: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page .
Salome-Meca6salome-mecaOpen source software that provides a generic platform for pre- and post-processing for numerical simulation. It is based on an open and flexible architecture made of re-usable components. Salome is a cross platform solution. It is distributed as open source under the terms of the GNU LGPL license. See external link: http://www.code-aster.org/V2/UPLOAD/DOC/Presentation/SALOME6_brochure-3.pdf .
Scalasca1.4.2scalasca/1.4.2A software tool that supports the performance optimisation of parallel programs by measuring and analysing their run time behaviour. The analysis can identify potential performance bottlenecks, in particular those concerning communication and synchronisation, and can offer guidance in identifying their causes. Scalasca is available under a BSD license from Juelich Forschungszentrum, see external link: http://www.scalasca.org/about/about.html .
SIESTA4.0siesta/4.0SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.A very important feature of the code is that its accuracy and cost can be tuned in a wide range. Free license for academic use. See external link: http://icmab.cat/leem/siesta/ .
Star-CCM+9.02.007, 11.02.010, 11.04.010star-ccm+/9.02.007, star-ccm+/11.02.010, star-ccm+/11.04.010Licensed software from CD-Adapco is a leading global provider of full-spectrum engineering simulation (CAE) solutions for fluid flow, heat transfer and stress. CD-adapco core products are the technology-leading simulation packages, STAR-CCM+ and STAR-CD. STAR-CCM+ is an engineering process oriented Computational Fluid Dynamics tool that delivers the latest CFD technology in a single integrated environment. STAR-CD is an integrated platform for performing powerful multi-physics simulations, un-rivalled in its ability to tackle problems involving multi-physics and complex geometries.
STAR-CD4.28.033star-cd/4.28.033Designers of modern Internal Combustion engines face huge challenges to deliver power units which satisfy legislation and have competitive economy, performance and manufacturing cost. In particular, technology advances in fuel injection systems, alternative fuels, combustion systems, multi-fuel operation, downsizing and engine management coupled to ever shorter engine development timescales dictate that analysis is used widely to deliver optimum solutions. STAR-CD has been actively used for in-cylinder analysis for over 30 years and there are many engines in production around the world today that have benefitted from its use. These range from the smallest motorcycle, through to car and truck engines, to the largest stationary and marine engines. To keep pace with developments in engine technology, STAR-CD/es-ice is continually developing new capabilities and functionality, increasing the star-cd and ease with which powertrain engineers can execute projects. See external link: https://mdx.plm.automation.siemens.com/star-cd
SWAN40.91, 41.01swan/40.91, swan/40.01SWAN is a 3rd generation shallow water wave model, developed at Delft University of Technology, that computes random, short-crested wind-generated waves in coastal regions and inland waters. See external link: http://swanmodel.sourceforge.net .
TAU2.24tau/2.24Tuning and Analysys Utilities, TAU, provides a suite of static and dynamic tools that provide graphical user interaction and inter-operation to form an integrated analysis environment for parallel Fortran, C++, C, Java, and Python applications. In particular, a robust performance profiling facility available in TAU has been applied extensively in the ACTS toolkit. Also, recent advancements in TAU's code analysis capabilities have allowed new static tools to be developed, such as an automatic instrumentation tool. See external link: https://www.cs.uoregon.edu/research/tau .
TELEMAC6.1, 6.3telemac/6.1, telemac-gcc/6.3TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free surface flow. Having been used in the context of many studies throughout the world, it has become one of the major standards in its field. TELEMAC-MASCARET is used by most partners for dimensioning and impact studies, where safety is prevailing and, for this reason, reliability, validation and a worldwide recognition of our tools are of utmost importance. Open source (commercial support available), see external link: http://www.opentelemac.org .
TotalView8.14.0, 8.15.0totalview/8.14.0, totalview/8.15.0RogueWave TotalView is a tool for dynamic source code and memory debugging for C, C++ and Fortran applications, see external link: http://www.roguewave.com/products/totalview.aspx . This is a licensed application from RogueWave available to Hartree Centre users, see external link: http://www.roguewave.com/products/totalview.aspx .
Valgrind3.11.0valgrind-gcc/3.11.0Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools. The Valgrind distribution currently includes six production-quality tools: a memory error detector, two thread error detectors, a cache and branch-prediction profiler, a call-graph generating cache and branch-prediction profiler, and a heap profiler. See external link: http://valgrind.org
Vampir8.0.0vampir/8.0.0Vampir is a tool for performance analysis and optimisation, see external link: http://www.vampir.eu/ . Vampir is a licensed product available to Hartree Centre users.
VASP5.2.11, 5.2.12, 5.3.3vasp/5.2.11, vasp/5.2.12, vasp/5.3.3Vienna Ab Initio Simulation Package. VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. See external link: http://www.vasp.at/ and external link: http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html . An academic group license is required to use this code.
VirtualGL2.5.0virtualgl/5.2.0VirtualGL is an open source package which provides hardware-accelerated 3D rendering capabilities to thin clients. Normally, when you run a Unix or Linux OpenGL application inside a thin client environment (such as VNC, remote X11, NX, etc.), the 3D application either does not work at all, is forced to use a slow software 3D renderer, or (worse) is forced to send every 3D command and piece of 3D data over the network to be rendered on the client machine. With VirtualGL, the OpenGL commands from the application are redirected onto a dedicated server’s 3D accelerator hardware. The resulting rendered images are then read back from the 3D hardware and composited into the appropriate window on the user’s desktop. This produces a completely seamless shared 3D environment that performs fast enough to take the place of a dedicated 3D workstation. See external link: http://www.virtualgl.org/vgldoc/2_0/ .
VisIt2.6.2, 2.8.2, 2.9.1, 1.10.3visit/2.6.2, v.sit/2.8.2, visit/2.9.1, visit/1.10.3VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool from LLNL. Users can interactively visualize and analyze data ranging in scale from small (<101 core) desktop sized projects to large (>105 core) computing facility simulation campaigns. Users can quickly generate visualizations, animate them through time, manipulate them with a variety of operators and mathematical expressions, and save the resulting images and animations for presentations. VisIt contains a rich set of visualization features to enable users to view a wide variety of data including scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured, adaptive and unstructured meshes. Owing to its customizeable plugin design, VisIt is capabable of visualizing data from over 120 different scientific data formats (see this partial list). See external link: https://wci.llnl.gov/simulation/computer-codes/visit
VisNow1.2visnow/1.2VisNow is a generic visualization framework in Java technology, developed by Interdisciplinary Centre for Mathematical and Computational Modelling at University of Warsaw. See external link: https://visnow.icm.edu.pl/ .
VSim (Vorpal)5.2.2, 6.0.0vorpal/5.2.2, vorpal/6.0.0VSim is a framework that uses PIC (Particle-in-Cell) methods to model particles, so it allows you to simulate the kinetic behavior of particles as well as electromagnetic phenomena. Because VSim supports massively parallel computing that scales to tens of thousands of processor cores, you are able to model complex geometries and more physical phenomena while still obtaining results within a reasonable amount of elapsed time. Vorpal is licensed software from Tech-X Inc. see external link: http://www.txcorp.com .
Vtune Amplifier, Advisor and Inspector2015.1intel_vtuneIntel tools VTune Amplifier (for performance profiling), Inspector (for memory and thread debugging) and Advisor (for thread design and prototyping).
Warp4.4warp/4.4WARP is a 2- and 3D, parallel, electrostatic and electromagnetic PIC framework, aware of the accelerator lattice, that is used to model the generation, transport, and neutralization of charged-particle beams. It also has uses in modeling ion traps and laser-plasma accelerators. It is part of the Berkeley Lab Accelerator Simulation Toolkit (BLAST), see external link: http://blast.lbl.gov/BLASTcodes_Warp.html .
WPS and WRF3.4.0, 3.4.1wps/3.4.1, wrf/3.4.0, wrf/3.4.1The Weather Research and Forecast (WRF) Model is a fully functioning modeling system for atmospheric research and operational weather prediction communities. With an emphasis on efficiency, portability, maintainability, scalability and productivity, WRF has been successfully deployed over the years on a wide variety of HPC clustered compute nodes connected with high speed interconnects - the most used system architecture for high-performance computing. As such, understanding WRF dependency on the various clustering elements, such as the CPU, interconnects and the software libraries are crucial for enabling efficient predictions and high productivity. Our results identify WRF’s communication-sensitive points and demonstrate WRF’s dependency on high-speed networks and fast CPU-to-CPU communication. Both factors are critical to maintaining scalability and increasing productivity when adding cluster nodes. We conclude with specific recommendations for improving WRF performance, scalability, and productivity as measured in jobs per day. Because proprietary hardware and software can quickly erode cluster architecture’s favorable economics, we have restricted our investigation to standards based hardware and open source software readily available to typical research institutions.
XBeach8Oct15xbeach/8Oct15XBeach is a 2D model for wave propagation, long waves and mean flow, sediment transport and morphological changes of the nearshore area, beaches, dunes and back-barrier during storms. It is a public domain model that has been developed with major funding from the US Army Corps of Engineers, Rijkswaterstaat and the EU, supported by a consortium of UNESCO-IHE, Deltares (formerly WL-Delft Hydraulics), Delft University of Technology and the University of Miami. See external link: https://oss.deltares.nl/web/xbeach .
XDBView2xdbview/2CFD post-processing application from IntelligentLight See external link: http://www.ilight.com/en/ .
XFLOW96.01xflow/96.01XFlow is a next generation CFD software system that uses a proprietary state-of-the-art Lattice Boltzmann technology, and is specifically designed for companies who require accurate feedback on flow simulation, transient aerodynamics, water management and fluid-structure interaction. The XFlow approach to CFD simplifies the workflow, minimizes the presence of algorithmic parameters and avoids the traditionally time consuming meshing process. See external link: http://xflowcfd.com
Yambo4.0.2yambo/4.0.2Yambo is a Fortran-C code for Many Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wave functions generated by two DFT public codes: ABINIT, and PWscf. The code was originally developed in the Condensed Matter Theoretical Group of the Physics Department at the University of Rome "Tor Vergata" by Andrea Marini. Its is available under a GPL license, see external link: http://www.yambo-code.org

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