Software
Aus PC2 Doc
In the following a list of available software is shown. Not all software is available on all systems. The availability of an application can be restricted by the terms of its license. Detailed information are available on request.
Inhaltsverzeichnis
Software List
- Scientific and Technical Applications
- ABAQUS - software suite for finite element analysis and computer-aided engineering
- ARGOS - a physics-based simulator designed to simulate large-scale robot swarms.
- CAFFE - Deep Learning Framework
- COMSOL - Modelling and Simulation of Physic based Systems
- ELMER - Open Source Multiphysical Simulation Software
- FEniCS Project - Automated Solution of Differential Equations by Finite Element Methods
- Gurobi Solver for linear programming
- ILOG CPLEX - Mathematical Programming Solver for Linear Programming, Mixed Integer Programming, and Quadratic Programming
- LS-DYNA - A Strongly Coupled Multi-Physics Solver
- MATLAB - Technical Computing
- OpenFoam - Finite element Analysis
- OpenModelica - Open-Source Modelica-based Modeling and Simulation Environment
- Octave - Open Source alternative to Matlab
- R-Project - Free software environment for statistical computing and graphics
- Scilab - Open source software for numerical computation
- SCIP - Solving Constraint Integer Programs
- SIMULIA Abaqus - Unified Finite Element Analysis
- SciPY - Scientific Computing Tools for Python
- Chemical and Physical Applications
- ABINIT - find total energy, charge density and electronic structure of systems made of electrons and nuclei within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
- AutoDock Vina - Molecular Docking and Virtual Screening Program
- BigDFT - Ab initio code based on Daubechies wavelet
- CP2K - Open Source Molecular Dynamics
- Dalton Suite - Dalton code, a powerful tool for a wide range of molecular properties at different levels of theory and LSDALTON, a linear-scaling HF and DFT code suitable for large molecular Systems
- ESPRESSO - Suite of Open-Source computer codes for electronic-structure calculations and materials modeling at nanoscale
- Gaussian - Electronic Structure
- Gromacs - Molecular Dynamics
- HOOMD - General-purpose Particle Simulation Toolkit
- LAMMPS - Open Source Molecular Dynamics Code, an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
- MEEP - Finite-Difference Time-Domain (FDTD) Simulation
- MPB - Electromagnetic Eigenmode Solver
- NAMD - Scalable Molecular Dynamics
- NWChem - Ab-initio and Semiempirical Computational Chemistry Package
- ORCA - Electronic Structure Program Package
- Turbomole - Ab-initio Electronic Structure Calculations
- VASP - Ab-initio quantum-mechanical molecular dynamics
- Libraries
- ACML - AMD Core Math Library
- Boost C++ Libraries
- FFTW3 - Library for Computing the Discrete Fourier Transform (DFT) in one or more Dimensions
- GHMM - General Hidden Markov Model library
- GSL - Gnu Scientific Library
- Intel MKL - Math Kernel Libraries (part of Intel Cluster Studio)
- Intel MPI - Message Passing Interface (part of Intel Cluster Studio)
- MAGMA - Matrix Algebra on GPU and Multicore Architectures is a linear algebra library
- Mono - Open source implementation of Microsoft's .NET Framework
- MVAPICH2 - supporting MPI 3.0 standard, delivers best performance, scalability and fault
- OpenBLAS - Optimized BLAS Library based on GotoBLAS2
- OpemFst - library for constructing, combining, optimizing, and searching weighted finite-state transducers (FSTs)
- OpenMPI - is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community.
- PETSc - Portable, Extensible Toolkit for Scientific Computation
- PLASMA - Parallel Linear Algebra Software for Multicore Architectures
- Visualization
- Blender - Open source 3D Animation Suite
- Grace - a free WYSIWYG 2D graph plotting tool, for Unix-like operating systems.
- MathGL - making high-quality scientific graphics
- ParaView - an Open-Source Data Analysis and Visualization Application
- Tools
- Anaconda - Python distribution including Intel Python
- CAPSCompilers - directive-based compiler (conform to OpenACC and OpenHMPP Standards)
- CDO - Climate Data Operators
- Chapel - Imperative block-structured parallel programming language
- CilkPlusSDK - Intel Cilk screen race detector and Intel Cilk view scalability analyzer
- EasyBuild - a software build and installation framework
- evince - GNOME document Viewer (pdf,ps)
- HDF5 - a data model, library, and file format for storing and managing data
- Intel Cluster Studio - High Performance MPI Hybrid Fortran, C/C++ Development Suite (CPU x86 and Intel Phi)
- Intel vTune - Performance Analysis Tool
- likwid - Toolsuite with Command Line Applications for Performance Oriented Programmers tolerance for high-end computing systems and servers using InfiniBand, 10GigE/iWARP and RoCE networking technologies.
- modules - dynamic modification of a user's environment via modulefiles
- Ncview - a netCDF visual browser
- NCO - manipulates data stored in netCDF format.
- NetCDF - self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data
- Open64 - Open Source, Optimizing Compiler for x86-64 Microprocessor Architectures
- OpenSpeedShop - Open Source Performance Tool for Performance Analysis of Applications
- PGI Accelerator Fortran,C and C++ Compilers (conform to OpenACC)
- Scalasca - Software Tool for Performance Optimization of Parallel Programs
- SINGULARITY - Linux Containers for HPC Systems
- UNICORE - Uniform Interface to Computing Resources
- UPC - Unified Parallel C
- Valgrind - An Instrumentation Framework for Building Dynamic Analysis Tools
Software Availability
You will find cluster specific examples for a lot of the software packages in $PC2SW/examples.
| OCuLUS | Arminius | HTC | |
|---|---|---|---|
| ABAQUS | Yes (CPU/GPU) | No | No |
| ABINIT | Yes (CPU/GPU) | No | No |
| ACML | Yes | No | No |
| ANACONDA | Yes | Yes | Yes |
| ARGOS | Yes | No | Yes |
| AutoDock Vina | Yes | No | No |
| BigDFT | Yes | No | No |
| Blender | Yes | No | No |
| Boost C++ Libs | Yes | Yes | Yes |
| CAFFE | Yes (CPU/GPU) | No | No |
| CAPSCompilers | Yes (CPU/GPU) | No | No |
| CDO | Yes | No | No |
| Chapel | Yes | No | No |
| CilkPlusSDK | Yes | No | No |
| COMSOL | Yes | Yes | No |
| CP2K | Yes | No | No |
| Dalton Suite | Yes | No | No |
| ELMER | Yes | No | No |
| EasyBuild | Yes | No | No |
| ESPRESSO | Yes | No | No |
| FEniCS | Yes | No | No |
| FFTW3 | Yes | Yes | No |
| Gaussian | Yes | Yes | Yes |
| GHMM | Yes | Yes | Yes |
| Grace | Yes | Yes | No |
| Gromacs | Yes (CPU/GPU) | Yes | Yes |
| Gurobi | Yes | Yes | Yes |
| GSL | Yes | No | Yes |
| HDF5 | Yes | No | No |
| HOOMD | Yes (CPU/GPU) | No | No |
| ILOG CPLEX | Yes | Yes | No |
| Intel Cluster Studio | Yes | Yes | No |
| Java | Yes | Yes | Yes |
| JAGS | No | Yes | Yes |
| likwid | Yes | No | No |
| LAMMPS | Yes (CPU/GPU) | No | No |
| LS-DYNA | Yes | Yes | Yes |
| MAGMA | Yes (CPU/GPU) | Yes | No |
| MathGL | No | Yes | Yes |
| MATLAB | Yes (CPU/GPU) | Yes | Yes |
| MEEP | Yes | No | No |
| modules | Yes | Yes | Yes |
| Mono | Yes | Yes | Yes |
| MPB | Yes | No | No |
| MVAPICH2 | Yes | Yes | No |
| NAMD | Yes (CPU/GPU) | No | No |
| Ncview | Yes | No | No |
| NCO | Yes | No | No |
| NetCDF | Yes | No | No |
| Newton-X | Yes | No | Yes |
| NWChem | Yes | Yes | Yes |
| Octave | Yes | Yes | Yes |
| OpenBLAS | Yes | Yes | Yes |
| OpenFOAM | Yes | Yes | Yes |
| OpenFst | Yes | No | No |
| OpenModelica | Yes | No | No |
| OpenMPI | Yes | Yes | No |
| OpenSpeedShop | Yes | No | No |
| ORCA | Yes | No | No |
| ParaView | Yes | No | No |
| PETSc | Yes | No | No |
| PGI-Compilers | Yes (CPU/GPU) | No | No |
| PLASMA | Yes | No | No |
| Python | Yes | Yes | Yes |
| R-Project | Yes | Yes | Yes |
| Ruby | Yes | Yes | Yes |
| Scalasca | Yes | Yes | Yes |
| Scilab | Yes | No | Yes |
| SCIP | Yes | Yes | Yes |
| SINGULARITY | Yes | Yes | Yes |
| Turbomole | Yes | Yes | Yes |
| UPC | Yes | No | No |
| Valgrind | Yes | Yes | Yes |
| VASP | Yes | Yes | No |
| vTune | Yes | No | No |
Links To Software Homepages
See also
- ABAQUS, http://www.3ds.com/products-services/simulia/portfolio/abaqus/overview/
- ABINIT, http://www.abinit.org
- ACML, http://developer.amd.com/tools/cpu-development/amd-core-math-library-acml/
- ANACONDA, https://docs.continuum.io/anaconda/
- ARGOS, https://github.com/ilpincy/argos3
- ATLAS, http://math-atlas.sourceforge.net
- AutoDock Vina, http://vina.scripps.edu
- BigDFT, https://launchpad.net/bigdft
- Blender, http://www.blender.org
- Boost C++ Libs, http://www.boost.org
- CAFFE, http://caffe.berkeleyvision.org
- CAPSCompilers, http://www.caps-entreprise.com
- CDO, http://www.nersc.gov/users/software/vis-analytics/climate-data-operators-cdo/
- Chapel, http://chapel.cray.com
- CilkPlusSDK, http://www.cilkplus.org
- COMSOL, http://www.comsol.de
- CP2K, http://www.cp2k.org
- Dalton , http://daltonprogram.org
- EasyBuild, https://easybuild.readthedocs.io/en/latest/
- ELMER, https://www.csc.fi/web/elmer/elmer
- ESPRESSO, http://www.quantum-espresso.org
- FEniCS Project, http://fenicsproject.org
- FFTW3, http://www.fftw.org
- Gaussian, http://www.gaussian.com
- GMHH, http://ghmm.org
- Grace, http://plasma-gate.weizmann.ac.il/Grace/
- Gromacs, http://www.gromacs.org
- GSL, http://www.gnu.org/software/gsl
- Gurobi, http://www.gurobi.com
- HDF5, http://www.hdfgroup.org/HDF5/
- HOOMD-blue, http://codeblue.umich.edu/hoomd-blue
- ILOG CPLEX, http://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/index.html
- Intel Cluster Studio, http://software.intel.com/en-us/intel-cluster-studio-xe/
- JAGS http://mcmc-jags.sourceforge.net/
- LAMMPS, http://lammps.sandia.gov/
- likwid, http://code.google.com/p/likwid/
- LS-DYNA, http://www.ls-dyna.com
- MAGMA, http://icl.cs.utk.edu/magma/
- MATLAB, http://www.mathworks.de
- MathGL, http://mathgl.sourceforge.net/doc_en/Main.html
- MEEP, http://ab-initio.mit.edu/wiki/index.php/Meep
- modules, http://modules.sourceforge.net/ https://www.nersc.gov/users/software/nersc-user-environment/modules/
- Mono, http://www.mono-project.com/
- MPB, http://ab-initio.mit.edu/wiki/index.php/MIT_Photonic_Bands
- MVAPICH2, http://mvapich.cse.ohio-state.edu
- NAMD, http://www.ks.uiuc.edu/Research/namd/
- Ncview, http://meteora.ucsd.edu/~pierce/ncview_home_page.html
- NCO, http://nco.sourceforge.net
- NetCDF, http://www.unidata.ucar.edu/software/netcdf/
- Newton-X, http://www.univie.ac.at/newtonx/index.html
- NWChem, http://www.nwchem-sw.org
- Octave, http://www.gnu.org/software/octave/
- Open64, http://www.open64.net
- OpenBLAS, http://xianyi.github.com/OpenBLAS/
- OpenFOAM, http://www.openfoam.com
- OpenFst, http://www.openfst.org
- OpenModelica, https://www.openmodelica.org
- OpenMPI, http://www.open-mpi.org
- OpenSpeedShop, http://www.openspeedshop.org
- ORCA, http://www.cec.mpg.de
- ParaView, http://www.paraview.org
- PETSc, http://www.mcs.anl.gov/petsc/index.html
- PGI, http://www.pgroup.com
- PLASMA, http://icl.cs.utk.edu/plasma/index.html
- Python, https://www.python.org
- R-project, http://www.r-project.org
- Ruby, https://www.ruby-lang.org
- Scalasca, http://www.scalasca.org
- Scilab, http://www.scilab.org
- SCIP, http://scip.zib.de
- SciPY, http://www.scipy.org
- SIMULIA ABAQUS, http://www.3ds.com/de/products/simulia/
- SINGULARITY http://singularity.lbl.gov/index.html
- Turbomole, http://www.turbomole.com
- UNICORE, http://www.unicore.eu
- UPC, http://upc.lbl.gov
- Valgrind, http://valgrind.org
- VASP, https://www.vasp.at
Choosing a Software Package
On all clusters, we use the tool Modules to manage the different software packages.
The following table shows the most used commands.
For more information about Modules, please read the man page or refer to the Modules Project home page.
| Command | Purpose |
|---|---|
| module avail | list the available software packages |
| module list | show the loaded modules |
| module add | load a module |
| module del | unload a module |
| module display | show what the module does |
