Software

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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.

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
    • 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

OCuLUS Arminius BisGrid HTC
ABAQUS Yes (CPU/GPU) No No No
ABINIT Yes (CPU/GPU) No No No
ACML Yes No No No
ANACONDA Yes Yes No Yes
ARGOS Yes No No Yes
AutoDock Vina Yes Yes No No
BigDFT Yes No No No
Blender Yes No No No
Boost C++ Libs Yes Yes No Yes
CAFFE Yes (CPU/GPU) No No No
CAPSCompilers Yes (CPU/GPU) No No No
CDO Yes No No No
Chapel Yes No No No
CilkPlusSDK Yes No No No
COMSOL Yes Yes No No
CP2K Yes No No No
Dalton Suite Yes No No No
ELMER Yes No No No
ESPRESSO Yes No No No
FEniCS Yes No No No
FFTW3 Yes Yes Yes No
Gaussian Yes Yes Yes Yes
GHMM Yes Yes NO Yes
Grace Yes Yes No No
Gromacs Yes (CPU/GPU) Yes Yes Yes
Gurobi Yes Yes No Yes
GSL Yes No No Yes
HDF5 Yes No No No
HOOMD Yes (CPU/GPU) No No No
ILOG CPLEX Yes Yes No No
Intel Cluster Studio Yes Yes No No
Java Yes Yes No Yes
JAGS No Yes No Yes
likwid Yes No No No
LAMMPS Yes (CPU/GPU) No No No
LS-DYNA Yes Yes No Yes
MAGMA Yes (CPU/GPU) Yes No No
MathGL No Yes No Yes
MATLAB Yes (CPU/GPU) Yes No Yes
MEEP Yes No No No
modules Yes Yes No Yes
Mono Yes Yes No Yes
MPB Yes No No No
MVAPICH2 Yes Yes No No
NAMD Yes (CPU/GPU) No No No
Ncview Yes No No No
NCO Yes No No No
NetCDF Yes No No No
Newton-X Yes No No Yes
NWChem Yes Yes No Yes
Octave Yes Yes No Yes
OpenBLAS Yes Yes No Yes
OpenFOAM Yes Yes No Yes
OpenFst Yes No No No
OpenModelica Yes No No No
OpenMPI Yes Yes No No
OpenSpeedShop Yes No No No
ORCA Yes Yes No Yes
ParaView Yes No No No
PETSc Yes No No No
PGI-Compilers Yes (CPU/GPU) No No No
PLASMA Yes No No No
Python Yes No Yes Yes
R-Project Yes Yes No Yes
Ruby Yes Yes No Yes
Scalasca Yes Yes No Yes
Scilab Yes No No Yes
SCIP Yes Yes No Yes
SINGULARITY Yes No No No
Turbomole Yes Yes No Yes
UNICORE No No Yes No
UPC Yes No No No
Valgrind Yes Yes No Yes
VASP Yes Yes No No
vTune Yes No No No

Links To Software Homepages

See also

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