• Name: Florian & De Vuyst, Super-Home: http://www.google.fr
• Home : http://www.mas.ecp.fr/labo/equipe/devuyst/
• Email: florian.de-vuyst at ecp.fr
• Location: Ecole Centrale PARIS, Laboratoire Mathématiques Appliquées aux Systèmes, Grande Voie des Vignes, 92295 Châtenay-Malabry cedex

MARQUE-PAGES DE CODES DE CALCUL SCIENTIFIQUE / CALCUL NUMERIQUE - BOOKMARKS OF SCIENTIFIC COMPUTING CODES

• Acts : The DOE Advanced Computational Software Collection project : http://acts.nersc.gov/
• Overture : OO tools for solving fluid dynamics and combustion problems in moving geometries : http://acts.nersc.gov/overture/index.html
• Mouse : a C++ library for Finite Volume Simulations : http://www.vug.uni-duisburg.de/MOUSE/
• Lifev : Modern Finite Element Library : http://www.lifev.org/
• Palm : Projet d'assimilation par logiciel multi-methodes : http://www.cerfacs.fr/globc/PALM_WEB/index.html
• Gerris : Gerris Flow Solver : http://gfs.sourceforge.net/
• UG : Flexible software tool, 2D/3D Unstructured + DDM + Multigrid : http://cox.iwr.uni-heidelberg.de/~ug/
• Openfoam : Open Field Operation and Manipulation : http://www.opencfd.co.uk/openfoam/
• MMTSB : Multiscale Modeling Tools for Structural Biology : http://mmtsb.scripps.edu/
• Amroc : Block Structured Mesh Refinement : http://amroc.sourceforge.net/html/intro.htm
• Dagh : Distributed Adaptive Grid Hierarchy : http://www.caip.rutgers.edu/~parashar/DAGH/
• Paramesh : Parallel adaptive mesh refinement : http://sourceforge.net/projects/paramesh/
• Aster : Code de calcul de structure EF d'Electricité de France : http://www.code-aster.org/
• Tahoe : Code de calcul de structure, techniques Meshless, C++ : https://tahoe.ca.sandia.gov/
• Geoframework : software suite for multiscale earth deformation analysis : http://www.geoframework.org/
• Zebulon : FE Analysis C++ code with Material database : http://www.nwnumerics.com/Downloads/
• Collela's Milestone project AMR C++, Particle NS : http://ct.gsfc.nasa.gov/milestones.colella.html
• Frontier Simulation Software for Industrial Science : http://www.fsis.iis.u-tokyo.ac.jp/en/result/software/
• Digital Material : http://www.lassp.cornell.edu/sethna/DM/Software.html
• AMAP : Plant Growing Simulation : http://wwww.cirad.fr/presentation/programmes/amap/logiciels/amap.shtml
• Flash : Astrophysical thermonuclear explosion simulation: http://flash.uchicago.edu/
• Sumaa3d : Scalable unstructured mesh : http://www-unix.mcs.anl.gov/sumaa3d/
• Survey of mesh generation technology : http://www.andrew.cmu.edu/user/sowen/softsurv.html
• Cubit : Sandia's Cubit mesh generation Tool suite : http://cubit.sandia.gov/
• Gmsh : 3D FE mesh generator with built-in pre- and post-processing facilities : http://www.geuz.org/gmsh/
• European synchrotron Radiation Facilities (ERSZF) : http://www.esrf.fr/Accelerators/Groups/InsertionDevices/Software
• Gyro : Eulerian gyrokinetic-Maxwell solver : http://fusion.gat.com/comp/parallel/gyro.html
• GS2 : Gyrokinetic turbulence particle-in-cell simulation : http://gs2.sourceforge.net/
• Camfr : Full vectorial Maxwell solver : http://camfr.sourceforge.net/
• Megawave : Free software intended for image processing : http://www.cmla.ens-cachan.fr/~megawave
• Scirun : Scientific computing and imaging : http://software.sci.utah.edu/

MATERIAL SIMULATION AT DIFFERENT SCALES

• Abinit : ab initio Quantum Chemistry computation : http://www.abinit.org/about/
• PWSCF : Plane wave self consistent field Package : http://www.pwscf.org/
• EON Project : Long time scale simulation of solids : http://eon.cm.utexas.edu
• MMTK : The Molecular Moddeling Toolkit : http://starship.python.net/crew/hinsen/MMTK/
• LAMMPS : Large-scale Atomic-Molecular Massively Parallel Simulator : http://www.cs.sandia.gov/~sjplimp/lammps.html
• ASE : Atomic Simulation Environment : http://dcwww.fysik.dtu.dk/campos/ASE/
• Dacapo : A planewave ultra-soft pseudopotential code : http://dcwww.fysik.dtu.dk/campos/Dacapo
• ASAP : Effective Medium theory code : http://dcwww.fysik.dtu.dk/campos/Asap
• SIESTA : Density-functional method for very large systems with LCAO basis sets : http://dcwww.fysik.dtu.dk/campos/ASE/calculators/SIESTA/SIESTA.html
• Gridpaw : Grid-based real-space PAW code : http://dcwww.fysik.dtu.dk/campos/GridPAW
• NAMD : Scalable molecular dynamics : http://charm.cs.uiuc.edu/research/moldyn/
• Leanmd : molecular dynamics for Petaflops machines : http://charm.cs.uiuc.edu/research/leanmd/
• Octopus : implementation of TDFDT : http://www.tddft.org/programs/octopus
• APE : Relativistic Atomic Code and pseudo-potential generator : http://www.tddft.org/programs/APE
• GAMGI : General Atomistic Modelling Graphic Interface : http://www.gamgi.org/
• CP2K : state-of-the-art methods for atomistic simulation (DFT, GPW,...) : http://cp2k.berlios.de/
• Piny_md : multipurpose, object-oriented molecular simulation package : http://www.indiana.edu/~rac/hpc/PINY_MD/
• Gromacs : simulation of millions of particles : http://www.gromacs.org/

COMPUTATIONAL LIBRARIES AND C++ TOOLS

• Blitz++ : Optimal Array, Tensor, Matrix C++ implementation : http://sourceforge.net/projects/blitz/
• Gmm++ : Iterative solvers and useful APIs (like Super-LU) : http://www.gmm.insa-tlse.fr/getfem/gmm_intro
• GSL : The gnu Scientific Library : http://www.gnu.org/software/gsl/
• MUMPS : Multi Frontal Massively Parallel Solver : http://graal.ens-lyon.fr/MUMPS
• Free Pooma : C++ library for parallel stencil-based physics computations : http://savannah.nongnu.org/projects/freepooma/
• PETSc : Portable, Extensible Toolkit for Scientific Computation : http://www-unix.mcs.anl.gov/petsc/petsc-as
• UMFPack : Unsymmetric Multi-Frontal sparse linear solver : http://www.cise.ufl.edu/research/sparse/umfpack/
• Sandia's Computational Software Site : http://software.sandia.gov/
• SGOPT : a C++ Library for Stochastic (Global) Optimization : http://www.cs.sandia.gov/SGOPT/
• COOOL : Object-Oriented Optimization library : http://coool.mines.edu/
• LAM/MPI : LAM/MPI Parallel Computing : http://www.lam-mpi.org/
• MPICH : http://www-unix.mcs.anl.gov/mpi/mpich/
• GA : Global Arrays, SMP Interface for Distributed Memory Computers : http://www.emsl.pnl.gov/docs/global/ga.html
• PLplot : a scientific plotting library : http://plplot.sourceforge.net/
• C Interface for Gnuplot : http://ndevilla.free.fr/gnuplot/
• Netcdf : Network Common Data Form : http://my.unidata.ucar.edu/content/software/netcdf/index.html
• Freesteam : opensource water and steam tables package : http://pye.dyndns.org/freesteam/
• vtkqt : classes for vtk GUI using QT : http://www.matthias-koenig.net/vtkqt/
• Spherepack : spherical harmonics (SH) development facilities : http://www.scd.ucar.edu/css/software/spherepack/
• Spharmonickit : http://www.cs.dartmouth.edu/~geelong/sphere/
• FFTPACK : http://www.scd.ucar.edu/softlib/FFTPACK.html
• FFTW : Fastest Fourier Transform in the West : http://www.fftw.org/
• ccSHT: A Fast Parallel Spherical Harmonic Transform : http://crd.lbl.gov/~cmc/ccSHTlib/doc/
• SCRIP : From grid to spherical coordinates : http://climate.lanl.gov/Software/SCRIP/
• VXL : C++ Libraries for Computer Vision and Implementation : http://vxl.sourceforge.net/
• Javaparty : a distributed companion to java : http://wwwipd.ira.uka.de/JavaParty/
• Mesa3d : 3D graphic library : http://www.mesa3d.org/
• Sundials : SUite of Nonlinear and DIfferential/Algebraic equation Solvers : http://www.llnl.gov/CASC/sundials/
• parasails : Parallel Sparse Approximate Inverse Preconditioner : http://www.llnl.gov/CASC/parasails/
• mpimap : A Tool for Visualizing MPI Datatypes : http://www.llnl.gov/CASC/mpimap/
• Easy-to-use C++ library for unconstrained optimization : http://math.ipm.ac.ir/scc/sourcecode/uncoptim.zip
• CLHEP : a Class library for High energy Physics : http://wwwasd.web.cern.ch/wwwasd/lhc++/clhep/index.html
• FML : The Fitting and Minimization Library : http://anaphe.web.cern.ch/anaphe/documentation/FML/index.html

SCIENTIFIC COMPUTING ENVIRONMENTS AND DEVELOPMENT ENVIRONMENTS

• Scilab : Rapid scientific development environment : http://scilabsoft.inria.fr/
• Wxmaxima : wxwidgets GUI for the computer algebra system Maxima : http://wxmaxima.sourceforge.net/
• ROOT : OO large scale data acquisition, simulation and data analysis : http://root.cern.ch/
• Salome : the Open-Source Platform for Numerical Simulation Integration : http://www.salome-platform.org/
• Open-FEM : an open source finite Element toolbox : http://www.openfem.net/
• Freefem : a finite element C++ environment : http://www.freefem.org
• Rheolef : a finite element C++ environment : http://www-lmc.imag.fr/lmc-edp/Pierre.Saramito/rheolef/index-normal.html
• R : The R project for statistical computing : http://www.r-project.org/
• Python/SciPy: http://www.python.org/ , http://www.scipy.org/

VISUALISATION - VISUALIZATION

• VTK : The Visualization Toolkit : http://public.kitware.com/VTK/
• Opendx : general 3D visualization : http://www.opendx.org/
• VMD : Molecular Dynamics Visualization : http://www.ks.uiuc.edu/Research/vmd/
• Visad : Java environment visu : http://www.ssec.wisc.edu/~billh/visad.html
• Scirun : Computation + Visu : http://software.sci.utah.edu/scirun.html
• Vis5d : Fluid-based visualization : http://www.ssec.wisc.edu/~billh/vis5d.html
• Chombovis : block-per-block AMR visualization : http://seesar.lbl.gov/anag/chombo/chombovis.html
• Graph visualization software : http://www.graphviz.org/
• Qplotter : 2D and pseudo-3D graphical plotter based on Qt : http://anaphe.web.cern.ch/anaphe/inDepth.html
• Visit : High-level VTK-based visualization : http://www.llnl.gov/visit/
• Paraview : Parallel vizualization application : http://www.paraview.org
• Labplot : Data analysis and visualization : http://labplot.sourceforge.net/
• Xd3d : tool for scientific visualization : http://www.cmap.polytechnique.fr/~jouve/xd3d/index.php
• Mayavi : the Maya-Vi Data Visualizer : http://mayavi.sourceforge.net/
• Xdraw : http://nimrodteam.org/xdraw
• Grace (ex-ACE/gr, ex-Xmgr) : WYSIWYG 2D plotting tool for the X Window System : http://plasma-gate.weizmann.ac.il/Grace/
• Hivision : Multi-purpose VTK-based scientific visualization : http://gaia.iwr.uni-heidelberg.de/~heuvelin/HiFlowProject/HiVision/index.html
• Popiplot : http://www.lmm.jussieu.fr/MEMBRES/POPINET/popiplot/index.html
• Scigraphica : "Microcal Origin"-like graphical software : http://scigraphica.sourceforge.net/
• Jsynoptic : http://jsynoptic.sourceforge.net/
• Visusimple : interactive visualization and graphics/mpeg-generation for VTK 2D/3D-data : http://dunne.uni-hd.de/VisuSimple/
• Lizard : new Python high-level interactive analysis and visualisation tool : http://anaphe.web.cern.ch/anaphe/lizard2.html
• Vpython : 3D Programming for Ordinary Mortals : http://vpython.org/

COMPILING / EDITING / DEBUGGING / PROFILING / VERSION CONTROL / DOCUMENTATION

• Eclipse CDT : Eclipse C/C++ Development Tool : http://www.eclipse.org/cdt/
• Mingw : Minimalist GNU C/C++/F77 for windows : http://www.mingw.org
• Cmake : Cross platform make : http://www.cmake.org
• Scintilla and Scite lightweight editors : http://www.scintilla.org
• Kdevelop : An Integrated Development Environment : http://www.kdevelop.org/
• Vdkbuilder : http://vdkbuilder.sourceforge.net/
• Insight : redhat gdb-based Graphic User Interface : http://sources.redhat.com/insight/
• DDD : The Data Display Debugger : http://www.gnu.org/software/ddd/
• TAU : Tuning and Analyzing Utility : http://acts.nersc.gov/tau/index.html
• Gprof : http://www.gnu.org/software/binutils/manual/gprof-2.9.1/gprof.html
• mpiP : Lightweight, Scalable MPI Profiling : http://www.llnl.gov/CASC/mpip/
• CVS : Concurrent Version Systems : https://www.cvshome.org/
• Robodoc : Automatic software documentation : http://sourceforge.net/projects/robodoc/

LINUX CLUSTER SOLUTIONS

• Xcat : extreme cluster administration toolkit : http://www.xcat.org
• Clustermatic : http://www.clustermatic.org
• Warewulf : the warewulf cluster toolkit : http://warewulf-cluster.org/
• Oscar : open source cluster application resources : http://oscar.openclustergroup.org/
• Rocks : Open source linux cluster solution : http://www.rocksclusters.org

GRID COMPUTING ENVIRONMENTS

• Xtremweb : Globat computing experimental java-based platform : http://www.xtremweb.net/
• Diet : Ditributed Interactive Engineering Toolbox : http://graal.ens-lyon.fr/DIET/
• MPICH-v : MPI Implementation for volatile resources : http://www.lri.fr/~bouteill/MPICH-V/
• Condor : High throughput computing (GRID) : http://www.cs.wisc.edu/condor/
• Cactus : GRID-enabled scientific computing : http://www.cactuscode.org
• RPC-based Netsolve/Gridsolve (GRID) : http://icl.cs.utk.edu/netsolve/
• Ninf-G : Implementation of Grid RPC system using Globus Toolkit : http://ninf.apgrid.org/
• MICO : Open source CORBA implementation : http://www.mico.org/

OTHER BOOKMARK PAGES AND PORTALS

• The Open Science Project : http://www.openscience.org/
• LCIC : Linux Clustering Information Center : http://lcic.org/index.html
• CIEL : Codes Informatiques En Ligne : http://ciel.ccsd.cnrs.fr/
• CODICIEL : Coordination et Diffusion des Logiciels : http://www.codiciel.fr/
• Sourceforge : http://www.sourceforge.net
• Globalgridforum GGF : http://www.globalgridforum.org/
• SCIDAC : Scientific Discovery through Advanced Computing : http://www.scidac.org/
• INRIA : Tools for scientific computing : http://www.inria.fr/valorisation/logiciels/calcul.fr.html
• OONumerics : the object-oriented Numerics page : http://www.oonumerics.org/oon/
• SAL : Scientific Applications on Linux : http://sal.jyu.fi/sal1.shtml
• Statlib : softwares and tools for Statistics community : http://lib.stat.cmu.edu/
• Netlib : netlib repository : http://www.netlib.org/
• Softwares for manipulating or visualizing Netcdf data : http://www.unidata.ucar.edu/packages/netcdf/software.html
• Generic Programming : http://www.ccrl-nece.de/~berti/generic/
• Le monde du calcul scientifique : http://gersoo.free.fr/calsci/calsci1.html
• Liste de logiciels gratuits d'Analyse Numérique : http://www.ann.jussieu.fr/gratuit.htm
• Solutions informatiques sur internet : http://zaimi.free.fr/informatique/
• Mathematical software : http://solon.cma.univie.ac.at/~neum/software.html
• Logiciels libres et calcul formel : http://www.lapcs.univ-lyon1.fr/~nthiery/CalculFormelLibre/
• Logiciels orientés traitement données/images : http://www.tsi.enst.fr/~rousseau/update.htm
• GPGPU : Scientific computation using Graphic processors GPU : http://www.gpgpu.org/cgi-bin/blosxom.cgi/Scientific%20Computing/index.html
• Fortran reloaded : http://www.fortran-2000.com/

MISCELLANEOUS

• Software for data analysis and pattern recognition : http://www.ph.tn.tudelft.nl/PRInfo/software.html
• QT Widgets for technical applications : http://qwt.sourceforge.net/
• Open-Cascade : http://www.opencascade.org/
• C/C++ wrapper Swig : http://www.swig.org/
• CFD codes from Los Alamos NL : http://www.lanl.gov/orgs/t/t3/codes.shtml
• Pyre : OO Python-based Framework for complex multi-physics simulation : http://www.cacr.caltech.edu/projects/pyre/index.html
• PSO : global optimization by particle swarm : the Matlab(TM) PSO toolbox : http://psotoolbox.sourceforge.net/
• pstoedit : transform postscript and pdf graphics into other vector graphics : http://www.pstoedit.net/

LATEX

• Miktex : complete Latex package : http://www.miktex.org
• Texniccenter : http://sourceforge.net/projects/texniccenter/
• GNU Texmacs : WYSIWYG Latex editor : http://www.texmacs.org
• Kile : an Integrated Latex environment : http://kile.sourceforge.net/
• The Latex beamer package : http://latex-beamer.sourceforge.net/
• Texpoint : a Latex add-in for MS Powerpoint : http://raw.cs.berkeley.edu/texpoint/
• Thloria : la classe de These du Loria : http://www.loria.fr/~roegel/TeX/TL.html

LANGUAGES

• The openSource FORTRAN 95 g95 project : http://g95.sourceforge.net/
• Free (for non-commercial use) Intel C++ and Fortran Compiler under Linux : http://www.intel.com/software/products/noncom/
• Cint : C/C++ interpreter : http://root.cern.ch/root/Cint.html

OPEN SOURCE OFFICE SUITE : OPENOFFICE . ORG 2.0 BETA :

• http://www.openoffice.org/

HTML WEB EDITOR

• NVU (say N'View) : The complete web authoring system : http://www.nvu.com

OPEN SOURCE DESKTOP PUBLISHING

• Scribus : http://www.scribus.org.uk/

SYSTEMES COLLABORATIFS INTERNET / INTERNET COLLABORATIVE SYSTEMS

• SPIP : Sytème de publication pour l'internet partagé : http://www.spip.net/fr
• Sympa : Rich open source mailing list software : http://www.sympa.org
• Plone : Content Management System based on Zope : http://www.plone.org
• Savane : Web-based Libre Software hosting system : https://gna.org/projects/savane
• Koha : Systeme integre de gestion de bibliotheque : http://www.koha-fr.org/

APPEL A PROJETS

• European Research Support : http://www.cordis.lu/guidance/services.htm
• Ministere de la recherche : http://www.recherche.gouv.fr/appel/index.htm
• Region Ile de France : http://www.iledefrance.fr/
• Region idf - systemes complexes et logiciels : http://www.polelsc.org/
• http://www.rrrt.cict.fr/module/lettre.php

CONTRIBUTIONS, CALL FOR SOFTWARE, TOOLBOX,...

• You think it would be interesting to add an interesting url to this page : please send it to florian.de-vuyst AT ecp.fr with "bookmarks" as subject.

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