Voici la liste des applications disponibles sur le Centre de Calcul en tant que modules.

Vous pourrez également trouver une liste d'applications installées directement par l'Institut Français de Bioinformatique (IFB) : lien vers les modules de l'IFB.

## SOFTWARES

Name | Description |
---|---|

abinit | Software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials |

adf | Quantum chemistry software package based on Density Functional Theory (DFT). |

alphafold | Artificial Intelligence program developed by Alphabets's/Google's DeepMind which performs predictions of protein structure |

amber | Suite of biomolecular simulation programs |

ccp4 | Integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques |

cdo | The Climate Data Operators (CDO) software is a collection of many operators for standard processing of climate and forecast model data |

cp2k | Quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems |

elk | All-electron full-potential linearised augmented-plane wave (LAPW) code with many advanced features |

freefem | Partial differential equation solver for non-linear multi-physics systems in 2D and 3D |

gaussian | Electronic structure program |

gmsh | A three-dimensional finite element mesh generator |

gromacs | Package to perform molecular dynamics |

gulp | General Utility Lattice Program |

harminv | Harmonic inversion program |

imagic | High end environment for the analysis of images, spectra and other multi-dimensional data-sets |

julia | Programming language |

matlab | Multi-paradigm programming language and numerical computing environment |

meep | Software package for electromagnetics simulation via the finite-difference time-domain (FDTD) method spanning a broad range of applications |

MGLTools | Visualization and analysis of molecular structures |

MPB | MIT Photonic-Bands. Software package for computing the band structures, or dispersion relations, and electromagnetic modes of periodic dielectric structure |

namd | Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems |

nvidia_hpc_sdk | Suite of compilers, Libraries and Tools for HPC |

opencv | Open source computer vision and machine learning software library. |

openfoam | Open source CFD toolbox |

openmpi | Open source Message Passing Interface implementation |

opentelemac | Integrated suite of solvers for use in the field of free-surface flow |

orca | Ab initio, DFT and semiempirical SCF-MO package |

osu-micro-benchmarks | Benchmark collection for MPI communications |

phenix | Software suite for the automated determination of molecular structures using X-ray crystallography and other methods |

python | Interpreted, high-level, general-purpose programming language |

quantumespresso | Electronic structure |

R | R is a free software environment for statistical computing and graphics. |

root | Toolkit for big dataset analysis and processing |

scilab | Numerical computation |

sidesplitter | Local SNR filter for Single Particle reconstruction |

siesta | Ab-initio molecular dynamics simulations / electronic structure |

singularity | Singularity is a free, cross-platform and open-source computer program that performs operating-system-level virtualization also known as containerization. |

slurm | Batch scheduler |

towhee | Monte-Carlo Molecular simulation |

vasp | Ab-initio package / Quantum-mechanical molecular dynamics |

Vina-GPU | A heterogeneous OpenCL implementation of AutoDock Vina |

WRF | Atmospheric modeling system designed for both meteorological research and Numerical Weather Prediction |

## LIBRARIES

Name | Description |
---|---|

arpack | Large scale eigenvalue problems library |

boost | Clean C++ Library |

CGAL | C++ library providing easy access to efficient and reliable geometric algorithms |

fftw | Fast-Fourier-Transform Library |

harminv | Harmonic inversion program |

hdf5 | High performance data software library and file format to manage, process, and store heterogeneous data |

intel | Intel high-end compilers and Math Kernel Library (MKL) |

lapack | Linear Algebra PACKage |

libctl | Flexible control files library for scientific simulations |

netcdf | Scientific portable I/O |

nvidia_hpc_sdk | Suite of compilers, Libraries and Tools for HPC |

openmpi | Open source Message Passing Interface implementation |

scalapack | High-performance linear algebra routines for parallel distributed memory machines |

## COMPILERS

Name | Description |
---|---|

clang | C, C++ and Objective-C compilers |

cmake | Cross-platform family of tools designed to build, test and package software |

cuda | CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia to use a CUDA-enabled graphics processing unit (GPU) for general purpose processing. |

gcc | Gnu Compiler Collection |

go | Open source programming language |

intel | Intel high-end compilers and Math Kernel Library (MKL) |

nvidia_hpc_sdk | Suite of compilers, Libraries and Tools for HPC |

pgi | PGI high-end compilers |

## DEBUGGERS

Name | Description |
---|---|

## VISUALIZATIONS

Name | Description |
---|---|

X2Go | Remote visualization software |

## NOT DOCUMENTED YET

Name | Description |
---|---|

abaqus | Abaqus FEA (formerly ABAQUS) is a software suite for finite element analysis and computer-aided engineering. |

acpype | |

automake | |

avogadro | |

binutils | |

bskan | |

caffe | |

charmm | |

chimera | |

chimerax | |

chimplot | |

cistem | |

Code_Aster | Structures and Thermomechanics Analysis for Studies and Research |

CPMD | The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. |

cryodrgn | |

ctffind | |

dgrid | |

dislin | |

dl_poly_4 | |

edp | |

eigen | |

FEniCS | |

ffmpeg | |

flex | |

fluent | |

gate | |

gdal | |

gdl | |

geant4 | |

geos | |

gflags | |

gmap | |

gmt | |

gnuplot | |

grace | |

grass | |

guile | |

idl | |

intelmpi | |

java | |

jq | |

kcachegrind | |

kokkos | |

lafter | |

lammps | |

lsdalton | |

make | |

math | |

metis | |

molden | |

molpro | |

motioncor2 | |

mumax3 | |

MUMPS | |

NCARG | NCAR Graphics is a Fortran and C based software package for scientific visualization |

ncview | |

nfft | |

ngc | |

nodejs | |

nvidia_OptiX | |

nwchem | |

octave | |

openbabel | |

opendx | |

openmotif | |

openTURNS | |

paraview | |

perl | |

petsc | |

photoscan | |

qt | |

relion | |

RSPt | |

scalasca | Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks - in particular those concerning communication and synchronization - and offers guidance in exploring their causes. |

scipion | |

scons | |

scotch | |

Seg3D | |

slepc | |

starccm | |

swig | |

TACC | |

tcl | |

THUNDER | A particle-filter framework for robust cryoEM 3D reconstruction |

tophat | |

totalview | |

triqs | TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems |

valgrind | |

visit | |

vmd | |

vtk | |

wannier90 | |

xcrysden | |

xplor-nih | |

zsh |