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 |
lammps | Large-scale Atomic/Molecular Massively Parallel Simulator |
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 |
openmolcas | Quantum Chemistry software package |
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. |
freepascal | Mature, versatile, open source Pascal compiler |
gcc | Gnu Compiler Collection |
go | Open source programming language |
intel | Intel high-end compilers and Math Kernel Library (MKL) |
lazarus | Open-source cross platform IDE powered by Free Pascal |
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 | |
appli | |
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 | |
kraken | |
lafter | |
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 | |
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 |