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).
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
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
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
alphafold
automake
avogadro
binutils
bskan
caffe
charmm
chimera
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.
ctffind
dgrid
dislin
edp
eigen
FEniCS
ffmpeg
flex
fluent
gate
gdal
gdl
geant4
geos
gflags
gmap
gmt
gnuplot
grace
grass
guile
idl
intelmpi
java
jq
kcachegrind
lammps
make
math
metis
molden
molpro
motioncor2
mumax3
MUMPS
NCARG NCAR Graphics is a Fortran and C based software package for scientific visualization
ncview
ngc
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
xcrysden
zsh