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 |
| kraken | Turn-key OCR system optimized for historical and non-Latin script material |
| 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 | Integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. Based on density-functional theory, plane waves, and pseudopotentials |
| 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 | |
| ams | Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials science, from quantum mechanics to fluid thermodynamics |
| appli | |
| automake | |
| avogadro | Advanced molecule editor and visualizer |
| binutils | |
| bskan | |
| caffe | Deep learning framework |
| charmm | Molecular simulation program with broad application to many-particle systems |
| chimera | Program for the interactive visualization and analysis of molecular structures |
| chimerax | Molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI) |
| chimplot | |
| cistem | |
| Code_Aster | Structures and Thermomechanics Analysis for Studies and Research |
| comsol | General-purpose simulation software based on advanced numerical methods |
| CPMD | The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. |
| cryodrgn | |
| ctffind | Program for finding CTFs of electron micrographs |
| dgrid | |
| dislin | |
| dl_poly_4 | |
| edp | |
| eigen | |
| esmfold | |
| FEniCS | |
| ffmpeg | |
| flex | |
| fluent | |
| gate | Opensource software dedicated to numerical simulations in medical imaging and radiotherapy |
| gdal | |
| gdl | |
| gdrcopy | Low-latency GPU memory copy library based on GPUDirect RDMA technology |
| geant4 | Toolkit for the simulation of the passage of particles through matter |
| geos | |
| gflags | |
| GlobalArrays | Portable Non-Uniform Memory Access (NUMA) shared-memory programming environment for distributed and shared memory computers |
| gmap | |
| gmt | |
| gnuplot | |
| grace | |
| grass | |
| guile | |
| idl | |
| intelmpi | |
| java | |
| jq | |
| kcachegrind | |
| kokkos | |
| lafter | |
| libxc | |
| lsdalton | |
| luscus | Portable GUI for MOLCAS and other quantum chemical software |
| make | Tool which controls the generation of executables and other non-source files of a program from the program's source files |
| math | |
| mctdh | |
| med | |
| metis | |
| molden | |
| molpro | |
| motioncor2 | |
| mumax | |
| mumax3 | |
| MUMPS | |
| NCARG | NCAR Graphics is a Fortran and C based software package for scientific visualization |
| nccl | |
| ncview | |
| nfft | |
| nodejs | |
| nvidia_OptiX | |
| nvshmem | Parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters |
| nwchem | |
| octave | |
| openbabel | |
| opencascade | |
| opendx | |
| openmotif | |
| openTURNS | |
| paraview | |
| perl | |
| petsc | |
| photoscan | |
| plumed | Library that provides a wide range of different methods, which include enhanced-sampling algorithms, free-energy methods, tools to analyze the vast amounts of data produced by molecular dynamics (MD) simulations |
| psi4 | Open-Source Quantum Chemistry |
| 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 | |
| sharc | Surface Hopping including Arbitrary Couplings created by the González group |
| slepc | |
| starccm | |
| swig | |
| TACC | |
| tcl | |
| TensorRT | Platform for high performance deep learning inference |
| 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 | |
| vaspkit | |
| vim | |
| visit | |
| vmd | Molecular visualization program for displaying, animating, and analyzing large biomolecular systems |
| vtk | |
| wannier90 | Maximally-Localised Generalised Wannier Functions Code |
| xcrysden | |
| xplor-nih | |
| xtb | Semiempirical Extended Tight-Binding Program Package |
| zsh |