HSE Supercomputer Application Software
If your research team has difficulty installing any open source software on a supercomputer or if you think that some software should be installed centrally and be accessible to all users, write a request (with details) to firstname.lastname@example.org.
Detailed instructions and examples of startup scripts are available on the Russian version of the page.
|GROMACS||A software package for modeling physicochemical processes in molecular dynamics.|
|GNU Octave||A free math system using MATLAB compatible high-level language.|
|BEAST, BEAST2||Cross-platform program for Bayesian phylogenetic analysis of molecular sequences|
|IQ-TREE||User-friendly and widely used software package for phylogenetic inference using maximum likelihood.|
PRIMME, MAGMA, EEGLAB
|Multi-paradigm numerical computing environment and proprietary programming language developed by MathWorks.|
|OpenBUGS, JAGS||Software packages for the analysis of Bayesian hierarchical models using Markov Monte Carlo Chain Modeling (MCMC).|
|fMRIPrep||Application for the preprocessing of task-based and resting-state functional MRI (fMRI).|
|CP2K||CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.|
|Quantum ESPRESSO||Is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.|
|LAMMPS||LAMMPS is a classical molecular dynamics code with a focus on materials modeling.|
Specialized Software Libraries
|OpenPose||Real-time multi-person keypoint detection library for body, face, hands, and foot estimation.|
|FFTW||A C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.|
|GSL, SAMtools, ANGSD, HTSlib||A suite of programs for interacting with high-throughput sequencing data.|
|BEAGLE||General purpose library for evaluating the likelihood of sequence evolution on trees.|
|cnpy||Lbrary to read/write .npy and .npz files in C/C++.|
|AdmixTools||Libraries and utilities for processing population data.|
|OpenBlas||An open source implementation of the BLAS and LAPACK APIs with many manually created optimizations for specific processor types.|
See also HSE Supercomputer System Software.
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