HSE Supercomputer Application Software

Dear users!

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 hpc@hse.ru.
Detailed instructions and examples of startup scripts are available on the Russian version of the page.

Software systems

Name	Description
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.
MATLAB 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

Name	Description
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.

Have you spotted a typo?
Highlight it, click Ctrl+Enter and send us a message. Thank you for your help!
To be used only for spelling or punctuation mistakes.

Supercomputer Modeling Unit

HSE Supercomputer Application Software

Software systems

Specialized Software Libraries