Application software

Under this area you will find information about the installed software and applications on HPC2N’s systems (except debuggers, profiling tools, compilers, and libraries which have their own sections), as well as some information about accessing and using the various pieces of software and applications.

Important

The list is NOT complete. Login to Kebnekaise and run the command

ml spider

to get a full list.

If there is a program you need and it is not installed, you can either install it yourself or ask (mail support at support@hpc2n.umu.se) if it can be installed on Kebnekaise. If the program needs a license you will have to provide that yourself. If the license requires a license server, that will have to be provided either by yourself or through your department or similar.

Most of the software is accessed through the module system. You can read more about using modules on our ‘The modules system’ page.

Newer versions of the provided software will be installed regularly. However, if you need a new version quickly, please send an email to support@hpc2n.umu.se.

Bioinformatics

Biopython

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. Python libraries and applications which address the needs of current and future work in bioinformatics.

GTDB-Tk

A software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.

Kraken

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.

Computational Structural Biology

AlphaFold

AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known.

cryosparc

CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art HPC software solution for complete processing of single-particle cryo-electron microscopy (cryo-EM) data. CryoSPARC is useful for solving cryo-EM structures of membrane proteins, viruses, complexes, flexible molecules, small particles, phase plate data and negative stain data.

RELION

RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class
averages in electron cryo-microscopy (cryo-EM).

Scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy.

Atomistic and Molecular simulations

ASE

ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.

GPAW

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).

  • Local documentation: GPAW
  • External info: GPAW

AMBER

Amber is a molecular dynamics software package that simulates the Amber force fields.

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.

Dalton

Dalton is an ab initio quantum chemistry computer program. It is capable of calculating various molecular properties using the Hartree–Fock, MP2, MCSCF and coupled cluster theories.

ESPResSO

ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft matter research in physics, chemistry and molecular biology.

GAMESS-US

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.

gaussian

Gaussian provides state-of-the-art capabilities for electronic structure modeling.

GROMACS

A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.

LAMMPS

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

OpenMM

A high-performance toolkit for molecular simulation. Use it as an application, a library, or a flexible programming environment. We include extensive language bindings for Python, C, C++, and even Fortran.

PLUMED

PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.

QuantumESPRESSO

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

Schrödinger

The Schrödinger suite contains various computational chemistry and molecular modelling codes.

Siesta

Siesta performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

VASP

Performs ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.

  • Local documentation: VASP
  • External info: VASP

Wannier90

A tool for obtaining maximally-localised Wannier functions.

Climate modelling

WRF

Advanced Research WRF (ARW) Modeling System is a flexible, state-of-the-art atmospheric simulation system.

Mathematics

Gurobi

The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.

MATLAB

MATLAB is a numerical computing environment and fourth generation programming language.

Physics and Multiphysics

OpenFOAM

OpenFOAM (Open Field Operation and Manipulation) is primarily a C++ toolbox for the customisation and extension of numerical solvers for continuum mechanics problems, including computational fluid dynamics (CFD).

OpenFOAM-Extend

See OpenFOAM.

ACTC

ACTC converts independent triangles into triangle strips or fans.

Gurobi

The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.

MATLAB

MATLAB is a numerical computing environment and fourth generation programming language.

COMSOL

COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating.

Trilinos

The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.

Python modules

JupyterLab, Jupyter

JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface.

Keras

Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.

matplotlib

matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.

mpi4py

MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.

numba

Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.

numpy

NumPy is a library for the Python programming language, adding support for large, multi-dimensional arrays and matrices, along with a large collection of high-level mathematical functions to operate on these arrays.

numpy is part of the module SciPy-bundle. See this for more information.

pandas

pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language.

pandas is part of the module SciPy-bundle. See this for more information.

PyTorch/torch

Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.

scikit-learn

scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering.

scipy

SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.

scipy is part of the module SciPy-bundle. See this for more information.

SciPy-bundle

(Easybuild) Bundle of Python packages for scientific software. Contains (some variation with version): beniget, Bottleneck, deap, gast, mpmath, numexpr, numpy, pandas, ply, pythran, scipy, tzdata, versioneer

Seaborn

Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.

sympy

SymPy is a Python library for symbolic mathematics.

tensorboard

TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs.

TensorFlow

An open-source software library for Machine Intelligence

Theano

Theano is a numerical computation library for Python. In Theano, computations are expressed using a NumPy-esque syntax and compiled to run efficiently on either CPU or GPU architectures.

Visualization

GaussView

GaussView is a graphical interface to design small compounds and produce input files for Gaussian software.

Molden

MOLDEN is a pre- and post processing program of molecular and electronic structure.

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Other

Apptainer / containers

Apptainer is a is a free, cross-platform and open-source computer program that performs operating-system-level virtualization also known as containerization.

CUDA

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

  • Local documentation: CUDA
  • External info: CUDA

HDF5

HDF5 is a data model, library, and file format for storing and managing data.

hwloc

The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, …) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs.

Julia

Julia is a high-level, high-performance, dynamic programming language.

numactl

The numactl program allows you to run your application program on specific cpu’s and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

R

R is a free software environment for statistical computing and graphics.