Software

Under this area you will find information about the installed software and applications on HPC2N's systems, as well as some information about accessing it.

Note that is is NOT a complete list. 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 (check if it can easily be installed with Easybuild) 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 deparment or similar.

Much of the software is accessed through the module system. You can read more about using modules on our 'Using modules (Lmod)' page and the 'Accessing software with Lmod' page. When you are looking for a piece of software, try running either

  • module avail
  • ml spider

to see if it is installed.

For information about versions, login to the cluster (Kebnekaise) and run

ml spider <software>

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.

More detailed information about using numerical and MPI libraries can be found on our Libraries page.

[Application software | Compilers | Debuggers and performance tools | MPI Libraries | Numerical, communications, and other libraries ]

Program Description
Application software
Abinit Abinit is a freely available program to find the total energy, charge density and electronic structure of systems.
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ACTC ACTC converts independent triangles into triangle strips or fans.
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AMBER AMBER is a molecular dynamics software package that simulates the Amber force fields.
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ASE ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.
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Caffe Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors.
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Comsol COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating
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CP2K CP2K is a freely available program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems.
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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.
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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.
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FDTD_Solutions (Lumerical) High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.
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galamost GALAMOST is a versatile molecular simulation package which is designed to fully utilize computational power of graphics processing units (GPUs). It is developed specially for coarse-graining simulations of polymeric systems by including some latest techniques
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GAMESS-US The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
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Gaussian Gaussian provides state-of-the-art capabilities for electronic structure modeling.
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GPAW GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
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Gromacs A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.
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HDF5 HDF5 is a data model, library, and file format for storing and managing data.
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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.
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Keras Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.
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MATLAB MATLAB is a numerical computing environment and fourth generation programming language.
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Molden MOLDEN is a pre- and post processing program of molecular and electronic structure.
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NAMD NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
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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.
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NWChem NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality.
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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).
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OpenFOAM-Extend 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).
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OpenMM OpenMM is a high performance toolkit for molecular simulation. Use it as a library, or as an application. It includes extensive language bindings for Python, C, C++, and even Fortran.

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ORCA

ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.

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PLINK 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.
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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.
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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).
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R R is a free software environment for statistical computing and graphics.
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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).
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Schrodinger The Schrödinger suite contains various computational chemistry  and molecular modelling codes.
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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.
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Scipion Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy.
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Siesta Siesta performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. External info:
Turbomole TURBOMOLE is a quantum chemical program package
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VASP Performs ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.
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VMD VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
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WRF Advanced Research WRF (ARW) Modeling System is a flexible, state-of-the-art atmospheric simulation system.
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Compilers
GCC

GNU Compiler Collection. Has C, C++, Fortran 77, Fortran 90, and Fortran 95. Available for serial, OpenMP, and MPI code for all languages, with the exception of Fortran 95 MPI programs.

Part of several compiler toolchains.
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Intel Intel Compilers. Has C, C++, Fortran 77, Fortran 90, and Fortran 95. Available for serial, OpenMP, and MPI code for all languages.
Part of several compiler toolchains.
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PGI Portland Group Compilers. Has C, C++, Fortran 77, Fortran 90, and Fortran 95. Avaliable for serial, OpenMP, and MPI code for all languages, with the exception of Fortran 96 MPI programs.
Part of several compiler toolchains.
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Debuggers and performance tools
Allinea, DDT The Allinea environment is an essential toolkit for developers and computational scientists looking to get results faster.
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Cube Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity.
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Extrae Extrae is the core instrumentation package developed by the Performance Tools group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered by Extrae typically includes timestamped events of runtime calls, performance counters and source code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application.
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Intel Inspector Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications
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itac The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace  Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.
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LLVM The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
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OPARI2 OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.
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PAPI PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.
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PDT Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations.
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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.
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Score-P The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
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Valgrind Debugging and profiling tools
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VTune Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
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MPI Libraries
Intel MPI (impi) Intel MPI (impi) is a high performance MPI implementation that can run on multiple cluster interconnects chosen by the user at runtime.
Part of several compiler toolchains.
External info:
Loading and using: Libraries->MPI
OpenMPI Open MPI is an open source combination of technologies from several other MPI projects.
Part of several compiler toolchains.
External info:
Loading and using: Libraries->MPI
Other libraries
BLACS The BLACS (Basic Linear Algebra Communication Subprograms) project aims to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms.
BLACS is now part of ScaLAPACK.
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ELPA Eigenvalue SoLvers for Petaflop-Applications.
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Eigen Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
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FFTW A fast, free C FFT library; includes real-complex, multidimensional, and parallel Fourier transforms.
Part of several compiler toolchains.
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GSL The GNU Scientific Library (GSL) is a numerical library for C and   C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
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Intel MKL Intel® Math Kernel Library (Intel® MKL) is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
Part of several compiler toolchains.
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Linking with Intel MKL.
ipp Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.
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Lapack LAPACK (Linear Algebra PACKage) is a software library for numerical linear algebra. It provides routines for solving systems of linear equations and linear least squares, eigenvalue problems, and singular value decomposition. It also includes routines to implement the associated matrix factorizations such as LU, QR, Cholesky and Schur decomposition.
Included with OpenBLAS.
Part of several compiler toolchains.
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Libint Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.
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libxc Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
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LIBXSMM LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
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METIS METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
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MPFR The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
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netCDF NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
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OpenBLAS OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
Part of several compiler toolchains.
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ParMETIS ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
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ScaLAPACK ScaLAPACK is a library of high-performance linear algebra routines for distributed-memory message-passing computers and networks of workstations supporting PVM and/or MPI. It is a continuation of the LAPACK project, which designed and produced analogous software for workstations, vector supercomputers, and shared-memory parallel computers.
Part of several compiler toolchains.
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SCOTCH Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
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SIONlib SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version.
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StarPU A Unified Runtime System for Heterogeneous Multicore Architectures StarPU is a task programming library for hybrid architectures.
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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.
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Tensorflow An open-source software library for Machine Intelligence
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Updated: 2020-12-01, 11:31