Software on Abisko

Software on Abisko

(For information about software on Kebnekaise, go to our 'Software on Kebnekaise' page.)

In this section you will find information about the installed software and applications on Abisko at HPC2N, as well as some information about available commercial programs.

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 Abisko. If the program needs a license, you will in some cases have to provide that.

HPC2N provides a large selection of application software on Abisko. This section will contain a brief overview of the programs, as well as (sometimes) recommendations for which version to use.  In the cases where there is a recommended or default version, it will be emphasized in bold. This will often, but not always, be the newest version. You can always run module avail and look for the program you want to use, to see all available versions. If you know the name of the module (like psc for PathScale compilers), but not which versions are available, you can use the command module avail <module name>.

You can read more about using modules on the Abisko: Using modules page.

Follow the links below to get more information about running the applications or linking with the libaries.

Many of the modules have a small 'help' text included. Type module help <module name> to get the help text.

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.

If you need a program not listed below, try running module avail or looking in /lap to see if it is installed. If not, you can send a suggestion to have it installed to support@hpc2n.umu.se. More detailed information can be found here:

  • Numerical and MPI libraries: here

 [ Appl. software | Compilers | Debuggers | MPI Lib. | Num. & Comm. Lib. ]

Program Description Availability/
newest version
Application software
Abinit Abinit is a freely available program to find the total energy, charge density and electronic structure of systems.
External info:
6.12.3, 7.4.3
AMBER AMBER is a molecular dynamics software package that simulates the Amber force fields.
External info:
12.0.21, 14.0.12
Ansys Ansys provides various engineering simulation solution sets for structural mechanics, fluid dynamics, electromagnetics, etc.
External info:  
14.0, 17.2
ASE ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.
External info:  
3.6.0
CP2K CP2K is a freely available program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems.
External info:
2.4, 2.6
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.
External info:
2011, 2013, 2015
ESPRESSO (QM) 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).
External info:
5.1.0, 5.2.1, 6.0
FEniCS FEniCS is free software for automated solution of differential equations.
External info:
1.5.0
GAMESS-US GAMESS (US) is a computational chemistry software program that stands for General Atomic and Molecular Electronic Structure System.
External info:

20120501-r1, 20130501-r1

Gaussian Gaussian provides state-of-the-art capabilities for electronic structure modeling.
External info:
09.d.01
GPAW GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
External info:  
0.9.0, 0.11.0
Gromacs A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.
External info:
4.6.2, 4.6.5, 4.6.7, 5.0.4, 5.0.5, 5.1, 2016
HDF5 HDF5 is a data model, library, and file format for storing and managing data.
External info:
1.8
MATLAB MATLAB is a numerical computing environment and fourth generation programming language.
External info:
2011b, 2014b, 2016a, 2016b
MOLDEN MOLDEN is a pre- and post processing program of molecular and electronic structure.
External info:
5.1
NWChem NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality.
External info:
6.1.1, 6.3, 6.5
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).
External info:
2.1.1, 2.2.2, 2.3.1, 2.4.0, 3.0.1
OpenMX OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories, norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.
External info:
3.7.8
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. External info: 1.07, 1.9_beta
R R is a free software environment for statistical computing and graphics.
External info:
3.2.5
Schrodinger The Schrodinger suite contains various computational chemistry  and molecular modelling codes.
External info:
2013u02, 2014u01, 2014u04
Siesta Siesta performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. External info:

3.2.3

SPM SPM (Statistical Parametric Mapping) is a software package for MATLAB for the analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG, MEG).
Extern info:
12
Tau TAU (Tuning and Analysis Utilities) is a portable profiling and tracing toolkit for performance analysis of parallel programs.
Extern info:
2.23
TURBOMOLE TURBOMOLE is a quantum chemical program package
Extern info:
6.3.1
VASP Performs ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.
Extern info:
5.3.3, 5.3.5, 5.4.1
WRF Advanced Research WRF (ARW) Modeling System is a flexible, state-of-the-art atmospheric simulation system.
Extern info:
3.4.0, 3.6.1, 3.7.1
Compilers
PathScale (psc) PathScale Compilers. Has C, C++, Fortran 77, Fortran90, and Fortran 95. Avaliable for serial, OpenMP, and MPI code for all languages.
External info:
5.0.0, 6.0.0, 6.0.9
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.
External info:
4.6.3
Intel Intel Compilers. Has C, C++, Fortran 77, Fortran 90, and Fortran 95. Available for serial, OpenMP, and MPI code for all languages.
External info:
12.1, 13.0, 13.1, 14.0, 15.0, 16.0
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.
External info:
15.7, 16.1
Debuggers
DDT DDT (Allinea DDT) - the Distributed Debugging Tool - is an advanced debugging tool available for scalar, multi-threaded and large-scale parallel applications.
External info:
5.0.1, 6.0.0, 6.0.1
MPI Libraries
OpenMPI

Open MPI is an open source combination of technologies from several other MPI projects.
External info:
Loading: here
Using: here.

1.6.5, 1.8.1, 1.8.8, 1.10.1
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.
External info:
Loading: here
Using: here 

4.0.3, 4.1.0, 4.1.3, 5.0.1, 5.1.1, 5.1.2, 5.1.3
Numerical & Communciation 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.
External info:
 
FFTW A fast, free C FFT library; includes real-complex, multidimensional, and parallel Fourier transforms.
External info:
2.1.5, 3.3.2, 3.3.3, 3.3.4
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.
External info:
3.4.2, 3.5.0
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.
External info:
Linking: here.
10.3.6, 11.0.0, 11.0.4, 11.1.2, 11.2.0, 11.3.0, 11.3.1
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.
External info:
4.1.3
OpenBLAS OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
External info:
0.2.8.a, 0.2.9, 0.2.13
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.
External info:
3.1.1, 4.0.2  
PETSc PETSc, is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
External info:
3.4.3
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.
External info:
2.0.2
Slepc SLEPc is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc.
External info:
3.4.3

 

Updated: 2017-05-22, 17:38