In this section you will find information about the installed software and applications at the 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 HPC2N's systems. If the program needs a license, you will in some cases have to provide that.

HPC2N provides a large selection of application software. This section will contain a brief overview of the programs, as well as (sometimes) recommandations for which version to use.  In the cases where there is a recommended 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 module 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 | 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:	Akka: 5.4.4, 5.8.3, 6.0.2
CHARMM	Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. External info:	Akka: c33b2
CP2K	CP2K is a freely available program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. External info:	Akka: cvs-20110308
Dacapo	Dacapo is a total energy program based on density functional theory. It uses a plane wave basis for the valence electronic states and describes the core-electron interactions with Vanderbilt ultrasoft pseudo-potentials. External info:	Akka: 2.7.7 Ritsem: 2.7.7
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:	Abisko: 3.0 Akka: 2.6.1
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:	Abisko: 4.3.2 Akka: 4.1.3, 4.3.0
ESPResSo (MD)	ESPResSo is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research, with emphasis on charged systems. External info:	Akka: 2.2.0b
GAMESS-UK	The General Atomic and Molecular Electronic Structure System (GAMESS-UK) is a general ab initio quantum chemistry package. External info:	Akka: 8.0
Gaussian	Gaussian provides state-of-the-art capabilities for electronic structure modeling. External info:	Akka: 09.c.01 Ritsem: 09.c.01
Gromacs	A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software. External info:	Abisko: 4.5.4 Akka: 4.0.5, 4.5.3
HDF5	HDF5 is a data model, library, and file format for storing and managing data. External info:	Abisko: 1.8 Akka: 1.6, 1.8
MATLAB	MATLAB is a numerical computing environment and fourth generation programming language. External info:	Abisko: 2010a Akka: 2010a
MOLDEN	MOLDEN is a pre- and post processing program of molecular and electronic structure. External info:	Akka: 4.7
NWChem	NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality. External info:	Abisko: 6.0.0 Akka: 6.0
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:	Abisko: 2.0 Akka: 1.5, 1.6, 2.0
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:	Akka: 3.0.0-p7 Ritsem: 2.3.3-p13
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:	Abisko: 1.07 Akka: 1.07
R	R is a free software environment for statistical computing and graphics. External info:	Abisko: 2.10.1 Akka: 2.10.0
Siesta	Siesta performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. External info:	Abisko: 3.1 Akka: 3.1
TURBOMOLE	TURBOMOLE is a quantum chemical program package Extern info:	Abisko: 6.3.1
VASP	Performs ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. Extern info:	Abisko: 5.2.12 Akka: 5.2.8
WRF	Advanced Research WRF (ARW) Modeling System is a flexible, state-of-the-art atmospheric simulation system. Extern info:	Akka: 3.2, 3.3
Compilers
PathScale	PathScale Compilers. Has C, C++, Fortran 77, Fortran90, and Fortran 95. Avaliable for serial, OpenMP, and MPI code for all languages. External info:	Abisko: 4.0.12 Akka: 4.0.9, 3.2 Ritsem: 3.2
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:	Abisko: 4.4.3 Akka: 4.1.2 Ritsem: 4.2.4
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:	Abisko: 11.1, 12.0 Akka: 11.1 Ritsem: 11.1
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:	Abisko: 10.4, 10.9, 11.9 Akka: 10.4, 10.9 Ritsem: 10.0
MPI Libraries
Open MPI	Open MPI is an open source combination of technologies from several other MPI projects. External info: Loading: here Using: here.	Abisko: 1.5.4 Akka: 1.4.2, 1.4.3 Ritsem: 1.3.3
MVAPICH	This is MPI over InfiniBand and iWARP. It is only installed on Akka, as that is the only cluster which has InfiniBand. External info: Loading: here Using: here	Akka: 1.4rc1
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. External info:	Abisko: 1.1 Akka: 1.1 Ritsem: 1.1
FFTW	A fast, free C FFT library; includes real-complex, multidimensional, and parallel Fourier transforms. External info:	Abisko, 2.1.5, 3.3 Akka: 3.2.2 Ritsem: 3.2.2
GOTOBLAS	The GOTO BLAS codes are a fast implementation of the Basic Linear Algebra Subroutines. External info:	Akka: 1.13 Ritsem: r1.26
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:	Abisko: 3.3.1, 3.4.0 Akka: 3.2.1 Ritsem: 3.1.1
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.	Abisko: 10.0, 10.2.5, 10.3.3 Akka: 10.2.5 Ritsem: 10.2.5
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:	Abisko: 4.1.3 Akka: 4.1.1, 4.1.2
OpenBLAS	OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. External info:	Abisko: 0.1
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:	Akka: 3.1.1
RECSY	RECSY is a library for solving triangular Sylvester-type matrix equations. External info:	Akka: 1.0 Ritsem: 1.0
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:	Abisko: 2.0.1 Akka: 1.8.0 Ritsem: 1.8.0
SLICOT	The subroutine library SLICOT provides Fortran 77 implementations of numerical algorithms for computations in systems and control theory. It is based on numerical linear algebra routines from BLAS and LAPACK libraries. External info:	Akka: 5.0 Ritsem: 4.0