The table below shows an overview of the software available on the
machines in the Notur project. Select a discipline from the menu to
restrict the list to only relevant entries.
Selecting a package name expands the entry with a short description,
which includes a link to the software provider if available. Any pages
describing a given installation are linked from the corresponding
available version.
Note that the listing may be incomplete or out-of-date. Application
software installed by users is not included. Please contact the local support staff to find out about the availability of
specific software that is not listed in the table, especially if you
consider to apply for access to a machine.
| | hexagon | njord | stallo | titan |
|---|
| abaqus | | x | | |
| Finite element analysis. |
| ACML | 4.0.1a
| | | |
| AMD Core Math Library
ACML |
| ADF | | 2005.1
2006.1
| 2007.01
2008.01
| |
| ADF is the Amsterdam Density Functional program system for electronic structure calculations. ADF |
| ADF-BAND | | d.s.
| | |
| BAND is a first-principles periodic structure program for the study of bulk crystals, polymers, as well as surfaces. ADF-BAND |
| ADFview | | | 2007.01
2008.01
| |
|
| AMBER | | 9.0
| 10
| |
| AMBER |
| ANTLR | | x | | |
| ANTLR, ANother Tool for Language Recognition, is a language tool that provides a framework for constructing recognizers, interpreters, compilers, and translators from grammatical descriptions containing actions in a variety of target languages. |
| ATLAS | | | 3.8.2
| |
| Automatically Tuned Linear Algebra Software |
| Biopython | | | 1.4.5
| |
|
| BLAST | | | | x |
| Searches a protein or DNA sequence data bank. BLAST |
| BOM | x | | | |
| Bergen Ocean Model |
| CAM | x | | | |
| Community Atmosphere Model |
| ClustalW-MPI | | | 0.13
| |
|
| COMSOL | | | 3.4
| |
|
| CPMD | | 3.11.1
| | |
| The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. CPMD |
| CrayPat | 4.1.1
| | | |
| Cray Performance Analysis Tool. Evaluates program execution on Cray systems. |
| Dalton | | 2.0
| 2.0
| x |
| Dalton QCP (Quantum Chemistry Program) represents a powerful quantum chemistry program for the calculation of molecular properties. Dalton |
| Diffpack | | 4.0
| | |
| An object-oriented problem-solving environment for PDEs. |
| Dirac | | | | x |
| Program for atomic and molecular Direct Iterative Relativistic All-electronic Calculations. Dirac |
| EMBOSS | | | | x |
| Package for seqence analysis. Tools for molecular biology |
| ESSL | | 4.2
| | |
| IBM core math library ESSL |
| FAMHAP | | | | x |
|
| Fasta | | | | x |
| Searches a protein or DNA sequence data bank.
Download the FASTA package. Fasta |
| FFTW | 3.1.1
| 3.1.2
| 3.1.2
| |
| FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of both real and complex data, and of arbitrary input size. FFTW |
| FLUENT | | 6.3.26
| | |
| CFD application |
| Freeesurfer | | | 4.0.4
| |
| FreeSurfer is a set of semi-automated tools for reconstruction of the brain\'s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.
Freesurfer |
| FSL | | | 4.0.2
| |
| FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
| GAMESS | | | | x |
| GAMESS (General Atomic and Molecular Electronic Structure System) is a general ab initio quantum chemistry package. GAMESS-US |
| Gaussian G03 | | c.02
| e01
| x |
| Gaussian 03 is the successor to Gaussian 98. |
| GNU Tools | x | | | x |
| The GNU Project was launched in 1984 to develop a complete Unix-like operating system which is free software: the GNU system. GNU |
| GotoBLAS | x | | 1.22
| |
| Fast implementation of the Basic Linear Algebra Subroutines. GotoBLAS |
| GrADS | 1.8
| | | |
| The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. The format of the data may be either binary, GRIB, NetCDF, or HDF-SDS (Scientific Data Sets).
GrADS |
| GROMACS | | | 3.3.3.
| |
| Package for molecular dynamics. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS |
| GSL | | 1.8
1.9
| | |
| he GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
GSL |
| GTS | | | 071220
0.7.6
| |
| Library for the manipulation of triangulated surfaces |
| HDF5 | 1.6.6
| 1.6.5
| | |
| HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file.HDF |
| HMMER | | | | x |
| Profile hidden Markov models. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. Basically, you give HMMER a multiple sequence alignment as input; it builds a statistical model called a "hidden Markov model" which you can then use as a query into a sequence database to find (and/or align) additional homologues of the sequence family. HMMER |
| HYCOM | x | | | |
| Hybrid Coordinate Ocean Model |
| IHPCT | | x | | |
| IBM High Performance Computing Toolkit |
| Intel compilers | | | 10.0
| x |
| Intel® Compilers help Linux* software run at top speeds. Using Intel Compilers for Linux, developers can write high-performance software for desktops and servers. These compilers are compatible with existing development environments on Linux, so it's easy to start using them. Intel compilers |
| Intel MKL | | | 10.0
| |
|
| LoadLeveler | | 3.3.2
| | |
| LoadLeveler is the workload manager on the Regatta. CXperf |
| Maple | | | | x |
|
| Matlab | 2007b
| | 2007b
| x |
| MATLAB is a language for technical computing that combines numeric computation, advanced graphics and visualization, and a high-level programming language. It is the natural environment for analysis, algorithm prototyping and application development. MatLab |
| MICOM | x | | | |
| Miami Isopycnic Coordinate Ocean Model |
| Modeltest | | | | x |
|
| Modules | 3.1.6
| | | |
| Provides dynamic modification of a user's environment via modulefiles. |
| Molden | | | 4.6
| |
| Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. Jaguar |
| MPI | x | x | | x |
| MPI (Message Passing Library) is a widely used standard for writing message-passing programs. The interface attempts to establish a practical, portable, efficient, and flexible standard for message passing. MPI |
| mpiBLAST | | | 1.5.0-pio
| x |
| Searches a protein or DNA sequence data bank. BLAST |
| Mpiexec | | | 0.82
0.83
| |
| Mpiexec is a replacement program for the script mpirun, which is part of the mpich package. It is used to initialize a parallel job from within a PBS batch or interactive environment.
Mpiexec |
| MrBayes | | | | x |
| Program for the Bayesian inference of phylogeny. MrBayes |
| NAMD | 2.6
| 2.6
| 2.6
2.6-TCP
| |
| NAMD is a parallel, object-oriented molecular dynamics code designed
for high-performance simulation of large biomolecular systems.
NAMD |
| NCARG | | x | | |
| NCAR Graphics |
| NCO | x | 3.1.8
3.9.1
| | |
| The netCDF Operators, or NCO, are a suite of programs known as operators. The operators take netCDF files as input, then perform a set of operations (e.g., deriving new data, averaging, hyperslabbing, or metadata manipulation) and produce a netCDF file as output.NCO |
| ncview | x | | | |
| Ncview is a visual browser for netCDF format files.ncview |
| NetCDF | 3.6.2
| 3.6.1
3.6.2
| 3.6.2
| |
| NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data.NetCDF |
| Netlib | | | 1.8.0
| |
|
| Newmat | | x | | |
|
| Newran | | x | | |
| Newran is a C++ library for generating sequences of random numbers from a wide variety of distributions. |
| NPMLE | | | | x |
|
| Octave | | x | | |
| GNU Octave is a high-level language, primarily intended for numerical computations. |
| OpenMPI | | | 1.2.4
| |
| Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation.OpenMPI |
| PAUP | | | | x |
| Tools for inferring and interpreting phylogenetic trees.PAUP |
| PBS/Torque | 2.3.0
| | 2.3.0
| x |
| PBS Pro (Portable Batch System) is the workload manager on the HP installations. Link to Maui, the advanced job scheduler. Link to OpenPBS. PBS |
| Perl | 5.8.3
| 5.8.2
| | |
| Scripting language of choice for most CGI scripts. Perl |
| PETSc | 2.3.3a
| 2.3.2.3
2.3.2.8
2.3.3.3
| | |
| PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for all message-passing communication.PETSc |
| PGPLOT | 5.2
| | | |
| The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent, graphics pacakge for making simple scientific graphs. |
| Phase | | | | x |
|
| Phylip | | | | x |
| PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. Phylip |
| PMDR | | x | | |
| Parallel Multifactor Dimensionality Reduction |
| Portland compilers | 7.1.6
| | | x |
| PGI High-Performance Compilers Portland |
| Purify | | x | | |
| IBM Rational Purify is a runtime analysis solution designed to help developers write more reliable code. |
| Python | 2.3.3
2.5.1
| 2.5.0
| 2.5.1
| |
| Python, an interpreted, interactive, object-oriented, extensible programming language. Link to a tutorial. Python |
| R | | | | x |
| R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. R |
| Ruby | | x | | |
| Ruby is a dynamic, reflective, general purpose object-oriented programming language. |
| Schrödinger | | | 2008-5
| |
| provides accurate, reliable, and high performance computational technology to
solve real-world problems in pharmaceutical, biotechnology, and materials
science research. |
| Simwalk2 | | | | x |
|
| Subversion | 1.4.6
| 1.4.2
1.4.3
| | |
| Subversion version control system clients |
| Tcl/Tk | | x | | |
| Tcl programming language and Tk graphical user interface toolkit. |
| TotalView | 8.4.1
| 8.0.1-0
| 8.3.0-1
| |
| TotalView, a source- and machine-level debugger with support for Fortran, C, C++, OpenMP, MPI, and threads. TotalView |
| Turbomole | | | 5.10
| |
|
| UNPHASED | | | | x |
|
| vasp | | x | 4.6.34
| |
|
| VPA | | x | | |
| Visual Performance Analyzer (VPA) is an Eclipse-based performance visualization toolkit. |
| WSMP | | x | | |
| Watson Sparse Matrix Package |
| XLC | | x | | |
| XL C is a standards-based, high performance C compiler with advanced optimizing and debugging features. |
| XLF | | x | | |
| XL Fortran |
| XT-libsci | 10.2.0
| | | |
| Cray Scientific Library that includes optimized LAPACK, BLAS, BLACS, ScaLAPACK, SuperLU, IRT |
