Basic software documentation at NSC


Directory list:

VersionDescription
CESM The Community Earth System Model (CESM) is a software suite for performing global climate simulations.
EC-Earth3 EC-Earth 3 is a software suite for performing global climate simulations.
NCARdiag The NCAR AMWG diagnostics package produces over 600 plots and tables from CCSM (CAM) monthly netcdf files.
OpenFOAM OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. It includes tools for meshing, notably snappyHexMesh, a parallelised mesher for complex CAD geometries, and for pre- and post-processing. [Link].
R R environment for statistical computing and graphics. [Link]
abinit ABINIT electronic structure program
abyss N/A
allinea-DDT Allinea DDT is an advanced debugging tool for multi-threaded and large-scale parallel applications. [Link]
amber Amber Molecular Dynamics [Link]
ansys The ANSYS application package. See the vendor website for more information.
arpack ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. [Link]
ase Atomic Simulation Environment [Link]
atompaw PAW pseudopotential generation software
avogadro Avogadro -- Free cross-platform molecule editor [Link]
beagle library for Bayesian and Maximum Likelihood phylogeny computations
castep CASTEP [Link]
ccp4 CCP4 -- Software for Macromolecular Crystallography [Link]
cdo Climate Data Operators project site. CDO is a collection of command line operators to manipulate and analyze climate and NWP model output.
comp_wrapper NSC Compiler wrapper
comsol COMSOL Multiphysics is a general-purpose software platform for modeling and simulating physics-based problems.
cp2k CP2K, ab initio electronic structure molecular dynamics [Link]
cpmd CPMD, Car-Parinello Molecular Dynamics [Link]
cyana program suite for automated NMR protein structure calculation
dalton ab initio and DFT quantum chemistry code
desmond Desmond, molecular dynamics code for biomolecular simulations [Link]
dl_poly dl_poly Molecular dynamics simulation software [Link]
elk Elk is a FPLAPW electronic structure code package [Link]
emto EMTO is a Green's function method
emtox EMTOx is a Green's function method
espresso Quantum Espresso ab initio package [Link]
exciting Exciting is a FPLAPW electronic structure code
ferret FERRET - An analysis tool for gridded and non-gridded data.
gabedit Gabedit -- A graphical user interface to computational chemistry packages [Link]
gamess-US GAMESS-US, ab initio quantum chemistry software [Link]
gaussian Gaussian [Link]
gcc The GNU Compiler Collection with C, C++ and Fortran compilers
gmp GNU Multiple Precision Arithmetic Library[Link]
gpaw A grid-based DFT/PAW code.
grib_api The ECMWF GRIB API application program interface.
gribex The ECMWF GRIBEX is a library for encoding and decoding FM-92 WMO code messages.
gromacs GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles [Link]
hdf5 Hierarchical Data Format (HDF5) is a data model, library, and file format for storing and managing data.
irods IRODS - the Integrated Rule-Oriented Data System. [Link]
jchempaint JChemPaint, an editor and viewer for 2D chemical structures [Link]
jobstats CPU and memory monitoring tool
julia Julia Programming Language
kkrasa KKRASA (GREENS) is a Green's function method software package [Link]
lammps LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. [Link]
llvm+clang LLVM compiler infrastructure with C language frontend
macmolplt wxMacMolPlt [Link]
mathematica Mathematica [Link]
matlab Matlab [Link]
mc text-based file manager
mpc GNU library for complex numbers
mpfr GNU multiple-precision floating-point library
mpprun NSC mpprun wrapper
mrbayes Bayesian inference of phylogeny
namd NAMD
ncl NCAR Command Language (NCL) is an interpreted language designed for scientific data analysis and visualization.
nco NetCDF Operator (NCO) is set of binary operators designed to manipulate data stored in netCDF format.
ncview ncview netCDF visual browser homepage.
netcdf NetCDF is a set of software libraries that support the creation, access, and sharing of array-oriented scientific data.
nmag Nmag [Link]
nmrpipe process, analyze, and exploit NMR spectroscopic data
nwchem NWChem -- High-Performance Computational Chemistry Software [Link]
octopus Octopus TDDFT electronic structure software [Link]
openmx OpenMX -- a DFT-based code with atomic localized basis functions.
orca ORCA, a modern electronic structure program package [Link]
p4vasp P4VASP -- visualization suite for VASP http://www.p4vasp.at/
papi PAPI tool for accessing the hardware performance counters.[PAPI]
paraview ParaView data analysis and visualization application homepage.
pdt PDT (Program Database Toolkit) is a framework for analyzing source code written in several programming languages.[PDT]
phenix software suite for automated macromolecular structure determination
phonopy Calculates phonons with the supercell method
povray POV-Ray -- The Persistence of Vision Raytracer [Link]
pyrosetta python interface to Rosetta protein structure suite
python NSC-provided custom Python builds
raxml Randomized Axelerated Maximum Likelihood
rosetta protein structure prediction suite
schrodinger Schrödinger suite of software [Link]
siesta SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids [Link].
sparsehash Sparsehash hash_map library.
spglib library for finding and handling crystal symmetries
star-ccm+ Star-CCM+ is a commercial CFD solver distributed by CD-adapco. [Link]
szip szip is a set of software libraries for lossless compression of scientific data.
tau TAU is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C++, C, Java and Python.[TAU]
totalview TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. [Link].
vasp Vienna ab initio simulation package [Link]
vasp-vtst VASP + VTST patches (for NEB)
vasptools A collection of useful VASP scripts
vesta VESTA [Link]
visit VisIt is a interactive parallel visualization and graphical analysis tool for viewing scientific data.
vmd VMD -- Visual Molecular Dynamics [Link]
wannier90 Calculates maximally-localized Wannier functions.
wien2k WIEN2k is a FPLAPW software package [Link]
xcrysden XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It can run on most UNIX platforms, without any special hardware requirements. [Link].
xds process rotation method chrystallographic data
yambo Yambo is a code for many-body calculations in solid state and molecular physics [Link]
zlib zlib is a set of software libraries for general-purpose, lossless data-compression.

How it works

Software installed by NSC staff for general usage is found in /software/apps/ and its subdirectories. We use an hierarchical scheme like this:

/software/apps/[program name]/[version]/[installation name]/

It means, for example, that the binary distribution of Gaussian 09 Rev. C01 is installed in:

/software/apps/gaussian/G09RevC.01/bdist/

In order to provide some minimal documentation, each directory contains a “README.NSC” file with important information about this particular installation and how to run the program. So for the above version of Gaussian, you have three relevant files to read for a quick start:

/software/apps/gaussian/README.NSC
/software/apps/gaussian/G09RevC.01/README.NSC
/software/apps/gaussian/G09RevC.01/bdist/README.NSC

The first one contains information about Gaussian in general, the second one contains information about G09 Rev. C01 version, and the third one contains notes about that particular installation/compilation.

There is a also a web version based of the content of these files, with much prettier formatting. You may look at it here:

http://www.nsc.liu.se/systems/triolith/software/

Software support tiers

Each software installation is categorized into one of three software support tiers, depending on the level of help we can provide for that particular program.

Tier 1

A program gets placed into tier 1 if NSC has at least one application expert on staff with deep knowledge about it, and we will try to help you with any problems. We have also done some internal tests to make sure that the program is working as intended. NSC also commits to installing updates as they become available.

The current list of tier 1 software at NSC is:

  • CESM
  • EC-Earth 3
  • Gaussian
  • NCL
  • Tau
  • VASP
  • Wien2K

Tier 2

The tier 2 is used when NSC has only limited experience with the software, but we will try to help as much as possible. For example, if the program comes with a test suite, we will run it, and attempt to evaluate the results. We will try to install and test new versions, as soon as we can.

List of tier 2 software:

  • Abinit
  • Allinea-DDT
  • Amber
  • Beagle
  • CDO
  • CP2K
  • Elk
  • Exciting
  • GAMESS
  • GPAW
  • grib-api
  • Mathematica
  • MrBayes
  • NAMD
  • NCAR diagnostics package
  • NCO
  • netcdf
  • NWCHEM
  • Rosetta
  • Schrödinger
  • Quantum Espresso

Tier 3

Tier 3 is used for test installations or custom software we helped install by request of a users. In general, we will not be able to help you much with such programs. Note that these types of installations can be completely untested, and will not be updated unless you send a request to NSC.

Disclaimer

NSC takes no responsibility for the correctness of results produced with the binaries! Hence, always evaluate the binaries against known results for the systems and properties you are investigating before using the binaries for production jobs.

About default versions

There are no “default” versions of software anymore on Triolith. Instead we will only recommend a certain version, and it will be up to the user to decide. So module add intel will now display a message stating what the recommended version is:

$ module load intel

************** NO MODULE LOADED *************
**** Please also specify desired version ****

The currently recommended version of the Intel compilers is:
intel/12.1.4

If you previously have been using a 12.x version, upgrading to 12.1.4
is recommended, and low risk.

If you have been using an earlier Intel version (e.g 10.x or 11.x),
upgrading is still recommended, but you might want to use more
caution.

If you have any questions regarding this version recommendation,
please contact support@nsc.liu.se.

The recommended versions represent our best effort to produce installations that are as fast and correct as possible. In general, we take a conservative approach, i.e. we do not recommend a new version of a program unless it has been tested in some way. Please note that old versions are never changed or removed unless there are very strong reasons to do so (e.g. severe security issues, or if discovered to always produce erroneous results). In order to prevent you from running very old or broken versions, we might add a warning to the module urging you to stop using it.