Basic software documentation at NSC


Directory list:

VersionDescription
apps installation directory for scientific software and libraries
intel Intel's compilers, math libraries, and tools
mpi MPI packages, excluding Intel MPI

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
  • Schr√∂dinger
  • 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.