Software documentation for Bi


Directory list:

VersionDescription
apps installation directory for scientific software and libraries
devel-tools Different compilers, math libraries, mpi etc

Software included in the operating system

Bi runs the CentOS 6 operating system (a rebuild of Red Hat Enterprise Linux 6). This means that a lot of common (and some not so common) programs and libraries are available on the login node and the compute nodes. We also install packages from EPEL 6, a set of Fedora Linux packages rebuilt as additional packages on top of CentOS/RHEL 6.

This means that basic utilities and programs like ls, top, wget, vim, emacs, git, etc. are available, installed in their normal system locations (for example /usr/bin).

If you need something that is packaged as part of CentOS 6 or EPEL 6 you can ask us to install it on the login node and/or the compute nodes. You can list both installed and available packages using yum list.

Note: to access the system gcc, g++ and gfortran compilers, you have to load a special module (see the output you get when you try to run gcc). This is done to remind you to actively choose between the system GCC, future separate installations of newer GCC versions, and the Intel compilers.

Software installed by NSC

For some software, packages may be missing in CentOS/EPEL. It may also be the case that we need a newer version, several versions at the same time, differently configured builds, etc. In that case, we install it ourselves from source code (or binary vendor archives for proprietary software).

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 first Python 2.7.9 installation built for SMHI needs is installed in:

/software/apps/python/2.7.9/smhi-1/

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 Python, you have three relevant files to read for a quick start:

/software/apps/python/README.NSC
/software/apps/python/2.7.9/README.NSC
/software/apps/python/2.7.9/smhi-1/README.NSC

The first one contains information about Python in general, the second one contains information about Python 2.7.9, and the third one contains notes about the specific smhi-1 installation.

There is a also a web version based of the content of these files, with much prettier formatting for be found at http://www.nsc.liu.se/systems/bi/software/ - if you read this in the web browser, you are already there!

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 Bi. Instead we will sometimes 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 ********
*** i.e. use the full name with version number ***

The currently recommended version of the Intel compilers is:
intel/15.0.1.133

If you have any questions regarding this version recommendation,
please contact smhi-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.