|apps||installation directory for scientific software and libraries|
|devel-tools||Different compilers, math libraries, mpi etc|
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
git, etc. are available, installed in their normal
system locations (for example
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
Note: to access the system
gfortran compilers, you
have to load a special module (see the output you get when you try to
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.
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:
In order to provide some minimal documentation, each directory
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
/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
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!
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/22.214.171.124 If you have any questions regarding this version recommendation, please contact email@example.com.
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.