Operating System Extension Stacks

This document describes how to configure and use software extensions on LRZ's HPC systems. These are based on public repositories that for various reasons cannot be directly installed on the systems themselves. They are provided as a convenience and have only limited support by LRZ.

Rationale

A lot of additional software packages are available for the SuSE Enterprise Server operating environment deployed on LRZ's HPC systems. Due to limited disk space or - in the case of compute nodes on some of these systems - diskless installations, such packages cannot be provided with the system installation. Also, many of these packages conflict with the LRZ-provided environment. Therefore, a set of software extensions has been separately installed that avoids the need for user-specific installations in at least some cases.

Availability

The software extension stack is available as a special set of environment modules on the LRZ HPC systems. The following table shows which extensions may be used.

Extension name Description Remarks
devel Development packages For use of system include files on diskless compute nodes
mysql MySQL packages

science Packages from Scientific Linux

The parallel programs make use of MVAPICH and GCC 4.3
X11 X11 libraries and baseline applications For use on diskless compute nodes.

The command

module load os_extension/<Extension name>

sets appropriate environment variables for each extension. The usual "module show" and "module help" commands indicate the performed environment settings and provide further guidance.

Risks

  1. The extension modules are considered experimental. Therefore, LRZ reserves the right to make changes to the provided extensions as well as the modules that do the extension setup at any time.
  2. Only limited support by LRZ is available. Some packages may not work at all, because non-relocatable packages have been installed in a non-system directory. LRZ support staff is likely to deny service requests if problems that cannot be trivially resolved arise with the provided packages.
  3. For packages that contain SUID root binaries, such binaries will not work.
  4. There may be destructive interactions with other packages from the LRZ module system. Conversely, some other modules may be needed to enable use of a specific software package. Therefore, care is needed to properly set up the environment.
  5. Software packages from the extension are likely to run at significantly reduced performance compared to installations optimized for the target architecture. This specifically applies for MPI programs.

Further information on specific extensions

science

  • Some software packages in this extension use GCC-based MVAPICH for MPI parallelization. The LoadLeveler or SLURM job scripts need to be configured as if an Intel MPI program should be run.  
  • Some software packages need to load the fftw module to run ("module load fftw")

X11

  • Xvfb: Using Xvfb, you will be able to start a XSession without a physical display. To create a virtual DISPLAY at :99, do
module load os_extension/X11
Xvfb :99 -ac -screen 0 1024x768x24 -fp $X11_FONT -kb -extension GLX  2>&1 &
export DISPLAY=:99
... # - run your application that requires x11 -
killall Xvfb
  • vncserver: This can be used to start a Tightvnc X server on a compute node for pseudo-interactive work. You need to connect to that X server using the vncviewer on the login node. Simple window managers like fvwm2 are available, but configuration is very rudimentary.