Software Stack Changes during Carter Maintenance

July 8, 2013
Coates, Hansen, Rossmann

Between July 8 and July 16, Carter will be unavailable due to scheduled maintenance. On July 8, there will be changes made to the software stack on most of ITaP's community clusters. Changes will include updates to the default version of the Intel compiler and associated software stack as well to the default OpenMPI library. Some older versions of other software will also be removed.

WHAT WILL BE THE IMPACT TO OPENMPI?

We will be upgrading the default version of OpenMPI from 1.4.4 to 1.6.3. This new versions offers stability and performance enhancements and some new features. Version 1.6.3 has been available since the beginning of the year and many researchers have already moved to 1.6.3. This version has proved to be the most stable and best performing OpenMPI version available on ITaP clusters.

This change only impacts those that invoke OpenMPI with "module load openmpi" or by the "devel" module. If your submission scripts explicitly ask for 1.4.4, you will not be impacted by this change. The default version for the following libraries will be updated.

  • openmpi
  • devel
  • fftw It is recommended that you upgrade to 1.6.3, however if you need to keep using 1.4.4 you may do so by switching to "openmpi/1.4.4" instead of "openmpi."

WHAT WILL BE THE IMPACT TO INTEL COMPILERS?

In support of the new Conte cluster, scheduled for later this year, the default Intel compiler will be upgraded from Intel 12 to Intel 13.1. This new version will be 13.1.1.163. On Coates, Rossmann, and Hansen the default version will be upgraded from 12.1 to 13.1.1.163. On Carter, Radon, and Peregrine1 it will be upgraded from 12.0.084 to 13.1.1.163. Steele will not be upgraded due to proximity to its end of life.

These upgrades will provide the best performance for the new and existing clusters and will provide a consistent Intel version stack across all of our clusters. This version and associated software stack is currently available on the clusters for testing and upgrade. ITaP research computing staff recommends testing out the new compilers and upgrading prior to July 8.

This change only impacts those that invoke the Intel compilers with "module load intel" or other libraries that default to Intel versions when loading without a specific version. If you load Intel compilers or other libraries with a specific version this will not impact you. The following libraries will be impacted.

Coates, Rossmann, Hansen:

  • intel
  • devel Carter, Pegrine1, Radon:- intel
  • devel
  • fftw
  • mvapich2 (Carter, Peregrine1 only)
  • mpich2 (Radon only)
  • netcdf
  • hdf5

It is recommended that you upgrade to these new libraries, however, if you need to continue using the old default versions you may do so by switching your "module load" to the specific version. The Intel 12 stack will remain available for those who require it. These new compilers offer bug fixes and enhanced performance and stability. Users are encouraged to send in any experiences with these new compilers to help us evaluate the direction of new compilers on RCAC systems.

WHAT OTHER SOFTWARE WILL BE IMPACTED?

There will be several changes to other miscellaneous software. Older versions of some software will be removed in favor of newer versions. Default versions of a few software will be updated to the latest version. In most cases, these older versions are being infrequently used so most should not be impacted by these changes.

If any software you are using will be impacted by these changes you will see a notice message being printed to your session or in your job output files when loading an affected module. This notice will provide recommendations on the latest version. For software versions being removed it is recommended that you switch to the latest version, however, these older versions will remain available for use via the "unsupported" module archive.

For software versions undergoing a default upgrade you can continue using the old default by switching your "module load" to explicitly load the version. Most of these changes only impact Steele, Coates, Rossmann, and Hansen as the Carter, Peregrine1, and Radon stack is more up to date. The following software will see a default version update.

  • comsol
  • gamess
  • gromacs
  • impi
  • ncl
  • octave
  • openfoam
  • r

Some software (but not all) that will have older versions removed include the following.

  • cmake
  • eclipse
  • gnuplot
  • ncl
  • r

    HOW DO I KNOW IF MY WORKFLOW WILL BE IMPACTED?

    Whenever a module that will be impacted is loaded a notice is printed to your screen or job output log. Please take a look at your job output over the couple of weeks and make note of any changes being advertised. You may continue using these modules as-is until July 8th to allow time to make any changes necessary. Users are encouraged to make any changes necessary to avoid disruption when changes are made.

    WHAT IF AN IMPACTED MODULE IS REQUIRED BY MY RESEARCH?

    We understand some users may not be able to change compilers or MPI libraries in the middle of a research project. Modules involved in a default version update will continue to be available, however, you will need to update your job scripts to request the specific version of the module. If you are already loading specific versions no changes are necessary.

    Older versions of software being removed will continue to be available in the "unsupported" module archive. You may use the archive by adding "module load unsupported" to your job scripts (prior to loading the affected modules).

    WHY ARE YOU CHANGING THE SOFTWARE STACK?

    ITaP aims to provide a software stack that allows for optimal use (performance and stability) of the clusters. This necessitates periodic updates to the stack as compilers, libraries, and software are improved over time. By removing older modules from the main stack we help ensure the selection is simple and easy for users to find the best compilers and libraries to use. If no modules were removed the selection would become difficult to navigate as well become difficult for ITaP staff to manage. Any major changes will be coordinated with scheduled maintenance periods to minimize impact.

If you have any questions or concerns with the upcoming changes please contact rcac-help@purdue.edu

Originally posted: June 10, 2013