GPC OS upgrade – what you need to know

October 17, 2011 in for_users

The operating system of the General Purpose Clusters will be updated from CentOS 5.6 to CentOS 6.0 in a few weeks. Note that the ARC already uses the newer OS. This upgrade includes updates to other programs/modules, and will mean that you will have to recompile your code.

To prepare for this transition, ten (ethernet) nodes are currently reserved for test purposes already, and have the most common modules already installed. We encourage all users to try and compile their code there and to submit short test runs to the centos6 compute nodes.

Here’s how you can access the centos 6 nodes:

  • Log in to one of the centos6 development nodes, gpc05 and gpc06.
  • Make sure the right modules are loaded, as they likely will have changed in the upgrade.
  • Recompile your code (don’t forget a “make clean” or equivalent).
  • Submit test jobs to the centos6 compute nodes using an extra flag “os=centos6computeA” in the “-l” argument, i.e. “-l nodes=2:ppn=8,walltime=1:00:00,os=centos6computeA”

To make your .bashrc work for both versions of CentOS, check out the example .bashrc on the wiki page on how to distiguish the two OSes.

Note that most modules that were available under the CentOS 5 are available with CentOS 6, but often their version number has changed. Use “module avail” on the centos6 compute nodes to see what module are available, or check the Software & Libraries wiki page .

Let us know if there is anything that is not working as it should, or if there are modules that you need which are missing.