Transition to CentOS 6

GPC OS switch

The default operating system of the GPC has been upgraded from CentOS 5 to CentOS 6. The switch occured on Monday December 5th 2011 at noon. It is possible to specifically request the old OS for at least 2 weeks after the switchover (see below) but only a small subset of such nodes will be available.

This upgrade includes updates to other programs/modules, and will mean that you will have to recompile your code, if you have not done so already.

Transition

• The development nodes gpc01-4 are running CentOS 6
• The development nodes gpc05-6 are running CentOS 5
• 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 jobs without any "os=" flag; the CentOS 6 operating system is now the default.
• Submit jobs to the centos53 compute nodes using an extra flag "os=centos53computeA" in the "-l" argument, i.e.

 -l nodes=2:ppn=8,walltime=1:00:00,os=centos53computeA

To make your .bashrc work for both versions of CentOS during the transition, check out the example .bashrc on the wiki page http://wiki.scinet.utoronto.ca/wiki/index.php/Important_.bashrc_guidelines on how to distiguish the two OSes.

Modules

Note that most modules that were available under the CentOS 5 are available with CentOS 6, but often their version numbers have changed. Use "module avail" or "/scinet/gpc/bin6/modulefind" on the centos6 devel nodes to see what module are available, or check the wiki page http://wiki.scinet.utoronto.ca/wiki/index.php/Software_and_Libraries. 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.

Known issues

Modules not found

If modules that you used to load on CentOS 5 no longer load on CentOS 6, it is likely because you are loading the modules with their full name, including the version number. Since all software modules had to be rebuilt for centOS 6, we took the opportunity to upgrade them, so version numbers will have changed.

You can see what modules are installed with module avail [start-of-a-modulename] or modulefind [part-of-a-modulename].

Note that this does not affect you if you loaded the modules by their short name, i.e., module load gcc.

Module command failing --- resolved

There is an issue with the module command which causes it to fail if to many modules are loaded in one line. The module command has been upgraded and this should no longer be an issue.

A workaround was to split a single long module load line in your .bashrc file into multiple commands.

ie replace

   module load openmpi gcc extras python gnuplot

with

   module load openmpi gcc
   module load extras python
   module load gnuplot

The newest version of the module command has been installed and should not see these issues anymore, but let us know if you experience other difficulties.

External packages Python 2.7.1 -- resolved, use 2.7.2

Some external packages (matplotlib, cython) for the current default python (2.7.1) did not survive the transition to CentOS 6. A new python has been built, 2.7.2, which is now the default.

Screen command missing -- resolved

In the new OS setup, the 'screen' command is placed in the module 'extras'.

 module load extras

will make it available to you again.

CentOS 5 Phase-out

Only 84 ethernet and 32 infiniband CentOS 5 nodes are still available, and will be phased out by mid-January at the latest.