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 (that we're working on)

Module command failing

There is an issue with the module command which causes it to fail if to many modules are loaded in one line. As a temporary workaround, split your single 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.

Largemem jobs

To submit a job to the largemem nodes, for now, you still have to request the centos6 image explicitly, e.g.

 qsub -l nodes=1:ppn=8,walltime=6:00:00,os=centos6computeA -q largemem  -I

External packages Python 2.7.1

Some external packages (matplotlib, cython) for the current default python (2.7.1) did not survive the transition to CentOS 6. If you have problems with packages in the default python, there is a new python module, 2.7.2, which currently has to be selected explicitly (module load python/2.7.2) which you can try. This will probably become the default shortly.

Screen command missing

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.