SciNet News July 2012

July 5, 2012 in for_researchers, for_users, newsletter


Mon July 9, 12:00 noon – 1:30 pm: INTRO TO SCINET

Learn what SciNet resources are available, how to compile your code and how to use the batch system, in approximately 90 minutes.

Intended for new users, but experienced users may still pick up some valuable pointers.

Sign up at

Mon July 9, 12:00 noon – 2:00 pm: SOSCIP INFORMATION SESSION FOR PI’S

SOSCIP, the Southern Ontario Smart Computing and Innovation Platform, is a consortium of UoT and six other Ontario Universities collaborating with IBM, and is the organization behind the new Blue Gene/Q system that SciNet will host in the near future.

This information session is open to any PI at the University of Toronto and its affiliated hospitals. PIs can learn more about the consortium and how to apply for access to the platform’s resources.

This event will not take place at the SciNet Headquarters, but at the Bahen Centre for Information Technology, Room 1210.

Fri Jul 27: 1:00 am – 6:00 am: CONNECTION OUTAGE TO DATA CENTRE

At some time within this maintenance window, there will be a 30 minute outage for connecting to the data centre. Login sessions will be broken, but jobs will continue to run as usual.

Wed Sep 12, 12:00 noon – 1:00 pm: SEPTEMBER SNUG MEETING

The SciNet Users Group (SNUG) meetings are every month on the second Wednesday, and involve pizza, user discussion, feedback, and one or two short talks on topics or technologies of interest to the
SciNet community.

TechTalk: TBA
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Oct 10, Nov 14, Dec 12, 12:00 noon – 1:00 pm: FUTURE SNUG MEETINGS

TechTalks: TBA (want to present? email
Sign up at (Oct) (Nov) (Dec)


  • GPC: The InfiniBand upgrade done in the spring has landed the GPC in the number 66 spot on the June 2012 TOP500 list (see It would have been at number 105 without the upgrade. This is currently the highest ranked of the ten Canadian systems on the list.
  • GPC: A versions of the Intel compilers are available as intel/12.1.5. Version 12.1.3 is still the default.
  • Scratch purging: the allowed time is still three months, but now files that were modified in the last three months will not get purged, even if they were never read in that period.
  • ARC: cuda/4.1 is now the default CUDA module. The module cuda/4.2 is available as well, and will work with the newer gcc 4.6.1 compiler.
  • ARC: Portland Group compilers are installed as the module pgi/12.5. This is one of the perks of being an “NVIDIA CUDA Research Center”. These PGI compilers have support for GPGPU programming through Fortran CUDA and OpenACC, in addition, of course, to the traditional support for C, C++, Fortran, OpenMP and MPI.   For more info, see the wiki page for the GPU nodes of the ARC.
  •  ARC: The scheduler has been integrated into the GPC scheduler. This will allow a fairer way of sharing the utilization of this resource. To submit jobs, you should now use “qsub -q arc” instead of just “qsub”. To check the arc queue, use “showq -w class=arc”. Commands like checkjob and showstart work as well.


All new wiki content below is listed and linked on the main page:

  • Updated ARC page with basic information on using the PGI compilers and the new queue structure.
  • Links to the PGI Compiler documentation, including User Guide and Reference Manual, on the Manual and Tutorial page.
  • Ontario Summerschool on High Performance Computing Central: slides and code. (Linux shell, HPC Intro, OpenMP, MPI, CUDA, Debugging, Best Practices).
  • Slides of the June TechTalk “Remote Development on SciNet”


  • Thu Jun 7: Scheduled shutdown of all SciNet systems
  • Wed Jun 13: June SNUG meeting with TechTalk on “Remote development on SciNet systems”.
  •  Jun 25 and 26: Two separate power glitches took down the data centre. In both cases, systems were brought back up on the same day.
  • Jun 25-28: Ontario Summerschool on High Performance Computing / Central.