SciNet News December 2010

December 4, 2010 in for_users, newsletter


(All events take place at the SciNet Headquarters at 256 McCaul St., Rm 235)

  • Dec 8, 2010, 12:00 noon: SNUG (SciNet Users Group) meeting

    • 1/2 hour TechTalk “Performance & profiling”
    • User discussion
    • Pizza!

    Free registration at

  • Dec 8, 2010, 3:10 pm: Talk “Fault Tolerant Scientific Computing with Erlang” Qiyu Zhu and Colin Morris, undergraduates at UoT’s Computer Science department, will speak about work implementing the Cowichan Problems, a set of model problems similar to numerical HPC “kernels”, in Erlang. Erlang is a language designed to support distributed, fault-tolerant, soft-real-time, non-stop applications. Discussion of their work can be found at
  • New SciNet classes for next term (winter/spring 2011) have been planned.

    Jan 18 Intro to SciNet (90 minutes) Jan 20 Intro to Parallel Programming (1 day) Feb 22,23 Science Illustrated (2 day visualization workshop) Mar 15 Introduction to Scientific Programming with C++ (1 day) Apr 19 Introduction to Scientific Programming with modern FORTRAN (1 day) May 9-13 5-day Parallel Programming course: OpenMP, MPI and more will be covered. The aim is for you to leave the course able to start parallelizing your code. There will likely be a fee for this one. See for details and registration.

  • Further SNUG meetings will be held on Jan 12, Feb 9, Mar 9, Apr 13.


  • Tips on running serial jobs more easily using GNU parallel.
  • How to set up a local perl module library in your home folder.
  • How to use job arrays, a way to submit similar jobs.
  • Pdf of the slides of the last TechTalk on debuggers.
  • Updated module information, including which modules were recently renamed or added (see below).


  • File system:

    Starting already this December, the scratch purging policy will be implemented a bit more strictly. Files that are not accessed for more than 3 months by the actual deletion day on the 15th of the month will be scheduled for purging. This constitutes a change only because our previous 2 weeks grace period was in addition to those 3 months, effectively keeping old files around for about 105 days. The regular notices on the 1st and the 12th of the month will still be sent. Scratch is getting heavily used these days so this half month’s worth of space is really needed, especially given the upcoming Holiday break.

    A thank-you goes out to all the users that already cleaned up a good deal of their scratch disk space upon our request!

  • GPC: A module for R was installed.
  • GPC: padb was installed as a module.
  • GPC: GNU parallel was installed as module ‘gnu-parallel’.
  • TCS: CDO (Climate Data Operators) was installed as module ‘cdo/1.4.6’
  • TCS: compilers xlf 13.1 and xlc 11.1 are available as modules as modules xlf/13.1 and vacpp/11.1, respectively.


  • A SNUG meeting with TechTalk on Debuggers was held on Nov 10.