SciNet News April 2011

April 5, 2011 in for_researchers, for_users, newsletter


  • Wed Apr 13, 12:00 noon: SNUG (SCINET USERS GROUP) MEETING

    • TechTalk by Peter Colberg (Chemical Physics Theory Group)

      “Scripting HALMD with Lua and Luabind”

      Lua is a lightweight, embeddable scripting language. Luabind is a library that exposes C++ classes and functions to Lua. HALMD, a highly accelerated large-scale molecular dynamics packqage for GPUs, uses Lua and Luabind to couple a set of high-performance C++ and CUDA modules in a flexible and extensible manner.

    • User discussion
    • Pizza!

    Sign up if you are planning to come, at


    Fortran, as the only major programming language designed explicitly for scientific programming, has come a long way since it’s 1977 version which was sensitive to spacing layout, used computed gotos and with only arrays whose sizes could only be changed by recompiling.

    This is a full-day course which will will demonstrate the use of modules to break code into type-safe pieces; optional arguments and the use of interface; portable ways of using different sizes of integers and reals; an introduction to object-oriented programming in Fortran 2003.; and a preview of co-arrays for parallel programming in Fortran 2008.

    Prerequisite is a significant experience in scientific programming with FORTRAN. If you are unsure about the prerequisites, contact us at

    Sign up at

  • Wed May 4, 12:00: SNUG (the first Wednesday on the month this time!)

    Sign up if you are planning to come, at


    The goal of the workshop is to enable young researchers already experienced in scientific computing to leave with the knowledge necessary to begin writing the parallel codes needed for their research. The workshop will be a mix of lectures and immediate feedback on practical assignments, designed to ensure that students leave with significant experience in both OpenMP and MPI, two of the standards for parallel computing today. We aim for this workshop to be useful for graduate students and postdocs for a wide range of disciplines.

    The course will be given in a yet-to-be determined location on the St. George Campus.

    There will be NO FEE, but you are responsible to get the recommended BOOKS, and your own COFFEE and LUNCH.

    There is LIMITED AVAILABILITY, so please only register if you are serious about attending. Registration and further details (topics, books, location) are (or will be) available at

  • Wed Jun 8, 12:00: SNUG

    Sign up if you are planning to come, at


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

  • Links to the videos of the presentations given at the Science Illustrated symposium.
  • Slides of the two March SNUG TechTalks by Abdul Mroue and Jaochim Harnois-Déraps.
  • An explanation of the change of the temporary location of the standard error/output file for GPC jobs; see the FAQ on the wiki.
  • Updated techniques to installed user-space Perl modules.
  • Slides, videos and sample code of the 1-day course on Scientific C++.
  • Instructions on how to install optional R packages from CRAN, including Rmpi.


  • TCS: The bug in the showstart command was fixed, and showstart may be used again to estimate the start time of your job.
  • GPC: Issues regarding simultaneously loading the gcc/4.4.0 and the Intel compiler modules were resolved.
  • GPC: A newer version of the gcc compiler suite, v4.6.0, has been installed. The default version is still 4.4.0, and in any case, we recommend using the Intel compilers for optimal performance. You should consider 4.6.0 as somewhat experimental for now, especially gfortran, as many other modules still depend require 4.4.0 for now. Let us know if you experience any unexpected difficulties with it.
  • GPC: Octave version 3.2.4 has been installed on the GPC. You should for now consider this an experimental module. Let us know about your experience with it!


  • A SNUG meeting was held on Mar 9, with TechTalks by Abdul Mroue and Joachim Harnois-Deraps.
  • On Mar 15, a 1-day course “Introduction to scientific C++” was given.
  • There was unexpected downtime on March 23. A VSD controller failed in the cooling system at 11:30AM which resulted in an emergency shutdown of all SciNet systems. A temporary solution has allowed us to bring systems back online. There will likely need to be downtime in the near future in order to replace the controller.