SciNet News April 2015

April 9, 2015 in for_researchers, for_users, newsletter

First of all, we want to take this opportunity to thank all of you who cleaned up their scratch directories last week when /scratch it was 99% full. You saved the file system!

Below you will find the salient points of what else happened or changed recently and what will happen in the near future. Among these is the announcement of the Ontario High Performance Computing Summerschool, which has three installments, one of which is to be held in Toronto in July. As always, details on SciNet events are available on the wiki and the SciNet education website.



Unless stated otherwise, all events take place at the SciNet Conference Room on the second floor of 256 McCaul Street, Toronto. All events at SciNet are free for users but we ask that you enroll on the education website:

    Wednesday April 8, 10:30 am – 11:30 am

    The “Intro to SciNet” is a class of approximately 90 minutes where you will learn how to use the systems. Experienced users may still pick up some valuable pointers during these sessions.

    Participation counts towards the SciNet HPC Certificate.

    For more information and enrollment, go to

    More intro sessions to be held in the near future: May 13, 10:30 am – 11:30 am:

    Jun 10, 10:30 am – 11:30 am:

    Wednesday April 8, 12:00 noon – 1:00 pm

    The SciNet Users Group (SNUG) meetings are every month on the second Wednesday, and involve pizza, user discussion, feedback, and a half-hour talk on topics or technologies of interest to the SciNet community.

    TechTalk: “Smoothed Particle Hydrodynamics” by Marcelo Ponce (SciNet)

    In this talk I’m planning to review the main concepts used in “Smoothed Particle Hydrodynamics”, a technique widely used for simulating fluid dynamics. In particular I will focus in the basic concepts and their applications to astrophysical simulations, such as, the effects on accretion disks surrounding a gravitational recoiled black hole, and “mergerburst” events where the interaction between stars may trigger luminosity outburst (suhc as the outburst of V838 Monocerotis observed some years ago).

    For more information and enrollment, go to

    Future SNUGs: May 13, 2015, 12:00 noon – 1:00 pm, TechTalk TBD
    Jun 10, 2015, 12:00 noon – 1:00 pm, TechTalk TBD

    Tuesday April 14, 9:00 am – 5:00 pm

    The goal of this course is for incoming students, new to GPGPU but familiar with scientific programming in C or C++, to leave being able to start writing simple kernels for their own problems, and understand the tools, techniques and libraries that will be needed to improve and optimize the results.

    Participation counts towards the SciNet HPC Certificate.

    For more information (soon) and enrollment, go to

    Wednesday May 6, 9:30 – 5:00 pm

    As a form to manage data, relational databases are widely used in the back-end of many websites as well as for data mining computations. In this course, we will look at the basics of relational databases: What are they, and what are they useful for? We will also consider why they are not all that much used in the context of scientific computing, using SQLite and Python.

    Participation counts towards the SciNet Scientific Computing Certificate.

    For more information (soon) and enrollment, go to

    Tuesday May 19 and Wednesday May 20, 9:30 am – 4:30 pm

    On May 19 and 20, 2015, Intel is giving a two-day workshop in Toronto for software developers on the foundation needed for modernizing their code to take advantage of parallel architectures found in both the Intel Xeon processor and the Intel Xeon Phi co-processor.

    Note that a substantial difference with the one-day workshop on the same topic given in Toronto on October 27, 2014, is the second day, which consists of a hands-on lab in which you get to use the material and techniques presented in the first day.

    This is an external event organized by Intel. For more information and registration please go to

    Day 1:

    Day 2:

    Thursday May 21 Conestoga College Institute of Technology and Advanced Learning Cambridge, Ontario

    A day filled with high performance computing related research done in Ontario. Have an interesting research story for which you used high performance computing (such as the facilities at SharcNet, SciNet, and HPCVL)? Want to share you experience with other Ontario HPC users? Consider giving a talk at the meeting.

    More details and registration at


    The Compute Ontario Summer School on High Performance Computing provides attendees with opportunities to learn and share knowledge and experience in high performance and technical computing.

    As in previous years, the Summer School on High Performance Computing 2015 will have three installments:

    “West” May 25 – 29 Western U. (London) “Central” July 13 – 17 U. Toronto (Toronto) “East” July 27 – 31 Queen’s U. (Kingston)

    The format will be a five day workshop with mixed lectures and hands-on sessions on a number of selected subjects such as MPI, CUDA, OpenMP, Python, and Visualization (the subjects will vary slightly depending on the location). These sessions will be organized in two parallel streams.

    Parts of this event may count towards the SciNet HPC Certificate.

    More details regarding the summer school program, location, and registration (for either of the three installments), will become available at

    Montreal, June 15-19

    Registration is now open for the 29th annual HPCS conference (Canada’s foremost supercomputing conference). This conference will take place in Montreal, June 15-19, the first two days of which are tutorials on advanced research computing and high performance computing. This year’s theme is `Advanced Computing and Big Data – Driving Competitiveness and Discovery’.

    More information and registration can be found at

    Sunday June 21 – Friday June 26 Toronto, Canada

    The application deadline for this event has passed. For more information see



Note that most software changes for the GPC also hold for ARC, Sandy and Gravity.

  • BGQ: software stack upgraded to version V1R2M2.
  • BGQ: module hdf5/1812-v18-mpich2-gcc is deprecated; please use hdf5/1814-v18-mpich2-gcc instead.
  • BGQ: module fftw/3.3.3-gcc4.8.1 is deprecated; please use fftw/3.3.4-gcc4.8.1 instead.
  • GPC: Allinea Forge (DDT & MAP) available as module ddt/5.0.This includes Allinea Performance Reports.
  • GPC: OpenBLAS 0.2.13 installed as modules.
  • GPC and BGQ: Namd 2.10 installed as modules.
  • GPC: Gromacs 4.6.7 installed as a module.
  • GPC: Gromacs 5.0.4 installed as an experimental module (“module load use.experimental gromacs/5.0.4”).
  • GPC: Stacks/1.29 installed as a module.


The SciNet Wiki contains technical information on how to use the systems and can be found at The SciNet Education and Training site can be found at and contains the material of SciNet’s training and education activities.

  • Wiki: Documentation of SciNet command line utilities to help with storage management, jobs and queues, and modules.
  • Wiki: PDF of the January SNUG Techtalk about “Data Management and Transfer Tools at SciNet”
  • Education: pdfs and recordings of the lectures of the “Scientific Computing” mini-courses.
  • Education: pdf of the TechTalk on “Job and Queue Management at SciNet”.