SciNet News January 2014

January 15, 2014 in for_researchers, for_users, newsletter, Uncategorized

To keep users posted on what’s going on at SciNet, we send monthly emails with the new features, planned courses and events and accomplishments at SciNet.

Taking of accomplishments, we are compiling user success stories and testimonials (http://www.scinethpc.ca/testimonials). If you want to share your SciNet-powered success stories, please let us know by emailing to support@scinet.utoronto.ca.

Below you will find the salient points of what has happened or changed during the last month and what will happen in the near future. Among these is the start of the term-long graduate course in Scientific Computing, which can be taken for credit by physics, astrophysics and chemistry graduate students.

As always, details are available on the wiki or the SciNet education website.

Happy new year!

– The SciNet team

Events Coming Up

Unless stated otherwise, all events take place at the SciNet Headquarters, Rm 235 of 256 McCaul Street, Toronto. All events below are free for users but we ask that you sign up (“enroll”) on the education website.

  • January 15, 7:00 am – January 16, 6:00 pmSCHEDULED MAINTENANCE DOWNTIME

    Systems will be taken down around 7 am on Wednesday Jan 15, andare expected to be back up by 6 pm on Thursday Jan 16. Check the wiki for updates.

  • January 18SCRATCH PURGING

    Because of the maintenance downtime we will postpone the scratch
    purging from the 15th of January to the 18th of January.

  • Jan-Mar, Tuesdays, almost bi-weekly, 2:30 pm – 3:30 pmCOAST-TO-COAST SEMINAR SERIES

    The Coast to Coast Seminar is an hour-long presentation given on a scientific topic and is made accessible to audiences at a number of remote sites across Canada through collaboration technology.

    SciNet is a local seminar location for this series.

    The topic of the Spring 2014 Coast to Coast seminar series is “Technology for Aging Well” and it is built around a pan-Canadian project titled AGE-WELL (Aging Gracefully across Environments using Technology to Support Wellness, Engagement and Long Life.) The focus of the series will be a discussion how to use technology in helping support the Canadian aging population to ensure that all Canadians can grow older with dignity and grace.

    Jan 14: Arlene Astell (U.Toronto), Uwe Glaesser (Simon Fraser U) Jan 28: Andrew Sixmith (Simon Fraser U) Feb 25: Ron Baecker (U.Toronto) and David Kaufman (Simon Fraser U) Mar 11: Geoff Fernie (U.Toronto) Mar 25: Alex Mihailidis (U.Toronto) and Rafik A. Goubran (Carleton U)

    For more information see
    the irmacs site or the westgrid seminar site

  • Wednesday January 15, 12:00 noon – 1:00 pmSCINET USER GROUP (SNUG) MEETING

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

    This time, we will have

    • TechTalk:IPython Notebook: Accessing IPython running on the GPC from your browser
    • User discussion
    • Pizza!

    For more information and enrollment, go to the course website.

  • Winter 2014SCIENTIFIC COMPUTING COURSE

    Many computational projects start off with knowledge of the science you want to do, and with a bit of programming experience. It can be an arduous journey to get to a (maintainable) piece of code which you trust to compute the right thing. This course is aimed at reducing your struggle, and make you a more efficient computational scientist. Topics include well-established best practices for developing software as it applies to scientific computations, common numerical techniques and packages (so you don’t reinvent the wheel), and aspects of high performance computing.

    The course consists of three parts:

    • Part 1: Scientific Software Development & Design
    • Part 2: Numerical Tools for Physical Scientists
    • Part 3: High Performance Scientific Computing

    Each part consists of eight lectures of one hour.

    Note that these parts can be taken as “mini-courses” by astrophysics graduate students and as “modular courses” by physics and chemistry graduate students at the University of Toronto. (Feel left out? Talk to your graduate office!)

    Participation in parts 1 and 2 counts towards the SciNet Scientific Computing Certificate.

    Participation in part 3 counts towards the SciNet HPC Certificate.

    For more information and enrollment, go to the course websites for
    part 1, part 2, and part 3.

  • January 7, 9, 14, 16, 21, 23, 28, 30: 11:00 am – 12:00 noonSCIENTIFIC SOFTWARE DEVELOPMENT

    Lectures of Part 1 of the Scientific Computing Course

    Topics: C++, version control, make, modular programming, testing, debugging, profiling

    For more information and enrollment, go to the
    course website.

  • Wednesday February 12, 10:30 am – 11:30 amINTRO TO SCINET

    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 the course website.

  • Wednesday February 12, 2014, 12:00 noon – 1:00 pmSCINET USER GROUP (SNUG) MEETING

    TechTalk: TBA

    For more information and enrollment, go to the course website.

  • February 4, 6, 11, 13, 25, 27, and March 4 and 6: 11am-12noonNUMERICAL TOOLS FOR PHYSICAL SCIENTISTS

    Lectures of Part 2 of the Scientific Computing Course

    Topics: Modelling, floating point computations, random numbers and Monte Carlo, ODEs and Molecular Dynamics, linear algebra, fast Fourier transforms

    For more information, go to the course website.

  • Wednesday March 12, 2014, 12:00 noon – 1:00 pmSCINET USER GROUP (SNUG) MEETING

    TechTalk: TBA

    For more information and enrollment, go to the course website.

  • Wednesday March 12, 14:30 pm – 15:30 pmINTRODUCTION TO GPU COMPUTING USING CUDA

    Scott Northrup (SciNet)

    The CUDA (Compute Unified Device Architecture) parallel programming model harnesses the power of Nvidia graphics processing units (GPUs) to enable dramatic increases in computing performance for graphics, 3D content, video and scientific processing-intensive applications. This talk will provide an introduction to CUDA and examples of applications within research. Participants should be familiar with C/C++ development.

    For more information, go to the course web site.

    This talk is also offered remotely, see here for details.

  • March 11, 13, 18, 20, 25, 27, and April 1 and 3: 11am-12noonHIGH PERFORMANCE SCIENTIFIC COMPUTING

    Lectures of Part 3 of the Scientific Computing Course

    Topics: parallel programming concepts, shared memory parallel programming with openmp, distributed memory parallel programming with mpi, hybrid programming.

    For more information and enrollment, go to the course website.

  • Wednesday April 9, 2014, 12:00 noon – 1:00 pmSCINET USER GROUP (SNUG) MEETING

    TechTalk: TBA

    For more information and enrollment, go to the course website.

  • Wednesday May 14, 2014, 12:00 noon – 1:00 pmSCINET USER GROUP (SNUG) MEETING

    TechTalk: TBA

    For more information and enrollment, go to the course website.

System News

  • The new resource allocations will take effect on January 10, 2014, for groups who were awarded an allocation.
  • Scheduled maintenance downtime on January 15-16 (see above).
  • GPC: discovar, a genome assember, installed as a module.
  • GPC: allpaths-lg, a short read genome assembler, installed as a module.
  • GPC: Of the ab initio quantum chemistry package gamess, the version of May 1, 2013 has been installed as a module.
  • TCS: HDF4 file format library version 4.2.6 installed.
  • TCS: Newest IBM compilers (xlf 14.1 and xlc 12.1) are now the default.
  • TCS: zlib and slib compression libraries installed as module ‘compression’
  • BGQ: cmake version 2.8.12.1 installed as a module.
  • BGQ: serial and parallel HDF5 v1.8.12 libraries installed as modules.

What Else Happened at SciNet in the Last Month?

  • Dec 11: Intro to SciNet session
  • Dec 11: SNUG w/TechTalk about Resources at SciNet