International Summer School 2014 on HPC Challenges

February 13, 2014 in blog, blog-general, for_educators, for_researchers, for_users, frontpage, news

intlsummerschool4
Apply by 9 March, decisions in early April
Expenses paid by program
Sponsored by PRACE, XSEDE, Riken, and Compute Canada
website: http://summerschool.niif.hu

Compute Canada/Calcul Canada invites students and researchers at Canadian post-secondary institutions to apply for one of 10 spots allocated to Canada for the fifth International Summer School on HPC Challenges in Computational Sciences. This is a great opportunity for Canadian students and postdocs to attend an Advanced Summer School on High Performance Computing Challenges, all expenses paid.

The workshop is aimed primarily at graduate students or postdocs; however, junior faculty or advanced undergraduates are also welcome to apply. Attendees will be expected to have some experience in HPC parallel programming (for instance, MPI, OpenMP, or CUDA/OpenCL), preferably on software used in successful research projects, and must be at least 18 years of age at time of application. Attendees from all disciplines are invited to participate.

The summer school is sponsored by the European Union Seventh Framework Program’s Partnership for Advanced Computing in Europe Implementation Phase project (PRACE-3IP), U.S. National Science Foundation’s Extreme Science and Engineering Discovery Environment (XSEDE) project, RIKEN Advanced Institute for Computational Science (RIKEN AICS), and Compute Canada / Calcul Canada.

Leading American, Canadian, European and Japanese computational scientists and HPC technologists will offer instruction on a variety of topics, including:

  • Access to EU, Canadian, Japanese and U.S. HPC-infrastructures
  • HPC challenges by discipline (e.g., bioinformatics, computer science, chemistry, and physics)
  • HPC Programming Proficiencies
  • Performance analysis & profiling
  • Algorithmic approaches & numerical libraries
  • Data-intensive computing
  • Scientific visualization

The expense-paid program will benefit advanced scholars from European, Canadian, Japanese and U.S. institutions who use HPC to conduct research. Interested students should apply by March 9, 2014.

Meals, housing, and travel from Canada, Japan and the U.S. will be covered for the selected participants. Applications from students in all science and engineering fields are welcome. Preference will be given to applicants with parallel programming experience, and a research plan that will benefit from the utilization of high performance computing systems.

For further information and to apply online, please click here.

Why Data Centre Providers Love the Greater Toronto Burbs

February 5, 2014 in blog, blog-general, in_the_news, news

The recent announcements of continued IT infrastructure building in Markham (and across the other southern York Region municipalities of Richmond Hill and Vaughan) reflect an established data centre cluster in the area, including recognizable names such as IBM, Rogers, Compugen, OnX, and HP. Of particular noteworthiness is Vaughn-based SCINET—Canada’s largest supercomputer data centre—a High Performance Computing consortium of the University of Toronto and affiliated Ontario hospitals.

Read the full article on TechVibes.

2014 Call for Compute Canada Resource Allocation Proposals

September 24, 2013 in blog, blog-general, for_educators, for_researchers, for_users, news

2014RAC
Any Canadian academic researcher may obtain a default allocation on any Compute Canada system, including those at SciNet, at any time by registering with the Compute Canada DataBase (CCDB) and requesting accounts at one or more consortia. The size of default allocations vary by system.

A Principal Investigator who requires more than the default allocation (be it computing time or storage space), and who is eligible to apply to national granting councils for funding, must submit a proposal to Compute Canada’s Resource Allocation Committee (RAC). The Call for Proposals is posted on the Compute Canada site each fall, with awarded allocations running 1 Jan to 31 Dec of every year.

The 2014 call for resource proposals is now open. Proposals with details about the scientific and technical aspects, are to be submitted via the Compute Canada website CCDB site.

More details can be found in Compute Canada’s Call for Proposal Announcement.

Note: The Resource Allocation deadline has been extended. Proposals must be submitted electronically to Compute Canada on or before October 21, 2013 at 3pm (Eastern). It is however necessary to have started the application process by October 16.

SciNet’s Top 5 of 2012

December 17, 2012 in blog, blog-general

scinet-new-year

 

It’s been a great, busy, year here at SciNet in 2012;  here’s our take on a SciNet Year in Review as a countdown to what’s already shaping up to be an exciting 2013…

5!  SciNet Training

Training and education have always been important to SciNet; it’s one thing to provide computer resources, but we enable research at scale by teaching researchers how to make use of the computers for their work.   In 2012:

  • We held 100 hours of courses, seminars, and Tech Talks,
  • Representing 1,138 student hours of teaching; and
  • Started a new SciNet Certificate program so that attendees could get recognition for all the effort they were putting in.

..4! SciNet Websites

We launched our new and clearer SciNetHPC.ca website this year, which will be the one-stop-shop for news, events and features about the science being enabled here at SciNet; but don’t worry, our technical wiki, wiki.SciNetHPC.ca, will still be there for all your documentation and training material needs.  Some website highlights:

  • Our new Careers page keeps track of Ontario jobs for researchers with HPC experience;
  • Our technical wiki served it’s 750,000th page view this year, and that doesn’t even count the downloads of PDFs of training materials or views of video-recorded educational sessions.

…3! Big Storage for SciNet Users

This was the year we made available our large HPSS system for long-term storage available to our users.  This sophisticated large-scale storage system allows our users reliable near-line storage for very-large data sets.  On tape we already have

  • Over 63 million files, and
  • Over 1.4 petabytes of usage

….2! SOSCIP and the Blue Gene/Q

As part of the SOSCIP project for accelerating research and innovation across Southern Ontario, SciNet took delivery of and is running and supporting the SOSCIP Blue Gene/Q systems.   These new systems are:

…..1! Future SciNet-ers; Outreach to High Schools

And the top highlight of the year has to go to working with the great high school students at SATEC in Toronto, who built a supercomputer of their own, learned to program it with MPI and OpenMP, and demo’ed it to their local MPP.    These students will be the supercomputing experts and data scientists of the future, and it was a pleasure to work with them.

So thanks for all your emails, tweets, and support through the year, have a wonderful holiday, and…

Happy New Year!

SciNet Runs Canada’s Fastest, Greenest Computers

November 19, 2012 in blog, blog-general, frontpage

SciNet-run computers tops in Canada on Green500, Graph500, and Top500.
 
 

The two new Blue Gene/Q systems that are part of the Southern Ontario Smarter Computing and Innovation Platform (SOSCIP) for joint commercial/academic applications are Canada’s biggest, fastest, and greenest big compute platforms – indeed, among the greenest and fastest in the world.  And they’re in just the right place.

“SciNet was the natural choice to host, run, and support these supercomputers,” said Dr. Chris Loken, CTO of SciNet.  “We’ve built a centre that has the concentration of expertise to support users looking to make use of this system for research and development; and we have one of the largest, most energy-efficient, research computing datacentres in Canada, and still have lots of room to grow.”

SciNet’s green datacentre, which makes use of Canada’s cold winters to help reduce the costs and energy needed to cool these behemoth computers, means that the computer’s rankings on the twice-annual Green 500 list, where the machines are tied for 6th and 24th in the world for energy efficiency,  actually understates the case for how energy efficiently they actually run.  Because of judicious use of “free cooling” provided by Ontario’s mild climate whenever possible, almost all the energy used by SciNet’s datacentre goes into compute equipment, not air conditioning infrastructure.  Partly as a result, SciNet uses less than one half of the possible four megawatts of power to which the facility has access.

But although the systems only sip energy compared to similarly large-scale systems, they can tear through “big data” or raw number-crunching computational problems with ease.   On the Graph 500 ranking of supercomputers, which ranks the worlds largest computing resources by how well they can handle the sort of big-data problems that business analytics or digital humanities problems need, the new systems rank the 13th and 35th fastest in the world.  And for raw, brute-force number crunching capability, the larger of the two systems ranks 68th.

While researchers look eagerly forward to use such computational engines for discovery and innovation, some need some help in scaling their research software up to effectively utilize such powerful computers. “And that’s where SciNet really shines,” says Dr. Daniel Gruner, CTO-Software of SciNet. “We’ve got an amazing team of expert analysts – second to none – who can help researchers and innovative companies retool in order to take advantage of the largest machines in the world, and realize their full potential.”

More information about the computers, SOSCIP, and SciNet’s role can be found at

SciNet is Canada’s largest supercomputer centre, providing Canadian researchers with computational resources and expertise necessary to perform their research on scales not previously possible in Canada. SciNet powers work from the biomedical sciences and aerospace engineering to astrophysics and climate science, and is funded by CFI, NSERC, the Ontario Government, the Federal Economic Development Agency for Southern Ontario, and the University of Toronto.  SciNet runs computers for, and provides computational expertise to users of, Compute Canada’s National Platform, the Southern Ontario Water Consortium, and the Southern Ontario Smarter Computing and Innovation Platform.

Computing and Planet-Finding

October 17, 2012 in blog, blog-general, blog-technical

An Earth-sized planet has been found around the star closest to the Sun, Alpha Centauri – and while the astronomers used a telescope, it was only with big computing that they could first “see” the planet.

Read the rest of this entry →

SciNet News, Oct 2012

October 1, 2012 in blog, for_users

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

Events Coming Up

Unless stated otherwise, all events take place at the SciNet Headquarters, Rm 235 of 256 McCaul Street, Toronto, ON. All events below are free but we ask that you sign up on the courses website: https://support.scinet.utoronto.ca/courses.

Monday October 1

MAINTENANCE DOWNTIME OF ALL SCINET SYSTEMS

At 7:50AM, all systems were shutdown for annual cooling tower maintenance. We expect to come back up in the evening of today. Check the wiki in the late afternoon for status updates.

Tuesdays, bi-weekly, 2:30 pm – 3:30 pm

COAST-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.

This fall, the theme is “Open Communication of Science”.

  • Oct 2: “Climate Delusions”, Dr. Mark Jaccard (Simon Fraser University)
  • Oct 16: “Disease, Aquaculture, and Pacific Salmon Management”, Dr. Rick Routledge (Simon Fraser University)
  • Oct 30: “The Role of Science in Marine Policy-Making: from Global to Local”, Dr. Jake Rice (Fisheries and Oceans Canada)
  • Nov 13: “Oil & Fish Tails: Cuts to Canada’s environment and the changing face of Metro Vancouver’s oil and gas industry”, Mr. Fin Donnelly and Mr. Kennedy Stewart (Members of Parliament)
  • Nov 27: TBA, Dr. Rob Macdonald (Fisheries and Oceans Canada)

More info at http://c2c.irmacs.sfu.ca

Thursday October 4, 10:30 am

ORGANIZATIONAL MEETING MINI-COURSE ON GPU COMPUTING

McLennan Physical Laboratories MP1318

Graphical Processing Units (GPUs) can perform certain computations tremendously faster than traditional CPU processors. Harald Pfeiffer (CITA) and Jonathan Dursi (SciNet/CITA) are offering a modular course / mini-course in GPU computing. They will introduce the students to the basics of GPU programming, with an emphasis on the practical knowledge of how to write, run, and optimize GPU-code.

The class-times will be decided in the organizational meeting. The primary audience are graduate students, but postdocs or undergraduate students are also very welcome

For more information, attend the organizational meeting on Thursday.

Wednesday October 10, 10:00 am – 12:00 noon

INTRO TO THE LINUX SHELL

Extremely useful for new users of SciNet that are not yet familiar with the Linux shell or other command-line interfaces.

For more information and sign up, see https://support.scinet.utoronto.ca/courses/?q=node/77

Wednesday October 10, 12:00 noon – 1:00 pm

SNUG MEETING W/TECHTALK: OVERVIEW OF THE NEW BLUE GENE/Q SYSTEM AT SCINET

Sign up at https://support.scinet.utoronto.ca/courses/?q=node/70

Thursday October 11, 2012, 3:00 pm (Eastern)

DEADLINE FOR 2013 COMPUTE CANADA RESOURCE ALLOCATION PROPOSALS

For more info see the Compute Canada website:

https://computecanada.ca/index.php/en/about-us/news/general-news/224-compute-canada-resource-allocation-2013-call-for-proposals-allocation-nationale-des-ressources-de-calcul-canada-demande-de-ressources

Tuesday October 23, 2:00 pm – 4:00 pm

SCINET DEVELOPER SEMINAR – THE JULIA LANGUAGE

By Michael Nolta (CITA, Toronto)

Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments.

Sign up at https://support.scinet.utoronto.ca/courses/?q=node/78

Wednesday November 7, 10:00 am – 11:30 am

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 https://support.scinet.utoronto.ca/courses/?q=node/80

Wednesday November 7, 12:00 noon – 1:00 pm

SNUG MEETING

TechTalk: TBA (Want to present? Email support@scinet.utoronto.ca)

There will also be pizza and discussion.

Sign up at https://support.scinet.utoronto.ca/courses/?q=node/71

Friday November 9, 12:30 pm – 14:00 pm

SCINET DEVELOPER SEMINAR

By Fernando Perez, the inventor of the IPython Notebook.

Because of the lunch-hour scheduling, we will also be providing pizza!

For pizza planning purposes, please sign up at https://support.scinet.utoronto.ca/courses/?q=node/84

Wednesday November 28, 10:00 am 5:00 pm

PARALLEL DEBUGGING WITH DDT

For more information and sign up, see https://support.scinet.utoronto.ca/courses/?q=node/82

Wednesday December 12, 12:00 noon – 1:00 pm

SNUG MEETING

TechTalk: TBA (Want to present? Email support@scinet.utoronto.ca)

There will also be pizza and discussion.

Sign up at https://support.scinet.utoronto.ca/courses/?q=node/72

SYSTEM NEWS

  • Scratch usage: Users will now get emailed when they reach 90% and 95% of their allowed disk usage, or of their allowed number of files. As a safety measure, in the near future, their compute jobs will be blocked when the 95% threshold is reached.
  • GPC and HPSS: A parallel implementation of gzip called ‘pigz’ has been installed as part of the “extras” module.
  • HPSS: A new version of hsi has been installed that allows for checksums.
  • BGQ: The Blue Gene/Q has been delivered. We are in the process of setting up the software environment and will let beta-users in later this month.

ADDED TO THE WIKI

All new wiki content below is listed and linked on the main page: http://wiki.scinethpc.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

  • Slides for the course: “Workflow Optimization for Large Scale BioInformatics”
  • “Intro to SciNet” slides
  • How to use checksums with hsi.
  • How to use pigz (parallel implementation of gzip) with HPSS
  • Slides of the September 2012 SNUG TechTalk “Science=Data”

WHAT ELSE HAPPENED AT SCINET IN SEPTEMBER?

  • September 12: Intro to SciNet
  • September 12: SNUG Meeting with a TechTalk on “Science=Data”
  • September 17: SciNet Developer Seminar by Kit Barton from IBM on “IBM XL compilers and optimization”
  • September 18: SciNet Developer Seminar by Mark Ebersole from NVIDIA on “OpenACC”.
  • September 25: 1-day session on “Workflow optimization for large scale bioinformatics”

SciNet and the Discovery of the Higgs Boson

July 4, 2012 in blog, blog-general, frontpage, in_the_news

“SciNet is absolutely central to make anything out of what happens,” Teuscher [a University of Toronto ATLAS Researcher] said in this Toronto Star article.

SciNet, and the other Compute Canada centres, play a significant role in the work of the Large Hadron Collider and the physicists who use it.

Want to learn more about computation and the Higgs? This PC Advisor article has a very good overview of the massive data challenges that the worlds largest scientific experiment faces, and this blog post describes how the frontiers of computing and of science affect each other.

There are many excellent video descriptions of the physics such as What is the Higgs boson? by theoretical physicist John Ellis, and this explanation of the Higgs mechanism by CMS (one of the CERN experiments) spokesperson Joe Incandela. And this week’s CERN Bulletin has a number of articles describing both the physics and the experimental details that went into this discovery.

For a University of Toronto perspective, the University of Toronto news has a good writeup.

The resulting science papers are starting to come out, and some are freely available:
Landmark Papers on the Higgs Boson Published and Freely Available in Elsevier’s Physics Letters B, and Observation of a new particle in the search for the Standard Model Higgs boson with the ATLAS detector at the LHC.

Ontario HPC Summer School 2012 (Central ON: Toronto)

June 28, 2012 in blog, blog-general

For the last three years, the coming of summer has meant one thing — the Ontario HPC Summer School. The three Ontario HPC Consortia have worked together to teach a week-long intensive “boot camp” introducing HPC and parallel computing to an audience including attendees from academia, government labs, and industry. This year, to better reach our Ontario-wide target audience, multiple sections are being taught; one was taught in early June in London  (Summer School West), one in late July in Ottawa (Summer School East), and one in Toronto is just winding up today.

Students learned about working at the shell, the basics of HPC, OpenMP, MPI or CUDA, parallel debugging, and the current state of HPC best practices.

It was a tremendous experience, and we look forward to doing something similar next year!

SciNet’s Infiniband Upgrade on The HPC Rich Report

June 16, 2012 in blog, blog-general, in_the_news

Our CTO, Dr. Chris Loken, was on this week’s Rich Report HPC podcast with Gilad Shainer of Mellanox and the HPC Advisory Council describing our recent Infiniband upgrade and the improvements that means for our user community; the podcast was also featured on Inside HPC.

 Using Mellanox end-to-end InfiniBand solutions, SciNet has improved reliability and stability of their file systems, greatly improving the performance of parallel user jobs and user efficiency. SciNet is experiencing at least 15-20% increased performance out their upgraded cluster and expects to be high on the TOP500 list when the update is issued at ISC.