SciNet Training 2022/2023

September 9, 2022 in for_researchers, for_users, news, newsletter

The following training events will be offered by SciNet in 2022/2023. Some events take place online, others are in-person in out teaching room at the SciNet offices on the St. George Campus of the University of Toronto (https://www.scinethpc.ca/contact-us/). The in-person events are usually also broadcasted and recorded.
All times below are in Eastern Time. All events listed below are free of charge. With a few execptions, these training courses can be taken for SciNet certificate credits.

To register for these events, log into https://scinet.courses with your Alliance/CCDB account, go to “Home”, select the course, and click on “Enrol me in this course”.

A number of courses may still be added later for the Winter 2023 term.
For any questions, contact

INTRO TO NIAGARA AND MIST

  1. Wed Sep 14, 10 am – 11:30 am | https://scinet.courses/1232 (online)
  2. Wed Oct 12, 10 am – 11:30 am | https://scinet.courses/1235
  3. Wed Nov 9, 10 am – 11:30 am | https://scinet.courses/1236
  4. Wed Dec 14, 10 am – 11:30 am | https://scinet.courses/1237
  5. Wed Jan 11, 10 am – 11:30 am | https://scinet.courses/1238
  6. Wed Feb 8, 10 am – 11:30 am | https://scinet.courses/1239
  7. Wed Mar 8, 10 am – 11:30 am | https://scinet.courses/1240
  8. Wed Apr 12, 10 am – 11:30 am | https://scinet.courses/1241
  9. Wed May 10, 10 am – 11:30 am | https://scinet.courses/1242
  10. Wed Jun 14, 10 am – 11:30 am | https://scinet.courses/1243

This is a class of approximately 90 minutes to introduce SciNet and the Niagara and Mist supercomputers and teach you how to use them.

Except for the September instance, these events take place in-person in the SciNet Teaching Room.

Participation counts towards the SciNet HPC Certificate.

INTRODUCTION TO APPTAINER

Mon Sep 26, 1 pm – 4 pm | https://scinet.courses/1247

Container computing is gradually changing the way researchers are developing, sharing, and running software applications. Apptainer (formerly called Singularity) is gaining popularity in HPC for its performance, ease of use, portability, and security. In this course, we will explore: what is a container, why use a container, and how to use and create one.

Format: On-line

Participation counts towards the SciNet Scientific Computing Certificate.

SCINET USER GROUP MEETING

  1. Wed Oct 12, 12 noon – 2:00 pm | https://scinet.courses/1253
  2. Wed Nov 9, 12 noon – 2:00 pm | https://scinet.courses/1254
  3. Wed Dec 14, 12 noon – 2:00 pm | https://scinet.courses/1255
  4. Wed Jan 11, 12 noon – 2:00 pm | https://scinet.courses/1256
  5. Wed Feb 8, 12 noon – 2:00 pm | https://scinet.courses/1257
  6. Wed Mar 8, 12 noon – 2:00 pm | https://scinet.courses/1258
  7. Wed Apr 12, 12 noon – 2:00 pm | https://scinet.courses/1259
  8. Wed May 10, 12 noon – 2:00 pm | https://scinet.courses/1260
  9. Wed Jun 14, 12 noon – 2:00 pm | https://scinet.courses/1261

The SciNet Users Group (SNUG) meetings happen every month on the second Wednesday and involve a techtalk (a hybrid in-person/online webinar) on topics or technologies of interest to the SciNet community, followed by an in-person session at the SciNet headquarters in Toronto where users can bring questions and issues.

These events take place in-person in the SciNet Teaching Room.

Topics of the TechTalks are TBA.

INTRODUCTION TO PROGRAMMING

Oct 3, 5, 10, 12, 17, 19, 24, 26 | https://scinet.courses/1233

New to programming? Learn the basics of programming using python in eight one-hour sessions over the course of four weeks. Sessions will consist of a mix of lectures and hands-on exercises.

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Scientific Computing Certificate.

INTRODUCTION TO THE LINUX COMMAND LINE

  1. Fri Oct 14, 1 pm – 4 pm | https://scinet.courses/1244
  2. Mon Jan 16, 1 pm – 4 pm | https://scinet.courses/1262

Working with many of the HPC systems (like those at SciNet) involves using the Linux/UNIX command line. This provides a very powerful interface, but it can be quite daunting for the uninitiated. In this half-day session, you can become initiated with this course which will cover basic commands. It could be a great boon for your productivity.

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Scientific Computing Certificate.

ENABLE YOUR RESEARCH WITH CYBERSECURITY!

Oct 24, 26, 29, 12:30 pm – 2:00 pm | https://scinet.courses/1245

In three sessions over the course of one week, we will cover different aspects of cybersecurity to help you enable your research! We will explore cybersecurity concepts, cyberattack models, as well as best practices to protect your research. We will talk about cryptography and apply the concept to a real life scenario via SSH keys. Finally, we will approach cybersecurity in the context of the Research Ethics Board. This session will be a mix of theory and practical exercises. We hope you will learn something new and, most importantly, enjoy the sessions!

The format is virtual, but for the second session there is the option to attend in person in the SciNet Boardroom to get in-person help with setting up ssh key authentication.

Participation counts towards the SciNet Scientific Computing Certificate.

PARALLEL PROGRAMMING AT SCALE WITH MPI

Nov 21, 23, 25, 12:30 pm – 2:00 pm | https://scinet.courses/1251

Learn the basics of Message Passing Interface (MPI) programming. Examples and exercises will be based on parallelization of common scientific computing problems.

Format: On-line

Participation counts towards the SciNet HPC Certificate.

INTRO TO GIT VERSION CONTROL

Mon Nov 21, 1:00 pm – 4:00 pm | https://scinet.courses/1249

Using version control for your scripts, codes, documents, papers, and even data, allows you to track changes, keep backups, and facilitate collaboration. In this workshop, you will learn the basics of version control with the popular distributed version control software GIT. This workshop assumes that students have an understanding of basic Linux shell commands.

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Scientific Computing Certificate.

FILE MANAGEMENT – PACKING SMALL FILES

Mon Nov 28, 1:00 pm – 4:00 pm | https://scinet.courses/1248

Managing large amount of files can be a challenging task. This course explores options such as using Apptainer Overlay and SQLite to pack and reduce large number of files to few files.

Format: Online.

Participation counts towards the SciNet Data Science Certificate.

ADVANCED LINUX COMMAND LINE

Mon Dec 19 17, 1 pm – 4 pm | https://scinet.courses/1250

Working with Advanced Research Computing and High Performance Computing systems involves using the Linux command line. This workshop will cover Linux commands to improve your productivity on the command line.

Participation counts towards the SciNet Scientific Computing Certificate.

FROM PYTHON TO C++

Jan 23, 25, 27, 12:30 noon – 2:00 pm | https://scinet.courses/1263

Python is a wonderful programming language, but it is not the fastest. If execution speed is an issue for your project, it can be worthwhile moving to a so-called compiled language such as C++. This three-session workshop is intended to get Python programmers started with the basics of C++.

Format: TBD, but hopefully in-person. In any case, sessions are broadcast and recorded as well.

Participation counts towards the SciNet Scientific Computing Certificate.

MICROSOFT WINDOWS SUBSYSTEM FOR LINUX

Mon Feb 13, 1:00 pm – 4:00 pm | https://scinet.courses/1264

Windows Subsystem for Linux (WSL) is Microsoft’s implementation of Linux container on Windows. WSL allows users to run various Linux distributions inside Windows and provides fully functional Linux environments for routine tasks. This course explores the use of WSL and Docker Desktop on Windows.

Format: TBD

Participation counts towards the SciNet Scientific Computing Certificate.

INTRODUCTION TO GPU PROGRAMMING

Feb 21, 22, 24, 12:30 noon – 2:00 pm | https://scinet.courses/1266

An overview of GPUs and their use in supercomputers. This workshop will cover the basic ideas of GPU use in scientific computing and introduce several GPU programming frameworks. Prior knowledge of programming (any language) is recommended.

Format: TBD, but hopefully in-person. Sessions will be broadcast and recorded.

Participation counts towards the SciNet HPC Certificate.

LINUX SHELL SCRIPTING

Mon Mar 13, 1:00 pm – 4:00 pm | https://scinet.courses/1267

Learn how to write bash scripts, use environment variables, how to control process, and much more. Requires some linux basic command line experience.

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Scientific Computing Certificate.

HIGH PERFORMANCE PYTHON

Mon Mar 27, 1:00 pm – 4:00 pm | https://scinet.courses/1268

Parallel programming in Python. We will cover subprocess, numexpr, multiprocessing, MPI, and other parallel-enabling python packages.

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet HPC Certificate.

ADVANCED LINUX II

Mon Apr 17, 1:00 pm – 4:00 pm | https://scinet.courses/1265

GNU tools provide powerful commands that facilitate the usage of HPC systems. This course explores some efficient ways of working with bash shell for routine tasks. It is complementary to the “Advanced Linux Command Line I”. Attending this class requires basic knowledge of GNU/Linux shell.

Format: TBD

Participation counts towards the SciNet Scientific Computing Certificate.

NEURAL NETWORK PROGRAMMING

Apr 25 – Jun 1, 11:00 am – 12:00 noon | https://scinet.courses/1271

This six-week class will introduce neural network programming concepts, theory and techniques. The class material will begin at an introductory level, intended for those with no experience with neural networks, eventually covering intermediate-to-advanced concepts. The programming language will be Python 3.9; experience with Python programming will be assumed. The Keras neural network framework will be used for neural network programming; no experience with Keras will be expected.

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Data Science Certificate.

RELATIONAL DATABASES BASICS

Mon May 29, 1:00 pm – 4:00 pm | https://scinet.courses/1270

Principles and uses of relational databases with practical examples using python and sqlite on the Niagara supercomputer.

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Data Science Certificate.

2022 Compute Ontario Summer School

May 13, 2022 in for_researchers, for_users, frontpage, news


This Summer School, jointly organized by SHARCNET, SciNet and Centre for Advanced Computing, will start on May 30th, 2022.

We are pleased to announce the 2022 Compute Ontario Summer School jointly organized by the three consortia, Centre for Advanced Computing, SciNet and SHARCNET. The Summer School is a free series of workshops on skills and technologies for compute and data intensive research delivered by advanced research computing (ARC) specialists.. 

The Summer School will begin on May 30th, 2022 and will run until August 5th, 2022 offering virtual workshops on a variety of topics, including introductory ARC basics, High Performance Computing tools, programming languages, machine learning, visualization, bioinformatics, and more. The Summer School is intended for beginner-to-intermediate participants. Prerequisites are listed in each workshop description. 

Sign up now to receive notifications to register for your favourite workshops. Registration will open two weeks prior to each workshop. Sign up for one, some, or all of the workshops in the Summer School. We look forward to hosting you this summer!


Participants are encouraged to have a user account with the Digital Research Alliance of Canada (formerly Compute Canada), both to facilitate using the digital research infrastructure in the hands-on components of the workshops, and for continued access after the summer school. Apply for an account today.

International HPC Summer School, Greece, June 19-24, 2022

December 8, 2021 in for_researchers, for_users, frontpage, news

Graduate students and postdoctoral scholars from institutions in Canada, Europe, Japan and the United States, are being invited to apply to participate in the 12th International HPC Summer School, to be held June 19-24 in Athens, Greece, hosted by the Partnership for Advanced Computing in Europe (PRACE). To apply, visit the event’s website at https://ss22.ihpcss.org. The deadline for application is 23:59 AOE on February 14, 2022.

The summer school is sponsored by PRACE, the Extreme Science and Engineering Discovery Environment (XSEDE), the RIKEN Center for Computational Science (R-CCS) and the SciNet HPC Consortium.

The summer school will familiarize the best students in computational sciences with major state-of-the-art aspects of HPC and Big Data Analytics for a variety of scientific disciplines, catalyze the formation of networks, provide advanced mentoring, facilitate international exchange and open up further career options.

Leading Canadian, European, Japanese and American computational scientists and HPC technologists will offer instruction in parallel sessions on a variety of topics such as:

  • HPC and Big Data challenges in major scientific disciplines
  • HPC programming proficiencies
  • Performance analysis and profiling
  • Software engineering
  • Numerical libraries
  • Big data analysis and analytics
  • Deep learning
  • Scientific visualization
  • Canadian, European, Japanese and U.S. HPC-infrastructures

The expense-paid program will benefit scholars from Canadian, European, Japanese and U.S. institutions who use advanced computing in their research. The ideal candidate will have many of the following qualities, however this list is not meant to be a “checklist” for applicants to meet all criteria:

  • A graduate student in computational sciences with a strong research plan or a postdoctoral fellow in the early stages of their research efforts
  • Familiar with HPC, not necessarily an HPC expert, but rather a scholar who could benefit from including advanced computing tools and methods into their existing computational work
  • Regular practice with parallel programming
  • Science or engineering background, however, applicants from other disciplines are welcome provided their research activities include computational work

Students from under-represented groups in computing are highly encouraged to apply (i.e. women, racial/ethnic minorities, persons with disabilities, etc.). If you have any questions regarding your eligibility or how this program may benefit you or your research group, please do not hesitate to contact the individual(s) associated with your region.

The school is currently being organised as an in-person event (no remote participation) in order to create the best experience for all attendees. Everyone from participants to staff on-site is expected to be fully vaccinated. Please refer to the COVID-19 Rules & Measures section of the School’s website for further information.

Niagara at Scale – Oct 2021

September 12, 2021 in for_press, for_researchers, for_users, news

SciNet held a successful event “Niagara at Scale” in the Spring of 2021, during which Niagara was reserved for 48 hours for large parallel computations on the order of the size of the cluster. Such “heroic computations” are Niagara’s mandate, but they are hard to run within the regular batch scheduler.

Because of further demand for such large computations, another “Niagara at Scale” event will be held for two days in October 2021. Exact dates will be announced in the near future.

Purpose of “Niagara at Scale”

These events enable pre-approved projects that require all or nearly all of the capacity of the Niagara supercomputer at once. Such heroic computations are Niagara’s mandate, as it is the “Large Parallel cluster within the national systems of the Compute Canada Federation, and the fastest machine of its kind in Canada according to the TOP500 List. But computations of this size — think massively parallel codes running on tens of thousands of cores — are hard or impossible to run within the regular batch scheduler.

How to apply

Announcements of this event went out to Niagara users on August 16, 2021, with an application deadline of September 7. The selection of participants is currently being made.

Future events

There will be more Niagara at Scales events in the future. If you are a Niagara user that has massively parallel jobs or workflows that could take advantage of this opportunity, keep an eye out for future announcements.

SciNet Virtual Summer Training Program 2021

June 2, 2021 in for_educators, for_researchers, for_users, frontpage, news

For the second summer in a row, in lieu of its annual Ontario Summer School, SciNet will be offering weekly virtual summer training on Advanced Research Computing from June through to early September. Topics will include parallel programming, Linux shell, cybersecurity, large scale batch processing, and performance Python and R.

The program will start on June 14th, 2021 and currently consists of the following 8 courses (more may be added later), each with 3 online vents of 90 minutes on successive days within one week.

  • Enable your Research with Cybersecurity!
  • Advanced Linux Command Line
  • Introduction to Supercomputing
  • Parallel Programming at Scale on Supercomputers with MPI
  • Python and High Performance Computing
  • Parallel Programming on Multicore Computers with OpenMP
  • R and High Performance Computing
  • Debugging and Performance

See the program site on the SciNet education website for further details.

Niagara at Scale Pilot

March 5, 2021 in blog-general, for_press, for_researchers, for_users, frontpage, news

SciNet will be reserving the Niagara cluster for two days in March for the first-ever “Niagara at Scale”, from March 30th, 2021, at 12 noon EST, to April 1st, 2021, at 12 noon EST.

Purpose of the “Niagara at Scale” event

This event will enable pre-approved projects that require all or nearly all of the capacity of the Niagara supercomputer at once. Such heroic computations are Niagara’s mandate, as it is the “Large Parallel cluster within the national systems of the Compute Canada Federation, and the fastest machine of its kind in Canada according to the TOP500 List. But computations of this size — think massively parallel codes running on tens of thousands of cores — are hard or impossible to run within the regular batch scheduler.

How to apply

We already have some groups interested in participating, but we would like to extend our invitation to the whole Canadian high-performance computing community before committing to a particular date. Users that have massively parallel jobs or workflows that could take advantage of this opportunity, are encourage to contact us at support@scinet.utoronto.ca by Friday, March 12, 2021 (note: this is an extension of the original deadline of March 5).

In the email, please briefly describe your intended computation, as well as the size and duration of the jobs you would like to run at scale.  Successful proposals will need to show evidence that their codes can run efficiently on at least 20,000 cores on Niagara and include strong and/or weak scaling data and plots.

In addition, your codes must be able to checkpoint and restart, especially since jobs will be restricted to shorter wall time.

Information session on March 10, 2021

We will hold an online information session regarding this program on March 10, 2021 at our SciNet User Group Meeting at noon EST. Attend to learn what kind of computations this program is aimed at. We will also provide guidance on how to get your computation to such a large scale if it needs it but your code does not yet scale to that size. For more information and sign-up for the event, go to https://scinet.courses/569

Future “Niagara at Scale” Events

The current event is a pilot project. If this initiative proves successful, we are planning to hold several of these events per year.

SciNet Virtual Summer Training Program

June 12, 2020 in blog, for_researchers, for_users

In lieu of its annual in person Ontario Summer School, this year, SciNet, in collaboration with CAMH, will be offering weekly virtual summer training on High Performance Computing from June through to August. The program consists of the following 11 courses, each with 3 online vents of 90 minutes on successive days within one week: a lecture, a hands-on session, and a wrap-up session.

The first of these courses, the “Introduction to Supercomputing” has just finished, with over 70 participants. Still to come in the next weeks are

  • Intro to Linux Shell
  • Parallel Programming on Multicore Computers with OpenMP
  • Parallel Programming at Scale on Supercomputers with MPI
  • Neuroimaging Analysis at Scale
  • Python for MRI Analysis
  • Python and High Performance Computing
  • Brain Network Modeling
  • R and High Performance Computing
  • Whole-Genome Association Analysis with PLINK
  • Debugging and Performance

See the program site on the SciNet education website for further details.

2020 International Summer School on HPC Challenges in Computational Sciences, University of Toronto, Canada, July 7-12

November 29, 2019 in for_press, for_researchers, for_users, frontpage, news


Update April 17, 2020: This event has been postponed to 2021.

Applications open November 29, 2019, and are due January 27, 2020

Who can apply: Graduate students and postdoctoral scholars from institutions in Canada, Europe, Japan and the United States, especially if you use advanced computing in your research. Students from underrepresented groups in computing are highly encouraged to apply (e.g., women, racial/ethnic minorities, persons with disabilities, etc.).

Who are the teachers: Leading computational scientists and HPC technologists from the U.S., Japan, Europe and Canada will teach classes and provide mentoring to attendees.

What will you learn: Topics include:

  • HPC challenges by discipline
  • HPC programming proficiencies
  • Performance analysis & profiling
  • Scientific visualization
  • Big Data Analytics
  • Mentoring
  • Networking
  • Machine Learning
  • Canadian, EU, Japanese and U.S. HPC-infrastructures

Preferred qualifications, but not required:

  • Familiarity with HPC, not necessarily an HPC expert, but rather a scholar who could benefit from including advanced computing tools and methods into their existing computational work
  • A graduate student with a strong research plan or a postdoctoral fellow in the early stages of their research careers
  • Utilize parallel programming at least on monthly basis, more frequently preferred
  • A science or engineering background, however, applicants from other disciplines are welcome, provided your research activities include computational work.

Cost: School fees, meals, and housing are covered for all accepted applicants, also intercontinental flight costs.

Further information and application: https://ss20.ihpcss.org

Questions? Reach out to the contact for your region listed on the back of this page to have questions answered about eligibility, the application process, or the summer school itself.

This summer school is organized by:

            
            

Contacts

Reach out to the contact for your region listed to get questions answered about eligibility, the application process, or the summer school itself.

CANADA
SciNet HPC Consortium: www.scinethpc.ca

Ramses van Zon
SciNet, Univ. of Toronto, Canada
Email: rzon@scinet.utoronto.ca

EUROPE
PRACE: www.prace-ri.eu

Hermann Lederer Simon Wong
Max Planck Computing and Data Facility, Germany ICHEC, Ireland
Email: lederer@mpcdf.mpg.de Email: simon.wong@ichec.ie

JAPAN
RIKEN: www.r-ccs.riken.jp/en

Toshiyuki Imamura
CCS, RIKEN
Email: Imamura.toshiyuki@riken.jp

UNITED STATES
XSEDE: www.xsede.org.

Jay Alameda
NCSA, University of Illinois at Urbana-Champaign, United States
Email: alameda@illinois.edu

SciNet News October 2019

October 10, 2019 in for_researchers, for_users, newsletter

SUMMARY

  • The Resource Allocation Competition is open.

  • Scheduled maintenance downtime on October 16th.

  • Training and education program continues.

  • UofT Visualization Discussion Group hosted at SciNet.

Details can be found below and are also available on the SciNet education website courses.scinet.utoronto.ca and the SciNet wiki docs.scinet.utoronto.ca.

SYSTEM CHANGES

  • Research groups that require more computational or storage resources than those that come with a default account on any of the Canadian national systems, can request more in the annual Resource Allocation Competition, organized by Compute Canada. The invitation for applications went out on September 24, and will be open until November 7, 2019

  • Scheduled maintenance on Wednesday October 16, 2019 at the SciNet Datacenter. This will require a full system power-off, so starting 7am all systems should be shutdown. We expect the systems to be back late that evening day. A two-day upgrade of the HPSS tape library will be started during the shutdown, so HPSS and the backup of home and project is not expected to be operational until one or two days after Niagara.

EVENTS COMING UP

To sign up for the events below, go to https://scinet.courses. Most events are recorded and posted on that site within a few work days. Some events are broadcast, but remote participation currently cannot count towards SciNet certificate credits.

The SciNet Teaching Room and Boardroom, where many of the events are held, are located in the SciNet office space on the eleventh floor of the MaRS West Tower, Suite 1140, 661 University Avenue, Toronto, Ontario, M5G 1M1.

  • SHARED MEMORY PARALLEL PROGRAMMING WITH OPENMP
    Friday October 11, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Students will learn the basics of shared memory programming with OpenMP. In particular, we will discuss the OpenMP’s execution and memory model, performance, reductions and load balancing. Prerequisites: C or C++.

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/521

  • INTRO TO NIAGARA
    Wednesday October 16, 2019, 10:00 am – 11:30 am
    SciNet Boardroom

    This is a class of approximately 60-90 minutes to introduce SciNet and the Niagara supercomputer and teach you how to the system.

    Participation counts towards the HPC Certificate.

    For more information and sign-up, go to https://scinet.courses/484

    Further sessions of this Intro are planned for November 13, December 11, January 8, February 12, March 11, April 8, May 13 and June 10.

  • SCINET USER GROUP MEETING (SNUG) Wednesday October 16, 2019, 12:00 noon – 1:00 pm
    SciNet Boardroom

    Pizza, user discussion, and presentations about:

    1. Using the newer 2019b Niagara software stack.

    2. The Compute Canada Resource Allocation Competition.

    For sign-up and more information, see https://scinet.courses/499

    Further SNUG meetings will be held on November 13, December 11, January 8, February 12, March 11, April 8, May 13 and June 10.

  • ADVANCED LINUX COMMAND LINE
    Wednesday October 23, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Increase your Linux (bash) command line productivity. Requires some basic Linux command line experience.

    Participation counts towards the Scientific Computing Certificate.

    For sign-up and more information, see https://scinet.courses/508

    Another “Advanced Linux Command Line” will be held on April 15.

  • DISTRIBUTED MEMORY PARALLEL PROGRAMMING WITH MPI
    Monday October 28, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Learn the basics of Message Passing Interface (MPI) programming in this three-hour workshop. Prerequisites: C/C++ or Fortran programming.

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/517

  • UofT Viz Discussion Group November 1 and 29, 2019 SciNet Boardroom

    Meetings for visualization enthusiasts to discuss and share ideas about visualization and novel data representations.

    For more information, see https://scinet.courses/523

  • NUMERICAL COMPUTING WITH PYTHON
    Tuesdays and Thursdays, 1:00 pm – 2:00 pm
    November 5 to December 5, 2019 (8 lectures)
    SciNet Teaching Room

    Learn about numerical computing even with little programming experience. Covers numerical computing in Python, best practices and visualization. Experience with Python is required.

    Participation counts towards the Scientific Computing Certificate.

    For sign-up and more information, see https://scinet.courses/473

  • GPU PROGRAMMING WITH CUDA
    Monday November 25, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    The goal of this three-hour workshop is for students, new to GPU programming but familiar with programming in C/C++, to leave being able to write simple kernels for their own problems, and understand the tools and techniques needed to improve the results.

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/516

  • INTRO TO THE LINUX COMMAND LINE
    Wednesday November 27, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Learn the basics of how to use the Linux shell in two hours. Very useful for new users of SciNet that have little or no experience with Linux.

    Participation counts towards the Scientific Computing Certificate.

    For sign-up and more information, see https://scinet.courses/495

    Further “Intro to the Linux Command Line” sessions will be held on January 15, March 18 and May 20, 2020.

  • SCIENTIFIC COMPUTING FOR PHYSICISTS (PHY1610)
    Winter 2020, starting January 7.
    SciNet Teaching Room

    This course is aimed at reducing your struggle in getting started with computational projects, 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, and aspects of high performance computing. While we will introduce the C++ language, in one language or another, students should already have some programming experience. Despite the title, this course is suitable for many physical scientists (chemists, astronomers, …).

    This course is part of the physics graduate program. Students willing to take the course as part of their graduate program have to enroll through Acorn/ROSI.

    For more information, see https://scinet.courses/468

  • QUANTITATIVE APPLICATIONS FOR DATA ANALYSIS (EES1137)
    Winter 2020, starting January 8.
    University of Toronto Scarborough Campus

    In this course data analysis techniques utilizing Python and R statistical language, will be discussed and introduced, as well as, the basics of programming and scientific computing. The goal of this course is to prepare graduate students to perform scientific data analysis. Successful students will learn how to use statistical inference tools to gain insight into large and small data sets, as well as be exposed to cutting-edge techniques and best practises to store, manage and analyze (large) data.

    Topics include: Python and R programming, version control, automation, modular programming and scientific visualization.

    Students willing to take the course as part of their graduate program have to enroll through Acorn/ROSI. This course is part of the EES graduate program and to be taught at the UTSc campus.

    For more information, see https://scinet.courses/513

  • PARALLEL PERFORMANCE TUNING
    Monday January 13, 2020, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    A three-hour workshop on profiling, performance analysis, and tuning of applications.

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/518

  • ADVANCED DISTRIBUTED MEMORY PARALLEL PROGRAMMING WITH MPI
    Monday February 3, 2020, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    In this three-hour workshop, you will learn advanced MPI techniques such as MPI Datatypes, MPI-IO and one-sided communications.

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/519

  • LINUX SHELL SCRIPTING
    Monday February 19, 2020, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Learn how to write bash scripts, use environment variables, how to control process, and much more. Requires some basic Linux command line experience.

    Participation counts towards the Data Science Certificate.

    For sign-up and more information, see https://scinet.courses/511

    Another “Shell Scripting” session will be held on June 17.

  • INTRO TO NEURAL NETWORK PROGRAMMING
    Starting April 14, 2020, 7 weeks, Tuesdays and Thursdays
    10:00 am – 11:00 noon
    SciNet Teaching Room

    This seven-week class will introduce neural network programming concepts, theory and techniques. The class material will begin at an introductory level, intended for those with no experience with neural networks, eventually covering intermediate-to-advanced concepts. The programming language will be Python 3.7; experience with Python programming will be assumed. The Keras neural network framework will be used for neural network programming; no experience with Keras will be expected.

    Participation counts towards the Data Science Certificate.

    For sign-up and more information, see https://scinet.courses/514

  • RELATIONAL DATABASE BASICS
    Monday May 4, 2020, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Principles and uses of relational databases with practical examples using Python and sqlite.

    Participation counts towards the Data Science Certificate.

    For sign-up and more information, see https://scinet.courses/520

SciNet News September 2019

September 6, 2019 in for_researchers, for_users, newsletter

SUMMARY

  • Announcing SciNet’s 2018-2019 Training and Education Schedule on Scientific Computing, High Performance Computing and Data Science.
  • To acknowlegde the Niagara supercomputer in your publications, please cite our recent PEARC19 paper:

    M Ponce, R van Zon, S Northrup, D Gruner, J Chen, F Ertinaz, A Fedoseev, L Groer, F Mao, B C Mundim, M Nolta, J Pinto, M Saldarriaga, V Slavnic, E J Spence, Ch-H Yu, and W R Peltier. 2019. “Deploying a Top-100 Supercomputer for Large Parallel Workloads: the Niagara Supercomputer”. In “Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) (PEARC ’19)”. ACM, New York, NY, USA, Article 34, 8 pages. DOI: https://doi.org/10.1145/3332186.3332195

  • This summer, SciNet organized or co-organized three successful week-long training events: The Compute Ontario Summer School Central, The International HPC Summer School, and the Petascale Computing Institute.
  • Easier procedure to enable access to Niagara.
  • BGQ and P7 clusters have been decommisioned.

Details can be found below and are also available on the SciNet education website courses.scinet.utoronto.ca and the SciNet wiki docs.scinet.utoronto.ca.

SYSTEM CHANGES

  • The procedure to enable access to Niagara is now easier: once you have your Compute Canada account, go to the CCDB opt-in page at https://ccdb.computecanada.ca/services/opt_in and click on the Niagara “Join” button. Your access will be enabled in a day or two. Before, you needed to fill out a form to request a SciNet account that you would then not need to use. Note that if you’re receiving this email, you likely already have access to Niagara, in which case no action is required, but this information may be helpful for new members of your research group.
  • The SOSCIP BGQ has been decommissioned on June 30, 2019. The P7 cluster was decommisioned at the same time.

SCINET EVENTS DURING THE PAST SUMMER

  • June 24 – 28, 2019: Ontario Summer School Central (Toronto, Canada)

    • Allows graduate and undergraduate students, postdocs, and researchers to learn and share knowledge and experience in high performance and technical computing on modern HPC platforms.
    • Three such schools are organized annually by SHARCNET, SciNet, and CAC, see https://www.sharcnet.ca/help/index.php/Summer_Schools
    • The HPC, Data Science, and Biomedical streams of the SciNet school drew a total of 225 unique participants.
    • 159 participants earned certificates for attending at least three days of the school.
    • See https://scinet.courses/438 for access to the slides and training materials of this event.
  • July 7 – 12, 2019: International HPC Summer School (Kobe, Japan)

    • Aims to familiarize the best students in computational sciences with major state-of-the-art aspects of HPC for a variety of scientific disciplines, catalyze the formation of networks, provide advanced mentoring, facilitate international exchange and open up further career options.
    • This expenses-paid event is a collaboration between XSEDE, PRACE, RIKEN and SciNet.
    • Eleven Canadian graduate students were selected to participate.
    • SciNet also delivered three of the sessions.
    • A team of three Canadian students took on the school’s parallel programming challenge and won the award for fastest GPU+MPI implementation of a Laplace code!
    • See http://www.ihpcss.org for details regarding next year’s IHPCSS, to be held in Toronto.
  • August 19-23, 2019: Petascale Computing Institute (Virtual, but also at SciNet)

    • Virtual training to enable computational and data-enabled discovery in all fields of study by teaching the participants to scale their computational codes to leadership-class computing systems.
    • A collaboration between Argonne National Laboratory (ANL), the Blue Waters project at NCSA, the National Energy Research Scientific Computing Center (NERSC), Oak Ridge Leadership Computing Facility (OLCF), Pittsburgh Supercomputing Center, SciNet at the University of Toronto, and the Texas Advanced Computing Center (TACC).
    • Broadcast to hunderds of participants in 22 hosts in four countries, with local staff helping the participants.
    • SciNet delivered two of the sessions.
    • Visit https://bluewaters.ncsa.illinois.edu/petascale-computing-2019 for recordings of this event.

EVENTS COMING UP

To sign up for the events below, go to https://scinet.courses. Most events are recorded and posted on that stite within a few work days. Some events are broadcast, but remote participation currently cannot count towards SciNet certificate credits.

The SciNet Teaching Room and Boardroom, where many of the events are held, are located in the SciNet office space on the eleventh floor of the MaRS West Tower, Suite 1140, 661 University Avenue, Toronto, Ontario, M5G 1M1.

  • INTRO TO COMPUTATIONAL BIOSTATISTICS WITH R (MSC1090)
    Mondays and Thursday, 1 pm – 2pm
    24 lectures from September 9 to December 5, 2019

    In this course data analysis techniques utilizing the R statistical language, will be discussed and introduced, as well as, the basics of programming and scientific computing. The goal of this course is to prepare graduate students to perform scientific data analysis. Successful students will learn how to use statistical inference tools to gain insight into large and small data sets, as well as be exposed to cutting-edge techniques and best practises to store, manage and analyze (large) data. Topics include: R programming, version control, automation, modular programming and scientific visualization.

    Students willing to take the course as part of their graduate program have to enroll through Acorn/ROSI. This course is part of the IMS graduate program and to be taught at the UofT St. George campus (i.e., not in the SciNet classroom). Contact us if you wish to audit the course without credit.

    For more information, see https://scinet.courses/475

  • INTRO TO NIAGARA
    Wednesday September 11, 2019, 10:00 am – 11:30 am
    SciNet Boardroom

    This is a class of approximately 60-90 minutes to introduce SciNet and the Niagara supercomputer and teach you how to the system.

    Participation counts towards the HPC Certificate.

    For more information and sign-up, go to https://scinet.courses/484

    Further sessions of this Intro are planned for October 16, November 13, December 11, January 8, February 12, March 11, April 8, May 13 and June 10.

  • INTRO TO THE LINUX COMMAND LINE
    Wednesday September 16, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Learn the basics of how to use the Linux shell in two hours. Very useful for new users of SciNet that have little or no experience with Linux.

    Participation counts towards the Scientific Computing Certificate.

    For sign-up and more information, see https://scinet.courses/494

    Further “Intro to the Linux Command Line” sessions will be held on November 27, January 15, March 18 and May 20.

  • INTRODUCTION TO PROGRAMMING
    Tuesdays and Thursdays, 1:00 pm – 2:00 pm
    From October 1 – October 29, 2019
    SciNet Teaching Room

    New to programming? Learn the basics of programming using Python in eight one-hour sessions over the course of five weeks. Sessions will consist of a mix of lectures and hands-on exercises.

    Participation counts towards the Scientific Computing Certificate.

    For sign-up and more information, see https://scinet.courses/472

  • GIT VERSION CONTROL
    Friday October 4, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Introductory workshop to get started in the usage of version control GIT. This workshop is held in collaboration with UofT-Libraries and UofT graduate students could gain GPS credits.

    For sign-up and more information, see https://scinet.courses/467

  • SHARED MEMORY PARALLEL PROGRAMMING WITH OPENMP
    Friday October 11, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Students will learn the basics of shared memory programming with OpenMP. In particular, we will discuss the OpenMP’s execution and memory model, performance, reductions and load balancing.

    For sign-up and more information, see https://scinet.courses/521

  • SCINET USER GROUP MEETING (SNUG)
    Wednesday October 16, 2019, 12:00 noon – 1:00 pm
    SciNet Boardroom

    Pizza, user discussion, and a tech talk TDB

    For sign-up and more information, see https://scinet.courses/499

    Further SNUG meetings will be held on November 13, December 11, January 8, February 12, March 11, April 8, May 13 and June 10.

  • ADVANCED LINUX COMMAND LINE
    Wednesday October 23, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Increase you Linux (bash) command line productivity. Requires some basic Linux command line experience.

    Participation counts towards the Scientific Computing Certificate.

    For sign-up and more information, see https://scinet.courses/508

    Another “Advanced Linux Command Line” will be held on April 15.

  • DISTRIBUTED MEMORY PARALLEL PROGRAMMING WITH MPI
    Monday October 28, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Learn the basics of Message Passing Interface (MPI) programming in this three-hour workshop. Prerequisites: C/C++ or Fortran programming.

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/517

  • NUMERICAL COMPUTING WITH PYTHON
    Tuesdays and Thursdays, 1:00 pm – 2:00 pm
    November 5 to December 5, 2019 (8 lectures)
    SciNet Teaching Room

    Learn about numerical computing even with little programming experience. Covers numerical computing in Python, best practices and visualization. Experience with Python is required.

    Participation counts towards the Scientific Computing Certificate.

    For sign-up and more information, see https://scinet.courses/473

  • GPU PROGRAMMING WITH CUDA
    Monday November 25, 2019, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    The goal of this three-hour workshop is for students, new to GPU programming but familiar with programming in C/C++, to leave being able to write simple kernels for their own problems, and understand the tools and techniques needed to improve the results.

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/516

  • SCIENTIFIC COMPUTING FOR PHYSICISTS (PHY1610)
    Winter 2020, starting January 7.
    SciNet Teaching Room

    This course is aimed at reducing your struggle in getting started with computational projects, 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, and aspects of high performance computing. While we will introduce the C++ language, in one language or another, students should already have some programming experience. Despite the title, this course is suitable for many physical scientists (chemists, astronomers, …).

    This course is part of the physics graduate program. Students willing to take the course as part of their graduate program have to enroll through Acorn/ROSI.

    For more information, see https://scinet.courses/468

  • QUANTITATIVE APPLICATIONS FOR DATA ANALYSIS (EES1137)
    Winter 2020, starting January 8.
    University of Toronto Scarborough Campus

    In this course data analysis techniques utilizing Python and R statistical language, will be discussed and introduced, as well as, the basics of programming and scientific computing. The goal of this course is to prepare graduate students to perform scientific data analysis. Successful students will learn how to use statistical inference tools to gain insight into large and small data sets, as well as be exposed to cutting-edge techniques and best practises to store, manage and analyze (large) data.

    Topics include: Python and R programming, version control, automation, modular programming and scientific visualization.

    Students willing to take the course as part of their graduate program have to enroll through Acorn/ROSI. This course is part of the EES graduate program and to be taught at the UTSc campus.

    For more information, see https://scinet.courses/513

  • PARALLEL PERFORMANCE TUNING
    Monday January 13, 2020, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    A three-hour workshop on profiling, performance analysis, and tuning of applications.

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/518

  • ADVANCED DISTRIBUTED MEMORY PARALLEL PROGRAMMING WITH MPI
    Monday February 3, 2020, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    In this three-hour workshop, you will learn advanced MPI techniques such as MPI Datatypes, MPI-IO and one-sided communications.

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/519

  • LINUX SHELL SCRIPTING
    Monday February 19, 2020, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Learn how to write bash scripts, use environment variables, how to control process, and much more. Requires some basic Linux command line experience.

    Participation counts towards the Data Science Certificate.

    For sign-up and more information, see https://scinet.courses/511

    Another “Shell Scripting” session will be held on June 17.

  • INTRO TO NEURAL NETWORK PROGRAMMING
    Starting April 14, 2020, 7 weeks, Tuesdays and Thursdays
    10:00 am – 11:00 noon
    SciNet Teaching Room

    This seven-week class will introduce neural network programming concepts, theory and techniques. The class material will begin at an introductory level, intended for those with no experience with neural networks, eventually covering intermediate-to-advanced concepts. The programming language will be Python 3.7; experience with Python programming will be assumed. The Keras neural network framework will be used for neural network programming; no experience with Keras will be expected.

    Participation counts towards the Data Science Certificate.

    For sign-up and more information, see https://scinet.courses/514

  • RELATIONAL DATABASE BASICS
    Monday May 4, 2020, 1:00 pm – 4:00 pm
    SciNet Teaching Room

    Principles and uses of relational databases with practical examples using Python and sqlite.

    Participation counts towards the Data Science Certificate.

    For sign-up and more information, see https://scinet.courses/520