SciNet News November 2019

November 4, 2019 in newsletter

SUMMARY

  • Scheduled maintenance downtime was postponed, now on November 15th.

  • Learn about the upcoming Niagara expansion at the SciNet User Group Meeting on November 13.

  • Training and education program continues with “Numerical Computing with Python”, “GPU Programming with CUDA”, “Intro to Niagara” and “Intro to Linux” this month.

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 Friday November 15, 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.

  • After the shutdown, the SLURM scheduler will have been upgraded to version 19. This should not require any changes from users.

EVENTS COMING UP

To sign up for the events below, go to https://scinet.courses. Most events are recorded and posted on the courses site within a few work days.

The SciNet Teaching Room and Boardroom in the SciNet office space on the eleventh floor of the MaR
S West Tower, Suite 1140, 661 University Avenue, Toronto, Ontario, M5G 1M1.

  • 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

  • INTRO TO NIAGARA
    Wednesday November 13, 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/486

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

  • SCINET USER GROUP MEETING (SNUG) Wednesday November 13, 2019, 12:00 noon – 1:00 pm
    SciNet Boardroom

    Pizza, user discussion, and presentations about:

    Upcoming New Resources at SciNet: Niagara Expansion and GPU System

    For sign-up and more information, see https://scinet.courses/500

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

  • 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.

  • UofT Viz Discussion Group November 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

  • 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

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

    Apply MPI to realistic scientific computing examples and learn to use advanced MPI techniques such as non-blocking 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.

  • ADVANCED DISTRIBUTED MEMORY PARALLEL PROGRAMMING WITH MPI
    Monday April 6, 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/525

  • 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 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

SciNet News June 2019

June 4, 2019 in for_researchers, for_users, newsletter

Summary

  • Increased security of the SciNet data centre
  • Decommissioning of the SOSCIP BlueGene/Q at the end of June.
  • Announcement of several training opportunities.

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

System News

  • The security level of the data centre has been increased by disabling certain weak encryption algorithms and certain weak public key types and by regenerating Niagara’s host keys. The latter requires users to replace their ssh clients stored host key for Niagara upon first login after the shutdown. If you have not done so yet, the details of how to do this can be found on https://docs.scinet.utoronto.ca/index.php/SSH_Changes_in_May_2019.
  • The SOSCIP BGQ will be decommissioned on June 30, 2019. The P7 cluster will be decommisioned at the same time. The file system of the BGQ, which is shared with the SOSCIP GPU Cluster, will remain active, and the BGQ front-end node (bgqdev.scinet.utoronto.ca) will remain up for the foreseeable future to allow users to access their files. If you have further questions regarding the decommisioning of the BGQ, write to support@scinet.utoronto.ca. For general questions regarding SOSCIP, write to info@soscip.org.

Events Coming Up

Unless stated otherwise, all events listed below are free of charge and take place at the SciNet Teaching Room or Boardroom at our offices on the eleventh floor of the MaRS West Tower, suite 1140A (661 University Avenue, Toronto ON M5G 1M1).

Most events are recorded and some are broadcast, but only some of the courses can be taken remotely for SciNet certificate credits.

Registration for SciNet courses should be done by logging into https://courses.scinet.utoronto.ca with your Compute Canada account (the same one that you use to log into Niagara).

  • INTRO TO SCINET AND NIAGARA Wednesday June 12, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and registration, go to https://scinet.courses/465

  • SCINET USER GROUP MEETING Wednesday June 12, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk by Ramses van Zon on

    “No Conda: Using Python, Installing Packages, and Accessing Jupyter Notebooks on Niagara”

    Abstract: If you want to know how to use install specific Python packages or how to use jupyter notebooks, most instructions that you find these days will tell you to use anaconda or miniconda. While very convenient on your own personal computer, conda comes with substantial storage inefficiencies and conflicts with other software, and is therefore not the recommended option on supercomputers. In this techtalk, we will explain and demonstrate how you can instead use virtual environments instead of conda environments, and use Niagara’s JupyterHub instance (which also supports R and can be made to work with Julia as well).

    For sign up and more information, see https://scinet.courses/471

  • COMPUTE ONTARIO SUMMER SCHOOL West – Hamilton June 10-14, 2019 Central – Toronto, June 24-28, 2019 East – Ottawa, July 8-12, 2019

    The Compute Ontario Summer School on Scientific and High Performance Computing is an annual educational event for graduate/undergraduate students, postdocs and researchers to learn and share knowledge and experience in high performance and technical computing on modern HPC platforms.

    As in previous years, the 2019 Summer School will have three instances, “West”, “Central”, and “East”. Each will be a week-long event with multiple parallel streams.

    Registration for the central instance will be open until June 17, 2019, see https://scinet.courses/438

  • SCALING TO PETASCALE INSTITUTE August 19-23, 2019

    This is a free virtual advanced HPC summer school, organized by a number of the US XSEDE sites and SciNet. include OpenMP, MPI, CUDA, and OpenACC.

    More details can be found at https://bluewaters.ncsa.illinois.edu/petascale-computing-2019

  • Intro to GIT Version Control Friday October 4, 2019, 1pm – 4pm Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    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

  • INTRODUCTION TO PROGRAMMING October 2019 Tuesdays and Thursdays, 1:00 pm – 2:00 pm Four weeks starting Oct 1. Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

  • NUMERICAL COMPUTING WITH PYTHON November 2019 Tuesdays and Thursdays, 1:00 pm – 2:00 pm Four weeks, starting Nov 5, 2019 Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    Learn about research computing even with little programming experience. Covers programming in python, best practices and visualization. Experience with python is required. Four home work sets will be the basic of the evaluation.

    Participation counts towards the SciNet Scientific Computing Certificate.

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

  • SCIENTIFIC COMPUTING FOR PHYSICISTS (PHY1610) Winter 2019 Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    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

SciNet News March 2019

March 4, 2019 in for_researchers, for_users, newsletter

Summary

  • Two additional ways to interact with the nearline/archive HPSS system: Globus and a Virtual File System.
  • Compute jobs on Niagara now have access to temporary burst buffer space.
  • Announcement of several techtalks at the SciNet User Group Meetings.

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 News

  • The Globus interface to the nearline/archive HPSS system is now operational. The endpoint name is computecanada#hpss. See https://docs.scinet.utoronto.ca/index.php/Globus and https://docs.scinet.utoronto.ca/index.php/HPSS for more details.
  • A Virtual File System (VFS) interface to the nearline/archive HPSS system is now available on a special dedicated node which you access through the scheduler. This interface makes HPSS seem like a regular file system, which is really only suited for small scale data management. See https://docs.scinet.utoronto.ca/index.php/HPSS for more details.
  • Compute jobs on Niagara now get access to temporary space on the Burst Buffer (a faster file system than scratch). For every job on Niagara, the scheduler now creates a temporary directory on the burst buffer called $BB_JOB_DIR. The $BB_JOB_DIR directory will be empty when your job starts and its content gets deleted after the job has finished. The directory is shared among the nodes of a job. This can be useful for I/O heavy jobs whose temporary files do not fit in ramdisk. See https://docs.scinet.utoronto.ca/index.php/Burst_Buffer for more details.
  • For consistency with the general purpose clusters Cedar and Graham, the environment variable $SLURM_TMPDIR will be set in Niagara compute jobs. This variable will point to ramdisk, not to local hard drives (since Niagara has none).

Events Coming Up

Unless stated otherwise, all events listed below are free of charge and take place at the SciNet Teaching Room or Boardroom at our offices on the eleventh floor of the MaRS West Tower, suite 1140A (661 University Avenue, Toronto ON M5G 1M1).

Most events are recorded and some are broadcast, but only some of the courses can be taken remotely for SciNet certificate credits.

Registration for SciNet courses should be done by logging into https://courses.scinet.utoronto.ca with your Compute Canada account (the same one that you use to log into Niagara).

  • INTRO TO SCINET AND NIAGARA Wednesday February 13, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and registration, go to https://courses.scinet.utoronto.ca/419

  • SCINET USER GROUP MEETING Wednesday February 13, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk by Mubdi Rahman, Ph.D, on

    “The Grammar and Tools of Data Visualization in the Era of Big Data”

    For sign up and more information, see https://courses.scinet.utoronto.ca/424

  • ADVANCED LINUX SHELL PROGRAMMING Wednesday February 13, 1:00 pm – 4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/431

  • INTRO TO SCINET AND NIAGARA Wednesday March 13, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and registration, go to https://courses.scinet.utoronto.ca/420

  • SCINET USER GROUP MEETING Wednesday March 13, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk TBA.

    For sign up and more information, see https://courses.scinet.utoronto.ca/425

  • INTRODUCTION TO THE LINUX SHELL Wednesday March 13, 1:00 pm -4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/429

  • INTRO TO SCINET AND NIAGARA Wednesday April 10, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and registration, go to https://courses.scinet.utoronto.ca/420

  • SCINET USER GROUP MEETING Wednesday April 10, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk by Anjali Silva on

    “Bayesian Model-Based Clustering Approaches for Discrete-Valued Gene Expression Data”

    For sign up and more information, see https://courses.scinet.utoronto.ca/425

  • ADVANCED LINUX COMMAND LINE Wednesday April 10, 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 SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/432

  • INTRODUCTION TO NEURAL NETWORK PROGRAMMING Starting April 23, 6 weeks, Tuesdays and Thursdays 11:00 am – 12:00 noon SciNet Teaching Room

    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 3.7; 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 SciNet Data Science Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/417

  • RELATIONAL DATABASE BASICS Wednesday May 1, 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 SciNet Data Science Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/433

  • INTRO TO SCINET AND NIAGARA Wednesday May 8, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and registration, go to https://courses.scinet.utoronto.ca/422

  • SCINET USER GROUP MEETING Wednesday May 8, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk TBA.

    For sign up and more information, see https://courses.scinet.utoronto.ca/427

  • INTRODUCTION TO THE LINUX SHELL Wednesday May 8, 1:00 pm -4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/430

  • COMPUTE ONTARIO SUMMER SCHOOL Summer 2019

    The Compute Ontario Summer School on Scientific and High Performance Computing is an annual educational event for graduate/undergraduate students, postdocs and researchers to learn and share knowledge and experience in high performance and technical computing on modern HPC platforms.

    As in previous years, the 2019 Summer School is expected to have three installments, “West”, “Central”, and “East”. Each will be a week-long event with multiple parallel streams.

    More details will be announced later in 2019.

  • SCALING TO PETASCALE INSTITUTE August 19-23, 2019

    This will be a free virtual advanced HPC summer school, organized by a number of the US XSEDE sites, also hosted at SciNet. Topics will likely include OpenMP, MPI, CUDA, and OpenACC.

    More details will be announced later in 2019.

SciNet News February 2019

February 4, 2019 in for_researchers, for_users, newsletter

Summary

  • Two additional ways to interact with the nearline/archive HPSS system: Globus and a Virtual File System.
  • Announcement of several techtalks at the SciNet User Group Meetings.

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 News

Events Coming Up

Unless stated otherwise, all events listed below are free of charge and take place at the SciNet Teaching Room or Boardroom at our offices on the eleventh floor of the MaRS West Tower, suite 1140A (661 University Avenue, Toronto ON M5G 1M1).

Most events are recorded and some are broadcast, but only some of the courses can be taken remotely for SciNet certificate credits.

Registration for SciNet courses should be done by logging into https://courses.scinet.utoronto.ca with your Compute Canada account (the same one that you use to log into Niagara).

  • INTRO TO SCINET AND NIAGARA Wednesday February 13, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and registration, go to https://courses.scinet.utoronto.ca/419

  • SCINET USER GROUP MEETING Wednesday February 13, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk by Mubdi Rahman, Ph.D, on

    “The Grammar and Tools of Data Visualization in the Era of Big Data”

    For sign up and more information, see https://courses.scinet.utoronto.ca/424

  • ADVANCED LINUX SHELL PROGRAMMING Wednesday February 13, 1:00 pm – 4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/431

  • INTRO TO SCINET AND NIAGARA Wednesday March 13, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and registration, go to https://courses.scinet.utoronto.ca/420

  • SCINET USER GROUP MEETING Wednesday March 13, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk TBA.

    For sign up and more information, see https://courses.scinet.utoronto.ca/425

  • INTRODUCTION TO THE LINUX SHELL Wednesday March 13, 1:00 pm -4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/429

  • INTRO TO SCINET AND NIAGARA Wednesday April 10, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and registration, go to https://courses.scinet.utoronto.ca/420

  • SCINET USER GROUP MEETING Wednesday April 10, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk by Anjali Silva on

    “Bayesian Model-Based Clustering Approaches for Discrete-Valued Gene Expression Data”

    For sign up and more information, see https://courses.scinet.utoronto.ca/425

  • ADVANCED LINUX COMMAND LINE Wednesday April 10, 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 SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/432

  • INTRODUCTION TO NEURAL NETWORK PROGRAMMING Starting April 23, 6 weeks, Tuesdays and Thursdays 11:00 am – 12:00 noon SciNet Teaching Room

    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 3.7; 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 SciNet Data Science Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/417

  • RELATIONAL DATABASE BASICS Wednesday May 1, 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 SciNet Data Science Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/433

  • INTRO TO SCINET AND NIAGARA Wednesday May 8, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and registration, go to https://courses.scinet.utoronto.ca/422

  • SCINET USER GROUP MEETING Wednesday May 8, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk TBA.

    For sign up and more information, see https://courses.scinet.utoronto.ca/427

  • INTRODUCTION TO THE LINUX SHELL Wednesday May 8, 1:00 pm -4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/430

  • COMPUTE ONTARIO SUMMER SCHOOL Summer 2019

    The Compute Ontario Summer School on Scientific and High Performance Computing is an annual educational event for graduate/undergraduate students, postdocs and researchers to learn and share knowledge and experience in high performance and technical computing on modern HPC platforms.

    As in previous years, the 2019 Summer School is expected to have three installments, “West”, “Central”, and “East”. Each will be a week-long event with multiple parallel streams.

    More details will be announced later in 2019.

  • SCALING TO PETASCALE INSTITUTE August 19-23, 2019

    This will be a free virtual advanced HPC summer school, organized by a number of the US XSEDE sites, also hosted at SciNet. Topics will likely include OpenMP, MPI, CUDA, and OpenACC.

    More details will be announced later in 2019.

SciNet News January 2019

January 4, 2019 in for_researchers, for_users, newsletter

Summary

  • Full datacentre maintenance shutdown on January 15 and 16, 2019.
  • Winter training and education schedule open for registration.
  • Application for International HPC Summer School in Japan in July are still open until February 4th 2019.

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 News: Maintenance Shutdown

The SciNet datacentre will undergo a two-day maintenance shutdown on January 15th and 16th 2019, starting at 7 am EST on the 15th. There will be no access to any of the SciNet systems (Niagara, P7, P8, BGQ, SGC, HPSS, Teach cluster, or the filesystems) during this time.

This is in preparation for the upcoming installation of an emergency power generator and a larger UPS, which will result in increased resilience to power glitches and outages.

It is expected that the system will be available to users late on Wednesday January 16th, 2019

The status of the Niagara cluster can be checked on status.computecanada.ca. For up-to-date and more detailed information on the status of all the SciNet systems, check https://docs.scinet.utoronto.ca.

Events Coming Up

Unless stated otherwise, all events listed below take place at the SciNet Teaching Room or Boardroom at our offices on the eleventh floor of the MaRS West Tower, suite 1140A (661 University Avenue, Toronto ON M5G 1M1).

Most events are recorded and some are broadcast, but only some of the courses can be taken remotely for SciNet certificate credits.

Registration for SciNet courses should be done by logging into https://courses.scinet.utoronto.ca with your Compute Canada account (the same one that you use to log into Niagara).

  • INTRO TO SCINET AND NIAGARA Wednesday Jan 16, 2019, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and (free) registration, go to https://courses.scinet.utoronto.ca/418

    Further sessions of this Intro are planned for February 13, March 13, April 10 and May 8, 2019.

  • SCINET USER GROUP MEETING Wednesday Jan 16, 2019, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk TDB

    For sign up and more information, see https://courses.scinet.utoronto.ca/423

    Further SNUG sessions are planned for: February 13, March 13, April 10, and May 8, 2019.

  • INTRODUCTION TO THE LINUX SHELL Wednesday January 16, 10:00 am – 12:00 noon SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/428

    Further “Intro to the Linux shell” sessions are planned for: March 13 and May 8, 2019.

  • APPLICATION DEADLINE FOR INTERNATIONAL HPC SUMMER SCHOOL Applications due: February 4, 2019 Event dates: July 7-12, 2019 Location: Kobe, Japan

    This summer school will 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. Leading Canadian, European, Japanese and American computational scientists and HPC technologists will offer instruction in parallel sessions on a variety of topics as: HPC challenges in major scientific disciplines, HPC programming proficiencies, Performance analysis and profiling, Software engineering, Numerical libraries, Big data analysis and analytics, Machine learning, Scientific visualization, and Canadian, European, Japanese and US HPC infrastructure.

    SciNet invites students and early-career post-docs in science, engineering, and other fields at Canadian post-secondary institutions to apply for one of the eight spots allocated to Canada. Travel, lodging and meal expenses of the selected candidates will be covered.

    For more information and application see https://ss19.ihpcss.org.

  • ADVANCED LINUX SHELL PROGRAMMING Wednesday February 13, 1:00 pm – 4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/431

    Another “Advanced Shell Programming” session is planned for April 10, 2019.

  • SCIENTIFIC COMPUTING FOR PHYSICISTS (PHY1610) Winter 2019, starting January 8 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://courses.scinet.utoronto.ca/398

  • QUANTITATIVE APPLICATIONS FOR DATA ANALYSIS Winter 2019, starting January 9 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://courses.scinet.utoronto.ca/403

  • INTRODUCTION TO NEURAL NETWORK PROGRAMMING Starting April 23, 2019, 6 weeks, Tuesdays and Thursdays 11:00 am – 12:00 noon SciNet Teaching Room

    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 3.7; 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 SciNet Data Science Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/417

  • RELATIONAL DATABASE BASICS Wednesday May 1, 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 SciNet Data Science Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/433

  • COMPUTE ONTARIO SUMMER SCHOOL Summer 2019

    The Compute Ontario Summer School on Scientific and High Performance Computing is an annual educational event for graduate/undergraduate students, postdocs and researchers to learn and share knowledge and experience in high performance and technical computing on modern HPC platforms.

    As in previous years, the 2019 Summer School is expected to have three installments, “West”, “Central”, and “East”. Each will be a week-long event with multiple parallel streams.

    More details will be announced later in 2019.

  • SCALING TO PETASCALE INSTITUTE August 19-23, 2019

    This will be a free virtual advanced HPC summer school, organized by a number of the US XSEDE sites, also hosted at SciNet. Topics will likely include OpenMP, MPI, CUDA, and OpenACC.

    More details will be announced later in 2019.

SciNet News December 2018

December 4, 2018 in for_researchers, for_users, newsletter

Summary

  • The full datacentre shutdown that was originally scheduled for December 18, 2018, is postponed to January 15 and 16, 2019, and combined with annual maintenance.
  • While the University of Toronto will be closed from Dec 22 to Jan 6. SciNet support will be on a “best effort” basis.
  • Time limits of jobs on Niagara are now 24 hours for all users.
  • Winter training and education schedule announced.
  • Application for International HPC Summer School in Japan in July is open.

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 News

  • The SciNet datacentre will undergo a two-day maintenance shutdown on January 15th and 16th 2019, starting at 7 am EST on the 15th. There will be no access to any of the SciNet systems (Niagara, P7, P8, BGQ, SGC, HPSS, Teach cluster, or the filesystems) during this time.

    This is in preparation for the upcoming installation of an emergency power generator and a larger UPS, which will result in increased resilience to power glitches and outages.

    The status of the Niagara cluster can be checked on status.computecanada.ca. For up-to-date and more detailed information on the status of all the SciNet systems, you can always check https://docs.scinet.utoronto.ca.

  • The walltime limit of jobs on Niagara is now 24 hours for all users.
  • While the University of Toronto is closed from December 22, 2018 to January 6, 2019, the SciNet systems will remain available. However, support will be on a “best effort” basis during the break.

Events Coming Up

Unless stated otherwise, all events listed below take place at the SciNet Teaching Room at our offices on the eleventh floor of the MaRS West Tower, suite 1140A (661 University Avenue, Toronto ON M5G 1M1).

Most events will be recorded and some are broadcast, but only some of the courses can be taken remotely for SciNet certificate credits, as indicated below.

Registration for SciNet courses is done by logging into https://support.scinet.utoronto.ca/education with your Compute Canada account (the same one that you use to log into Niagara).

  • INTRO TO SCINET AND NIAGARA Wednesday Jan 16, 2019, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and (free) registration, go to https://courses.scinet.utoronto.ca/418

    Further sessions of this Intro are planned for February 13, March 13, April 10 and May 8, 2019.

  • SCINET USER GROUP MEETING Wednesday Jan 16, 2019, 12:00 noon – 1:00 pm SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

    Pizza, user discussion, and a tech talk TDB

    For sign up and more information, see https://courses.scinet.utoronto.ca/423

    Further SNUG sessions are planned for: February 13, March 13, April 10, and May 8, 2019.

  • INTRODUCTION TO THE LINUX SHELL Wednesday January 16, 10:00 am – 12:00 noon SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/428

    Further “Intro to the Linux shell” sessions are planned for: March 13 and May 8, 2019.

  • ADVANCED LINUX SHELL PROGRAMMING Wednesday February 13, 1:00 pm – 4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/431

    Another “Advanced Shell Programming” session is planned for April 10, 2019.

  • SCIENTIFIC COMPUTING FOR PHYSICISTS (PHY1610) Winter 2019, starting January 8 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://courses.scinet.utoronto.ca/398

  • QUANTITATIVE APPLICATIONS FOR DATA ANALYSIS Winter 2019, starting January 9 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://courses.scinet.utoronto.ca/403

  • INTRODUCTION TO NEURAL NETWORK PROGRAMMING Starting April 23, 2019, 6 weeks, Tuesdays and Thursdays 11:00 am – 12:00 noon SciNet Teaching Room

    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 3.7; 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 SciNet Data Science Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/417

  • RELATIONAL DATABASE BASICS Wednesday May 1, 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 SciNet Data Science Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/433

  • INTERNATIONAL HPC SUMMER SCHOOL July 7-12, 2019 Kobe, Japan

    This summer school will 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. Leading Canadian, European, Japanese and American computational scientists and HPC technologists will offer instruction in parallel sessions on a variety of topics as: HPC challenges in major scientific disciplines, HPC programming proficiencies, Performance analysis and profiling, Software engineering, Numerical libraries, Big data analysis and analytics, Machine learning, Scientific visualization, and Canadian, European, Japanese and US HPC infrastructure.

    SciNet invites students and early-career post-docs in science, engineering, and other fields at Canadian post-secondary institutions to apply for one of the eight spots allocated to Canada. Travel, lodging and meal expenses of the selected candidates will be covered.

    Applications are due February 4, 2019.

    For more information and application see https://ss19.ihpcss.org.

  • COMPUTE ONTARIO SUMMER SCHOOL Summer 2019

    The Compute Ontario Summer School on Scientific and High Performance Computing is an annual educational event for graduate/undergraduate students, postdocs and researchers to learn and share knowledge and experience in high performance and technical computing on modern HPC platforms.

    As in previous years, the 2019 Summer School is expected to have three installments, “West”, “Central”, and “East”. Each will be a week-long event with multiple parallel streams.

    More details will be announced later in 2019.

  • SCALING TO PETASCALE INSTITUTE Summer 2019

    This will be a free virtual advanced HPC summer school, organized by a number of the US XSEDE sites, also hosted at SciNet. Topics will likely include OpenMP, MPI, CUDA, and OpenACC.

    More details will be announced later in 2019.

SciNet News September 2018

September 14, 2018 in for_researchers, for_users, newsletter

SUMMARY

  • Niagara takes the number 53 spot in the June 2018 TOP500 list of supercomputers (https://www.top500.org/list/2018/06).
  • Scratch purging policy on Niagara is in effect.
  • Burst buffer available on demand.
  • Various SciNet courses and events to start next week, including a “Intro to Niagara/SciNet” session and a TechTalk on “Machine Learning Cosmic Structure Formation” on Sept 12.
  • SciNet’s Jupyterhub with access to files on Niagara is online.
  • my.SciNet website with access to your Niagara jobs records is online.
  • Courses website now accessible with your Compute Canada password.

SYSTEM NEWS

EVENTS COMING UP

Registration for SciNet courses is done by logging into https://courses.scinet.utoronto.ca with your Compute Canada username
and password.

Many of the events are at the teaching room or boardroom in the SciNet offices on the eleventh floor of the MaRS West Tower, suite 1140A (661 University Avenue, Toronto ON M5G 1M1). SciNet events are often recorded and broadcast (see the courses site for links).

  • INTRO TO SCINET AND NIAGARA
    Wednesday Sept 12, 2018, 10:00 am – 11:30 am
    SciNet Boardroom (suite 1140, 661 University Avenue, Toronto).

    This is a class of approximately 90 minutes to introduce SciNet and the new supercomputer Niagara and teach you how to use Niagara.

    Participation counts towards the SciNet HPC Certificate.

    For more information and (free) registration, go to https://courses.scinet.utoronto.ca/404

  • SCINET USER GROUP MEETING
    Wednesday Sept 12, 2018, 12:00 noon – 1:00 pm
    SciNet Boardroom (suite 1140, 661 University Avenue, Toronto).

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

    The TechTalk will be on

    MACHINE LEARNING COSMIC STRUCTURE FORMATION

    by George Stein (Dept. of Astronomy-UofT, CITA).

    Abstract: In modern astrophysics and cosmology, accurate simulations of the large scale structure of the universe are necessary. Usually, this is accomplished by so called N-body simulations, which calculate the full gravitational collapse of a region of the universe over its 14 billion year history. Instead of calculating this costly gravitational evolution, we trained a three-dimensional deep Convolutional Neural Network (CNN) to identify dark matter proto-haloes directly from the cosmological initial conditions, and showed that a CNN of this type can be a viable alternative in some cases. In this talk I will discuss current cosmological simulations and the invasion of machine learning techniques, with a focus on our work. For more information see https://arxiv.org/abs/1805.04537.

    For sign up and more information, see https://courses.scinet.utoronto.ca/410

  • INTRODUCTION TO COMPUTATIONAL BIOSTATISTICS WITH R (MSC1090)
    Tuesdays and Thursday, 11 am – 12 noon
    Twelve weeks starting Sept 12.

    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.

    This course will be recorded, but not broadcast.

    For more information, see https://courses.scinet.utoronto.ca/399

  • INTRODUCTION TO THE LINUX SHELL
    Wednesday Sept 19, 1:00 pm – 4:00 pm
    Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    Working with many of the HPC systems in Ontario 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. This hands on session will cover basic commands and scripting. It could be a great boon for your productivity!

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/407

  • INTRODUCTION TO PROGRAMMING
    Tuesdays and Thursdays, 1:00 pm – 2:00 pm
    Four weeks starting Oct 2.
    Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    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.

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/401

  • INTRO TO SCINET AND NIAGARA
    Wednesday Oct 10, 2018, 10:00 am – 11:30 am
    SciNet Boardroom (suite 1140, 661 University Avenue, Toronto).

    This is a class of approximately 90 minutes to introduce SciNet and the new supercomputer Niagara and teach you how to use Niagara.

    Participation counts towards the SciNet HPC Certificate.

    For more information and (free) registration, go to https://courses.scinet.utoronto.ca/405

  • SCINET USER GROUP MEETING
    Wednesday Oct 10, 2018, 12:00 noon – 1:00 pm
    SciNet Boardroom (suite 1140, 661 University Avenue, Toronto).

    The SciNet Users Group (SNUG) meetings are every month on the second Wednesday (except during the summer), and involve pizza, user
    discussion, feedback, and a half-hour talk (TBA) on topics or technologies of interest to the SciNet community. We’ll likely
    discuss the upcoming Resource Allocation Competition.

    For sign up and more information, see https://courses.scinet.utoronto.ca/411

  • ADVANCED SHELL PROGRAMMING
    Wednesday Oct 17, 2018, 1:00 pm – 4:00 pm
    Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/409

  • NUMERICAL COMPUTING WITH PYTHON
    Tuesdays and Thursdays, 1:00 pm – 2:00 pm
    Four weeks, starting Nov 6, 2017 (skipping the week of Nov 12-16)
    Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    Learn about research computing even with little programming experience. Covers programming in python, best practices and
    visualization. Some experience with python is required. Four home work sets will be the basic of the evaluation.

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/402

  • INTRO TO SCINET AND NIAGARA
    Wednesday Nov 14, 2018, 10:00 am – 11:30 am
    SciNet Boardroom (suite 1140, 661 University Avenue, Toronto)

    This is a class of approximately 90 minutes to introduce SciNet and the new supercomputer Niagara and teach you how to use Niagara.

    Participation counts towards the SciNet HPC Certificate.

    For more information and (free) registration, go to https://courses.scinet.utoronto.ca/406

  • INTRODUCTION TO THE LINUX SHELL
    Wednesday Nov 21, 1:00 pm – 4:00 pm
    Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    Working with many of the HPC systems in Ontario 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. This hands on session will cover basic commands and scripting. It could be a great boon for your productivity!

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://courses.scinet.utoronto.ca/407

  • SCIENTIFIC COMPUTING FOR PHYSICISTS (PHY1610)
    Winter 2019
    Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    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://courses.scinet.utoronto.ca/398

  • QUANTITATIVE APPLICATIONS FOR DATA ANALYSIS
    Winter 2019
    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://courses.scinet.utoronto.ca/403

As always, further details can be found below on the SciNet courses siteand the SciNet wiki.

SciNet News June 2018

June 4, 2018 in for_users, newsletter

SUMMARY

  • Scratch purging policy on Niagara starts July 16.
  • Niagara takes it place at the number 53 spot in the top500.
  • Preliminary fall training and education schedule

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 NEWS

  • Scratch purging policy on Niagara starts July 16.
  • Niagara takes it place at the number 53 spot in the top500.
  • Burst Buffer, a fast storage tier between the general parallel file system and system memory, is sto;; available for groups with high I/O needs, upon request. See https://docs.scinet.utoronto.ca/index.php/Burst_Buffer

EVENTS COMING UP

Unless stated otherwise, all events listed below take place at the SciNet Teaching Room at our offices on the eleventh floor of the MaRS West Tower, suite 1140A (661 University Avenue, Toronto ON M5G 1M1).

Most events will be recorded and some are broadcast, but only some of the courses can be taken remotely for SciNet certificate credits, as indicated below.

Registration for SciNet courses is done by logging into https://support.scinet.utoronto.ca/education with your SciNet account.

More SciNet courses will be announced at the end of the summer.

  • INTRO TO SCINET/NIAGARA Wednesday Sept 23, 2018, 10:00 am – 11:30 am SciNet Boardroom (suite 1140, 661 University Avenue, Toronto ON M5G 1M1).

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and (free) registration, go to https://support.scinet.utoronto.ca/education/go.php/396/index.php

  • COMPUTE ONTARIO SUMMER SCHOOL EAST June 11 – 15, University of Toronto, St. George Campus New College, University of Toronto, 40 Willcocks St., Toronto, M5S 1C6

    The Compute Ontario Summer School on Scientific and High Performance Computing is an annual educational event for graduate/undergraduate students, postdocs and researchers to learn and share knowledge and experience in high performance and technical computing on modern HPC platforms.

    As in previous years, the Summer School on High Performance Computing 2014 will have three installments:

    “West” May 28 – June 1 Western University, London “Central” June 11 – June 15 University of Toronto, Toronto “East” July 30 – August 3 Queen’s University, Kingston

    Registration for the school in London and Kingston is at https://www.sharcnet.ca/summerschool/2018, while registration for the summer school in Toronto is at https://support.scinet.utoronto.ca/education/go.php/368/index.php

    The Toronto summer school hosted by SciNet will have the following three streams: Stream 1: High Performance computing; Stream 2: Data Science; Stream 3: Biomedical. Instructors are from SciNet, SHARCNET, and CAMH.

    This event will not be held at the SciNet Offices, rather it will be at New College on the Downtown St. George Campus of the University of Toronto.

    Parts of this event count towards the SciNet Certificates.

    More details and registration can be found at https://support.scinet.utoronto.ca/education/go.php/368/index.php

  • ADVANCED PARALLEL SCIENTIFIC COMPUTING Mondays and Wednesdays, 1 pm – 2pm Four weeks starting Sept 11. Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    In this course, we will be exploring advanced examples of parallel computing in scientific research. Topics include HPC tools, CUDA, molecular dynamics, Monte Carlo and random number generation, smoothed particle hydrodynamics, N-body simulations and computational fluid dynamics.

    The format of the course will be two lectures of one hour, for four consecutive weeks. The participants are expected to choose a project that involves analyzing and improving a parallel research code from one of the topic presented in the lectures, and to present their findings two weeks after the end of the course.

    The lectures of this course will be broadcast and recorded. Remote participation for credit may be possible upon request.

    Familiarity with parallel programming (MPI/OpenMP/CUDA) in a compiled language (C/C++/Fortran) is a prerequisite of this course.

    This class counts as 12 credit-hours towards the SciNet HPC Certificate. It can also be taken as a modular course by Physics grad students and as a mini course by Astrophysics students.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/317/index.php

  • INTRODUCTION TO CLINICAL BIOSTATISTICS (MSC1090) Tuesdays and Thursday, 11 am – 12 noon Twelve weeks starting Sept 12.

    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).

    Unfortunately, this course is full, but we are exploring the possibility of giving it again in the Winter term.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/324/index.php

  • INTRO TO SCINET Sept 13, 10:00 am – 11:30 am

    In about 90 minutes, you will learn how to use the SciNet systems. Experienced users may still pick up some valuable pointers.

    Participation counts towards the SciNet HPC Certificate.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/329/index.php

  • SCINET USER GROUP MEETING Sept 13, 12:00 noon – 1:00 pm Boardroom (MaRS West Tower, 661 University Ave, Toronto, suite 1140)

    Pizza, user discussion, and a tech talk: “ChIP-Seq analysis of the Interactive Bromodomain 1 protein (Ibd1) in Tetrahymena thermophila”, by Alejandro Saettone (Ryerson University)

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/301/index.php

  • INTRODUCTION TO NEURAL NETWORK PROGRAMMING Sept 25, 10:00 am – 3:00 pm Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    This workshop will introduce neural network programming concepts, theory, and techniques. The level of the material will be introductory, intended for those with no experience with neural networks. The programming language will be Python 2.7; experience with Python programming will be assumed. The Keras neural network framework, with a Theano back end, will be used for more-advanced programming; no experience with Keras or Theano will be expected. Students should come with the following Python packages installed on their laptops: numpy, matplotlib, scikit-learn, theano (version 0.9.0 or greater), keras.

    Participation counts towards the SciNet Data Science Certificate.

    You can also view this event’s broadcast, but this would not count towards the certificate.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/338/index.php

  • INTRODUCTION TO THE LINUX SHELL Sept 27, 10:00 am – 12:00 noon Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/330/index.php

  • ADVANCED NEURAL NETWORKS Mondays from 11:00 am to 12:00 noon Four weeks starting Oct 2. Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    This class will review advanced neural network programming theory and architectures. The level of the material will not be introductory, experience with neural networks will be assumed. This class is intended to continue the material covered in “Introduction to Neural Network Programming” (see above).

    Participation counts towards the SciNet Data Science Certificate.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/325/index.php

  • INTRODUCTION TO PROGRAMMING Tuesdays and Thursdays, 1:00 pm – 2:00 pm Four weeks starting Oct 10. Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    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.

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/328/index.php

  • ADVANCED SHELL PROGRAMMING Oct 25, 1:00 pm – 4:00 pm Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/331/index.php

  • INTRO TO SCIENTIFIC COMPUTING WITH PYTHON Tuesdays and Thursdays, 1:00 pm – 2:00 pm Four weeks, starting Nov 7, 2017 Teaching Room 1140A (MaRS West Tower, 661 University Ave, Toronto)

    Learn about research computing even with little programming experience. Covers programming in python, best practices and visualization. Some experience with python is required. Four home work sets will be the basic of the evaluation.

    Participation counts towards the SciNet Scientific Computing Certificate.

    The lectures of this course will be broadcast and recorded. Remote participation for credit may be possible upon request.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/327/index.php

  • SCIENTIFIC COMPUTING FOR PHYSICISTS (PHY1610) Winter 2018

    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, …).

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/326/index.php