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

SciNet News August 2016

August 29, 2016 in for_researchers, for_users, newsletter

The SciNet offices have moved to a new home! We are now located in the MaRS West Tower on the eleventh floor (address: 661 University Ave., Suite 1140 Toronto, ON M5G 1M1). As in our old spot, users, students, and friends are still welcome to visit our new abode, however, because we are still getting settled in, it is recommended to schedule a meeting (by emailing support AT scinet.utoronto.ca).

You will also find the announcement of SciNet course offerings in the 2016-2017 academic year. Users that take a sufficient number of courses can earn one of the SciNet certificates. In addition, many of our courses can now be taken for credit towards PhD and MSc programs by graduate students from several departments across the University of Toronto, including Institute of Medical Sciences, Ecology and Evolutionary Biology, Chemistry, Astrophysics, and Physics.

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

SUMMARY

  • SciNet offices have moved.
  • SciNet’s Courses that can also be taken for graduate credit at the University of Toronto:
    • Advanced Parallel Scientific Computing
    • Introduction to Data Analysis with R
    • Introduction to Scientific Computing with Python
    • Scientific Computing for Physicists
  • SciNet’s Training Events: Intro to SciNet, Intro to Linux Shell, Storage and I/O in Large Scale Scientific Projects, SciNet User Group Meetings.
  • HPSS: Now also accessible via Globus.
  • GPC: New versions of ParaView and VisIt, and beagle for GPUs available as modules.
  • GPC: New web portal with records of your completed GPC jobs available for testing at https://my.scinet.utoronto.ca.
  • BGQ: Upgraded toolchain and operating system.
  • P8: We now have two Power 8 boxes with GPUs available for testing.

SCINET OFFICE MOVE

The SciNet offices have moved to a new home! We are now located in brand new offices on the eleventh floor of the new MaRS West Tower at the corner of College Street and University Avenue. Our new address is

661 University Ave
Suite 1140
Toronto, ON M5G 1M1

As was the case when we were in our old spot, users, students, and friends are still welcome to visit, however, because we are still getting settled in, we recommend that you first schedule a meeting by emailing support AT scinet.utoronto.ca.

Many of our courses, training sessions and user group meetings will be given in the new location, either in our new conference room or in our new classroom.

EVENTS COMING UP

Unless stated otherwise, all events take place at the SciNet Headquarters, now located on the eleventh floor of 661 University Ave., MaRS West Tower, suite 1140 (look for the bright orange reception area).

Most events will be recorded and some are broadcasted, but only some of the courses can be taken remotely for SciNet certificate credits, as indicated below. All events at SciNet are free but we ask that you enroll on the education website: https://support.scinet.utoronto.ca/education .

Courses that can be taken for credit at the UoT

  • ADVANCED PARALLEL COMPUTING
    8 Lectures, Tuesdays and Thursdays starting Sept 20, 11:00 am – 12:00 pm

    Explore advanced use case examples of parallel computing in scientific research.

    The course can be taken as a mini/modular graduate course by Physics, Astronomy, and Chemistry students.

    This course counts toward the High Performance Computing Certificate.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/263/index.php

  • INTRODUCTION TO DATA ANALYSIS WITH R
    12 Lectures, Tuesdays and Thursdays starting Oct 11, 12:00 pm – 1:00 pm

    The goal of this course is to prepare 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 practices to store, manage and analyze (large) data.

    For students in the Institute of Medical Science, this course can be taken as “Seminars in Translational Research” (MSC1010Y-1011Y)

    Graduate students from the Department of Ecology & Evolutionary Biology (EEB) at UofT can take this course for graduate credit as well. Interested students from the EEB department should contact Prof. Helen Rodd in advance.

    Physics, Astrophysics and Chemistry students can take this course as part of the mini/modular graduate courses.

    This course also counts toward the SciNet’s Data Science Certificate.

    Location: St.George Campus, specific room TBD.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/262/index.php

  • SCIENTIFIC COMPUTING WITH PYTHON
    8 Lectures, Tuesdays and Thursdays starting Nov 15, 11:00 am – 12:00 pm

    Learn about research computing even with little programming experience. Covers basics of programming in Python, best practices and visualization. The course will last 4 weeks with 2 lectures per week.

    The course can be taken as a mini/modular graduate course by Physics, Astronomy and Chemistry students. This course can also be taken by students for graduate credits from the Department of Ecology & Evolutionary Biology (EEB) at the UofT. Interested students from the EEB department should contact Prof. Helen Rodd in advance.

    This course counts toward the Scientific Computing Certificate and (partially) toward the High Performance Computing Certificate.

    Although in-person attendance is highly preferred, SciNet users can take this course remotely by following the lectures online and submitting the assignments.

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/264/index.php

  • SCIENTIFIC COMPUTING FOR PHYSICISTS
    Physics graduate course (PHY1610)

    Winter 2017

    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 can be taken for credit by Physics graduate students, and by other graduate students that are allowed to take physics courses, however, they are strongly encourage to check this with their graduate coordinators first.

    Part of this course may be given as mini-courses as well. Details on this will follow later.

    This course counts toward the Scientific Computing Certificate and the High Performance Computing Certificate.

    Although in-person attendance is highly preferred, SciNet users can take this course remotely by following the lectures online and submitting the assignments.

SciNet Training Events

  • INTRO TO SCINET
    Wed 14th Sept 10:00 am – 11:30 am

    The “Intro to SciNet” is a class of approximately 60-90 minutes where you will learn how to use the systems. Experienced users may still pick up some valuable pointers during these sessions.

    Participation counts towards the SciNet HPC Certificate.

    If you are interested to participate remotely using Google Hangout, please send an email with your gmail address to which we can send the invitation.

    Location: SciNet conference room (MaRS West Tower, 11th floor)

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/267/index.php

    Future “Intro to SciNet” dates and enrollment links:
    Oct 12, 10:00 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/269/index.php
    Nov 9, 10:00 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/268/index.php
    Dec 14, 10:00 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/270/index.php
    Jan 11, 10:00 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/296/index.php
    Mar 8, 10:00 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/297/index.php
    May 10, 10:00 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/302/index.php

  • SCINET USER GROUP MEETING
    Wed 14th Sept 12:00 pm – 1:00 pm

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

    Location: SciNet conference room (MaRS West Tower, 11th floor)

    For sign up, see https://support.scinet.utoronto.ca/education/go.php/291/index.php

    Future “SNUG” dates and enrollment links:
    Oct 12, 12:00 noon – 1:00 pm: https://support.scinet.utoronto.ca/education/go.php/292/index.php
    Nov 9, 12:00 noon – 1:00 pm: https://support.scinet.utoronto.ca/education/go.php/293/index.php
    Dec 14, 12:00 noon – 1:00 pm: https://support.scinet.utoronto.ca/education/go.php/294/index.php
    Jan 11, 12:00 noon – 1:00 pm: https://support.scinet.utoronto.ca/education/go.php/295/index.php
    Feb 8, 12:00 noon – 1:00 pm: https://support.scinet.utoronto.ca/education/go.php/298/index.php
    Mar 8, 12:00 noon – 1:00 pm: https://support.scinet.utoronto.ca/education/go.php/299/index.php
    Apr 12, 12:00 noon – 1:00 pm: https://support.scinet.utoronto.ca/education/go.php/300/index.php
    May 10, 12:00 noon – 1:00 pm: https://support.scinet.utoronto.ca/education/go.php/301/index.php

  • STORAGE AND I/O IN LARGE SCALE SCIENTIFIC PROJECTS
    Wed 21th Sept 09:30 am – 5:00 pm

    Location: SciNet classroom (MaRS West Tower, 11th floor)

    Learn how to pinpoint and alleviate bottlenecks in large data-driven research projects. Techniques such as tar, compression, ramdisk, file format options, and job scheduling techniques will be covered.

    For sign up, see https://support.scinet.utoronto.ca/education/go.php/265/index.php

  • INTRODUCTION TO THE LINUX SHELL
    Wed 19th Oct 10:00 am – 1:00 pm

    The Linux shell (command line, or however you want to phrase it) is the most basic Linux interface that there is. If you don’t know what the Linux shell is then you need to take this course!

    In this course, you will learn the basics of how to use the Unix shell in three hours. Includes a mild introduction to bash scripting as well. This course counts toward the Scientific Computing Certificate.

    Location: SciNet classroom (MaRS West Tower, 11th floor)

    For sign up and more information, see https://support.scinet.utoronto.ca/education/go.php/266/index.php

SYSTEM CHANGES

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

  • HPSS: If you have an HPSS account, this is now also accessible from the Globus file transfer web-interface. Globus is accessible through https://globus.computecanada.ca, where you’d login with your Compute Canada account, while the name of the HPSS endpoint is “Compute Canada HPSS”, for which you separately authenticate with your SciNet account. For more information on using Globus, see https://docs.computecanada.ca/wiki/Globus .
  • GPC: New web portal with records of your completed GPC jobs available for testing at https://my.scinet.utoronto.ca.
  • GPC: Beagle GPU-version available for testing under the use.experimental module.
  • GPC: Python distribution Anaconda v4.x installed as a module
  • GPC: VisIt version 2.10.2 installed as a module
  • GPC: ParaView version 5.1.0 installed as a module
  • GPC: Versions 15.0.6 and 16.0.3 of the Intel Compilers are installed as modules.
  • GPC: Version 6.0 of Allinea Forge (containing the DDT parallel debugger, the profiler MAP and Performance Reports) installed as a module.
  • GPC: Gromacs v. 5.1.1 installed as modules (GPU and non-GPU).
  • GPC: Chemistry package Cantera installed as a module.
  • BGQ: Upgraded compute nodes and toolchain to V1R2M4 from V1R2M2. Note that this means that when recompiling applications, one has to start from scratch (i.e., no old object files).
  • BGQ: Front end nodes operating system was updated to RedHat 6.7. This should not change much for users.
  • P8: A new P8 system with two Power-8 machines, each with two NVIDIA Tesla K80 GPUs, is available for testing. For details, see wiki.scinet.utoronto.ca/wiki/index.php/P8

WHAT ELSE HAPPENED AT SCINET IN THE SUMMER OF 2016?

  • April: Participation of SciNet in Science Rendezvous 2016.
  • May: Visualization tutorial at 2016 “Chemical BioPhysics Symposium” and Best Practices at GLBIO 2016.
  • June: Participation of SciNet’s personnel at Canheit-HPCS 2016 (Edmonton, Alberta), and ISC (Frankfurt, Germany).
  • June: Participation of SciNet’s personnel at the International HPC Summer School (Ljubljana, Slovenia)
  • June: Intro to SciNet
  • June: SciNet User Group Meeting
  • June 21-26: International Summer School on HPC Challenges
  • May/August: Participation of SciNet’s personnel at the other instance of Ontario HPC Summer School 2016 (Hamilton and Ottawa)
  • July 11-15: Ontario HPC Summer School 2016 – Central
  • August 14-19: As part of the “2016 Industrial Problem Solving Workshop” to be hosted at the Fields Institute, SciNet will provide an introduction to High Performance Computing resources, as well as support for participants who decide to tackle this problems numerical utilizing supercomputer resources.

SciNet News April 2015

April 9, 2015 in for_researchers, for_users, newsletter

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

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

 

UPCOMING EVENTS

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

  • INTRO TO SCINET
    Wednesday April 8, 10:30 am – 11:30 am

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

    Participation counts towards the SciNet HPC Certificate.

    For more information and enrollment, go to https://support.scinet.utoronto.ca/education/go.php/172/index.php

    More intro sessions to be held in the near future: May 13, 10:30 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/173/index.php

    Jun 10, 10:30 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/174/index.php

  • SCINET USER GROUP MEETING
    Wednesday April 8, 12:00 noon – 1:00 pm

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

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

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

    For more information and enrollment, go to https://support.scinet.utoronto.ca/education/go.php/184/index.php

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

  • INTRODUCTION TO CUDA
    Tuesday April 14, 9:00 am – 5:00 pm

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

    Participation counts towards the SciNet HPC Certificate.

    For more information (soon) and enrollment, go to https://support.scinet.utoronto.ca/education/go.php/179/index.php

  • RELATIONAL DATABASE BASICS
    Wednesday May 6, 9:30 – 5:00 pm

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

    Participation counts towards the SciNet Scientific Computing Certificate.

    For more information (soon) and enrollment, go to https://support.scinet.utoronto.ca/education/go.php/186/index.php

  • XEON PHI DEVELOPER TRAINING
    Tuesday May 19 and Wednesday May 20, 9:30 am – 4:30 pm

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

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

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

    Day 1: http://events.constantcontact.com/register/event?llr=kpiwi7pab&oeidk=a07eapw56wscf327149

    Day 2: http://events.constantcontact.com/register/event?llr=kpiwi7pab&oeidk=a07eapwcqo3f9b22629

  • COMPUTE ONTARIO RESEARCH DAY
    Thursday May 21 Conestoga College Institute of Technology and Advanced Learning Cambridge, Ontario

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

    More details and registration at https://www.sharcnet.ca/events/CORD2015

  • ONTARIO HPC SUMMER SCHOOL 2015

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

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

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

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

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

    More details regarding the summer school program, location, and registration (for either of the three installments), will become available at https://www.sharcnet.ca/events/ss2015

  • HPCS 2015: HIGH PERFORMANCE COMPUTING SYMPOSIUM IN MONTREAL
    Montreal, June 15-19

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

    More information and registration can be found at http://www.hpcs.ca.

  • INTERNATIONAL SUMMER SCHOOL ON HPC CHALLENGES IN COMPUTATIONAL SCIENCES
    Sunday June 21 – Friday June 26 Toronto, Canada

    The application deadline for this event has passed. For more information see https://ihpcss2015.computecanada.ca.

 

SYSTEM NEWS

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

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

WHAT’S NEW ONLINE?

The SciNet Wiki contains technical information on how to use the systems and can be found at https://support.scinet.utoronto.ca/wiki. The SciNet Education and Training site can be found at https://support.scinet.utoronto.ca/education and contains the material of SciNet’s training and education activities.

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