SciNet Training 2024/2025

September 10, 2024 in for_researchers, for_users, frontpage, news, newsletter, Training

The following training events will be offered by SciNet in 2024/2025. Most events take place online, others are in-person in our teaching room at the SciNet offices on the St. George Campus of the University of Toronto (https://www.scinethpc.ca/contact-us/). Many of the events are recorded and posted afterwards on the sites listed below.
All events listed below are free of charge. With a few exceptions, these training courses can be taken for SciNet certificate credits.

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

A number of courses may still be added later for the Winter 2025 term.
For any questions, contact

INTRODUCTION TO NIAGARA AND MIST

Date/time: Any Time | https://scinet.courses/1352

This is new, self-guided course. At your own pace, learn how to use the SciNet systems Niagara and Mist, from securely logging in to running computations on the supercomputer. Highly recommended for new users of Niagara and Mist, but experienced users may still pick up some valuable pointers!

Format: Self-guided

Counts towards the SciNet HPC Certificate.

INTRODUCTION TO COMPUTATIONAL BIOSTATISTICS WITH R

Tue and Thu, 10:00 am – 11:30 am ET starting Sep 10 | https://scinet.courses/1353

The goal of this course is to prepare graduate students to perform scientific data analysis using the R programming language. Successful students will learn how to use statistical inference and machine-learning tools to gain insight into data sets, as well as be introduced to techniques and best practises for storing, managing and analyzing data. Topics will include: R programming, version control, modular programming, coding best practices, data analysis, machine learning and scientific visualization. This is a UofT course restricted to graduate students, but could be audited upon request.

Format: In Person

Counts towards the SciNet Scientific Computing and Data Science Certificates

INTRODUCTION TO LINUX COMMAND LINE

  1. Mon Sep 16, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1354
  2. Mon Nov 25, 1:00 pm – 4:00 pm EST | https://scinet.courses/1355
  3. Mon Mar 3, 1:00 pm – 4:00 pm EST | https://scinet.courses/1356

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

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

INTRODUCTION TO SUPERCOMPUTING

Sep 23, 25, 27, 12:30 pm – 2:00 pm EDT | https://scinet.courses/1357

An introduction to basic concepts in High-Performance Computing (HPC). This is intended to be a high-level primer for those largely new to HPC. Topic will include motivation for HPC, available HPC resources, essential issues, problem characteristics as they apply to parallelism and a high-level overview of parallel programming models.

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

SECURING FILE ACCESS PERMISSIONS ON LINUX

Fri Oct 4, 1:00 – 3:00 pm EDT | https://scinet.courses/1360

Did you know the Linux operating system has built-in tools to control which specific users and groups can access which files and directories? In this session, you will learn what these Linux permissions are, how to use the available tools to control access and sharing, and how to avoid common security pitfalls.

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

SCALING UP: MASTERING HPC

Mon Oct 28, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1359

Learn how to fully utilize the power of HPC. Discover proven strategies and tools to efficiently scale up from serial jobs to parallel runs across many compute nodes on Niagara.

Format: In Person

Counts towards the SciNet High-Performance Computing Certificate

INTRODUCTION TO PROGRAMMING WITH PYTHON

Tue and Thu from Nov 5 to Dec 5, 1:00 pm – 2:00 pm EDT | https://scinet.courses/1362

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

Format: In Person

Counts towards the SciNet Scientific Computing Certificate

INTRODUCTION TO APPTAINER

Fri Nov 29, 1:00 – 4:00 pm EST | https://scinet.courses/1363

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

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

LINUX SHELL SCRIPTING

  1. Fri Oct 25, 1:00 – 4:00 pm EDT | https://scinet.courses/1364
  2. Mon Jan 20, 1:00 – 4:00 pm EST | https://scinet.courses/1365
  3. Mon Apr 8, 1:00 – 4:00 pm EDT | https://scinet.courses/1366

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

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

GIT VERSION CONTROL

Wed Nov 6, 1:00 pm – 4:00 pm EST | https://scinet.courses/1367

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

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

INTRODUCTION TO PARALLEL PROGRAMMING

Dec 2, 4, 6, 12:30 pm – 2:00 pm EST | https://scinet.courses/1368

An introduction to concepts and techniques in parallel computing with compiled languages, e.g., C, C++ or Fortran. Both OpenMP and MPI will be introduced.

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

SCIENTIFIC COMPUTING FOR PHYSICISTS

Tue and Thu, 11:00 am – 12:00 pm ET, starting Jan 9 | https://scinet.courses/1369

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 is a UofT course restricted to graduate students, but could be audited online upon request.

Format: In Person

Counts towards the SciNet Scientific Computing and High Performance Certificates

QUANTITATIVE APPLICATIONS FOR DATA ANALYSIS

Winter 2025 | TBD

In this course data analysis techniques utilizing the Python and R languages will be introduced, as well as the basics of programming and scientific computing. The goal of this course is to prepare graduate students for performing 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. This is a UofT course restricted to graduate students, but could be audited online upon request.

Format: In Person

Counts towards the SciNet Scientific Computing and Data Science Certificates

BASH COMMAND LINE WITH COMMON IDIOMS, AWK, AND OTHERS

Mon Feb 3, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1370

This workshop explores various concise and useful constructs for working with bash shell. The goal is to improve your shell skills. Attending this class requires some basic GNU/Linux command line experience.

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

NEURAL NETWORK PROGRAMMING

Starting in April 2025 | TBD

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.

Format: TBD

Counts towards the SciNet Data Science Certificate

PYTHON AND HIGH PERFORMANCE COMPUTING

Tue Apr 22, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1371

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

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

PARALLEL DEBUGGING WITH DDT

Mon Apr 28, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1373

Debugging is an important step in developing a new code, or porting an old one to a new machine. In this session, we will discuss the debugging of frequently encountered bugs in serial code and debugging of parallel (MPI and threaded) codes using DDT.

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

RELATIONAL DATABASE BASICS

Mon May 5, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1372

Principles and uses of relational databases with practical examples using Python and Sqlite on the Niagara supercomputer.

Format: Virtual

Counts towards the SciNet Data Science Certificate

2025 COMPUTE ONTARIO SUMMER SCHOOL

June 2025, tentative, dates TBD | https://training.computeontario.ca

The Compute Ontario Summer School, jointly organized by SHARCNET, SciNet, Centre for Advanced Computing, and in collaboration with the RDM Network of Experts, offers a comprehensive curriculum packed with dozens of courses for researchers, students, and staff. These sessions are offered in parallel streams which cover a wide range of topics including Advanced Research Computing (ARC), High Performance Computing (HPC), and Research Data Management (RDM) and are available at introductory to advanced levels. Whether you are interested in a specific topic or wish to explore multiple areas, you have the freedom to register for one, some, or all of the workshops available.

Format: Virtual

SciNet Training 2023/2024

September 1, 2023 in for_researchers, for_users, frontpage, news, newsletter, Training

The following training events will be offered by SciNet in 2023/2024. Most events take place online, others are in-person in our teaching room at the SciNet offices on the St. George Campus of the University of Toronto (https://www.scinethpc.ca/contact-us/). Many of the events are recorded and posted afterwards on the sites listed below.
All events listed below are free of charge. With a few exceptions, these training courses can be taken for SciNet certificate credits.

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

A number of courses may still be added later for the Winter 2024 term.
For any questions, contact

INTRODUCTION TO NIAGARA AND MIST

  1. Wed Sep 13, 1:00 pm – 2:30 pm EDT | https://scinet.courses/1302
  2. Wed Oct 11, 1:00 pm – 2:30 pm EDT | https://scinet.courses/1306
  3. Wed Nov 8, 1:00 pm – 2:30 pm EST | https://scinet.courses/1311
  4. Wed Dec 13, 1:00 pm – 2:30 pm EST | https://scinet.courses/1315
  5. Wed Jan 10, 1:00 pm – 2:30 pm EST | https://scinet.courses/1316
  6. Wed Feb 14, 1:00 pm – 2:30 pm EST | https://scinet.courses/1319
  7. Wed Mar 13, 1:00 pm – 2:30 pm EDT | https://scinet.courses/1323
  8. Wed Apr 10, 1:00 pm – 2:30 pm EDT | https://scinet.courses/1326
  9. Wed May 8, 1:00 pm – 2:30 pm EDT | https://scinet.courses/1328
  10. Wed Jun 12, 1:00 pm – 2:30 pm EDT | https://scinet.courses/1331

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

Format: Virtual

Counts towards the SciNet HPC Certificate.

INTRODUCTION TO COMPUTATIONAL BIOSTATISTICS WITH R

Tue and Thu, 9:00 am – 10:30 am ET starting Sep 12 | https://scinet.courses/1301

The goal of this course is to prepare graduate students to perform scientific data analysis using the R programming language. Successful students will learn how to use statistical inference and machine-learning tools to gain insight into data sets, as well as be introduced to techniques and best practises for storing, managing and analyzing data. Topics will include: R programming, version control, modular programming, coding best practices, data analysis, machine learning and scientific visualization. This is a UofT course restricted to graduate students, but could be audited upon request.

Format: In Person

Counts towards the SciNet Scientific Computing and Data Science Certificates

INTRODUCTION TO LINUX COMMAND LINE

  1. Mon Sep 18, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1303
  2. Fri Dec 1, 1:00 pm – 4:00 pm EST | https://scinet.courses/1313
  3. Fri Feb 23, 1:00 pm – 4:00 pm EST | https://scinet.courses/1320

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

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

INTRODUCTION TO SUPERCOMPUTING

Sep 25, 27, 29, 12:30 pm – 2:00 pm EDT | https://scinet.courses/1304

An introduction to basic concepts in High-Performance Computing (HPC). This is intended to be a high-level primer for those largely new to HPC. Topic will include motivation for HPC, available HPC resources, essential issues, problem characteristics as they apply to parallelism and a high-level overview of parallel programming models.

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

INTRODUCTION TO PROGRAMMING WITH PYTHON

Tue and Thu from Oct 3 to Oct 26, 1:00 pm – 2:00 pm EDT | https://scinet.courses/1305

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

Format: In Person

Counts towards the SciNet Scientific Computing Certificate

INTRODUCTION TO APPTAINER

Mon Oct 16, 1:00 – 4:00 pm EDT | https://scinet.courses/1307

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

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

FROM PYTHON TO C++

Oct 31 and Nov 2 and 4, 12:30 pm – 2:00 pm EDT | https://scinet.courses/1309

C++ is a high level programming language that is extremely useful for scientific applications. The language has historically had a bad reputation, but modern C++ is much improved so that your code can be relatively short and elegant. In this workshop we will teach the basics of C++ for people who are familiar with the basics of programming, and we will especially compare and contrast C++ with Python (only the material covered in SCMP142 “Intro to Programming with Python” is required). Knowing multiple programming languages may be a useful skill: while Python is a wonderful programming language, execution speed is often a practical issue for pure Python applications. For applications where this is an issue, coding in C++ can significantly improve performance. As C++ can relatively easily be integrated in a Python project, it is also possible (and common) to code just the bottleneck in that language.

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

LINUX SHELL SCRIPTING

  1. Mon Nov 6, 1:00 – 4:00 pm EDT | https://scinet.courses/1310
  2. Mon Apr 8, 1:00 – 4:00 pm EDT | https://scinet.courses/1325

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

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

GIT VERSION CONTROL

Mon Nov 20, 1:00 pm – 4:00 pm EST | https://scinet.courses/1312

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

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

INTRODUCTION TO MPI

Dec 4, 6, 8, 12:30 pm – 2:00 pm EST | https://scinet.courses/1314

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

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

SCIENTIFIC COMPUTING FOR PHYSICISTS

Tue and Thu, 11:00 am – 12:00 pm ET, starting Jan 9 | https://scinet.courses/1296

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 is a UofT course restricted to graduate students, but could be audited online upon request.

Format: In Person

Counts towards the SciNet Scientific Computing and High Performance Certificates

EES1137 QUANTITATIVE APPLICATIONS FOR DATA ANALYSIS

Tue 10 am – 12 pm ET and Thu 11 am – 12 pm, starting Jan 9 | https://scinet.courses/1346

In this course data analysis techniques utilizing the Python and R languages will be introduced, as well as the basics of programming and scientific computing. The goal of this course is to prepare graduate students for performing 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. This is a UofT course restricted to graduate students, but could be audited online upon request.

Format: In Person

Counts towards the SciNet Scientific Computing and Data Science Certificates

FILE MANAGEMENT – PACKING SMALL FILES

Mon Jan 15, 1:00 pm – 4:00 pm EST | https://scinet.courses/1317

Managing large amounts of data can be a challenging task. Processing large numbers of files incur heavy overhead of IO communications. This course explores several options such as using Apptainer Overlay and SQLite to pack and reduce a large number of files to few files, and hence, improving IO performance. Python scripts are used throughout the course

Format: Virtual

Counts towards the SciNet Data Science Certificate

PYTHON AND HIGH PERFORMANCE COMPUTING

Mon Jan 22, 1:00 pm – 4:00 pm EST | https://scinet.courses/1318

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

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

INTRO TO GPU PROGRAMMING

Feb 26 and 28 and March 1, 12:30 pm – 2:00 pm EST | https://scinet.courses/1321

An overview of GPUs and their use in supercomputers. This workshop will explain what GPUs are, and cover the basic ideas of GPU use in scientific computing. We will introduce several GPU programming frameworks, and demonstrate how to accelerate a solution of a science problem using a GPU. Python or C++ could be used for the assignment.

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

INTRO TO OPENMP

Mon Mar 4, 1:00 pm – 4:00 pm EST | https://scinet.courses/1322

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

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

PARALLEL DEBUGGING WITH DDT

Mon Mar 25, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1324

Debugging is an important step in developing a new code, or porting an old one to a new machine. In this session, we will discuss the debugging of frequently encountered bugs in serial code and debugging of parallel (MPI and threaded) codes using DDT.

Format: Virtual

Counts towards the SciNet High Performance Computing Certificate

NEURAL NETWORK PROGRAMMING

Starting Tue Apr 23 onwards | https://scinet.courses/1327

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.

Format: TBA

Counts towards the SciNet Data Science Certificate

RELATIONAL DATABASE BASICS

Mon May 13, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1329

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

Format: Virtual

Counts towards the SciNet Data Science Certificate

BASH COMMAND LINE WITH COMMON IDIOMS, AWK, AND OTHERS

Mon May 27, 1:00 pm – 2:30 pm EDT | https://scinet.courses/1330

This workshop explores various concise and useful constructs for working with bash shell. The goal is to improve your shell skills. Attending this class requires some basic GNU/Linux command line experience.

Format: Virtual

Counts towards the SciNet Scientific Computing Certificate

INTRO TO QUANTUM COMPUTING

June 2024, dates TBD | https://scinet.courses/1332

This course will provide an introduction to the theory, formalisms and algorithms of quantum computing. The programming language will be Python; experience with Python will be assumed. Experience with quantum mechanics is not necessary; an introductory-level understanding of linear algebra will be assumed.

Format: In Person

Counts towards the SciNet Certificate

2024 COMPUTE ONTARIO SUMMER SCHOOL

June 2024, tentative, dated TDB | https://training.computeontario.ca

The Compute Ontario Summer School, jointly organized by SHARCNET, SciNet, Centre for Advanced Computing, and in collaboration with the RDM Network of Experts, offers a comprehensive curriculum packed with nearly 30 courses for researchers, students, and staff. These sessions are offered in two parallel streams which cover a wide range of topics including Advanced Research Computing (ARC), High Performance Computing (HPC), and Research Data Management (RDM) and are available at introductory to advanced levels. Whether you are interested in a specific topic or wish to explore multiple areas, you have the freedom to register for one, some, or all of the workshops available.

Format: Virtual

SciNet Training 2022/2023

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

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

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

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

INTRO TO NIAGARA AND MIST

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

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

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

Participation counts towards the SciNet HPC Certificate.

INTRODUCTION TO APPTAINER

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

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

Format: On-line

Participation counts towards the SciNet Scientific Computing Certificate.

SCINET USER GROUP MEETING

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

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

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

Topics of the TechTalks are TBA.

INTRODUCTION TO PROGRAMMING

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

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

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Scientific Computing Certificate.

INTRODUCTION TO THE LINUX COMMAND LINE

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

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

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Scientific Computing Certificate.

ENABLE YOUR RESEARCH WITH CYBERSECURITY!

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

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

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

Participation counts towards the SciNet Scientific Computing Certificate.

PARALLEL PROGRAMMING AT SCALE WITH MPI

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

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

Format: On-line

Participation counts towards the SciNet HPC Certificate.

INTRO TO GIT VERSION CONTROL

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

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

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Scientific Computing Certificate.

FILE MANAGEMENT – PACKING SMALL FILES

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

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

Format: Online.

Participation counts towards the SciNet Data Science Certificate.

ADVANCED LINUX COMMAND LINE

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

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

Participation counts towards the SciNet Scientific Computing Certificate.

FROM PYTHON TO C++

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

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

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

Participation counts towards the SciNet Scientific Computing Certificate.

MICROSOFT WINDOWS SUBSYSTEM FOR LINUX

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

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

Format: TBD

Participation counts towards the SciNet Scientific Computing Certificate.

INTRODUCTION TO GPU PROGRAMMING

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

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

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

Participation counts towards the SciNet HPC Certificate.

LINUX SHELL SCRIPTING

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

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

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Scientific Computing Certificate.

HIGH PERFORMANCE PYTHON

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

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

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet HPC Certificate.

ADVANCED LINUX II

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

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

Format: TBD

Participation counts towards the SciNet Scientific Computing Certificate.

NEURAL NETWORK PROGRAMMING

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

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

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Data Science Certificate.

RELATIONAL DATABASES BASICS

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

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

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Data Science Certificate.

INTRODUCTION TO QUANTUM COMPUTING

Jun 5, 6, 7, 8, 1:00 pm – 4:00 pm EDT | https://scinet.courses/1290

An introduction to the theory, formalisms and algorithms of quantum computing. The programming language will be Python; experience with Python will be assumed. Experience with quantum mechanics is not necessary; an introductory-level understanding of linear algebra will be assumed. The PennyLane quantum-computing programming framework (installation instructions here), provided by Xanadu, will be used. No experience with quantum computing will be expected.

Format: In-person in the SciNet Teaching Room.

Participation counts towards the SciNet Scientific Computing Certificate.

2023 COMPUTE ONTARIO SUMMER SCHOOL

June 12-29, 2023 | https://training.computeontario.ca/coss2023.php

Compute Ontario Summer School, jointly organized by SHARCNET, SciNet, Centre for Advanced Computing, and in collaboration with the RDM Network of Experts, offers a comprehensive curriculum packed with nearly 30 courses for researchers, students, and staff. These sessions are offered in two parallel streams which cover a wide range of topics including Advanced Research Computing (ARC), High Performance Computing (HPC), and Research Data Management (RDM) and are available at introductory to advanced levels. Whether you are interested in a specific topic or wish to explore multiple areas, you have the freedom to register for one, some, or all of the workshops available.

Format: Virtual

SciNet News November 2019

November 4, 2019 in newsletter

SUMMARY

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

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

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

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

SYSTEM CHANGES

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

  • Scheduled maintenance on Friday November 15, 2019 at the SciNet Datacenter. This will require a full system power-off, so starting 7am all systems should be shutdown. We expect the systems to be back late that evening day.

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

EVENTS COMING UP

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

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

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

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

    Participation counts towards the Scientific Computing Certificate.

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

  • INTRO TO NIAGARA
    Wednesday November 13, 2019, 10:00 am – 11:30 am
    SciNet Boardroom

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

    Participation counts towards the HPC Certificate.

    For more information and sign-up, go to https://scinet.courses/486

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

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

    Pizza, user discussion, and presentations about:

    Upcoming New Resources at SciNet: Niagara Expansion and GPU System

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

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the Scientific Computing Certificate.

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

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

  • UofT Viz Discussion Group November 29, 2019 SciNet Boardroom

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

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

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

    This course is aimed at reducing your struggle in getting started with computational projects, and make you a more efficient computational scientist. Topics include well-established best practices for developing software as it applies to scientific computations, common numerical techniques and packages, and aspects of high performance computing. While we will introduce the C++ language, in one language or another, students should already have some programming experience. Despite the title, this course is suitable for many physical scientists (chemists, astronomers, …).

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

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

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

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

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

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

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the Data Science Certificate.

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

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

  • ADVANCED DISTRIBUTED MEMORY PARALLEL PROGRAMMING WITH MPI
    Monday April 6, 2020, 1:00 pm – 4:00 pm
    SciNet Teaching Room

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

    Participation counts towards the HPC Certificate.

    For sign-up and more information, see https://scinet.courses/525

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

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

    Participation counts towards the Data Science Certificate.

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

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

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

    Participation counts towards the Data Science Certificate.

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

SciNet News October 2019

October 10, 2019 in for_researchers, for_users, newsletter

SUMMARY

  • The Resource Allocation Competition is open.

  • Scheduled maintenance downtime on October 16th.

  • Training and education program continues.

  • UofT Visualization Discussion Group hosted at SciNet.

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

SYSTEM CHANGES

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

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

EVENTS COMING UP

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

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Pizza, user discussion, and presentations about:

    1. Using the newer 2019b Niagara software stack.

    2. The Compute Canada Resource Allocation Competition.

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

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

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

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

    Participation counts towards the Scientific Computing Certificate.

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

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

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

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

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

    Participation counts towards the Scientific Computing Certificate.

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the Scientific Computing Certificate.

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

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

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

    This course is aimed at reducing your struggle in getting started with computational projects, and make you a more efficient computational scientist. Topics include well-established best practices for developing software as it applies to scientific computations, common numerical techniques and packages, and aspects of high performance computing. While we will introduce the C++ language, in one language or another, students should already have some programming experience. Despite the title, this course is suitable for many physical scientists (chemists, astronomers, …).

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

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

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

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

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

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

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the Data Science Certificate.

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

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

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

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

    Participation counts towards the Data Science Certificate.

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

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

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

    Participation counts towards the Data Science Certificate.

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

SciNet News September 2019

September 6, 2019 in for_researchers, for_users, newsletter

SUMMARY

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

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

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

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

SYSTEM CHANGES

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

SCINET EVENTS DURING THE PAST SUMMER

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

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

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

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

EVENTS COMING UP

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

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

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

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

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

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

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

    Participation counts towards the Scientific Computing Certificate.

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

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

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

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

    Participation counts towards the Scientific Computing Certificate.

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

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

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

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

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

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

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

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

    Pizza, user discussion, and a tech talk TDB

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

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

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

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

    Participation counts towards the Scientific Computing Certificate.

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

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the Scientific Computing Certificate.

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

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

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

    Participation counts towards the HPC Certificate.

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

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

    This course is aimed at reducing your struggle in getting started with computational projects, and make you a more efficient computational scientist. Topics include well-established best practices for developing software as it applies to scientific computations, common numerical techniques and packages, and aspects of high performance computing. While we will introduce the C++ language, in one language or another, students should already have some programming experience. Despite the title, this course is suitable for many physical scientists (chemists, astronomers, …).

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

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

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

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

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

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

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the HPC Certificate.

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

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

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

    Participation counts towards the Data Science Certificate.

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

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

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

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

    Participation counts towards the Data Science Certificate.

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

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

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

    Participation counts towards the Data Science Certificate.

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

SciNet News June 2019

June 4, 2019 in for_researchers, for_users, newsletter

Summary

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

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

System News

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

Events Coming Up

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

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

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

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

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

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

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

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

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

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

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

  • SCALING TO PETASCALE INSTITUTE August 19-23, 2019

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

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

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

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

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

    This course is aimed at reducing your struggle in getting started with computational projects, and make you a more efficient computational scientist. Topics include well-established best practices for developing software as it applies to scientific computations, common numerical techniques and packages, and aspects of high performance computing. While we will introduce the C++ language, in one language or another, students should already have some programming experience. Despite the title, this course is suitable for many physical scientists (chemists, astronomers, …).

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

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

SciNet News March 2019

March 4, 2019 in for_researchers, for_users, newsletter

Summary

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

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

System News

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

Events Coming Up

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

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

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

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

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

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

    Pizza, user discussion, and a tech talk TBA.

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

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

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

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

  • ADVANCED LINUX COMMAND LINE Wednesday April 10, 1:00 pm – 4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

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

    Participation counts towards the SciNet Data Science Certificate.

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

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

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

    Participation counts towards the SciNet Data Science Certificate.

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

    Pizza, user discussion, and a tech talk TBA.

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

  • COMPUTE ONTARIO SUMMER SCHOOL Summer 2019

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

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

    More details will be announced later in 2019.

  • SCALING TO PETASCALE INSTITUTE August 19-23, 2019

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

    More details will be announced later in 2019.

SciNet News February 2019

February 4, 2019 in for_researchers, for_users, newsletter

Summary

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

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

System News

Events Coming Up

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

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

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

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

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

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

    Pizza, user discussion, and a tech talk TBA.

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

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

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

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

  • ADVANCED LINUX COMMAND LINE Wednesday April 10, 1:00 pm – 4:00 pm SciNet Teaching Room

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

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

    Participation counts towards the SciNet Data Science Certificate.

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

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

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

    Participation counts towards the SciNet Data Science Certificate.

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

    Pizza, user discussion, and a tech talk TBA.

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

  • COMPUTE ONTARIO SUMMER SCHOOL Summer 2019

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

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

    More details will be announced later in 2019.

  • SCALING TO PETASCALE INSTITUTE August 19-23, 2019

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

    More details will be announced later in 2019.

SciNet News January 2019

January 4, 2019 in for_researchers, for_users, newsletter

Summary

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

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

System News: Maintenance Shutdown

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

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

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

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

Events Coming Up

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

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

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

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

    Pizza, user discussion, and a tech talk TDB

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

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

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

    This summer school will familiarize the best students in computational sciences with major state-of-the-art aspects of HPC for a variety of scientific disciplines, catalyze the formation of networks, provide advanced mentoring, facilitate international exchange and open up further career options. Leading Canadian, European, Japanese and American computational scientists and HPC technologists will offer instruction in parallel sessions on a variety of topics as: HPC challenges in major scientific disciplines, HPC programming proficiencies, Performance analysis and profiling, Software engineering, Numerical libraries, Big data analysis and analytics, Machine learning, Scientific visualization, and Canadian, European, Japanese and US HPC infrastructure.

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

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

  • SCIENTIFIC COMPUTING FOR PHYSICISTS (PHY1610) Winter 2019, starting January 8 SciNet Teaching Room

    This course is aimed at reducing your struggle in getting started with computational projects, and make you a more efficient computational scientist. Topics include well-established best practices for developing software as it applies to scientific computations, common numerical techniques and packages, and aspects of high performance computing. While we will introduce the C++ language, in one language or another, students should already have some programming experience. Despite the title, this course is suitable for many physical scientists (chemists, astronomers, …).

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

    For more information, see https://courses.scinet.utoronto.ca/398

  • QUANTITATIVE APPLICATIONS FOR DATA ANALYSIS Winter 2019, starting January 9 University of Toronto Scarborough Campus

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

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

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

    For more information, see https://courses.scinet.utoronto.ca/403

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

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

    Participation counts towards the SciNet Data Science Certificate.

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

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

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

    Participation counts towards the SciNet Data Science Certificate.

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

  • COMPUTE ONTARIO SUMMER SCHOOL Summer 2019

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

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

    More details will be announced later in 2019.

  • SCALING TO PETASCALE INSTITUTE August 19-23, 2019

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

    More details will be announced later in 2019.