SciNet concludes its biggest-ever training week in scientific, high performance, and data science computing

June 19, 2018 in blog-general, for_educators, for_press, for_researchers, for_users, frontpage, news, success_story

When summer arrives, it means the return of Ontario’s Summer School on Scientific and High Performance Computing. This annual set of educational events bring together graduate students, undergraduate students, postdocs and researchers and gives them an opportunity to learn and share knowledge and experience in technical computing, data science and biomedical computing on modern high-performance computing platforms.

The summer school has been given at three locations for the last seven years and is a collaborative effort of the three High-Performance Consortia in Ontario: SHARCNET, CAC, and SciNet. This year, the first was from May 28 to June 1 in London, while the second one was hosted by SciNet on the St. George campus of the University of Toronto from June 11 to 15, and the third will take place in Kingston from July 30 to August 3.

HPC Python session at the 2018 summer school

High Performance Computing with Python (“Parallel Python”) Session at the 2018 Ontario HPC Summer School in Toronto

The format of the school is that of a five-day intensive workshop with mixed lectures and hands-on sessions on a number of selected topics. The topics slightly vary by location, but may include shared memory programming, distributed memory programming and general purpose graphics processing unit programming, and Python, R, machine learning, neural networks, visualization, debugging, bioinformatics and bioimaging. To make all these topics fit in one week, the lectures are organized in different streams. In Toronto, there was a high performance computing stream, a data science stream, and a biomedical stream, given by instructors from SciNet, SHARCNET, and CAMH.

group photo HPC Summer School in Toronto

Group Photo of the 2018 Ontario HPC Summer School in Toronto

This year was SciNet’s biggest summer school yet. For the first time, there were more than two hundred participants, from widely varying academic background like Business Administration, Dentistry, Biology, Medicine, Economics, Health Sciences, Phyics, Chemistry, Engineering, and Astronomy. Those who attended at least three days received a certificate of attendance.

To get a sense of the tremendous growth of this event, consider that in 2012, one of the first years of the summer school, in Toronto, we had 35 participants in the summer school, issued 20 certificates, and a total of 400 contact-hours were delivered by a handful of instructors. In 2018, these numbers are 7 to 10 times larger: there were 211 participants, 135 certificates were issues, and 3800 contact-hours were delivered by 17 instructors. If that is not a clear enough indication of the demand for this kind of training, consider this: within one day of opening the registration, there were over 100 registrations, and just one week later, the 200 registration mark was crossed. There were people on the waiting list, although we made an effort to try and accommodate most people in the end.

The school is offered for free, but without support for travel, lodging or meals. It is therefore not surprising that most participants are from the Toronto area, but there was a sizeable number of attendants from outside Toronto (60), from outside of Ontario (15) and even from outside Canada (5).

The participants seem to really appreciate the event, as borne out by the preliminary results from the post-event survey. From the survey, we got suggestions for improvements for the future, such as (even) more hands-on and better explanation of prerequisites and software for the sessions. Nonetheless, 94% of the respondents was very satisfied with the summer school, and thought the overall value of the summer school was high. 92% would recommend the event to their peers. Interestingly, the answers to the question “What was the most important thing you learned or did during the summer school?” varied a lot, indicating, perhaps, that the broad range of offered topics allowed participants to pick what suits them best.

Organizing the school was a tremendous experience, made possible by 8 instructors and staff members from SciNet, 9 from CAMH, and 2 from SHARCNET. The University of Toronto provided the space for the session, while Compute Ontario sponsored the coffee-and-cookie breaks.

If you missed it this time, look for the announcement next spring of the 2019 Ontario Summer School on High Performance Computing.

2018 Compute Ontario Summer School Central

May 14, 2018 in blog, for_educators, for_researchers, for_users, frontpage, news

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.

Apart from the Compute Ontario Summer School Central, which will be hosted in Toronto by SciNet from June 11 to June 15, 2018, there are two other instances of the 2018 Compute Ontario summer school: One hosted by SHARCNET at Western University (May 28-Jun 1) one hosted by CAC at Queen’s University (Jul 30-Aug 3). Each of the three site has a slightly different list of courses, but all include both in-class lectures and hands-on sessions. Those who attend at least three full days cumulatively will receive an official certificate in HPC training.

The Toronto summer school (“Compute Ontario Summer School Central”), hosted by SciNet, will have the following three streams: Stream 1: High Performance computing; Stream 2: Data Science; Stream 3: Biomedical. Instructors are from SciNet, SHARCNET, and CAMH.

Location

Wilson Hall – New College
University of Toronto
St. George Campus
40 Willcocks St.
Toronto, ON M5S 1C6

Rooms: 524, 1016, 1017, 2006 (check the sessions for the room assignments)

Registration

Step 1: Log into the SciNet education site with your SciNet account, select the Compute Ontario Summer School in “Browse Courses”, and click on the “Register Me” link on the right. OR: if you do not have a SciNet account, register at tinyurl.com/toss2018reg, enter the required information such as login, password and email. In the latter case, you will receive an email with a link to confirm your email.

Step 2: Make your session selection (see program below). You can alter your selection at any time, but note that seats are limited.

Cost

The event is free of charge, though meals and lodging are at the participant’s own expense. We therefore thank the organizations who are providing the instructors (which they do free of
charge). This event is furthermore sponsored by Compute Ontario, the umbrella organization for Academic Advanced Research Computing in Ontario.

Program

HPC Stream Data Science Stream Biomedical Stream
Mon, Jun 11
Morning: 09:00-12:30
Welcome and Introduction to HPC and SciNet Welcome and Introduction to HPC and SciNet Welcome and Introduction to HPC and SciNet
Afternoon: 13:30-16:30
Programming Clusters with Message Passing Interface Introduction to the Linux Shell Python for MRI analysis
Tue, Jun 12
Morning: 09:30-12:30
Programming Clusters with Message Passing Interface Introduction to R Image Analysis at Scale
Afternoon: 13:30-16:30
Programming Clusters with Message Passing Interface Introduction to Python Machine Learning for Neuroimaging
Wed, Jun 13
Morning: 09:30-12:30
Programming GPUs with CUDA Parallel Python PLINK
Afternoon: 13:30-16:30
Programming GPUs with CUDA Machine Learning with Python Next Generation Sequencing
Thu, Jun 14
Morning: 09:30-12:30
Programming GPUs with CUDA Neural Networks with Python RNASeq Analysis
Afternoon: 13:30-16:30
Programming GPUs with CUDA Scientific Visualization Suites R for MRI analysis
Fri, Jun 15
Morning: 09:30-12:30
Shared Memory Parallel Programming with OpenMP Debugging, Profiling and Bring-Your-Own-Code Lab Public Datasets for Neuroimaging
Afternoon: 13:30-16:30
Shared Memory Parallel Programming with OpenMP Debugging, Profiling and Bring-Your-Own-Code Lab HCP with HPC: Surface Based Neuroimaging Analysis

Launch of the Niagara Supercomputer at SciNet

March 5, 2018 in for_educators, for_press, for_researchers, for_users, frontpage, in_the_news, news, Road_to_Niagara

The Niagara supercomputer was officially launched on March 5th, 2018. We were honoured by the presence and remarks of Reza Moridi (Ontario Minister of Research, Innovation and Science), Nizar Ladak (Compute Ontario President and CEO), Dr. Roseann O’Reilly Runte (CFI President and CEO), Prof. Vivek Goel (Vice-president of Research and Innovation at the University of Toronto), and Prof. W. Richard Peltier (Scientific Director of SciNet).

SciNet’s CTO Daniel Gruner gave an overview of the new system:

Niagara is located at University of Toronto and operated by the university’s high-performance computing centre SciNet, but the system is open to all Canadian university researchers.

Niagara is the fastest computer system in the country and is able to run a single job across all 60,000 cores thanks to a high-performance network which interconnects all the nodes. For more information on the configuration, see here.

A time-lapse of the building of Niagara is available (part of SciNet’s YouTube channel):

This system is jointly funded by the Canada Foundation for Innovation, the Government of Ontario, and the University of Toronto.

International HPC Summer School 2018 in Ostrava, by SciNet, XSEDE, PRACE and Riken

December 22, 2017 in for_educators, for_researchers, for_users, frontpage, in_the_news, news

A High-Performance Computing Summer Institute
July 8-13, Ostrava, Czech Republic
Expenses-paid program
Apply by February 13, 2018
Website: http://ihpcss18.it4i.cz


Graduate students and postdoctoral scholars from institutions in Canada, Europe, Japan and the United States are invited to apply for the ninth International Summer School on HPC Challenges in Computational Sciences, to be held July 8 to 13, 2018, in Ostrava, in the Czech Republic, and hosted by the IT4Innovations National Supercomputing Centre.

Applications are due Feb 13, 2018. The summer school is organized by the Partnership for Advanced Computing in Europe (PRACE), the Extreme Science and Engineering Discovery Environment (XSEDE), the RIKEN Advanced Insti­tute for Computational Science (RIKEN AICS), and the SciNet HPC Consortium.

Leading computational scientists and HPC technologists from the U.S., Europe, Japan and Canada will offer instructions on a variety of topics and also provide advanced mentoring. Topics include:

  • HPC challenges by discipline
  • HPC programming proficiencies
  • Performance analysis & profiling
  • Algorithmic approaches & numerical libraries
  • Data-intensive computing
  • Scientific visualization
  • Canadian, EU, Japanese and U.S. HPC-infrastructures

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

  • Familiar with HPC, not necessarily an HPC expert, but rather a scholar who could benefit from including advanced computing tools and methods into their existing computational work
  • A graduate student with a strong research plan or a postdoctoral fellow in the early stages of their research efforts
  • Regular practice with parallel programming (i.e., student utilizes parallel programming generally on a monthly basis or more)
  • May have a science or engineering background, however, applicants from other disciplines are welcome provided their research activities include computational work.

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

Interested students should apply by February 13, 2018. Participation, meals and housing will be covered for the selected participants, also support for intercontinental travel will be given (contingent to funding).

Further information and application, see http://ihpcss18.it4i.cz.

New Courses and New Initiatives for this Coming Semester

September 2, 2017 in for_educators, for_press, frontpage, news, Uncategorized


Excited about the beginning of a new academic year?

We, at SciNet, certainly are!

SciNet has created several new courses for this coming fall semester and we are really excited about that!
Take a look at our education website to learn about all the courses and workshops that we will be offering.

In addition to the traditional courses on Scientific Computing, we have also added courses on Computational BioStatistics, Machine Learning and Neural Networks, and basic level introductory courses for students without any previous background on computing or programming!

Additionally, several members of our team have obtained Graduate restricted appointed positions at the Institute of Medical Sciences and the Physics Department!

The number of SciNet courses that are listed as U of T graduate courses continues to increase (no small feat for a non-teaching unit like SciNet). Our full-term graduate courses in 2017/2018 are

Finally, starting this September we want to officially launch our “Research Initiative Program”!

This is a collaborative program, aimed to partner with research groups across the University, in order to boost and empower research.

Of course, research support is something that we have been doing since the beginning of SciNet, by providing technical support and the infrastructure to researchers for tackling their computational needs.
This program will go beyond that, by allowing researchers to explicitly partner with SciNet’s scientists, in order to pursue short and long term research projects.

More information about this program, ongoing collaborations and areas of expertise can be found at the
Research @ SciNet page.

2017 Compute Ontario Summer School Central

June 14, 2017 in blog, blog-general, for_educators, for_press, for_researchers, for_users, frontpage, news, Uncategorized

The Compute Ontario Summer School on Scientific and High Performance Computing is an annual educational event for graduate/undergraduate students, postdocs and researchers who are engaged in a compute intensive research. Held geographically in the west, centre and east of the province of Ontario, the summer school provides attendees with the opportunity to learn and share knowledge and experience in high performance and technical computing on modern HPC platforms.

Each site will have a slightly different list of courses. The summer school will include both in-class lectures and hands-on labs (done on the participants’ laptops). Those who attend at least three full days cumulatively will receive an official certificate in HPC training (i.e., a total of 6 full morning and afternoon sessions).

Instructors for this school have been provided by SciNet, CAMH and SHARCNET. Break refreshments are provided courtesy of Compute Ontario.

REGISTRATION

Registration for the central installment in Toronto from July 24-28, 2017 is now open!

The registration is free and is aimed at Compute Canada users as well as students, post-docs and other researchers from academic institutions. You do not need to have a SciNet account. Please be advised that seats are limited and tend to fill up.

More information and registration can be found on the summer school website.

SCHEDULE

High Performance Computing Stream Data Science Stream Biomedical Stream
Mon, Jul 24
Morning: 09:00-12:00
Welcome and Introduction to HPC and SciNet
Afternoon: 13:30-16:30
Shared Memory Programming with OpenMP Introduction to the Linux Shell PLINK
Tue, Jul 25
Morning: 09:00-12:00
Shared Memory Programming with OpenMP Introduction to R Next Generation Sequencing
Afternoon: 13:30-16:30
Programming Clusters with Message Passing Interface Data Science with Python RNASeq
Wed, Jul 26
Morning: 09:00-12:00
Programming Clusters with Message Passing Interface Parallel R for Data Science Python for MRI analysis
Afternoon: 13:30-16:30
Programming Clusters with Message Passing Interface Python for High Performance Computing (Parallel Python) Image Analysis at Scale
Thu, Jul 27
Morning: 09:00-12:00
Programming GPUs with CUDA Visualization with Python Machine Learning for Neuroimaging
Afternoon: 13:30-16:30
Programming GPUs with CUDA Scientific Visualization Suites R for MRI analysis
Fri, Jul 28
Morning: 09:00-12:00
Programming GPUs with CUDA Debugging, Profiling and Bring-Your-Own-Code Lab Public Datasets for Neuroimaging
Afternoon: 13:30-16:30
Programming GPUs with CUDA Debugging, Profiling and Bring-Your-Own-Code Lab Unit Testing / Neuroinformatics Pipeline Development

LOCATION

This event will be held in the Medical Science Building at the University of Toronto, 1 King Circle, Toronto, Ontario, M5S 1A8, Canada.

The nearest subway station is “Queen’s Park”. Paid parking is available on the St. George Campus.

LODGING

Lodging is not provided by the organization. If you require lodging, you will have to make arrangements yourself. It may be worthwhile checking out the University’s summer residence program at www.studentlife.utoronto.ca/hs/summer .

MEALS

Meals are *not* provided by the organization, but refreshments will be provided during the morning and afternoon breaks, courtesy of Compute Ontario.

COMPUTING FACILITIES

For the hands-on sessions, participants are to bring their own laptop with working wireless and with an ssh client with X-windows installed. The latter is needed to connect to one of SciNet or SHARCNET supercomputers, to which the participant will get access for the duration of the School.

CERTIFICATES

Participants that complete at least three days worth of instruction (i.e., a total of 6 morning and afternoon sessions combined) are to receive a Compute Ontario Summer School Certificate on the last day of the School. Note that this certificate is separate from the SciNet certificates, but parts of the school may count towards a SciNet certificate as well.

Grand Opening of the ArcNet Space at MaRS

May 15, 2017 in blog-general, for_educators, for_press, for_researchers, for_users, frontpage, news, Uncategorized

On May 9, 2017, the Grand Opening of the ArcNet space took place (despite having moved a while ago). What is ArcNet? It is a space where expertise and support of Advanced Research Computing (the “ARC” in ArcNet) from three organizations come together. SciNet is the oldest of the three; It is the supercomputing consortium at the University of Toronto, which has been providing Canadian researchers with computational resources and expertise necessary to perform their research on scales not previously possible in Canada, from the biomedical sciences and aerospace engineering to astrophysics and climate science. SOSCIP is a research and development consortium that pairs academic and industry researchers with advanced computing tools to fuel Canadian innovation. The third organization, Compute Ontario, partners with the four academic computing consortia in Ontario aims to drive advanced computing to accelerate research and enhance competitiveness in the global marketplace resulting in a more prosperous Ontario.

The Grand Opening brought together many of our stakeholders, and was also attended by the Ontario Minister of Research, Innovation and Science, MPP Rezi Moridi, by the President of the University of Toronto Meric Gertler, by the Vice-President of Research at the University of Toronto Prof. Vivek Goel, and by the Scientific Directory of SciNet Prof. W. Richard Peltier. We were honoured that each was willing to say a few words about the opening of this space.

“This facility is a true partnership between the University of Toronto’s SciNet High Performance Computing Consortium, SOSCIP and Compute Ontario. Bringing them together in a state-of-the-art facility will strengthen their partnership and undoubtably create new opportunities to drive innovation through advanced computing in Ontario.” said Prof. Goel, one of the driving forces of the creation of the space.

The President of the University of Toronto reminded us that “With ARCNet, we have created an amazing hub of talent and technology that fosters collaboration between the public and private sector.”

Minister Rezi Moridi remarked that “Today we are here to celebrate the grand opening of the Advanced Research Computing facility. It is great to see that three organizations got together and set up this wonderful facility: SOSCIP,
Compute Ontario, and University of Toronto’s SciNet. I wish you all the best in serving our research community.”


The speeches were given in the new teaching and visualization room. This room holds up to 40 students and is already frequently used for courses and other events. It features a large visualization wall, i.e., a 13 x 7.5 feet ultrahigh resolution screen (8K, to be precise).


Two presentations were given by SciNet analysts to demonstrate the capabilities of this visualization wall; Ramses van Zon showed how to get insight into the complexity of the software installed on SciNet’s main cluster by using graph visualizations, while Marcelo Ponce showed visualizations of several aspects of interacting neutron stars, with data from numerical general relativity simulations.

You can see the capabilities of the visualization wall in the following video:




Sheridan Cyber Security Symposium 3.0

May 6, 2017 in for_educators, for_industry, for_researchers, for_users, news

The Sheridan Cyber Security Symposium 3.0, will be held on Monday, May 15, 2017 at the Hazel McCallion Campus of Sheridan College in Mississauga.

This conference is hosted by the Sheridon College Faculty of Applied Science and Technology in collaboration with Sheridan Applied Research and Innovation, and will explore cyber security within public health & safety, community, education and business.

For more information and registration see the symposium’s website.

International HPC Summer School 2017 in Boulder, CO

January 25, 2017 in for_educators, for_researchers, for_users, frontpage, news, Uncategorized

boulder-jay-05apr2016-cropped

Apply by 6 March, 2017
Expenses-paid program
Sponsored by PRACE, XSEDE, Riken, and Compute Canada
website: https://confluence.xsede.org/display/IH17/International+HPC+Summer+School+2017

The eighth International Summer School on HPC Challenges in Computational Sciences will be held from June 25-July 30, 2017, Boulder, Colorado, USA. This is an advanced summer school on High Performance Computing which targets graduate students who already have some experience in HPC parallel programming (for instance, MPI, OpenMP, or CUDA/OpenCL), preferably on software used in successful research projects.

The organizers of this summer school are XSEDE, PRACE, Compute Canada, and RIKEN.

Leading American, Canadian, European and Japanese computational scientists and HPC technologists will offer instruction on a variety of topics. The program is still being finalized, but previous summer schools included the following:

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

Participation in the summer school is decided through an application process. Meals, housing, and travel will be covered for the selected participants. Applications from students in all science and engineering fields are welcome. Ten out of 80 student participants will be from Canada. Preference will be given to applicants with parallel programming experience, and a research plan that will benefit from using high performance computing systems.

Applications are due by March 6, 2017
For further information and to apply online, please click here.

SciNet News August 2016

August 29, 2016 in blog, blog-general, for_educators, for_researchers, for_users, news, newsletter

Below you will find the salient points of what happened or changed recently, and what will happen in the near future. Among these is that the SciNet offices have moved to a new home! We are now located in the MaRS West Tower on the eleventh floor (address: 661 University Ave., Suite 1140 Toronto, ON M5G 1M1). As in our old spot, users, students, and friends are still welcome to visit our new abode, however, because we are still getting settled in, it is recommended to schedule a meeting (by emailing support AT scinet.utoronto.ca).

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

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

SUMMARY

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

SCINET OFFICE MOVE

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

661 University Ave
Suite 1140
Toronto, ON M5G 1M1

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

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

EVENTS COMING UP

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

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

Courses that can be taken for credit at the UoT

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

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

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

    This course counts toward the High Performance Computing Certificate.

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

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

    The goal of this course is to prepare students to perform scientific data analysis. Successful students will learn how to use statistical inference tools to gain insight into large and small data sets, as well as be exposed to cutting-edge techniques and best practices to store, manage and analyze (large) data.

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

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

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

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

    Location: St.George Campus, specific room TBD.

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

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

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

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

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

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

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

  • SCIENTIFIC COMPUTING FOR PHYSICISTS
    Physics graduate course (PHY1610)

    Winter 2017

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

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

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

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

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

SciNet Training Events

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

SYSTEM CHANGES

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

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

WHAT ELSE HAPPENED AT SCINET IN THE SUMMER OF 2016?

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