SciNet Receives HPCwire Award

December 6, 2018 in blog, for_press, for_researchers, for_users, frontpage, in_the_news, news, Road_to_Niagara, success_story

We are very proud that SciNet has received the 2018 HPCwire Editor’s Award for Best Use of HPC in Physical Sciences. The award was announced at the 2018 International Conference for High Performance Computing, Networking, Storage and Analysis (SC18), in Dallas, Texas.

SciNet used Lenovo and Mellanox technologies on the new Niagara cluster to create spatial resolution models of the Pacific Ocean, helping to validate ocean waves movement and to assist in global warming calculations. These calculations were performed by a team of scientists involving University of Toronto’s Prof. W. Richard Peltier, University of Michigan oceanographer Prof. Brian Arbic, and NASA JPL’s Dr. Dimitris Menemenlis. More on this calculation can be found here.

This calculation was part of the “early science” program of the Niagara supercomputer at the SciNet HPC Consortion. In this short period in March of 2018, a number of scientists were given the opportunity to perform “heroic” calculations. These large scale calculation were essential to test, to tune and to get Niagara ready for use as a Canada’s fastest national academic supercomputer.

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, 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

HPCwire: SciNet Launches Niagara, Canada’s Fastest Supercomputer

March 9, 2018 in in_the_news, news, Road_to_Niagara

HPCwire reports on the launch on the new supercomputer Niagara at Scinet.

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.

Road to Niagara 3: Hardware setup

March 5, 2018 in blog-technical, for_press, for_researchers, for_users, news, Road_to_Niagara, Uncategorized

This is the fourth of a series of posts on the transition to SciNet’s new supercomputer called “Niagara”, which will replace the General Purpose Cluster (GPC) and Tightly Coupled Cluster (TCS). The transition to Niagara will take place in the fall of 2017, and the system is planned to be available to users in early 2018.

The University of Toronto has awarded the contract for Niagara to Lenovo, and some of the details of the hardware specifications of the Niagara system have been released:

The system will have the following hardware components:

  • 1,500 nodes.
  • Each node will have 40 Intel Skylake cores (making a total of 60,000 cores) at 2.4 GHz.
  • Each node will have 200 GB (188 GiB)of DDR4 memory.
  • The interconnect between the nodes will be Mellanox EDR Infiniband in a Dragonfly+ topology.
  • A ~9PB usable shared parallel filesystem (GPFS) will be mounted on all nodes.
  • A 256TB Excelero burst buffer (NVMe fabric, up to 160 GB/s) will be available for fast I/O.
  • Peak theoretical speed: 4.61 PetaFLOPS

Niagara is estimated to be installed and operational towards in March 2018, and ready for users not too long after.

Even before official ready-date, there will a period in which select users can try out and port their codes to Niagara.

After the friendly-user period, all current users of the GPC (and former users of the TCS) will get access to Niagara.

The large core count, ample memory per core, and fast interconnect support Niagara’s intended purpose to enable large parallel compute jobs of 512 cores or more.

The software setup will also be tailored to large parallel computations. Nonetheless, there will still be a fair amount of backfill opportunity for smaller jobs.

The setup of Niagara is intended to be similar in spirit to the GPC, but different in form: scheduling per node, a home, scratch and possibly project directory defined in environment variables, a module system, and access to our team of analyst to help you get your codes running, and running well.

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.

Road to Niagara 2: GPC Reduction

October 26, 2017 in news, Road_to_Niagara

This is the second of a series of posts on the transition to SciNet’s new supercomputer called “Niagara”, which will replace the General Purpose Cluster (GPC) and Tightly Coupled Cluster (TCS). The transition to Niagara will take place in the fall of 2017, and the system is planned to be available to users in early 2018.

The University of Toronto has awarded the contract for Niagara, which means its installation will start soon. To make room for this system, the General Purpose Cluster will be reduced from 30,912 to 16,800 cores on Tuesday November 28, 2017, at 12:00 noon.

Niagara is estimated to be installed, operational and ready for users towards the end of February 2018. At that time, the GPC will be decommissioned.

Even before official ready-date, there will a period in which select users can try out and port their codes to Niagara.

After the friendly-user period, all current users of the GPC (and former users of the TCS) will get access to Niagara (and their allocations on GPC or TCS will be carried over).

The setup will also be tailored to large parallel computations. Nonetheless, there will still be a fair amount of backfill opportunity for smaller jobs.

Although the details of the Niagara system are yet to be announced, existing SciNet users can get more information about the new system here.

Road to Niagara 1: Tightly Coupled Cluster Decommissioned

October 25, 2017 in frontpage, news, Road_to_Niagara


This is the first of a series of posts on the transition to SciNet’s new supercomputer called “Niagara”, which will replace our aging General Purpose Cluster (GPC) and Tightly Coupled Cluster (TCS). The transition to Niagara will take place in the fall of 2017, and the system is planned to be available to users in early 2018.

To make room for Niagara, old systems will have to go. Because enabling research computing is our priority, throughout the process of installting Niagara, at least 50% of the GPC will be kept running. The GPC will not be completely switched off until Niagara is available.

The first cluster to go was the TCS. This was SciNet’s first supercomputer, a 102-node, 3264-core, IBM Power 6 system installed in January of 2009.

The TCS was shut off on September 29, 2017, and physically removed in October. The end of an era.

As the pictures below show, you don’t just put your old supercomputer to the curb, there is a bit of work involved in removing it. It took about 8 hours, 14 pallets, 10 racks, and 3 truck loads. And a $5 bill was found under one of the TCS racks, so we made some money as well!

Currently we are in mids of finalizing the contract for Niagara, so the next post in this series will provided more details on the new system to come.

Decommissioning the old Power 6 TCS requires a little fork lift; those are heavy nodes.

TCS nodes taken out of their racks.


The empty space left behind by the TCS…


Decommissing TCS subfloor connections.

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.