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SciNet to be the site for the new Large Parallel System

May 11, 2015 in for_press, for_researchers, for_users, in_the_news, news, Road_to_Niagara

As part of its strategy for Advanced Research Computing and High Performance Computing in Canada, Compute Canada has conducted a site selection for four new systems. These systems are intended to replace and augment the currently aging computational systems available to Canadian academic researchers.

biligual-cc-web-logo-flat-white

Recognizing the diversity of ARC computing in academic research, Compute Canada is planning to install four systems. Three systems will be so-called General Purpose clusters, aimed at small to moderate sized jobs with a large variety of demands (e.g, IO, GPUS, memory, …).

The fourth machine will be a Large Parallel system, i.e. a tightly coupled parallel supercomputer intended for running large (on the order of at least 512 cores per job) parallel jobs, typically using the Message Passing Interface.

SciNet, at the University of Toronto, has been selected as the site for the LP system. The GP systems will be at the University of Victoria, at Simon Fraser University, and at the University of Waterloo.

Note that it is very hard at this stage to know when these new systems will be online. A rough, very tentative estimate is that they could start arriving sometime in 2016.

For more information regarding the selection, see the selection announcement by Compute Canada.

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Compute Ontario Research Day 2015

April 21, 2015 in blog-general, for_researchers, for_users, frontpage, news, Uncategorized

co

The Compute Ontario Research Day 2015 will be held on Thursday, May 21 at the Cambridge campus of Conestoga College Institute of Technology and Advanced Learning.

This will be a day filled with high performance computing related research done in Ontario. Have an interesting research story for which you used high performance computing (such as the facilities at SharcNet, SciNet, and HPCVL)? Want to share you experience with other Ontario HPC users? Consider giving a talk at the meeting.
This is the preeminent provincial high performance computing event at which professors, postdoctoral, graduate, and undergraduate students gather to learn about each other’s high performance computing related work.

The program will consist contributed and poster presentations and four invited speakers:

  • Prof. James Demmel
    Department of Mathematics, Computer Science Division, University of California, Berkeley
  • Anil K. Goel
    Vice President and Chief Architect, HANA, SAP
  • Prof. Harald Pfeiffer
    Canadian Institute for Theoretical Astrophysics, University of Toronto
  • Prof. Aristotelis Tsirigos
    Department of Pathology, School of Medicine, New York University

This conference is sponsored by Compute Canada and Compute Ontario, and is a collaborative event between SHARCNET, SciNet, HPCVL, and Conestoga College Institute of Technology and Advanced Learning.

For more information and registration, see https://www.sharcnet.ca/events/CORD2015.

conestogaCambridgeCampus

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SciNet News April 2015

April 9, 2015 in for_researchers, for_users, newsletter

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

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

 

UPCOMING EVENTS

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

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

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

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

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

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

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

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

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

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

    Participation counts towards the SciNet HPC Certificate.

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

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

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

    Participation counts towards the SciNet Scientific Computing Certificate.

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

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

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

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

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

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

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

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

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

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

  • ONTARIO HPC SUMMER SCHOOL 2015

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

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

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

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

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

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

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

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

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

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

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

 

SYSTEM NEWS

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

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

WHAT’S NEW ONLINE?

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

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

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SciNet News February 2015

February 26, 2015 in for_researchers, for_users, newsletter

ANNOUNCEMENTS

Dear SciNet users,

To keep users posted on what’s going on at SciNet, we send monthly emails with the new features, planned courses, events and accomplishments at SciNet.

Last month, the SciNet team was augmented with another analyst, Mike Nolta. Welcome, Mike!

Below you will find the salient points of what else happened or changed recently and what will happen in the near future. Among these is the announcement and call for participant applications for the International High Performance Computing Summer School, to be held in Toronto. As always, details on SciNet events are available on the wiki and the SciNet education website.

– The SciNet team

 

UPCOMING EVENTS

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

 

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

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

Participation counts towards the SciNet HPC Certificate.

For more information and enrollment, go to https://support.scinet.utoronto.ca/education/go.php/171/index.php

Future “Intro to SciNet” dates and enrollment links:

Apr 8, 10:30 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/172/index.php

May 13, 10:30 am – 11:30 am: https://support.scinet.utoronto.ca/education/go.php/173/index.php

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

 

  • SCINET USER GROUP MEETING
    Wednesday March 11, 12:00 noon – 1:00 pm

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

TechTalk: “Job and Queue Management Tools” by Mike Nolta (SciNet)

For more information and enrollment, go to https://support.scinet.utoronto.ca/education/go.php/183/index.php

Future SNUGs:
Apr 8, 2015, 12:00 noon – 1:00 pm, TechTalk TBD

May 13, 2015, 12:00 noon – 1:00 pm, TechTalk TBD

Jun 10, 2015, 12:00 noon – 1:00 pm, TechTalk TBD

 

  • SCIENTIFIC COMPUTING COURSE: HIGH PERFORMANCE COMPUTING
    March/April 2015

Part 3 of the Scientific Computing Course (part 1 was given in January and part 2 is in progress). Each part consists of eight lectures of one hour.

Note that these parts can be taken as “mini-courses” by astrophysics graduate students and as “modular courses” by physics and chemistry graduate students.

Participation in part 3 counts towards the SciNet HPC Certificate.

For more information (soon) and enrollment, go to https://support.scinet.utoronto.ca/education/go.php/178/index.php

Enrollment for part 1 and 2 is closed.

 

  • DEADLINE APPLICATION INTERNATIONAL SUMMER SCHOOL ON HPC IN TORONTO
    Wednesday March 11, 2015

See below for information regarding this summer school.

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

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

Participation counts towards the SciNet HPC Certificate.

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

 

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

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

Participation counts towards the SciNet Scientific Computing Certificate.

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

 

  • ONTARIO HPC SUMMER SCHOOL CENTRAL 2015
    Dates: TDB

Details to be posted soon.

 

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

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

More details to follow.

 

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

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

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

 

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

In this summer school, leading American, Canadian, European and Japanese computational scientists and HPC technologists will offer instruction on a variety of topics, including 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 and scientific visualization.

Compute Canada/Calcul Canada invites students enrolled in science and engineering fields, and researchers in those fields, at Canadian post-secondary institutions to apply for one of 10 spots allocated to Canada.

The application deadline is March 11, 2015.

For more information see https://ihpcss2015.computecanada.ca

 

SYSTEM NEWS

  • BGQ now a single 4-rack system. bgqdev-fen1 is the single login/devel/submission node.
  • GPC: Cmake 3.1.0 available as a module.
  • GPC: kernel upgraded to 2.6.32-504.3.3.el6.x86_64. Its base OS remains unchanged.
  • GPC: emacs 24.4 available as a module.
  • GPC: intel/15.0 module is deprecated — use 15.0.1 instead.
  • GPC, BGQ: git/1.9.5 is available as a module.
  • GPC: Nwchem 6.5 installed as a moduled.

 

WHAT’S NEW ONLINE?

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

  • Wiki: PDF of the January SNUG Techtalk about “Data Management and Transfer Tools at SciNet” Wiki: How to run parallel R.
  • Wiki: BGQ page updated to reflect its new 4-rack configuration.
  • Education: recordings of the first lectures on in the “Scientific
  • Computing” and “Numerical Tools” mini-course.

 

WHAT HAPPENED AT SCINET IN THE LAST MONTH?

  • Jan 14 and Feb 11: Intro to SciNet
  • Jan 21: Introduction to the Linux Shell
  • Jan: Eight lectures of the mini-course “Scientific Computing”
  • Feb: Four lectures of the mini-course “Numerical Tools for Physical Sciences”
  • Feb 11: SciNet User Group Meeting with TechTalk on “Data Management and Transfer Tools”
  • Feb 13: SciNet analysts participated as judges in the final of the Big Data Challenge for High School Students.

 

 

 

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International HPC Summer School 2015

January 20, 2015 in blog, for_educators, for_press, for_researchers, for_users, frontpage

toronto

Apply by 11 March, decisions on 1 April
Expenses paid by program
Sponsored by PRACE, XSEDE, Riken, and Compute Canada
website: https://ihpcss2015.computecanada.ca

The sixth International Summer School on HPC Challenges in Computational Sciences will be held from June 21-26, 2015, in Toronto, Canada. This is an advanced summer school on High Performance Computing which targets graduate students and postdocs 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. SciNet, a partner in the Compute/Calcul Canada national advanced research computing platform, acts as the local organizer and contact.

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. Although the school targets graduate students and postdocs, applications from research assistants and faculty are also welcome. Preference will be given to applicants with parallel programming experience, and a research plan that will benefit from the utilization of high performance computing systems.

Applications are due by March 11, 2015.
For further information and to apply online, please click here.

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2015 Call for Compute Canada Resource Allocation Proposals

September 17, 2014 in blog, blog-general, for_educators, for_researchers, for_users

Compute Canada is announcing the launch of the 2015 Resource Competitions.  In addition to the familiar Resource Allocation Competition (RAC), there are two other opportunities to access Compute Canada resources including the Fast Track and the NEW Research Platforms and Portals (RPP) Competition.

I invite you to consult the Compute Canada website for additional details on these three opportunities and to be mindful of the deadlines below.  If you have any questions please contact rac@computecanada.com.

Resource Allocation Application Deadlines

Resource Opportunity Deadline
Fast Track October 2nd, 2014
Resource Allocation Competition October 20th, 2014
Research Platform and Portal Competition (Letter of Intent) September 25th, 2014

Background:  Compute Canada is leading the creation of a powerful national Advanced Research Computing (ARC) platform for research. This national platform integrates ARC resources at six partner consortia across the country to create a dynamic computational resource. Compute Canada integrates high-performance computers, data resources and tools, and academic research facilities around the country. These integrated resources represent a substantial computing capability and online and long term storage with rapid access and retrieval over Canada’s national, provincial and territorial high-performance networks.

————————————————————————————-

Calcul Canada annonce le lancement de son concours d’allocation des ressources pour l’année 2015. En plus du Concours d’allocation des ressources (CAR) régulier, il existe désormais deux autres moyens d’obtenir des ressources, à savoir la procédure de demande accélérée et le NOUVEAU Concours plateformes et portails de recherche (PPR).

Je vous convie à visiter le site Web de Calcul Canada pour obtenir plus de précisions sur chacun de ces trois opportunités, en gardant à l’esprit les échéances indiquées ci-dessous. Pour toute question, écrivez à  rac@computecanada.com.

Échéances pour l’affectation des ressources

Possibilité Échéance
Demande accélérée 2 octobre 2014
Concours d’allocationdes ressources 20 octobre 2014
Concours plateformes et portails de recherche (lettre d’intention) 25 septembre 2014

Contexte:  Calcul Canada orchestre la création d’une puissante plateforme de CIP nationale pour la recherche. Cette plateforme rassemble les ressources de CIP de six consortiums partenaires situés  un peu partout au pays de manière à en créer une seule, dynamique, intégrant des ordinateurs de haute performance, des banques de données et leurs outils ainsi que des installations de recherche universitaires réparties aux quatre coins du Canada. Combinées, ces ressources représentent une capacité de calcul appréciable à laquelle s’ajoutent des capacités de stockage en ligne et de longue durée. Il est possible d’y accéder et de les utiliser rapidement grâce aux réseaux de pointe national, provinciaux et territoriaux.

Tags: , , , ,
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2014 Ontario High Performance Computing Summerschool (Central) open for registration

May 13, 2014 in for_researchers, for_users

consulting

The Ontario Summerschool on High Performance Computing provides attendees with opportunities to learn and share knowledge and experience in high performance and technical computing. The Ontario Summerschool on High Performance Computing will have three installments. The first will be in Waterloo (May 26-30), the second in Toronto (June 9-13), hosted by SciNet, while the third will be held in Ottawa (July 7-11).

The format of the Toronto installment will be a five-day workshop with mixed lectures and hands-on sessions on a number of selected subjects, including shared memory programming, distributed memory programming and general purpose graphics processing unit programming. The graphics cards and distributed memory sessions will be given in parallel, as will the visualization and debugging/optimization session.

SESSIONS

  • Linux command line: a primer
  • Introduction to High Performance Computing
  • Shared memory programming with OpenMP
  • Distributed memory programming with MPI
  • General Purpose GPU Programming with CUDA
  • HPC Debugging
  • HPC optimization and best practices
  • Visualization

LOCATION

This event will be held in Ramsey Wright Laboratories, University of
Toronto, 25 Harbord Street, Toronto, Ontario M5S 3G5.

CERTIFICATE

Participants that complete more than three days worth of instruction will be given an Ontario Summerschool Certificate. Note that this certificate is separate from the SciNet certificates.

MORE INFORMATION AND REGISTRATION

For more information and (free) registration, please go to the website for all three installments:

https://www.sharcnet.ca/events/ss2014/

The SciNet Team

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SciNet News April 2014

April 21, 2014 in for_researchers, for_users, newsletter

ANNOUNCEMENTS

We are pleased to announce that users can now keep track of their progress towards a SciNet certificate through their account on the Courses website.

UPCOMING EVENTS

Unless stated otherwise, all events take place in the SciNet Boardroom, 2nd floor of 256 McCaul Street, Toronto. Events are free for users but registration is required: https://support.scinet.utoronto.ca/education.

In a Nutshell

SCINET USER GROUP (SNUG) MEETING- Wednesday April 9, 12:00 noon – 1:00 pm

INTRO TO SCINET- Wednesday May 14, 10:30 am – 11:30 am

SCINET USER GROUP (SNUG) MEETING- Wednesday May 14, 12:00 noon – 1:00 pm

5TH INTERNATIONAL SUMMER SCHOOL ON HPC CHALLENGES IN COMPUTATIONAL
SCIENCES- Sunday June 1 – Friday June 6 (Budapest, Hungary)

COMPUTE ONTARIO SUMMER SCHOOL ON HIGH PERFORMANCE COMPUTING/CENTRAL- Monday June 9 – Friday June 13 (University of Toronto, St. George Campus)

SCINET USER GROUP (SNUG) MEETING – Wednesday Jun 18, 12:00 noon – 1:00 pm

HPCS 2014: HIGH PERFORMANCE COMPUTING SYMPOSIUM IN HALIFAX – Monday June 23 – Friday June 27

Details

  • SCINET USER GROUP (SNUG) MEETING
    Wednesday April 9, 12:00 noon – 1:00 pmTechTalk:
    Keep inventory of your data on different file systems with ISH
    by Ramses van Zon

    Want to be able to browse remote data on SciNet and HPPS as if you’re in a linux shell? With ‘ish’ , an inventory shell, you can use ls, cd, find, etc., to access and browse metadata of remote files and tar-balls. It allows you keep and peruse an inventory of your files stored in different locations.

    For more information and enrollment, go to the course website.

  • INTRO TO SCINET
    Wednesday May 14, 10:30 am – 11:30 amA class of approximately 60 minutes where you will learn how to use the SciNet systems. Experienced users may still pick up some valuable pointers during these sessions.

    For more information and enrollment, go to the course website.

  • SCINET USER GROUP (SNUG) MEETING
    Wednesday May 14, 12:00 noon – 1:00 pmTechTalk:
    Getting Started with Cilk Plus
    by Chris Szalwinski

    Intel’s Cilk Plus augments the C and C++ languages with three keywords for parallel programming on multi-core systems. These keywords inform the compiler that pertinent code may be parallelized. This talk will include code snippets showing how to implement map-reduce and fork-join patterns and will compare run times with those of serial code.

    For more information and enrollment, go to the course website.

  • 5TH INTERNATIONAL SUMMER SCHOOL ON HPC CHALLENGES IN COMPUTATIONAL SCIENCES
    Sunday June 1 – Friday June 6, Budapest, HungaryIn this summer school, leading American, Canadian, European and Japanese computational scientists and HPC technologists will offer instruction on a variety of topics, including HPC challenges by discipline (e.g., bioinformatics, computer science, chemistry, and physics), HPC programming proficiencies, performance analysis and profiling, algorithmic approaches & numerical libraries, data-intensive computing and scientific visualization.

    Compute Canada/Calcul Canada invites students enrolled in science and engineering fields at Canadian post-secondary institutions to apply for one of 10 (expenses-paid) spots allocated to Canada.

    The deadline for application has passed.

    For more information see http://www.prace-ri.eu/International-Summer-School-2014.

  • COMPUTE ONTARIO SUMMER SCHOOL ON HIGH PERFORMANCE COMPUTING/CENTRAL
    Monday June 9 – Friday June 13, University of Toronto, St. George CampusThe Compute Ontario Summer School on High Performance Computing provides attendees with opportunities to learn and share knowledge and experience in high performance and technical computing.

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

    “West” May 26 – 30 Waterloo

    “Central” June 9 – 13 Toronto

    “East” July (TBD) Ottawa

    The format will be a four day workshop with mixed lectures and hands-on sessions on a number of selected subjects, such as MPI, CUDA, OpenMP, and Visualization (these will vary slightly depending on the location).

    This event will *not* be held at the SciNet Headquarters.

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

    More details regarding the summer school will be announced here

  • SCINET USER GROUP (SNUG) MEETING
    Wednesday Jun 18, 12:00 noon – 1:00 pmTechTalk: TBA

    For more information and enrollment, go to
    the course website.

  • HPCS 2014: HIGH PERFORMANCE COMPUTING SYMPOSIUM IN HALIFAX
    Monday June 23 – Friday June 27The 28th annual HPCS conference, will take place in Halifax, June 3-27 (of which the first two days are tutorials). This year’s theme is `HPC Serving Society’. Sessions will focus on Bioinformatics, Big Data & Analytics, Computational Materials Science, Ocean & Atmosphere Modelling, Computational Chemistry, Data Cave Visualization, and more.

    We are seeking submissions for contributed works and posters relating to the conference theme. Submissions for contributed works will be due on April 30.

    More information is available at the conference website, http://2014.hpcs.ca.

System News

  • GPC: Ffmpeg v2.1.3, an audio and video software solution, installed as a module.
  • GPC: Python 3.3.4 installed as a module.
  • P7: Vapor 2.3.0, The Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers, installed as a module.
  • BGQ: Hpn-ssh, high-performance enabled ssh, installed as a module.
  • GPC: Petsc 3.4.4,the Portable, Extensible Toolkit for Scientific computation, installed as a module.
  • BGQ: OpenFOAM 2.3.0 installed as a module.
  • GPC: Quake 0.3.5, a program to detect and correct errors in DNA sequencing reads, installed as a module.
  • TCS: Cdo 1.6.1, a collection of command line Operators to manipulate and analyse climate and NWP model data, installed as a module.

What’s New On The SciNet Websites?

The SciNet Wiki can be found at http://wiki.scinethpc.ca, and the SciNet Education and Training site can be found at https://support.scinet.utoronto.ca/education.

  • Education site: Users can now keep track of their progress towards the SciNet certificates as they are take the courses. See the ‘Certificates’ tab on the education web site. For clarity, courses that count toward the certificates now have a course number.
  • Wiki and Education: Slides of the Seminar on Intro to GPU Computing Using CUDA.
  • Wiki and Education: Slides and Recordings of the lectures of the “High Performance Scientific Computing” mini-course.
  • Wiki and Education: Slides of the TechTalk “NetCDF4 binary files with Python, C++ and R”

What Else Happened at SciNet in the Last Month?

  • Mar 6: SciNet developer seminar on “OpenCL Middleware” by AJ Guillon
  • Mar 12: SciNet User Group meeting with TechTalk on “NetCDF4 binary files with Python, C++ and R” by Bertrand Brelier.
  • Mar 12: Introduction to GPU computing using CUDA
  • Mar 11-Apr 3: Lectures on “High Performance Scientific Computing” (Part 3 of the SciNet Scientific Computing Course)

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SciNet News March 2014

March 12, 2014 in for_researchers, for_users, newsletter

To keep users posted on what’s going on at SciNet, we send monthly emails with the new features, planned courses and events and accomplishments at SciNet.

Below you will find the salient points of what has happened or changed during the last month and what will happen in the near future. Among these is the announcement of the dates of the “Compute Ontario Summer School on HPC”. There will an installment in Waterloo in May, one in Toronto in June and one in Ottawa in July.

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

– The SciNet team

Events Coming Up

Unless stated otherwise, all events take place at the SciNet Headquarters, Rm 235 of 256 McCaul Street, Toronto. All events below are free for users but we ask that you sign up (“enroll”) on the education website.

  • Thursday March 6, 2:00 pm – 3:00 pm

    SCINET DEVELOPER SEMINAR

    OPENCL MIDDLEWARE

    By AJ Guillon

    AJ will demonstrate new C++11 OpenCL middleware that enables professional software development for heterogeneous computing. This framework significantly reduces programming complexity and extends OpenCL with new features. AJ will also provide an overview of the internal design of the middleware and supporting software stack.

    For more information and enrollment, go to the course website.

  • Sunday March 9, 2014

    APPLICATION DEADLINE INTERNATIONAL SUMMER SCHOOL ON HPC

    See below for more information about this expenses-paid summer school on challenges in HPC, held in June in Budapest, Hungary.

  • Wednesday March 12, 12:00 noon – 1:00 pm

    SCINET USER GROUP (SNUG) MEETING

    The SciNet Users Group (SNUG) meetings are every month on the second Wednesday, and involve (free) pizza, user discussion, feedback, and a one or two short talks on topics or technologies of interest to the SciNet community.

    This time, we will have

    • TechTalk:

      Introduction to NetCDF4 binary files with Python, C++ and R

      Bertrand Brelier (IBM@SciNet)

      During the presentation, Bertrand will review some features of NetCDF4, which is a portable binary file format and corresponding library. He will then show an example how to read and write a NetCDF4 compound variable in Python, C++ and R.

    • User discussion
    • Pizza!

    For more information and enrollment, go to the course website.

  • Wednesday March 12, 14:30 pm – 15:30 pm

    INTRODUCTION TO GPU COMPUTING USING CUDA

    Scott Northrup (SciNet)

    The CUDA (Compute Unified Device Architecture) parallel programming model harnesses the power of Nvidia graphics processing units (GPUs) to enable dramatic increases in computing performance for graphics, 3D content, video and scientific processing-intensive applications. This talk will provide an introduction to CUDA and examples of applications within research. Participants should be familiar with C/C++ development.

    For more information and enrollment, go to the course website.

    This talk is also offered remotely, for details see: https://www.westgrid.ca/events/introduction-to-gpu-computing-using-cuda

  • March 11, 13, 18, 20, 25, 27, and April 1 and 3: 11am-12noon

    HIGH PERFORMANCE SCIENTIFIC COMPUTING

    Lectures of Part 3 of the Scientific Computing Course

    Topics: parallel programming concepts, shared memory parallel programming with openmp, distributed memory parallel programming with mpi, hybrid programming.

    Participation counts towards the SciNet HPC Certificate.

    For more information and enrollment, go to the course website.

  • Tuesdays, almost bi-weekly, 2:30 pm – 3:30 pm

    COAST-TO-COAST SEMINAR SERIES

    The Coast to Coast Seminar is an hour-long presentation given on a scientific topic and is made accessible to audiences at a number of remote sites across Canada through collaboration technology.

    SciNet is a local seminar location for this series.

    The topic of the Spring 2014 Coast to Coast seminar series is “Technology for Aging Well” and it is built around a pan-Canadian project titled AGE-WELL (Aging Gracefully across Environments using Technology to Support Wellness, Engagement and Long Life.)

    The focus of the series will be a discussion how to use technology in helping support the Canadian aging population to ensure that all Canadians can grow older with dignity and grace.

    Mar 11: Geoff Fernie (U.Toronto)

    Mar 25: Alex Mihailidis (U.Toronto) and Rafik A. Goubran (Carleton U)

    For more information see http://www.irmacs.sfu.ca/events/coast-coast-seminars or https://www.westgrid.ca/events/coast-to-coast-seminar-series

  • Wednesday April 9, 12:00 noon – 1:00 pm

    SCINET USER GROUP (SNUG) MEETING

    TechTalk: TBA

    For more information and enrollment, go to the course website.

  • Wednesday May 14, 12:00 noon – 1:00 pm

    SCINET USER GROUP (SNUG) MEETING

    TechTalk: TBA

    For more information and enrollment, go to the course website.

  • Sunday June 1 – Friday June 6, Budapest, Hungary

    5TH INTERNATIONAL SUMMER SCHOOL ON HPC CHALLENGES IN COMPUTATIONAL SCIENCES

    In this summer school, leading American, Canadian, European and Japanese computational scientists and HPC technologists will offer instruction on a variety of topics, including HPC challenges by discipline (e.g., bioinformatics, computer science, chemistry, and physics), HPC programming proficiencies, performance analysis and profiling, algorithmic approaches & numerical libraries, data-intensive computing and scientific visualization.

    Compute Canada/Calcul Canada invites students enrolled in science and engineering fields at Canadian post-secondary institutions to apply for one of 10 (expenses-paid) spots allocated to Canada.

    Interested students should apply by March 9, 2014.

    For more information see http://www.prace-ri.eu/International-Summer-School-2014.

  • Monday June 9 – Friday June 13, University of Toronto, St. George Campus

    COMPUTE ONTARIO SUMMER SCHOOL ON HIGH PERFORMANCE COMPUTING/CENTRAL

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

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

    “West” May 26 – 30 Waterloo

    “Central” June 9 – 13 Toronto

    “East” July (TBD) Ottawa

    The format will be a four day workshop with mixed lectures and hands-on sessions on a number of selected subjects, such as MPI, CUDA, OpenMP, and Visualization (these will vary slightly depending on the location).

    This event will *not* be held at the SciNet Headquarters.

    More details regarding the summer school and how to register, will be announced in the future.

  • Monday June 23 – Friday June 27

    HPCS 2014: HIGH PERFORMANCE COMPUTING SYMPOSIUM IN HALIFAX

    The 28th annual HPCS conference, will take place in Halifax, June 3-27 (of which the first two days are tutorials). This year’s theme is `HPC Serving Society’. Sessions will focus on Bioinformatics, Big Data & Analytics, Computational Materials Science, Ocean & Atmosphere Modelling, Computational Chemistry, Data Cave Visualization, and more.

    We are seeking submissions for contributed works and posters relating to the conference theme. Submissions for contributed works will be due on April 30.

    More information is available at the conference website, http://2014.hpcs.ca.

System News

  • GPC: Ray 2.3.1 installed as a module.
  • GPC: Ghostscript added to the Xlibraries module.
  • GPC: CP2K (trunk of 25 Feb, 2014) installed as a module.
  • GPC: Valgrind 3.9.0 with openmpi 1.6 and intelmpi support installed as a modules.
  • ARC/Gravity: Cuda 5.5 installed as a module (cuda 4.1 still the default).

What’s New On The Wiki?

  • Slides and Recordings of 6 lectures of the “Numerical Tools for Physical Scientists” mini-course.
  • Slides of the TechTalk “Introduction to the Intel Xeon Phi”

What Else Happened at SciNet in the Last Month?

  • Feb 12: Intro to SciNet
  • Feb 12: SciNet User Group meeting with TechTalk on the Intel Xeon Phi.
  • Feb 4-27: Numerical Tools for Physical Scientists mini-course, 6 lectures.

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International Summer School 2014 on HPC Challenges

February 13, 2014 in blog, blog-general, for_educators, for_researchers, for_users, news

intlsummerschool4
Apply by 9 March, decisions in early April
Expenses paid by program
Sponsored by PRACE, XSEDE, Riken, and Compute Canada
website: http://summerschool.niif.hu

Compute Canada/Calcul Canada invites students and researchers at Canadian post-secondary institutions to apply for one of 10 spots allocated to Canada for the fifth International Summer School on HPC Challenges in Computational Sciences. This is a great opportunity for Canadian students and postdocs to attend an Advanced Summer School on High Performance Computing Challenges, all expenses paid.

The workshop is aimed primarily at graduate students or postdocs; however, junior faculty or advanced undergraduates are also welcome to apply. Attendees will be expected to have some experience in HPC parallel programming (for instance, MPI, OpenMP, or CUDA/OpenCL), preferably on software used in successful research projects, and must be at least 18 years of age at time of application. Attendees from all disciplines are invited to participate.

The summer school is sponsored by the European Union Seventh Framework Program’s Partnership for Advanced Computing in Europe Implementation Phase project (PRACE-3IP), U.S. National Science Foundation’s Extreme Science and Engineering Discovery Environment (XSEDE) project, RIKEN Advanced Institute for Computational Science (RIKEN AICS), and Compute Canada / Calcul Canada.

Leading American, Canadian, European and Japanese computational scientists and HPC technologists will offer instruction on a variety of topics, including:

  • 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

The expense-paid program will benefit advanced scholars from European, Canadian, Japanese and U.S. institutions who use HPC to conduct research. Interested students should apply by March 9, 2014.

Meals, housing, and travel from Canada, Japan and the U.S. will be covered for the selected participants. Applications from students in all science and engineering fields are welcome. Preference will be given to applicants with parallel programming experience, and a research plan that will benefit from the utilization of high performance computing systems.

For further information and to apply online, please click here.

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