EVENTS COMING UP

• Wed Dec 14, 2011: SciNet User Group (SNUG) Meeting

  The SciNet Users Group (SNUG) meetings are every month on the second Wednesday, and involve 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

  • Updates on the CentOS 6 switch.
  • “Compiler and optimization flags on the GPC” (TechTalk by Scott Northrup from SciNet)
  • User discussion
  • Pizza!
• Thu Dec 15, 2011: INTRODUCTION TO GPGPU WITH CUDA

  The goal of this course is for incoming students, new to GPGPU but familiar with scientific programming in 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.

  More info and sign up at https://support.scinet.utoronto.ca/courses/?q=node/42

• Mon Jan 9, 2012, 2:00 pm – 4:00 pm: INTRO TO THE LINUX SHELL

  Extremely useful for new users of SciNet that are not yet familiar with the Linux shell or other unix prompt systems.

  For more information and sign up, go to https://support.scinet.utoronto.ca/courses/?q=node/55

• Wed Jan 11, 2012, 10:00 am – 11:30 am: INTRO TO SCINET

  Learn what SciNet resources are available, how to recompile your code and how to use the batch system, in approximately 90 minutes.

  Intended for new users, but experienced users may still pick up some valuable pointers.

  Sign up at https://support.scinet.utoronto.ca/courses/?q=node/56

  Note that subsequently, at noon, there is a SciNet User group meeting (see below) that participants to the intro may be interested in too, but we do ask that you sign up for this separately.

• Jan 11/Feb 8/Mar 14/Apr 11/May 9, 2012, at noon: FUTURE SNUG MEETINGS

  We are still looking for users (students, postdocs, staff, faculty, it does not matter) willing to giving a short talk (20-30 minutes) about interesting work that they did on SciNet clusters and how they did it! If you are up for it, email support@scinet.utoronto.ca.

  More info on future SNUGs and sign-up at https://support.scinet.utoronto.ca/courses/?q=node/47 (Jan) https://support.scinet.utoronto.ca/courses/?q=node/48 (Feb) https://support.scinet.utoronto.ca/courses/?q=node/49 (Mar) https://support.scinet.utoronto.ca/courses/?q=node/50 (Apr) https://support.scinet.utoronto.ca/courses/?q=node/51 (May)

• Fri Jan 13,20,27, Feb 3, 2012: SCIENTIFIC COMPUTING 2: NUMERICAL TOOLS FOR PHYSICAL SCIENTISTS

  Part II of SciNet’s Scientific Computing couse. These parts can be taken as “mini-courses” or “modular courses” by astrophysics and physics graduate students.

  Topics of part II: Modelling, floating point computations, validation + verification, visualization, ODEs, Monte Carlo, linear algebra, FFT.

  More info: https://support.scinet.utoronto.ca/courses/?q=node/39 Sign-up: https://support.scinet.utoronto.ca/courses/?q=node/44

• Fri Feb 10,17, Mar 2,9, 2012: SCIENTIFIC COMPUTING 3: HIGH PERFORMANCE SCIENTIFIC COMPUTING

  Part III of SciNet’s Scientific Computing couse. These parts can be taken as “mini-courses” or “modular courses” by astrophysics and physics graduate students.

  Topics of part II: Profiling, optimization, openmp, mpi and hybrid programming.

  More info: https://support.scinet.utoronto.ca/courses/?q=node/39 Sign-up: https://support.scinet.utoronto.ca/courses/?q=node/45

SYSTEM CHANGES

• The home, scratch, project and hpss file systems have been restructured (note: not all users have access to the latter two). As a consequence, users’ files reside in different locations than before. The home and scratch file system are now group-based, and groups are furthermore clustered by the initial letter of the group name. For instance, the current home directory of user ‘resu’ in group ‘puorg’ is now /home/p/puorg/resu.

  The predefined variables $HOME, $SCRATCH, $PROJECT and $ARCHIVE point to the new directories.

• The High-Performance Storage System (HPSS) is in full production with a concurrent change in /project policies. Users with storage allocations greater than 5 TB will find all their former /project files will now reside in HPSS and their /project quotas will be reduced to 5 TB. Because HPSS recalls are much slower than expected (a bug that will hopefully be fixed soon), we closely follow any retrieval jobs that hpss users submit to try and streamline the recall.
• GPC: the OS update from CentOS 5.6 to CentOS 6 is completed. This update include updates to other programs (perl,gcc,python) as well, and to all modules. A small number of nodes still runs CentOS 5, but only for comparison runs. See the wiki on how to request these nodes, and be prepared for longer queuing times if you do.

ADDED TO THE WIKI IN NOVEMBER

All new wiki content below is listed and linked on the main page: 
http://wiki.scinethpc.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

• Important updates on the transition to CentOS 6.
• List of installed modules for the CentOS 6 nodes.
• Lectures slides and videos of the first four lectures of the Scientific Computing Course.

WHAT ELSE HAPPENED AT SCINET IN NOVEMBER?

• Transition to CentOS 6 (see above).
• Visualizing data with Paraview, given by SHARCNET collegue Alex Razoumov at SciNet on Wed Nov 23.
• Part I of SciNet mini-course Scientific Computing I – Scientific Software Development, consisting of four lectures.
• SNUG Meeting with a TechTalk on the file system restructuring was held on Nov 9, 2011.
• File system restructuring (see above) on Nov 8.

EVENTS COMING UP

• Tue Nov 8, 9:00 am: MAINTENANCE SHUTDOWN FOR FILE SYSTEM

  This is the first of two shutdowns intended to improve certain aspects of system performance and data centre stability. File systems are the focus of this first downtime. The most visible change for users is that their home and scratch directories will be moved. See “SYSTEM NEWS” below for details.

  Note that all logins and jobs will be killed at that 9:00 am. We expect to be back in the evening.

• Wed Nov 9, 12:00 noon: SNUG (SCINET USERS GROUP) MEETING

  The SciNet Users Group (SNUG) meetings are every month on the second Wednesday, and involve 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

  • “How to deal with the new file system setup at SciNet” (TechTalk by SciNet)
  • User discussion
  • Pizza!

  Sign up at https://support.scinet.utoronto.ca/courses/?q=node/35

• Dec 14, 2011, Jan 11/Feb 8/Mar 14/Apr 11/May 9, 2012: FUTURE SNUG MEETINGS

  We are still looking for users (students, postdocs, staff, faculty, it does not matter) willing to giving a short talk (20-30 minutes) about interesting work that they did on SciNet clusters and how they did it! If you are up for it, email support@scinet.utoronto.ca.

  More info on future SNUGs and sign-up at https://support.scinet.utoronto.ca/courses/?q=SNUG_Meetings

• Wed Nov 23: VISUALIZING DATA WITH PARAVIEW

  ParaView is a powerful open-source tool for analyzing and visualizing large multi-dimensional datasets. It is based on the Visualization Toolkit (VTK) and can run on all major platforms (Linux, Mac, Windows) both as a standalone application and as a front-end client connecting to a remote parallel server. In this two-hour long introduction I will talk about the basic workflow of a ParaView session, importing datasets in various formats, using filters, and scripting for automating ParaView tasks. This tutorial will have many hands-on exercises, so attendees are encouraged to bring a laptop with the latest copy of ParaView installed (http://www.paraview.org/paraview/resources/software.html). All sample codes and data will be provided.

  This workshop will be given at SciNet by our colleague from UOIT, Alex Razoumov.

  Sign-up at https://support.scinet.utoronto.ca/courses/?q=node/46.

• Fri Nov 4,11,18,25, 2011: SCIENTIFIC COMPUTING 1: SOFTWARE DEVELOPMENT AND DESIGN

  Note: in contrast to an earlier announcement, the lectures will be given on Fridays, from 9:30 to 11:30.

  See below for more details of the course. Sign-up for this part of the course is now closed.

• Fall/Winter: SCIENTIFIC COMPUTING COURSE

  Many computational projects start off with knowledge of the science you want to do, and with a bit of programming experience. It can be an arduous journey to get to a (maintainable) piece of code which you trust to compute the right thing. This course is aimed at reducing your struggle, 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 (so you don’t reinvent the wheel), and aspects of high performance computing.

  The course consists of three parts: Part 1: Scientific Software Development & Design (Nov 4,11,18,25) Part 2: Numerical Tools for Physical Scientists (Jan 13,20,27 & Feb 3) Part 3: High Performance Scientific Computing (Feb 10,17 & Mar 2,9) + A wrap-up lecture on Mar 16. Each part consists of four lectures of two hours. You can sign up for separate parts, or for the course as a whole.

  More details, including the full syllabus, grading, and sign-up, can be found at

  http://wiki.scinethpc.ca/wiki/index.php/Scientific_Software_Development_Course

  Note that these parts can be taken as “mini-courses” (AST3100) by astrophysics graduate students and as “modular courses” (PHYS2109) by physics students.

  Sign up for the full course and for part 1 is closed, but you can still sign up separately for parts 2 and 3 (see below) that will be give in the Winter.

• Mon Dec 12, 2011: INTRODUCTION TO GPGPU WITH CUDA

  The goal of this course is for incoming students, new to GPGPU but familiar with scientific programming in 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.

  More info and sign up at https://support.scinet.utoronto.ca/courses/?q=node/42

• Fri Jan 13,20,27, Feb 3, 2012: SCIENTIFIC COMPUTING 2: NUMERICAL TOOLS FOR PHYSICAL SCIENTISTS

  Sign-up: https://support.scinet.utoronto.ca/courses/?q=node/44

• Fri Feb 10,17, Mar 2,9, 2012: SCIENTIFIC COMPUTING 3: HIGH PERFORMANCE SCIENTIFIC COMPUTING

  Sign-up: https://support.scinet.utoronto.ca/courses/?q=node/45

SYSTEM CHANGES

• On November 8, we will be adding disks to the scratch file system and making scratch span both of our DDN controllers. The performance of /scratch should improve as a result of more spindles and the use of a second controller while the available space will increase by at least 40%.
• Furthermore, on November 8, 2011, the home, scratch, project and hpss file systems will be restructured (note: not all users have access to the latter two). As a consequence, users’ files will reside in different locations than before. The home and scratch file system will be group-based, and groups will furthermore be clustered by the initial letter of the group name. For instance, the current home directory of user ‘resu’ in group ‘puorg’ would move from /home/resu to /home/p/puorg/resu. Likewise, /scratch/resu would be moved to /scratch/p/puorg/resu.

  Users are responsible for making sure all their scripts and applications only use relative paths, or use the predefined variables $HOME, $SCRATCH and $PROJECT.

  Note that the TechTalk of the Nov 9 SNUG will address the issue how to deal with this new setup.

• The High-Performance Storage System (HPSS) goes into full production with a concurrent change in /project policies. Users with storage allocations greater than 5 TB will find all their former /project files will now reside in HPSS and their /project quotas will be reduced to 5 TB.
• GPC: an OS update from CentOS 5.6 to CentOS 6 is being prepared, which will include updates to other programs (perl,gcc,python) as well. The ARC already uses the newer OS, and a few of the gpc nodes are using this as a test already, while we are in the process of porting all the modules to the new OS. We encourage users to try the new environment out using the instructions on the wiki.
• SciNet has a new public web site, www.scinethpc.ca, with a new look. The wiki and portal sites can now be accessed though the same domain, as wiki.scinethpc.ca and portal.scinethpc.ca, respectively. The courses site remains at https://support.scinet.utoronto.ca/courses for now.

  Come take a look at our new website!

ADDED TO THE WIKI IN OCTOBER

 All new wiki content below is listed and linked on the main page: 
 http://wiki.scinethpc.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

• Tips on testing your codes for CentOS 6
• Syllabus of the Scientific Software Development Course
• Currently installed modules for the CentOS 6 nodes
• Slides of the SNUG talk by Manuel Saldaña on “MPI as a programming model for High-Performance Reconfigurable Computers”
• How to distinguish between CentOS 5 and 6 in your .bashrc

WHAT ELSE HAPPENED AT SCINET IN OCTOBER?

• Oct 6: Information session for NRAC applications
• Oct 12: SNUG meeting with a TechTalk by Manuel Saldaña (Arch Es Computing) on “MPI as a programming model for High-Performance Reconfigurable Computers”
• Oct 26: Introduction to scientific programming with modern FORTRAN

EVENTS COMING UP

• Tue Oct 4, 2:00 pm: MAINTENANCE SHUTDOWN FOR DATA CENTRE TRANSFORMERS

  All logins and jobs will be killed at that time. Power may not be restored until midnight.

• Thu Oct 6, 1:00-3:00 pm: INFORMATION SESSION FOR NRAC APPLICATIONS

  Meet with SciNet analysts to discuss your application for the yearly round of national resource allocations. The call for proposals can be found here: https://computecanada.org/?mod=cms&pageId=1663&lang=EN&

• Wed Oct 12, 12:00 noon: SNUG (SCINET USERS GROUP) MEETING

  The SciNet Users Group (SNUG) meetings are every month on the second Wednesday, and involve 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

  • A TechTalk by Manuel Saldana (Arch Es Computing) on “MPI as a programming model for High-Performance Reconfigurable Computers”
  • User discussion
  • Pizza!

  Sign up at https://support.scinet.utoronto.ca/courses/?q=node/34

• Tue Oct 18, 3:00 pm: DEADLINE FOR NRAC APPLICATIONS

  The application website is https://ccdb.computecanada.org/allocation/resource_applications. Note that an information session will be held on Oct 6 (see above).

• Wed Oct 26: INTRODUCTION TO SCIENTIFIC PROGRAMMING WITH MODERN FORTRAN

  This full-day course will demonstrate how to use modern features of Fortran. It will cover the use of modules to break code into type-safe pieces; optional arguments and the use of interface; portable ways of using different sizes of integers and reals; an introduction to object-oriented programming in Fortran 2003; and a preview of co-arrays for parallel programming in Fortran 2008.

  More info and sign-up at https://support.scinet.utoronto.ca/courses/?q=node/41

• Wed Nov 9 and Dec 14: FUTURE SNUG MEETINGS

  We are still looking for users (students, postdocs, staff, faculty, it does not matter) willing to giving a short talk (20-30 minutes) about interesting work that they did on SciNet clusters and how they did it! If you are up for it, email support@scinet.utoronto.ca.

  More info on future SNUGs and sign-up at https://support.scinet.utoronto.ca/courses/?q=SNUG_Meetings

• Wed Nov 23: VISUALIZING DATA WITH PARAVIEW

  Given at SciNet by our colleague from UOIT/SharcNet, Alex Razoumov.

  More details to come soon at https://support.scinet.utoronto.ca/courses/?q=node/46.

• Fri Nov 4,11,18,25, 2011: SCIENTIFIC COMPUTING 1: SOFTWARE DEVELOPMENT AND DESIGN

  Note: in contrast to an earlier announcement, the lectures will be given on Fridays, from 9:30 to 11:30.

  See below for more details of the course.

  Sign-up for this part only: https://support.scinet.utoronto.ca/courses/?q=node/43

  You can also sign up for all three parts, see below.

• Fall/Winter: SCIENTIFIC COMPUTING COURSE

  Many computational projects start off with knowledge of the science you want to do, and with a bit of programming experience. It can be an arduous journey to get to a (maintainable) piece of code which you trust to compute the right thing. This course is aimed at reducing your struggle, 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 (so you don’t reinvent the wheel), and aspects of high performance computing.

  The course consists of three parts: Part 1: Scientific Software Development & Design (Nov 4,11,18,25) Part 2: Numerical Tools for Physical Scientists (Jan 13,20,27 & Feb 3) Part 3: High Performance Scientific Computing (Feb 10,17 & Mar 2,9) + A wrap-up lecture on Mar 16. Each part consists of four lectures of two hours. You can sign up for separate parts, or for the course as a whole.

  More details, including the full syllabus, grading, and signup, can be found at https://support.scinet.utoronto.ca/courses/?q=node/39

  Note that these parts can be taken as “mini-courses” by astrophysics graduate students; we are talking to other departments to see if this can be extended to their grad students as well.

• Mon Dec 12, 2011: INTRODUCTION TO GPGPU WITH CUDA

  The goal of this course is for incoming students, new to GPGPU but familiar with scientific programming in 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.

  More info and sign up at https://support.scinet.utoronto.ca/courses/?q=node/42

• Thu Jan 13,20,27, Feb 3, 2012: SCIENTIFIC COMPUTING 2: NUMERICAL TOOLS FOR PHYSICAL SCIENTISTS Sign-up: https://support.scinet.utoronto.ca/courses/?q=node/44
• Thu Feb 10,17, Mar 2,9, 2012: SCIENTIFIC COMPUTING 3: HIGH PERFORMANCE SCIENTIFIC COMPUTING Sign-up: https://support.scinet.utoronto.ca/courses/?q=node/45

SYSTEM CHANGES

• File system: In the near future, the home, scratch, project and hpss file systems will be restructured (note: not all users have access to the latter two). As a consequence, users’ files will reside in different (absolute) locations than before. The home and scratch file system will be group-based, and groups will furthermore be clustered by the initial letter of the group name. For instance, the current home directory of user ‘resu’ in group ‘puorg’ would move from /home/resu to /home/p/puorg/resu. Likewise, /scratch/resu would be moved to /scratch/p/puorg/resu.

  To facilitate the transition, we ask the user’s cooperation in making sure all their scripts and applications only use relative paths, or use the predefined variables $HOME, $SCRATCH and $PROJECT.

• GPC: an OS update from Centos 5.6 to CentOS 6 is being prepared, which will include updates to other programs (perl,gcc,python) as well. A few nodes are using this as a test already, and we are in the process of porting all the modules to the new OS. We encourage users willing to try the new environment out to contact us. Note that the ARC already uses the newer OS.

ADDED TO THE WIKI AND COURSE WEBSITE IN SEPTEMBER

 All new wiki content below is listed and linked on the main page: 
 http://wiki.scinet.utoronto.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

• Slides of the latest INTRO TO SCINET session.
• Slides of the SciNet presentations given at the SciNet GPU Workshop Sept 2011
• Slides of the SNUG TechTalk on HPSS given on Sep 14.

WHAT ELSE HAPPENED AT SCINET IN SEPTEMBER?

• Fri Sept 9: Intro to SciNet
• Wed Sept 14: SNUG meeting with a TechTalk by Jaime Pinto (SciNet) on “HPSS – SciNet’s storage capacity expansion”.
• Mon Sept 26: GPGPU workshop with talks by Jianwen Zhu (Electrical and Computer Engineering) on “Some Applications of GPGPU on Electronic Design Automation” and by Peter Colberg (Chemical Physics Theory Group) on “Multi-Particle Collision Dynamics on GPUs”
• Fri Sept 30: full day Parallel I/O course

EVENTS COMING UP

• Fri Sept 9, 12:00 noon: INTRO TO SCINET

  Learn what SciNet resources are available and how to use them, in approximately 90 minutes. Extremely useful for new users, but experienced users may still pick up some valuable pointers. This is a repeat of the Aug 26 session.

  Sign up at https://support.scinet.utoronto.ca/courses/?q=node/32.

• Wed Sept 14, 12:00 noon: SNUG (SCINET USERS GROUP) MEETING

  The SciNet Users Group (SNUG) meetings are every month on the second Wednesday, and involve 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

  • A techTalk by Jaime Pinto (SciNet) on “HPSS – SciNet’s storage capacity expansion”
  • User discussion
  • Pizza!

  Sign up at https://support.scinet.utoronto.ca/courses/?q=node/33

• Wed Oct 12, Nov 9 and Dec 14: FUTURE SNUG MEETINGS

  We are still looking for users (students, postdocs, staff, faculty, it does not matter) willing to giving a short talk (20-30 minutes) about interesting work that they did on SciNet clusters and how they did it! If you are up for it, email support@scinet.utoronto.ca.

  More info on future SNUGs and sign-up at https://support.scinet.utoronto.ca/courses/?q=SNUG_Meetings

• Mon Sept 26, 2:00pm-5:00pm: GPGPU WORKSHOP

  SciNet presentation:

  • “GPGPU Activities and Support at SciNet”

  Research talks:

  • Jianwen Zhu (Electrical and Computer Engineering) “Some Applications of GPGPU on Electronic Design Automation”
  • Peter Colberg (Chemical Physics Theory Group) “Multi-Particle Collision Dynamics on GPUs”

  More info and sign-up at https://support.scinet.utoronto.ca/courses/?q=node/38

• Wed Sept 28, 10am-3:30pm: SCINET’S RESEARCH COMPUTING CONSULTING CLINIC

  Thinking of starting a compute-intensive research project? In the middle of one but stuck on what technique or method to use?

  Once a month, the experts at SciNet, Canada’s largest supercomputing centre, will have a consulting desk open for all research members of the larger University community to help them design and make decisions about their computational research tools. These clinics will usually be held on the days of the SciNet users group meetings, the 3rd Wednesday of the month, which attendees are welcome to attend.

  To mark the start of the school year, this month’s clinic will be at a special date: Wed, 28 Sept, 10am-4:30pm. For the rest of the semester, it will be held at the third Wednesday of the month, 10am-12pm, 1:30pm-3:30pm.

• Fri Sept 30: PARALLEL I/O COURSE

  Learn how to avoid I/O becoming the bottleneck in your large-scale computation; general strategies as well as true parallel I/O techniques (MPI-IO, HDF5, and NetCDF) will be covered in this one-day course.

  More info and sign-up at https://support.scinet.utoronto.ca/courses/?q=node/40

• Wed Oct 26: INTRODUCTION TO SCIENTIFIC PROGRAMMING WITH MODERN FORTRAN

  This full-day course will demonstrate how to use modern features of Fortran. It will cover the use of modules to break code into type-safe pieces; optional arguments and the use of interface; portable ways of using different sizes of integers and reals; an introduction to object-oriented programming in Fortran 2003; and a preview of co-arrays for parallel programming in Fortran 2008.

  More info and sign-up at https://support.scinet.utoronto.ca/courses/?q=node/41

• Fall/Winter: SCIENTIFIC COMPUTING COURSE

  Many computational projects start off with knowledge of the science you want to do, and with a bit of programming experience. It can be an arduous journey to get to a (maintainable) piece of code which you trust to compute the right thing. This course is aimed at reducing your struggle, 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 (so you don’t reinvent the wheel), and aspects of high performance computing.

  The course consists of three parts: Part 1: Scientific Software Development & Design (Nov 3,10,17,24) Part 2: Numerical Tools for Physical Scientists (Jan 13,20,27 & Feb 3) Part 3: High Performance Scientific Computing (Feb 10,17 & Mar 2,9) + A wrap-up lecture on Mar 16. Each part consists of four lectures of two hours. You can sign up for separate parts, or for the course as a whole.

  More details, including the full syllabus, grading, etc., can be found at https://support.scinet.utoronto.ca/courses/?q=node/39

  Note that these parts can be taken as “mini-courses” by astrophysics graduate students; we are talking to other departments to see if this can be extended to their grad students as well.

• Thu Nov 3,10,17,24, 2011: SCIENTIFIC COMPUTING 1: SOFTWARE DEVELOPMENT AND DESIGN Sign-up: https://support.scinet.utoronto.ca/courses/?q=node/43
• Mon Dec 12, 2011: INTRODUCTION TO GPGPU WITH CUDA

  The goal of this course is for incoming students, new to GPGPU but familiar with scientific programming in 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.

  More info and sign up at https://support.scinet.utoronto.ca/courses/?q=node/42

• Thu Jan 13,20,27, Feb 3, 2012: SCIENTIFIC COMPUTING 2: NUMERICAL TOOLS FOR PHYSICAL SCIENTISTS Sign-up: https://support.scinet.utoronto.ca/courses/?q=node/44
• Thu Feb 10,17, Mar 2,9, 2012: SCIENTIFIC COMPUTING 3: HIGH PERFORMANCE SCIENTIFIC COMPUTING Sign-up: https://support.scinet.utoronto.ca/courses/?q=node/45

SYSTEM CHANGES

• GPC: an OS update from Centos 5.6 to CentOS 6 is being prepared, which will include updates to other programs (perl,gcc,python) as well. A few nodes are using this as a test already, and we are in the process of porting all the modules to the new OS. We encourage users willing to try the new environment out to contact us. Note that the ARC already uses the newer OS.
• GPC: “Climate Data Operator” versions 1.4.6 and 1.5.1 are available as modules cdo/1.4.6 and cdo/1.5.1, respectively.
• GPC: The “Climate Model Output Rewriter” is installed as module cmor/2.7.1.
• GPC: a newer version of R can now be used by explicitly loading the module R/2.13.1, while R/2.11.1 remains the default.
• GPC: ffmpeg has been added to the ImageMagick module.

ADDED TO THE WIKI AND COURSE WEBSITE IN AUGUST

(All new wiki content below is listed and linked on the main page: http://wiki.scinet.utoronto.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

• Slides of the 1-day intro to GPGPU using CUDA Course.
• Slides of the latest INTRO TO SCINET session.
• Update info on how to distinguish what cluster you are on in the .bashrc file.
• The course website now has a link to past courses at the top, so it is now easier to find slides and/or movies of past events.

WHAT ELSE HAPPENED AT SCINET IN AUGUST?

• A one-day course on General Purpose GPU computing with CUDA was held on Aug 22. This is one of the first of many GPGPU activities to come, now that the University of Toronto has been recognized as a NVIDIA Teaching Centre as well as an NVIDIA Research Centre (a collaborative effort of SciNet and the Canadian Institute for Theoretical Astrophysics, the University of Toronto’s Institute for Aerospace Studies and Departments of Chemistry, Biochemistry, and Electrical and Computer Engineering, and the Medical Image Analysis Laboratory at Sunnybrooke Hospital).
• The first “Intro to SciNet” session held given on Aug 26.
• A leak in the cooling system was discovered in the data centre, leading to two emergency shutdowns. Repairs have been made.

EVENTS COMING UP

• Mon Aug 22: INTRODUCTION TO GPGPU WITH CUDA

  The goal of this one-day course is for incoming students, new to GPGPU but familiar with scientific programming in 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.

  For more information and to sign up, see: https://support.scinet.utoronto.ca/courses/?q=node/37

• Fri Aug 26, 12:00 noon: INTRO TO SCINET

  Learn how to use SciNet systems in approximately 90 minutes. Extremely useful for new users, but experienced users may still pick up some valuable pointers.

  More sessions may be given throughout the year depending on user interest, but only the first one (Aug 25) will feature pizza!

  Sign up on https://support.scinet.utoronto.ca/courses/?q=node/31.

• Tue Aug 30 (tentative): GPGPU WORKSHOP

  A GPGPU workshop at SciNet in which representatives from research groups will give short talks, and then we discuss.

  More info coming soon at https://support.scinet.utoronto.ca/courses/?q=node/38

• Fri Sep 9, 12:00 noon: INTRO TO SCINET

  A repeat of the Aug 26 session, but without the distraction of pizza.

  Sign up on https://support.scinet.utoronto.ca/courses/?q=node/32.

• Wed Sep 14, 12:00 noon: SNUG (SCINET USERS GROUP) MEETING
  • TechTalk by Jaime Pinto (SciNet) on “HPSS – SciNet’s storage capacity expansion”
  • User discussion
  • Pizza!

  Sign up on https://support.scinet.utoronto.ca/courses/?q=node/33

• Other SNUG meetings next term are scheduled on Oct 12, Nov 9 and Dec 14, and you can sign up on https://support.scinet.utoronto.ca/courses/?q=SNUG_Meetings.
• Fall Term: SCIENTIFIC COMPUTING COURSE

  This course will likely follow the format of a weekly 3-hour session. It will consist of three parts: Part 1: Scientific Software Development & Design Part 2: Numerical Tools for Physical Scientists Part 3: High Performance Scientific Computing Each part consists of 4 lectures, which include hands-on, and can be taken separately.

  More details (including whether you can get credit for this course!) will soon be available on the courses website: https://support.scinet.utoronto.ca/courses.

SYSTEM CHANGES

• SciNet has a mailing lists for people interested in GPGPU computing. To receive information on courses, workshop and other GPGPU related events, sign up at: https://support.scinet.utoronto.ca/mailman/listinfo/scinet-gpgpu .
• To deal with the security issue in July (see below), extensive updates and tightening of security measured were performed. Users were required to change there passwords and regenerate (pass-phrase protected) ssh keys if they used these (highly recommended, see wiki). We also updated the operating system on the gpc to ensure the security hole could not be used again.
• GPC: nedit installed as a module.
• P7: any user that has access to the power-6 cluster tcs, can now give the power-7 cluster (p7) a try. This cluster currently consists of 5 IBM Power 755 servers (3 or more servers to be added later this year). Each has four 8-core 3.3GHz Power7 CPUs and 128GB RAM, and features 4-way Simultaneous MultiThreading giving 128 threads per server. Linux is the operating system. Both the GCC and IBM compilers are installed, as well as POE. LoadLeveler is used as the scheduler. Instruction on usage are on the wiki.

ADDED TO THE WIKI IN JULY

(All new wiki content below is listed and linked on the main page: http://wiki.scinet.utoronto.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

• Update info on how to distinguish what cluster you are on in the .bashrc file.
• Improved help for the ish application, which can browse previously indexed directories on the hpss system.
• More material on HPSS was added.

WHAT ELSE HAPPENED AT SCINET IN JULY?

• We were hacked, as were several other hpc consortia in Canada. We needed more than 4 days of shutdown to make sure nothing vital was compromised, to reinstall and upgrade systems, and to safe-guard ourselves against any possible future attack. It seems that the attack started with a stolen user’s password. So be careful not to let your password fall in the wrong hands, and generate pass- phrase protected ssh keys for increased security!
• SciNet, in collaboration with the research groups at the Canadian Institute for Theoretical Astrophysics, the University of Toronto’s Institute for Aerospace Studies and Departments of Chemistry, Biochemistry, and Electrical and Computer Engineering, and the Medical Image Analysis Laboratory at Sunnybrooke Hospital, has successfully applied for the University of Toronto to become an NVIDIA Teaching Centre as well as an NVIDIA Research Centre. So you can expect more GPGPU training facilities from SciNet soon!

COMING UP

• Jul 11-13: HPCVL / Compute Canada Workshop July 2011

  Practical Parallel Programming With OpenMP and MPI HPCVL Training Room, 115-993 Princess St., Kingston, Ontario

  Schedule: Mon July 11, 2011: OpenMP Tue July 12, 2011: MPI Wed July 13, 2011: Hybrid Time: 9:00 am – 4:00 pm (EST)

  Lecturers: Hartmut Schmider and Gang Liu (HPCVL, Queen’s University, Kingston, Ontario)

  Also available via video conferencing at SciNet. Contact us if you want to participate remotely (support@scinet.utoronto.ca), or see https://support.scinet.utoronto.ca/courses/?q=node/29.

• Wed Jul 20, 12:00 – 13:00: Introduction to Linux for SHARCNET

  Speaker: Isaac Ye, HPTC Analyst

  An introductory seminar on Linux usage, aimed specifically at users new to the Linux operating system, and with an emphasis on usage typical to a user of the SHARCNET systems. Topics will include basic concepts related to the filesystem, shell usage and basic commands to help a new user be productive on SHARCNET clusters; key activities such as compilation, modules and the job scheduler will also be covered.

  Registration for this event is not necessary, just point your web browser at http://my.dimdim.com/sharcnet just before the talk.

• Thu Aug 25, 12:00 noon: Intro to SciNet Fri Sep 9, 12:00 noon: Intro to SciNet (these are identical sessions)

  Learn how to use SciNet systems in approximately 90 minutes. Extremely useful for new users, but experienced users may still pick up some valuable pointers.

  More sessions may be given throughout the year depending on user interest, but only the first one (Aug 25) will feature pizza!

  Sign up on https://support.scinet.utoronto.ca/courses.

• Wed Sep 14, 12:00 noon: SNUG (SCINET USERS GROUP) MEETING
  • TechTalk by Jaime Pinto (SciNet) on “HPSS – SciNet’s storage capacity expansion”
  • User discussion
  • Pizza!

  Sign up on https://support.scinet.utoronto.ca/courses/?q=node/33

• Other SNUG meetings next term are scheduled on Oct 12, Nov 9 and Dec 14, and you can sign up on https://support.scinet.utoronto.ca/courses/?q=SNUG_Meetings.
• More course announcements to come soon! Keep an eye on SciNet’s course web site https://support.scinet.utoronto.ca/courses.

SYSTEM CHANGES

• HPSS, the new tape-backed storage system that expands the current storage capacity of SciNet, has entered its pilot phase. This means that the installation is complete, and select users are trying out the system. HPSS will be one of the ways in which storage allocation will be implemented.
• New IBM Power-7 cluster: The P7 cluster currently consists of 5 IBM Power 755 servers (at least 3 more servers to be added later this year). Each has four 8-core 3.3GHz Power7 CPUs and 128GB RAM, and features 4-way Simultaneous MultiThreading giving 128 threads per server. Linux is the operating system. Both the GCC and IBM compilers are installed, as well as POE and OpenMPI. LoadLeveler is used as the scheduler. Instruction on usage are on the wiki, but you will first have to ask us if you want access (support@scinet.utoronto.ca).
• GPC: The Berkeley compiler for Unified Parallel C (UPC) has been installed as the module upc. The compiler command is ‘upcc’.
• GPC: Bugs in the gnuplot module were fixed.
• GPC: qhull support was added to octave.

ADDED TO THE WIKI IN JUNE

(All new wiki content below is listed and linked on the main page: http://wiki.scinet.utoronto.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

• The Acceptable Use Policy in the Essentials page
• Slides and source code of the Parallel I/O session at HPCS 2011, given by one of our analysts.
• A link to a 2009 INRIA Technical Report on existing linear algebra libraries for C++ was added to the Math section of the Tutorial page
• Slides of Pierre de Buyl’s TechTalk on f2py: Fortran and Python
• A lot of material on HPSS was added.

WHAT ELSE HAPPENED AT SCINET IN JUNE?

• A SNUG meeting was held on Jun 8, with a TechTalk by Pierre de Buyl on “f2py (Fortran Python interfacing)
• Jun 13-17: SciNet was involved in the technical sessions of HPCS2011 in Montreal, and many of us participated in the symposium (http://2011.hpcs.ca).
• May 30-Jun 3: The Ontario Summer School on HPC, jointly sponsored by SHARCNET, SciNet and HPCVL — your Ontario HPC consortia — was held at the Sheridan Institute of Technology and Advanced Learning in Trafalgar, Oakville, Ontario (http://ss2011.sharcnet.ca).
• We had a couple of chiller failures.

COMING UP

• Wed Jun 8, 12:00 noon: SNUG (SCINET USERS GROUP) MEETING
  • TechTalk by Pierre de Buyl (Chemical Physics Theory Group) on “f2py” (a Fortran-Python interface).
  • User discussion
  • Pizza!

  This event takes place at the SciNet Headquarters, Rm 235 of 256 McCaul Street, Toronto.

  Sign up if you are planning to come (so we won’t run out of pizza), at https://support.scinet.utoronto.ca/courses/?q=node/26

• June 13-17: HIGH PERFORMANCE COMPUTING SYMPOSIUM 2011

  HPCS2011 is a multidisciplinary conference that focuses on research involving High Performance Computing and its application.

  This year it is given in Montreal, and focuses on HPC in medical science.

  The actual symposium is from June 15 to 17. There are very worthwhile tutorial sessions on the two days before.

  More info can be found at http://2011.hpcs.ca.

SYSTEM CHANGES

• DDT, a parallel debugging program from Allinea, has been installed on the GPC, TCS, and ARC. DDT stands for “Distributed Debugging Tool” and is available as the module “ddt”. It supports debugging OpenMP, MPI and CUDA applications in a graphical environment.
• In the future, we may have to move your /home/USER and /scratch/USER directories to new locations. To prepare for this, you should try to avoid using absolute paths in your scripts and programs, i.e., use relative paths, or use ~ or ${HOME} instead of /home/USER.

ADDED TO THE WIKI IN MAY

(All new wiki content below is listed and linked on the main page: http://wiki.scinet.utoronto.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

• Slides of the May 2011 SNUG TechTalk by Peter Colberg on Lua.
• Slides, videos, and source code of the 5-day parallel programming course given in May.
• A link to the manual of the parallel debugger DDT (on the right side of the Tutorials and Manuals page).
• Our twitter feed can be found at the bottom of the main wiki page.

WHAT ELSE HAPPENED AT SCINET IN MAY?

• A SNUG meeting was held on May 4, with a TechTalk by Peter Colberg on “Scripting HALMD with Lua and Luabind”
• On May 9-13, an intensive 5-day course “Introduction to Practical Parallel Programming” was given.
• We had a few chiller failures. The main reasons of the failures have been found, but there were side effects that still caused issues.

COMING UP:

• Wed May 4, 12:00 noon: SNUG (SCINET USERS GROUP) MEETING
  • TechTalk by Peter Colberg (Chemical Physics Theory Group)

    “Scripting HALMD with Lua and Luabind”

    Lua is a lightweight, embeddable scripting language. Luabind is a library that exposes C++ classes and functions to Lua. HALMD, a highly accelerated large-scale molecular dynamics package for GPUs, uses Lua and Luabind to couple a set of high-performance C++ and CUDA modules in a flexible and extensible manner.

  • User discussion
  • Pizza!

  Sign up if you are planning to come, at https://support.scinet.utoronto.ca/courses/?q=node/25

  • MAY 9-13: 5 DAY PARALLEL PROGRAMMING COURSE

  The goal of the workshop is to enable young researchers already experienced in scientific computing to leave with the knowledge necessary to begin writing the parallel codes needed for their research. The workshop will be a mix of lectures and immediate feedback on practical assignments, designed to ensure that students leave with significant experience in both OpenMP and MPI, two of the standards for parallel computing today. We aim for this workshop to be useful for graduate students and postdocs for a wide range of disciplines.

  The course will be given in a yet-to-be determined location on the St. George Campus.

  There will be NO FEE, but you are responsible to get the recommended BOOKS, and your own COFFEE and LUNCH.

  There is LIMITED AVAILABILITY, so please only register if you are serious about attending. Registration and further details (topics, books, location) are (or will be) available at

  https://support.scinet.utoronto.ca/courses/?q=node/23

• May 30-June 3: ONTARIO SUMMER SCHOOL ON HIGH PERFORMANCE COMPUTING

  This Summer School is jointly sponsored by SHARCNET, SciNet and HPCVL — your Ontario HPC consortia. It is held at the Sheridan Institute of Technology and Advanced Learning in Trafalgar, Oakville, Ontario.

  This annual, intensive education event offers a week-long program of hands-on courses covering introductory HPC materials, programming for distributed systems (MPI) and shared memory environments (OpenMP), GPU programming, software best practices, debugging and much more.

  To maximize the ability for persons from the widest range of SHARCNET, SciNet and HPCVL institutions to attend, a subsidized rate will be available for those traveling a reasonable distance which includes up to 4 nights accommodation in the on-site residence, and a limited number of travel subsidies will be available, reserved for those traveling very long distances (Lakehead for example).

  Please watch the website (http://ss2011.sharcnet.ca) over the coming days as more information is put in place, and registration opens. Note that spaces are limited so register early!

  If you have additional questions in the meantime, please e-mail ss2011@sharcnet.ca .

• Wed Jun 8, 12:00: SNUG MEETING

  Let us know (support@scinet) if you’re interested in giving a TechTalk.

  Sign up if you are planning to come, at https://support.scinet.utoronto.ca/courses/?q=node/26

• June 13-17: HIGH PERFORMANCE COMPUTING SYMPOSIUM 2011

  HPCS2011 is a multidisciplinary conference that focuses on research involving High Performance Computing and its application.

  This year it is given in Montreal, and focuses on HPC in medical science.

  The actual symposium is from June 15 to 17. There are very worthwhile tutorial sessions on the two days before.

  More info can be found at at http://2011.hpcs.ca

ADDED TO THE WIKI IN APRIL:

(All new wiki content below is listed and linked on the main page: https://support.scinet.utoronto.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

• Slides and source code of the Scientific Modern Fortran class.
• Slides of the April 2011 SNUG on User-space modules and packages.
• Instructions on installing your own modules.
• Instructions on how to install your own Python Modules.

SYSTEM CHANGES:

• GPC: Two versions of Goto Blas were installed, a single and multi-threaded one. They can be loaded as modules “gotoblas/1.13-singlethreaded” and “gotoblas/1.13-multithreaded”, respectively.
• TCS: A temporary workaround for the development nodes tcs01 and tcs02 was in place, but things are back to usual.
• Accelerator Research Cluster (ARC): A 8-node GPU test-cluster has been setup with a total of 64 Nehalem CPUs and 16 GPUs (NVIDIA, Cuda capability 2.0). As with the TCS, you do not have access to this by default, but let us know if you want to do GPU computing. More information at https://support.scinet.utoronto.ca/wiki/index.php/GPU_Devel_Nodes
• SciNet is on Twitter! Our twitter feed can be found here: https://twitter.com/SciNetHPC

WHAT ELSE HAPPENED AT SCINET IN APRIL?

• A SNUG meeting was held on Apr 13, with a TechTalk by SciNet on “User-space modules and packages on SciNet”.
• On Apr 19, a 1-day course “Introduction to to Scientific Programming with Modern FORTRAN” was given.
• There was scheduled downtime on April 27 to make repairs and improvements to the cooling system.
• Problems with the TCS were largely remedied.
• A thank-you goes out to all the users that cleaned up a good deal of their scratch disk space upon our request, when scratch was reaching 98% utilization in early April!

COMING UP:

• Wed Apr 13, 12:00 noon: SNUG (SCINET USERS GROUP) MEETING
  • TechTalk by Peter Colberg (Chemical Physics Theory Group)

    “Scripting HALMD with Lua and Luabind”

    Lua is a lightweight, embeddable scripting language. Luabind is a library that exposes C++ classes and functions to Lua. HALMD, a highly accelerated large-scale molecular dynamics packqage for GPUs, uses Lua and Luabind to couple a set of high-performance C++ and CUDA modules in a flexible and extensible manner.

  • User discussion
  • Pizza!

  Sign up if you are planning to come, at https://support.scinet.utoronto.ca/courses/?q=node/18

• Tue Apr 19: INTRODUCTION TO SCIENTIFIC PROGRAMMING WITH MODERN FORTRAN

  Fortran, as the only major programming language designed explicitly for scientific programming, has come a long way since it’s 1977 version which was sensitive to spacing layout, used computed gotos and with only arrays whose sizes could only be changed by recompiling.

  This is a full-day course which will will demonstrate the use of modules to break code into type-safe pieces; optional arguments and the use of interface; portable ways of using different sizes of integers and reals; an introduction to object-oriented programming in Fortran 2003.; and a preview of co-arrays for parallel programming in Fortran 2008.

  Prerequisite is a significant experience in scientific programming with FORTRAN. If you are unsure about the prerequisites, contact us at support@scinet.utoronto.ca.

  Sign up at https://support.scinet.utoronto.ca/courses/?q=node/21

• Wed May 4, 12:00: SNUG (the first Wednesday on the month this time!)

  Sign up if you are planning to come, at https://support.scinet.utoronto.ca/courses/?q=node/25

  • MAY 9-13: 5 DAY PARALLEL PROGRAMMING COURSE *

  The goal of the workshop is to enable young researchers already experienced in scientific computing to leave with the knowledge necessary to begin writing the parallel codes needed for their research. The workshop will be a mix of lectures and immediate feedback on practical assignments, designed to ensure that students leave with significant experience in both OpenMP and MPI, two of the standards for parallel computing today. We aim for this workshop to be useful for graduate students and postdocs for a wide range of disciplines.

  The course will be given in a yet-to-be determined location on the St. George Campus.

  There will be NO FEE, but you are responsible to get the recommended BOOKS, and your own COFFEE and LUNCH.

  There is LIMITED AVAILABILITY, so please only register if you are serious about attending. Registration and further details (topics, books, location) are (or will be) available at

  https://support.scinet.utoronto.ca/courses/?q=node/23

• Wed Jun 8, 12:00: SNUG

  Sign up if you are planning to come, at https://support.scinet.utoronto.ca/courses/?q=node/26

ADDED TO THE WIKI IN MARCH:

(All new wiki content below is listed and linked on the main page: https://support.scinet.utoronto.ca/wiki/index.php/SciNet_User_Support_Library#What.27s_New_On_The_Wiki)

• Links to the videos of the presentations given at the Science Illustrated symposium.
• Slides of the two March SNUG TechTalks by Abdul Mroue and Jaochim Harnois-Déraps.
• An explanation of the change of the temporary location of the standard error/output file for GPC jobs; see the FAQ on the wiki.
• Updated techniques to installed user-space Perl modules.
• Slides, videos and sample code of the 1-day course on Scientific C++.
• Instructions on how to install optional R packages from CRAN, including Rmpi.

SYSTEM CHANGES:

• TCS: The bug in the showstart command was fixed, and showstart may be used again to estimate the start time of your job.
• GPC: Issues regarding simultaneously loading the gcc/4.4.0 and the Intel compiler modules were resolved.
• GPC: A newer version of the gcc compiler suite, v4.6.0, has been installed. The default version is still 4.4.0, and in any case, we recommend using the Intel compilers for optimal performance. You should consider 4.6.0 as somewhat experimental for now, especially gfortran, as many other modules still depend require 4.4.0 for now. Let us know if you experience any unexpected difficulties with it.
• GPC: Octave version 3.2.4 has been installed on the GPC. You should for now consider this an experimental module. Let us know about your experience with it!

WHAT ELSE HAPPENED AT SCINET IN MARCH?

• A SNUG meeting was held on Mar 9, with TechTalks by Abdul Mroue and Joachim Harnois-Deraps.
• On Mar 15, a 1-day course “Introduction to scientific C++” was given.
• There was unexpected downtime on March 23. A VSD controller failed in the cooling system at 11:30AM which resulted in an emergency shutdown of all SciNet systems. A temporary solution has allowed us to bring systems back online. There will likely need to be downtime in the near future in order to replace the controller.