WARNING: SciNet is in the process of replacing this wiki with a new documentation site. The links below may still contain valuable information, but for current information, please go to https://docs.scinet.utoronto.ca

Training material

For upcoming classes, see our Training and Education website!

SciNet Basics

SciNet User Tutorial
SciNet Command Line Utilities
Intro to SciNet May 2014: Video/Slides
SciNet Resources: Video/ Slides
Essentials
Frequenty asked questions
Ssh
GPC quickstart
TCS quickstart
ARC/GPU quickstart
ARC/Cell quickstart
Important .bashrc guidelines
Workflow Optimization (w/focus on Large Scale BioInformatics)
Software and libraries
Installing your own modules
User-space modules and packages (April 2011 SNUG TechTalk)
HPSS - SciNet's storage capacity expansion
BGQ Hardware Overview Slides / Video Recording
Intro to Using the BGQ Slides /Video Recording

Linux

Linux Tutorial (warning: the last part of this tutorial is specific to the csh shell, whereas SciNet uses the bash shell).
Linux Command Line: A Primer (June 2012) Slides, Files
Introduction to the Linux Shell, SciNet, Mar 2012: Slides and Data files

Batch job management

Job and Queue Management Tools (Techtalk Mar.11, 2015)
Workflow Optimization (w/focus on Large Scale BioInformatics)
GNU Parallel (Techtalk Nov 14, 2012)
Job Monitoring on SciNet and Job Efficiency
Wallclock time
Checkpoints
Signals
Moab
Serial Jobs (including GNU Parallel)
Ramdisk
Moab workload manager
Moab commands
Torque resource manager
Torque PBS commands
Parallel environment
Cluster information center (with error codes)
LoadLeveler: using & administering

Programming

General

Performance Tuning with the IBM XL Compilers: Slides fromt the SciNet Develop Seminar by Kit Barton, Sep 17, 2012.
Remote Development, slides from TechTalk Jun 13, 2012
Scientific Software Development Course, part I of the SciNet's Scientific Computing Course
Software Carpentry Resources
Version Control: Video/ Slides
IBM AIX Workshop, SciNet, Nov 2008
IBM Compiler Workshop, SciNet, Feb 2009
SNUG Techtalk Dec 2011 Intel Compiler Optimizations

Fortran

Modern Fortran Course (1 day), SciNet, 19 Apr 2011
- Slides
- Source Code
[http://support.scinet.utoronto.ca/Manuals/xlf-compiler.pdf IBM Fortran compiler language, optimization

C++

Slides and recording of the SciNet Developer Seminar on C++11, March 20, 2013
Scientific C++ Course (1 day), SciNet, 15 March 2011
- Slides (updated on Apr 26, 2012)
- Example source code
- Videos of the Scientific C++ class
Intel C & C++ compiler

ro/en-us/fortran/lin/compiler_f/index.htm Intel Fortran compiler]

IBM C++ compiler, language, optimization

C

C refresher: Video/ Slides
IBM C compiler, language, optimization

Cilk Plus

CilkPlus - Getting Started (slides of the May 2014 TechTalk by Chris Szalwinski)

Hadoop

Introduction to Hadoop for HPCers, Part I - MapReduce: Slides, Source Code, Virtual Machine

Lua

Scripting HALMD with Lua and Luabind (May 2011 TechTalk by Peter Colberg)

Parallel Programming

2014 Ontario Summerschool on High Performance Computing Central (incl. OpenMP and MPI)
High Performance Scientific Computing Course 2014 (OpenMP and MPI, with video recordings of lectures)
MPI 3 Developer Seminar
OpenMP 4 Developer Seminar
Ontario Summerschool on High Performance Computing Central (2013)
High Performance Scientific Computing, part 3 of SciNet's Scientific Computing Course (Winter 2012)
Parallel Programming Course (5 days), SciNet, May 2011
- Videos, slides and code
Parallel Computing for Computational Fluid Dynamics (CFD), SciNet, 23 March 2011
- Slides
- Source Code
Intro to Practical Parallel Programming (1 day), SciNet, 22 Sept 2010:
Parallel Scientific Computing Workshop (5 days), SciNet, Aug 2009:
- Slides
- Video
Virtual School for CSE Web courses (Jul/Aug 2010):
- Petascale programming environments and tools
- Big data for science
- Proven algorithmic techniques for many-core processors
LLNL MPI Tutorial: This was the basis for the MPI workshop at SciNet.
Intel MPI library
GPC MPI Versions
Co-array Fortran on the GPC
IBM MPI Workshop, SciNet, Feb 2009
IBM UPC compiler, language, optimization, library, user's guide, programmer's guide

GPU Computing

1-day "Introduction to GPGPU Programming with CUDA" Course (May 2015): [1].
2-day "Programming GPUs with CUDA" Course (2015 Summer School): [2]
New Features in CUDA 5 & 6, Nov. 2014
Intro to GPU Computing Using CUDA (WestGrid Spring 2014 Seminar Series)
1.5 hour intro to CUDA, March 2013: Slides and Source Code
CITA/SciNet CUDA Minicourse, Fall 2012
SciNet GPU Workshop July 2010
Intro to GPGPU Programming: Video/ Slides
(from 5 day parallel programming course at SciNet, May 2011)
1-day intro to GPGPU using CUDA Course (Aug 2011): Source Code, Slides.
NVidia archived courses for GPGPU Programming
PGI Compiler User's Guide
PGI Compiler Reference Manual
PGI Fortran reference
PGI CUDA Fortran Programming Guide and Reference
PGI OpenACC Getting Started Guide

Performance Tuning

Performance and Profiling Course, April 2013
Introduction To Performance
Performance tools for GPC and TCS
Dec 2010 SNUG TechTalk: Profiling Tools on GPC
Performance tuning
MPI Tuning Parameters - SNUG TechTalk, Feb 2012
High Performance Computing Book
Online version of an older O'Reilly book which covers the basics of (mostly serial) programming for performance. Covers the most important issues today (such as cache) very clearly.
How to Write Fast Numerical Code
Good introduction to thinking about performance and cache.

Debugging

Math libraries (BLAS, LAPACK, FFT)

Intel Math Kernel Library (MKL): An overview (TechTalk, March, 2012)
Numerical Tools for Physical Scientists, part 2 of SciNet's Scientific computing course, covers, random nubers, blas, lapack, fft, ...
Intel Compiler Floating Point Consistency
Math Kernel Library (MKL)
Math Kernel Library's Vector Statistical Library
Math Kernel Library link line advisor
($MKLPATH → ${MKLPATH} in makefiles)
ESSL high performance math library V4 (V3)
Parallel ESSL high performance math library V3.3
Linear Algebra Libraries by Claire Mouton. 2009 INRIA Technical Report on existing linear algebra libraries for C++ (also here: [3])

I/O

Introduction to NetCDF4 binary files with Python, C++ and R (TechTalk March 2014)
Using MySQL on the GPC
Relational Database Basics
Sep 2012 SNUG TechTalk: Science=Data
Data management
Intro to Parallel I/O, SciNet, Oct 6th, 2010:
Intro to Parallel I/O, SciNet, Feb, 2013
Half-day HPCS2012 Parallel I/O tutorial, covering MPI-IO, HDF5, NetCDF, based on the above: slides (pdf) and source code.
Sept 2010 SNUG TechTalk: Parallel File System and IO
Video
File System and I/O dos and don'ts
So you have 40TB of Data -- an overview of things to consider with large data sets.
May 2012 SNUG TechTalk: ADIOS for Parallel IO slides and source code
Writting / Reading a table in hdf5
Writting / Reading a table in NetCDF
Intro to Parallel I/O, SciNet, Sept 215
- MPI-IO Slides and Sample codes
- NETCDF & HDF5

Infiniband Networking

TechTalk on SciNet's Infiniband Network & MPI options

Visualization

Science Illustrated: Two-day symposium on Visualizing Science, Feb 2011
Videos of the talks given at Science Illustrated (recorded by KMDI at UoT):
- Opening remarks by Paul Young
- Information Visualization and the Myth of Information Overload by Christopher Collins
- Beyond Basic Visualization by Ramses Van Zon
- Network Visualization & Analysis by Igor Jurisica
- Simulation and Visualization of Blood Flow by David Steinman
- Scientific Visualizations: Does the Science Matter? by Thomas Lucas
- How can visualization impact public perception of science? Panelists: Jay Ingram, Peter Calamai, Reni Barlow, Hooley McLaughlin
- How Info Graphics are Created for the Mainstream Media by Peter Calamai
- Design Boot Camp by Graham Huber
- Visualization Large Datasets by Jonathan Dursi
- Visualizing Colliding Black Holes by Herald Pfeiffer
- Closing remarks by Mubdi Rahman

Applications

Currently, information on the following applications is available:

Development Systems

KNL

SNUG TechTalk October 2016 - Intel Xeon Phi Knights Landing

Manuals

Intel compilers and libraries (GPC)

C & C++ compiler
Fortran compiler
Intel Compiler Floating Point Consistency
Intel Compiler Optimization Guide
Math Kernel Library (MKL)
Math Kernel Library's Vector Statistical Library
Intel MPI library
Math Kernel Library link line advisor
($MKLPATH → ${MKLPATH} in makefiles)

IBM compilers and libraries (TCS/P7)

PGI compilers (ARC)

Compiler User's Guide
Compiler Reference Manual
Fortran reference
CUDA Fortran Programming Guide and Reference
OpenACC Getting Started Guide
(Note: $PGI/linux86-64/12.5/doc contains a newer version.)

Scheduler (Adaptive Computing/Cluster Resources)

DDT Debugger (Allinea)

Distributed Debugging Tool User Guide

Knowledge Base: Tutorials and Manuals

Contents