Knowledge Base: Tutorials and Manuals

Training material

For upcoming classes, see our Training and Education website!

SciNet Basics

• SciNet User Tutorial
• Intro to SciNet: Video/Slides, SciNet, November 2012
• 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 Command Line: A Primer (June 2012) Slides, Files
• Introduction to the Linux Shell, SciNet, Mar 2012: Slides and Data files

Batch job management

• 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

Hadoop

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

Perl

• Perl

Python

• Python
• IPython Notebook on GPC (January 2014 TechTalk)
• Research Computing with Python (Modular Course, Fall 2013)
• f2py: Fortran and Python (June 2011 TechTalk by Pierre de Buyl)

R

• R Statistical Package

Lua

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

Parallel Programming

• Ontario Summerschool on High Performance Computing Central
• 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:
  • Morning Slides, Intro and OpenMP
  • Afternoon Slides, MPI
  • Example source code
• 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

• 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
• 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 very clearly.
• How to Write Fast Numerical Code
  Good introduction to thinking about performance.
• Performance tuning
• MPI Tuning Parameters - SNUG TechTalk, Feb 2012

Debugging

• Debugging with GDB and DDT, half-day session at the Ontario HPC Summerschool 2012 Central
  Slides, Code.
• TechTalk: Debuggers & Parallel Debugging on SciNet - gdb, ddd, padb], SciNet User Group Meeting, Nov 2010
  Video
• Allinea DDT (Distributed Debugging Tool) User Guide

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: [1])

I/O

• Introduction to NetCDF4 binary files with Python, C++ and R (TechTalk March 2014)
• Using MySQL on the GPC
• Sep 2012 SNUG TechTalk: Science=Data
• Data management
• Intro to Parallel I/O, SciNet, Oct 6th, 2010:
  • Morning & MPI-IO Slides
  • NetCDF/HDF5 Slides
  • Source Code.
• 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

Infiniband Networking

• TechTalk on SciNet's Infiniband Network & MPI options

Visualization

• Using Paraview
• TechTalk on VNC (slides)
• Visualization Software on the GPC
• 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:

• Athena
• Amber
• CCSM3/CCSM4
• FLASH3
• Gamess. See also here
• Gromacs
• LAMMPS
• NAMD
• Paraview
• VASP
• See also User Codes

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)

• C compiler, language, optimization
• C++ compiler, language, optimization
• Fortran compiler language, optimization
• UPC compiler, language, optimization, library, user's guide, programmer's guide
• ESSL high performance math library V4 (V3)
• ESSL high performance math library V5.1 for Linux on Power
• Performance tuning
• Parallel environment
• Cluster information center (with error codes)
• LoadLeveler: using & administering

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)

• Moab workload manager
• Moab commands
• Torque resource manager
• Torque PBS commands

DDT Debugger (Allinea)

• Distributed Debugging Tool User Guide