Knowledge Base: Tutorials and Manuals

Manuals Intel (GPC): C & C++ compiler Fortran compiler C & C++ compiler 12.0 Fortran compiler 12.0 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 (TCS): 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) Performance tuning Parallel environment Cluster information center (with error codes) LoadLeveler: using & administering PGI (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 (Allinea) Distributed Debugging Tool User Guide

Training material

For upcoming classes, see our Courses website!

SciNet Basics

• SciNet User Tutorial
• Intro to SciNet, SciNet, July 2012
• Linux Command Line: A Primer (June 2012) Slides, Files
• Introduction to the Linux Shell, SciNet, Mar 2012: Slides and Data files
• SciNet Resources: Video/ Slides
• Essentials
• Frequenty asked questions
• Ssh
• GPC quickstart
• TCS quickstart
• ARC/GPU quickstart
• ARC/Cell quickstart
• Important .bashrc guidelines
• Software and libraries
• Installing your own modules
• User-space modules and packages (April 2011 SNUG TechTalk)
• HPSS - SciNet's storage capacity expansion

Batch job management

• Job Monitoring on SciNet and Job Efficiency
• Wallclock time
• Checkpoints
• Signals
• Moab
• Serial Jobs
• 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

• 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
• IBM Fortran compiler language, optimization

C++

• 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
• Intel Fortran compiler
• IBM C++ compiler, language, optimization

C

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

Perl

• Perl

Python

• Python
• 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

• 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

• 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

• 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

Infiniband Networking

• TechTalk on SciNet's Infiniband Network & MPI options

Visualization

• Using Paraview
• 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