Difference between revisions of "Knowledge Base: Tutorials and Manuals"

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Revision as of 13:59, 28 October 2011

Manuals Intel (GPC): C & C++ compiler Fortran compiler C & C++ compiler 12.0 Fortran compiler 12.0 Intel Compiler Floating Point Consistency 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 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, Sept 2010
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

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

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
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

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

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

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

Debugging

Math libraries (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:
Half-day HPCS2011 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

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:

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