Knowledge Base: Tutorials and Manuals
From SciNetWiki
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Manuals Intel (GPC):
IBM (TCS):
Scheduler (Adaptive Computing/Cluster Resources) DDT (Allinea) |
Training material
Contents |
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SciNet Basics
- SciNet User Tutorial
- Intro to SciNet, SciNet, Sept 2011
- 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
- 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
- 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
Python
- Python
- f2py: Fortran and Python (June 2011 TechTalk by Pierre de Buyl)
R
Lua
- Scripting HALMD with Lua and Luabind (May 2011 TechTalk by Peter Colberg)
Parallel Programming
- High Performance Scientific Computing, part 3 of SciNet's Scientific Computing Course (Winter 2012)
- Parallel Programming Course (5 days), SciNet, May 2011
- Parallel Computing for Computational Fluid Dynamics (CFD), SciNet, 23 March 2011
- Intro to Practical Parallel Programming (1 day), SciNet, 22 Sept 2010:
- Parallel Scientific Computing Workshop (5 days), SciNet, Aug 2009:
- 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
- MPI Tuning Parameters - SNUG TechTalk, Feb 2012
Debugging
- 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:
- 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
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:
