Difference between revisions of "Knowledge Base: Tutorials and Manuals"
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| − | + | __NOTOC__ | |
| − | + | <table class="infobox vcard" style="width:26em; font-size:90%; text-align:left;"> | |
| − | ''' | + | <tr><td> |
| + | '''Manuals''' | ||
| − | '' | + | ''Intel (GPC):'' |
| + | * [http://software.intel.com/sites/products/documentation/hpc/compilerpro/en-us/cpp/lin/compiler_c/index.htm C & C++ compiler] | ||
| + | * [http://software.intel.com/sites/products/documentation/hpc/compilerpro/en-us/fortran/lin/compiler_f/index.htm Fortran compiler] | ||
| + | * [https://support.scinet.utoronto.ca/wiki/images/f/f2/FP_Consistency.pdf Intel Compiler Floating Point Consistency] | ||
| + | * [http://software.intel.com/sites/products/documentation/hpc/mkl/lin/index.htm Math Kernel Library (MKL)] | ||
| + | * [http://software.intel.com/sites/products/documentation/hpc/mkl/vsl/vslnotes.pdf Math Kernel Library's Vector Statistical Library] | ||
| + | * [http://software.intel.com/sites/products/documentation/hpc/mpi/linux/reference_manual.pdf Intel MPI library] | ||
| + | * [http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor Math Kernel Library link line advisor]<br/>($MKLPATH → ${MKLPATH} in makefiles) | ||
| − | * | + | ''IBM (TCS):'' |
| − | * [ | + | * [http://support.scinet.utoronto.ca/Manuals/xlc-compiler.pdf C compiler], [http://support.scinet.utoronto.ca/Manuals/xlc-langref.pdf language], [http://support.scinet.utoronto.ca/Manuals/xlc-proguide.pdf optimization] |
| − | * [ | + | * [http://support.scinet.utoronto.ca/Manuals/xlC++-compiler.pdf C++ compiler], [http://support.scinet.utoronto.ca/Manuals/xlC++-langref.pdf language], [http://support.scinet.utoronto.ca/Manuals/xlC++-proguide.pdf optimization] |
| − | + | * [http://support.scinet.utoronto.ca/Manuals/xlf-compiler.pdf Fortran compiler] [http://support.scinet.utoronto.ca/Manuals/xlf-langref.pdf language], [http://support.scinet.utoronto.ca/Manuals/xlf-proguide.pdf optimization] | |
| + | * [http://support.scinet.utoronto.ca/Manuals/UPC/compiler.pdf UPC compiler], [http://support.scinet.utoronto.ca/Manuals/UPC/langref.pdf language], [http://support.scinet.utoronto.ca/Manuals/UPC/upcopt.pdf optimization], [http://support.scinet.utoronto.ca/Manuals/UPC/standlib.pdf library], [http://support.scinet.utoronto.ca/Manuals/UPC/upcusersguide.pdf user's guide], [http://support.scinet.utoronto.ca/Manuals/UPC/proguide.pdf programmer's guide] | ||
| + | * [http://publib.boulder.ibm.com/epubs/pdf/am501405.pdf ESSL high performance math library V4] ([http://publib.boulder.ibm.com/epubs/pdf/am601305.pdf V3]) | ||
| + | * [http://support.scinet.utoronto.ca/Manuals/JUMP-AIX-POWER6-AppsPerformanceTuning-wp032008.pdf Performance tuning] | ||
| + | * [http://support.scinet.utoronto.ca/Manuals/PE5.1-operationanduse.pdf Parallel environment] | ||
| + | * [http://publib.boulder.ibm.com/infocenter/clresctr/vxrx/index.jsp Cluster information center] (with error codes) | ||
| + | * [http://support.scinet.utoronto.ca/Manuals/LL-usingandadministering.pdf LoadLeveler: using & administering] | ||
| + | |||
| + | ''Scheduler (Adaptive Computing/Cluster Resources)'' | ||
| + | * [http://www.clusterresources.com/products/mwm/docs/index.shtml Moab workload manager] | ||
| + | * [http://www.clusterresources.com/products/mwm/docs/a.gcommandoverview.shtml Moab commands] | ||
| + | * [http://www.clusterresources.com/products/torque/docs/ Torque resource manager] | ||
| + | * [http://www.clusterresources.com/products/torque/docs/a.acommands.shtml Torque PBS commands] | ||
| + | |||
| + | </table> | ||
| + | =Tutorials and other training material= | ||
| + | For upcoming classes, see our [https://support.scinet.utoronto.ca/courses/ Courses website]! | ||
| + | ==SciNet Basics== | ||
| + | * [[Essentials]] | ||
* [https://support.scinet.utoronto.ca/wiki/images/5/54/SciNet_Tutorial.pdf SciNet User Tutorial] | * [https://support.scinet.utoronto.ca/wiki/images/5/54/SciNet_Tutorial.pdf SciNet User Tutorial] | ||
* [https://support.scinet.utoronto.ca/wiki/images/3/35/Introscinet.pdf Intro to SciNet], SciNet, Sept 2010 | * [https://support.scinet.utoronto.ca/wiki/images/3/35/Introscinet.pdf Intro to SciNet], SciNet, Sept 2010 | ||
| − | * [ | + | * [[FAQ|Frequenty asked questions]] |
| − | * [ | + | * [[Ssh]] |
| − | * | + | * [[GPC_Quickstart|GPC quickstart guide]] |
| − | * | + | * [[TCS_Quickstart|TCS quickstart guide]] |
| + | * [[Important .bashrc guidelines]] | ||
| + | * [[Software_and_Libraries | Software and libraries modules system]] | ||
| + | |||
| + | ==Batch job management== | ||
| + | * [[Wallclock time]] | ||
| + | * [[Checkpoints]] | ||
| + | * [[Using_Signals|Signals]] | ||
| + | * [[Moab]] | ||
| + | * [[User_Serial|Serial Jobs]] | ||
| + | * [[User_Ramdisk|Ramdisk]] | ||
| + | * [http://www.clusterresources.com/products/mwm/docs/index.shtml Moab workload manager] | ||
| + | * [http://www.clusterresources.com/products/mwm/docs/a.gcommandoverview.shtml Moab commands] | ||
| + | * [http://www.clusterresources.com/products/torque/docs/ Torque resource manager] | ||
| + | * [http://www.clusterresources.com/products/torque/docs/a.acommands.shtml Torque PBS commands] | ||
| + | * [http://support.scinet.utoronto.ca/Manuals/PE5.1-operationanduse.pdf Parallel environment] | ||
| + | * [http://publib.boulder.ibm.com/infocenter/clresctr/vxrx/index.jsp Cluster information center] (with error codes) | ||
| + | * [http://support.scinet.utoronto.ca/Manuals/LL-usingandadministering.pdf LoadLeveler: using & administering] | ||
| + | |||
| + | ==Programming== | ||
| + | * [http://software.intel.com/sites/products/documentation/hpc/compilerpro/en-us/cpp/lin/compiler_c/index.htm C & C++ compiler] | ||
| + | * [http://software.intel.com/sites/products/documentation/hpc/compilerpro/en-us/fortran/lin/compiler_f/index.htm Fortran compiler] | ||
* [[IBM_Nov_Workshop | IBM AIX Workshop, SciNet, Nov 2008 ]] | * [[IBM_Nov_Workshop | IBM AIX Workshop, SciNet, Nov 2008 ]] | ||
* [[IBM_Feb_Workshop | IBM MPI Workshop, SciNet, Feb 2009]] | * [[IBM_Feb_Workshop | IBM MPI Workshop, SciNet, Feb 2009]] | ||
* [[IBM_Compiler_Workshop | IBM Compiler Workshop, SciNet, Feb 2009]] | * [[IBM_Compiler_Workshop | IBM Compiler Workshop, SciNet, Feb 2009]] | ||
| + | * [http://support.scinet.utoronto.ca/Manuals/xlc-compiler.pdf C compiler], [http://support.scinet.utoronto.ca/Manuals/xlc-langref.pdf language], [http://support.scinet.utoronto.ca/Manuals/xlc-proguide.pdf optimization] | ||
| + | * [http://support.scinet.utoronto.ca/Manuals/xlC++-compiler.pdf C++ compiler], [http://support.scinet.utoronto.ca/Manuals/xlC++-langref.pdf language], [http://support.scinet.utoronto.ca/Manuals/xlC++-proguide.pdf optimization] | ||
| + | * [http://support.scinet.utoronto.ca/Manuals/xlf-compiler.pdf Fortran compiler] [http://support.scinet.utoronto.ca/Manuals/xlf-langref.pdf language], [http://support.scinet.utoronto.ca/Manuals/xlf-proguide.pdf optimization] | ||
| + | * [http://support.scinet.utoronto.ca/Manuals/UPC/compiler.pdf UPC compiler], [http://support.scinet.utoronto.ca/Manuals/UPC/langref.pdf language], [http://support.scinet.utoronto.ca/Manuals/UPC/upcopt.pdf optimization], [http://support.scinet.utoronto.ca/Manuals/UPC/standlib.pdf library], [http://support.scinet.utoronto.ca/Manuals/UPC/upcusersguide.pdf user's guide], [http://support.scinet.utoronto.ca/Manuals/UPC/proguide.pdf programmer's guide] | ||
| + | * [[Perl]] | ||
| + | * [https://support.scinet.utoronto.ca/wiki/images/7/7e/Snug_techtalk_revcontrol.pdf TechTalk: Version Control], SciNet User Group Meeting, Oct 2010. | ||
| + | * [http://software-carpentry.org/4_0/vc/ Software Carpentry Resources] | ||
| − | + | ==Parallel Programming== | |
| − | + | * One-day Intro to Practical Parallel Programming, SciNet, 22 Sept 2010: [[Media:PPP-Intro-Morning.pdf|Morning Slides, Intro and OpenMP ]], [[Media:PPP-Intro-Afternoon.pdf|Afternoon Slides, MPI]], [[Media:Intro-ppp.tgz|Example source code ]] | |
| − | * [http:// | + | * Five-day Parallel Scientific Computing Workshop, SciNet, Aug 2009: [[ Parallel_Scientific_Computing_-_Aug_09 | Slides ]]/[http://www.cita.utoronto.ca/~ljdursi/PSP/ Video] |
* [http://www.vscse.org/news/apply_summer2010.html Virtual School for CSE] Web courses (Jul/Aug 2010): | * [http://www.vscse.org/news/apply_summer2010.html Virtual School for CSE] Web courses (Jul/Aug 2010): | ||
** Petascale programming environments and tools | ** Petascale programming environments and tools | ||
** Big data for science | ** Big data for science | ||
** Proven algorithmic techniques for many-core processors | ** Proven algorithmic techniques for many-core processors | ||
| − | + | * [https://computing.llnl.gov/tutorials/mpi/ LLNL MPI Tutorial]: This was the basis for the MPI workshop at SciNet. | |
| − | * [https://computing.llnl.gov/tutorials/mpi/ LLNL MPI Tutorial] | + | * [http://software.intel.com/sites/products/documentation/hpc/mpi/linux/reference_manual.pdf Intel MPI library] |
| + | * [[GPC MPI Versions]] | ||
| + | |||
| + | ==Performance Tuning== | ||
| + | * [[Introduction To Performance]] | ||
| + | * Performance tools for [[Performance_And_Debugging_Tools:_GPC | GPC ]] and [[Performance_And_Debugging_Tools:_TCS | TCS ]] | ||
| + | * Dec TechTalk: [[Media:ProfillingTechTalk-Dec2010.pdf | Profiling Tools on GPC]] | ||
* [http://cnx.org/content/col11136/latest/ High Performance Computing Book]<br />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. | * [http://cnx.org/content/col11136/latest/ High Performance Computing Book]<br />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. | ||
* [http://www.ece.cmu.edu/~franzf/papers/gttse07.pdf How to Write Fast Numerical Code ]<br />Good introduction to thinking about performance. | * [http://www.ece.cmu.edu/~franzf/papers/gttse07.pdf How to Write Fast Numerical Code ]<br />Good introduction to thinking about performance. | ||
| − | + | * [http://support.scinet.utoronto.ca/Manuals/JUMP-AIX-POWER6-AppsPerformanceTuning-wp032008.pdf Performance tuning] | |
| − | + | ||
| + | ==Debugging== | ||
| + | * [https://support.scinet.utoronto.ca/wiki/images/2/27/Snugdebug.pdf TechTalk: Debuggers & Parallel Debugging on SciNet - gdb, ddd, padb], SciNet User Group Meeting, Nov 2010 | ||
| − | + | ==Math libraries== | |
| − | |||
| − | |||
* [https://support.scinet.utoronto.ca/wiki/images/f/f2/FP_Consistency.pdf Intel Compiler Floating Point Consistency] | * [https://support.scinet.utoronto.ca/wiki/images/f/f2/FP_Consistency.pdf Intel Compiler Floating Point Consistency] | ||
* [http://software.intel.com/sites/products/documentation/hpc/mkl/lin/index.htm Math Kernel Library (MKL)] | * [http://software.intel.com/sites/products/documentation/hpc/mkl/lin/index.htm Math Kernel Library (MKL)] | ||
| − | * [http://software.intel.com/sites/products/documentation/hpc/mkl/vsl/vslnotes.pdf Math Kernel Library's Vector Statistical Library | + | * [http://software.intel.com/sites/products/documentation/hpc/mkl/vsl/vslnotes.pdf Math Kernel Library's Vector Statistical Library] |
| − | * [http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor Math Kernel Library link line advisor]<br/> | + | * [http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor Math Kernel Library link line advisor]<br/>($MKLPATH → ${MKLPATH} in makefiles) |
| − | * [http:// | + | * [http://publib.boulder.ibm.com/epubs/pdf/am501405.pdf ESSL high performance math library V4] ([http://publib.boulder.ibm.com/epubs/pdf/am601305.pdf V3]) |
| + | |||
| + | ==I/O== | ||
| + | * [[Data_Management|Data management]] | ||
| + | * Intro to Parallel I/O, SciNet, Oct 6th, 2010: <br />[[Media:Parallel_io_course.pdf|Morning & MPI-IO Slides]]; [[Media:Netcdfhdf5.pdf|NetCDF/HDF5 Slides]]; [[Media:ParIO.tgz|Source Code]]. | ||
| + | * [https://support.scinet.utoronto.ca/wiki/images/c/c7/Snugio.pdf TechTalk: Parallel File System and IO], SciNet User Group Meeting, Sept 2010 | ||
| + | * [[File System and I/O dos and don'ts]] | ||
| + | |||
| + | ==GPU Computing== | ||
| + | * [[SciNet GPU Workshop July 2010]] | ||
| + | * [http://developer.nvidia.com/object/cuda_training.html NVidia archived courses for GPGPU Programming] | ||
| − | + | ==Visualization== | |
| − | * [ | + | * [[Using Paraview]] |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | =User Codes= | |
| − | + | {{User Codes}} | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Revision as of 17:36, 20 December 2010
|
Manuals Intel (GPC):
IBM (TCS):
Scheduler (Adaptive Computing/Cluster Resources) |
Tutorials and other training material
For upcoming classes, see our Courses website!
SciNet Basics
- Essentials
- SciNet User Tutorial
- Intro to SciNet, SciNet, Sept 2010
- Frequenty asked questions
- Ssh
- GPC quickstart guide
- TCS quickstart guide
- Important .bashrc guidelines
- Software and libraries modules system
Batch job management
- 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
- C & C++ compiler
- Fortran compiler
- IBM AIX Workshop, SciNet, Nov 2008
- IBM MPI Workshop, SciNet, Feb 2009
- IBM Compiler Workshop, SciNet, Feb 2009
- C compiler, language, optimization
- C++ compiler, language, optimization
- Fortran compiler language, optimization
- UPC compiler, language, optimization, library, user's guide, programmer's guide
- Perl
- TechTalk: Version Control, SciNet User Group Meeting, Oct 2010.
- Software Carpentry Resources
Parallel Programming
- One-day Intro to Practical Parallel Programming, SciNet, 22 Sept 2010: Morning Slides, Intro and OpenMP , Afternoon Slides, MPI, Example source code
- Five-day Parallel Scientific Computing Workshop, 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
Performance Tuning
- Introduction To Performance
- Performance tools for GPC and TCS
- Dec 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
- TechTalk: Debuggers & Parallel Debugging on SciNet - gdb, ddd, padb, SciNet User Group Meeting, Nov 2010
Math libraries
- 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)
I/O
- Data management
- Intro to Parallel I/O, SciNet, Oct 6th, 2010:
Morning & MPI-IO Slides; NetCDF/HDF5 Slides; Source Code. - TechTalk: Parallel File System and IO, SciNet User Group Meeting, Sept 2010
- File System and I/O dos and don'ts