Difference between revisions of "SciNet User Support Library"

Latest revision as of 14:59, 15 May 2018

WARNING: SciNet is in the process of replacing this wiki with a new documentation site. For current information, please go to https://docs.scinet.utoronto.ca

System Status

System status can now be found at docs.scinet.utoronto.ca

Mon 23 Apr 2018 GPC-compute is decommissioned, GPC-storage available until 30 May 2018

Thu 18 Apr 2018 Niagara system will undergo an upgrade to its Infiniband network between 9am and 12pm, should be transparent to users, however there is a chance of network interruption.

Fri 13 Apr 2018 HPSS system will be down for a few hours on Mon, Apr/16, 9AM, for hardware upgrades, in preparation for the eventual move to the Niagara side.

Tue 10 Apr 2018 Niagara is open to users.

Wed 4 Apr 2018 We are very close to the production launch of Niagara, the new system installed at SciNet. While the RAC allocation year officially starts today, April 4/18, the Niagara system is still undergoing some final tuning and software updates, so the plan is to officially open it to users on next week.

All active GPC users will have their accounts, $HOME, and $PROJECT, transferred to the new Niagara system. Those of you who are new to SciNet, but got RAC allocations on Niagara, will have your accounts created and ready for you to login.

We are planning an extended Intro to SciNet/Niagara session, available in person at our office, and webcast on Vidyo and possibly other means, on Wednesday April 11 at noon EST.

System News

April 23, 2018: GPC & Sandy decommissioned.
April 10, 2018: Niagara commissioned.
March 20th, 2018: Gravity decommissioned.
Dec 4, 2017 : scratchtcs decommissioned.
Nov 28, 2017: The GPC has been reduced from 30,912 to 16,800 cores to make room for the installation of Niagara.
Sept 29, 2017: The TCS has been decommissioned.

(Previous System News)

QuickStart Guides

Tutorials and Manuals

What's New On The Wiki

Dec 2014: Updated GPC Quickstart with info on email notifications from the scheduler.

Dec 2014: Hdf5 compilation page updated.

Dec 2014: Research Computing with Python 2014 lectures 5-8

Nov 2014: "Modern CUDA Features" TechTalk slides in SciNet TechTalks and Seminars.

Nov 2014: Research Computing with Python 2014 lectures 1-4

Sept 2014: Tip on reducing virtual memory consumption for multithreaded programs

Sept 2014: Improved information on the Python versions installed on the GPC, and which modules are included in each version.

Sept 2014: Description on using job arrays on the GPC on the Scheduler page.

Sept 2014: Tkinter instructions, slides and code for the TkInter workshop held in September.

Sept 2014: Instructions on using Hadoop (for the Hadoop workshop held in September).

Previous new stuff can be found in the What's new archive.

User-Supplied Content

Share your expertise with the SciNet Community!

@@ Line 1: / Line 1: @@
 __NOTOC__
-Welcome to the SciNet User Support library. Here you will find up-to-date manuals put together by SciNet staff and users, as well as links to external resources, to help you make use of SciNet resources for computational scientific discovery.
+{| style="border-spacing: 8px; width:100%"
+| valign="top" style="cellpadding:1em; padding:1em; border:2px solid; background-color:#f6f674; border-radius:5px"|
+'''WARNING: SciNet is in the process of replacing this wiki with a new documentation site. For current information, please go to [https://docs.scinet.utoronto.ca https://docs.scinet.utoronto.ca]'''
+|}
-{|
-| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#F0F0F0" colspan=2|
+{|  style="border-spacing: 8px;"
+| valign="top" style="cellpadding:1em; padding:1em; border:3px solid #0645ad; background-color:#f6f6f6; border-radius:7px"|
 {{SciNetWiki:System_Alerts}}
+| valign="top" style="cellpadding:1em; padding:1em; border:3px solid #0645ad; background-color:#f6f6f6; border-radius:7px"|
+==System News==
+* April 23, 2018: GPC & Sandy decommissioned.
+* April 10, 2018: Niagara commissioned.
+* March 20th, 2018: Gravity decommissioned.
+* Dec 4, 2017 : scratchtcs decommissioned.
+* Nov 28, 2017: The GPC has been reduced from 30,912 to 16,800 cores to make room for the installation of Niagara.
+* Sept 29, 2017: The TCS has been decommissioned.
+([[Previous System News]])
+|-
+| valign="top" width="50%" style="padding:1em; border:1px solid #aaaaaa; background-color:#f6e8e8; border-radius:7px" |
-|+
-| valign="top" width="50%" style="padding:1em; border:1px solid #8fa1b2; background-color:#F6DEDE" |
 == QuickStart Guides ==
-* [[Essentials|Login essentials]]
+* [[SciNet Command Line Utilities]]
-* [[GPC_Quickstart|GPC: General Purpose Cluster]]
+* [[Media:SciNet_Tutorial.pdf|SciNet User Tutorial]]
-* [[TCS_Quickstart|TCS: Tightly Coupled System]]
+* [[P7_Linux_Cluster|P7: Power 7 Linux cluster]]
-* [[Storage_Quickstart|Data storage]]
+* [[BGQ|BGQ: BlueGene/Q clusters]]
-* [[Data_Transfer|Data transfer]]
+* [[Software_and_Libraries|Software and libraries]]
-* [[Software_and_Libraries | Software and libraries]]
+* [[Data_Management|Data management]]
-* [[Moab | Job scheduling system (Moab) ]]
-* [[Introduction_To_Performance|Performance primer]], [[Performance_And_Debugging_Tools:_GPC | GPC tools]], [[Performance_And_Debugging_Tools:_TCS | TCS tools]]
 * [[FAQ | FAQ (frequently asked questions)]]
+* [[Acknowledging_SciNet | Acknowledging SciNet]]
+* [https://courses.scinet.utoronto.ca SciNet education]
+* [https://www.youtube.com/channel/UC42CaO-AAQhwqa8RGzE3daQ SciNet YouTube Channel]
+| valign="top" style="padding:1em; border:1px solid #aaaaaa; background-color:#e8f6e8; border-radius:7px" |
+== Tutorials and Manuals ==
+* [[Knowledge_Base:_Tutorials_and_Manuals#SciNet_Basics|SciNet basics]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Linux|Linux]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Batch_job_management|Batch job management]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Programming|Programming]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Parallel_Programming|Parallel programming]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#GPU_Computing|GPU computing]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Performance_Tuning|Performance tuning]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Debugging|Debugging]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Math_libraries_.28BLAS.2C_LAPACK.2C_FFT.29|Math libraries (BLAS, LAPACK, FFT)]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#I/O|I/O and databases]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Visualization|Visualization]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Applications|Applications]]
+* [[Knowledge_Base:_Tutorials_and_Manuals#Manuals|Manuals (compilers etc)]]
+* [[2016_Ontario_Summer_School_for_High_Performance_Computing_Central]]
+* [[2015_Ontario_Summer_School_for_High_Performance_Computing_Central]]
+|-
+| valign="top" style="padding:1em; border:1px solid #aaaaaa; background-color:#e8e8f6; border-radius:7px" |
+== What's New On The Wiki ==
+<div style='text-align:left;'>
-SciNet Accounts:
+* Dec 2014: Updated [[GPC Quickstart]] with info on email notifications from the scheduler.
-* [[Application_Process | Application process]]
+* Dec 2014: [[Hdf5]] compilation page updated.
-* [https://portal.scinet.utoronto.ca/usage_policy/ Usage policy]
-* [[SciNet_Usage_Reports | Usage reports]]
-* [[Acknowledging SciNet]]
-* [[SciNet_User_Support | User support]]
-| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#DEF6DE" |
+* Dec 2014: [[Research Computing with Python 2014]] lectures 5-8
-== Manuals ==
+* Nov 2014: "Modern CUDA Features" TechTalk slides in [[SciNet TechTalks and Seminars]].
-* GPC (Intel)
+* Nov 2014: [[Research Computing with Python 2014]] lectures 1-4
-** [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]
-** [http://software.intel.com/sites/products/documentation/hpc/mkl/lin/index.htm Math Kernel Library]
-** [http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor Math Kernel Library Link Line Advisor]
-** [http://software.intel.com/sites/products/documentation/hpc/mpi/linux/reference_manual.pdf Intel MPI Library]
-* TCS (IBM)
+* Sept 2014: [[User_Tips#Reducing_virtual_memory_consumption_for_multithreaded_programs| Tip on reducing virtual memory consumption for multithreaded programs]]
-** [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/LL-usingandadministering.pdf LoadLeveler: Using & Administering]
-** [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] has more (also explains error codes!)
-* Adaptive Computing/Cluster Resources
+* Sept 2014: Improved information on the [[Python]] versions installed on the GPC, and which modules are included in each version.
-** [http://www.clusterresources.com/products/mwm/docs/index.shtml MOAB Workload Manager]
-** [http://www.clusterresources.com/products/torque/docs/ TORQUE Resource Manager]
-|-
+* Sept 2014: Description on using job arrays on the GPC on the [[Scheduler]] page.
-| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#DEDEF6" |
-== Tutorials ==
+* Sept 2014: [[Intro to Tkinter|Tkinter instructions]], [[Media:Tkinter.pdf|slides]] and [[Media:Tkinter_code.tgz|code]] for the TkInter workshop held in September.
-* [https://support.scinet.utoronto.ca/wiki/images/5/54/SciNet_Tutorial.pdf SciNet User Tutorial]
-* Parallel Scientific Computing Workshop, SciNet, Aug 2009: [[ Parallel_Scientific_Computing_-_Aug_09  | Slides ]]/[http://www.cita.utoronto.ca/~ljdursi/PSP/ Video]
-* [[IBM_Nov_Workshop | IBM AIX Workshop, SciNet, Nov 2008 ]]
-* [[IBM_Feb_Workshop | IBM MPI Workshop, SciNet, Feb 2009]]
-* [[IBM_Compiler_Workshop | IBM Compiler Workshop, SciNet, Feb 2009]]
-* [http://www.vscse.org/news/apply_summer2010.html  Virtual School for CSE]: Free webinar-style courses (but must register):
-** Petascale programming environments and tools, Jul 6–9, 2010
-** Big data for science, Jul 26–30, 2010
-** Proven algorithmic techniques for many-core processors, Aug 2–6, 2010
-* [http://developer.nvidia.com/object/cuda_training.html  NVidia archived courses for GPGPU Programming]
-* [https://computing.llnl.gov/tutorials/mpi/ LLNL MPI Tutorial]: This was the basis for the MPI workshop at SciNet.
-* [http://cnx.org/content/col11136/latest/  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.
-* [http://www.ece.cmu.edu/~franzf/papers/gttse07.pdf  How to Write Fast Numerical Code ]: good introduction to thinking about performance.
-| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#DEDEDE" |
+* Sept 2014: Instructions on using [[Hadoop for HPCers|Hadoop]] (for the Hadoop workshop held in September).
-{{SciNetWiki:Current_events}}
+</div>
-|+
+Previous new stuff can be found in the [[What's new archive]].
-| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#FFFFDE" colspan=1|
+| valign="top" style="padding:1em; border:1px solid #aaaaaa; background-color:#f4f4fa; border-radius:7px" |
-== What's New On The Wiki ==
+<div style='text-align:left;'>
-* Tips for using [[GPC_Quickstart#HyperThreading | HyperThreading]] on the GPC ([[User:Rzon|Rzon]] 30 June)
-* How to [[Using_Signals | trap signals in C, C++ and Fortran]] ([[User:Rzon|Rzon]] 30 June)
-* Output in <tt>.bashrc</tt> can break lots of things. This and other tips in [[Important_.bashrc_guidelines | important .bashrc guidelines]] ([[User:Rzon|Rzon]] 24 June)
-* Instructions on using the [[ Using_Paraview | ParaView ]] Visualization Package on GPC ([[User:Ljdursi|Ljdursi]] 23 June)
-* Tips on using the [http://cms.mpi.univie.ac.at/vasp/ Vasp] code from the [[ User_Codes#Vienna_Ab-initio_Simulation_Package_.28VASP.29 | Polanyi Group ]] ([[User:Imcnab|Imcnab]] 21 June)
-* Updated tips on using [[ User_Ramdisk | Ram Disk ]] on GPC jobs ([[User:Rzon|Rzon]] 18 June)
-* More sophisticated methods to [[ User_Serial | run serial jobs on GPC ]] ([[User:Rzon|Rzon]] 16 June)
-* Continuing updates on the [[ Software_and_Libraries | Software and Libraries ]] Page (various)
-* `What's new' section on the wiki main page ([[User:Ljdursi|Ljdursi]] 23 June)
-| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#FFFFFF" colspan=1|
 {{SciNetWiki:Community_Portal}}
+</div>
 |}
+{{#Widget:Twitter|shell.background=#9fb1c2|tweets.links=#4775c1|tweets.color=#000000|tweets.background=#ffffff|user=SciNetHPC}}
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