Difference between revisions of "SciNet User Support Library"

From oldwiki.scinet.utoronto.ca
Jump to navigation Jump to search
m
 
(475 intermediate revisions by 8 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__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. Navigate using the links in the grid-style presentation below, or using the menu on the left.  
+
{| 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}}
 
{{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 ==
 
== 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]]
 +
* [[BGQ|BGQ: BlueGene/Q clusters]]
 +
* [[Software_and_Libraries|Software and libraries]]
 
* [[Data_Management|Data management]]
 
* [[Data_Management|Data management]]
−
* [[Software_and_Libraries | Software and libraries]]
 
−
* [[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)]]
 
* [[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" |
  
−
SciNet Accounts:
+
== 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" |
  
−
* [[Application_Process | Application process]]
+
== What's New On The Wiki ==
−
* [https://portal.scinet.utoronto.ca/usage_policy/ Usage policy]
+
<div style='text-align:left;'>
−
* [[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: Updated [[GPC Quickstart]] with info on email notifications from the scheduler.
  
−
== Manuals ==
+
* Dec 2014: [[Hdf5]] compilation page updated.
−
{{:Knowledge_Base:_Manuals}}
 
  
−
|-
+
* Dec 2014: [[Research Computing with Python 2014]] lectures 5-8
−
| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#DEDEF6" |
 
  
−
== Tutorials ==
+
* Nov 2014: "Modern CUDA Features" TechTalk slides in [[SciNet TechTalks and Seminars]].
−
{{:Knowledge_Base:_Tutorials}}
 
  
−
| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#DEDEDE" |
+
* Nov 2014: [[Research Computing with Python 2014]] lectures 1-4
  
−
{{SciNetWiki:Current_events}}
+
* Sept 2014: [[User_Tips#Reducing_virtual_memory_consumption_for_multithreaded_programs| Tip on reducing virtual memory consumption for multithreaded programs]]
−
|+
 
−
| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#FFFFDE" colspan=1|
 
  
−
== What's New On The Wiki ==
+
* Sept 2014: Improved information on the [[Python]] versions installed on the GPC, and which modules are included in each version.
  
−
''July 2010:''
+
* Sept 2014: Description on using job arrays on the GPC on the [[Scheduler]] page.
  
−
* Added an Intel Whitepaper on [https://support.scinet.utoronto.ca/wiki/images/f/f2/FP_Consistency.pdf Floating Point Consistency] to the Manual Section ([[User:Northrup|Northrup]] 13 July)
+
* Sept 2014: [[Intro to Tkinter|Tkinter instructions]], [[Media:Tkinter.pdf|slides]] and [[Media:Tkinter_code.tgz|code]] for the TkInter workshop held in September.
−
* Tips for running the [[ User_Codes#Climate_Modelling | climate modelling code]] [[ User_Codes#Running_CCSM4 | CCSM4 ]] on the TCS from the Peltier group (Guido 11 July)
 
−
* How to apply [[ Data_Management#File.2FOwnership_Management_.28ACL.29 | file access control to specific members of your group]] (Pinto 7 July)
 
−
* More tips on using [[ User_Codes#GAMESS_.28US.29 | GAMESS(US) on the GPC]] from the Fekl group (Mzd 7 July).
 
−
* Explanation of what [[FAQ#My_job_won.27t_start.2C_and_checkjob_says_.22Batch:PolicyViolation.22 | PolicyViolation]] means and why your job won't start with one ([[User:Ljdursi|Ljdursi]] 1 July)
 
  
−
''June 2010:''
+
* Sept 2014: Instructions on using [[Hadoop for HPCers|Hadoop]] (for the Hadoop workshop held in September).
  
−
* Tips for using [[GPC_Quickstart#HyperThreading | HyperThreading]] on the GPC ([[User:Rzon|Rzon]])
+
</div>
−
* How to [[Using_Signals | trap signals in C, C++ and Fortran]] ([[User:Rzon|Rzon]])
+
Previous new stuff can be found in the [[What's new archive]].
−
* Printing to standard output in <tt>.bashrc</tt> can break lots of things. This and other tips in [[Important_.bashrc_guidelines | important .bashrc guidelines]] ([[User:Rzon|Rzon]])
+
| valign="top" style="padding:1em; border:1px solid #aaaaaa; background-color:#f4f4fa; border-radius:7px" |
−
* Instructions on using the [[ Using_Paraview | ParaView ]] Visualization Package on GPC ([[User:Ljdursi|Ljdursi]])
+
<div style='text-align:left;'>
−
* 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 ]] (Imcnab)
 
−
* Updated tips on using [[ User_Ramdisk | Ram Disk ]] on GPC jobs ([[User:Rzon|Rzon]])
 
−
* More sophisticated methods to [[ User_Serial | run serial jobs on GPC ]] ([[User:Rzon|Rzon]])
 
−
* `What's new' section on the wiki main page ([[User:Ljdursi|Ljdursi]])
 
−
| valign="top" style="padding:1em; border:1px solid #8fa1b2; background-color:#FFFFFF" colspan=1|
 
 
{{SciNetWiki:Community_Portal}}
 
{{SciNetWiki:Community_Portal}}
 +
</div>
 
|}
 
|}
 +
 +
{{#Widget:Twitter|shell.background=#9fb1c2|tweets.links=#4775c1|tweets.color=#000000|tweets.background=#ffffff|user=SciNetHPC}}
  
 
<!-- [[Old Main Page]] --!>
 
<!-- [[Old Main Page]] --!>

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

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


Retrieved from ‘https://oldwiki.scinet.utoronto.ca/index.php?title=SciNet_User_Support_Library&oldid=9365’