SciNet User Support Library

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.

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.
QuickStart Guides Login essentials GPC: General Purpose Cluster TCS: Tightly Coupled System Data management Software and libraries Job scheduling system (Moab) Performance primer, GPC tools, TCS tools FAQ (frequently asked questions) SciNet Accounts: Application process Usage policy Usage reports Acknowledging SciNet User support	Manuals GPC (Intel) C & C++ compiler Fortran compiler Math Kernel Library Math Kernel Library link line advisor Intel MPI library Intel Compiler Floating Point Consistency TCS (IBM) 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) LoadLeveler: using & administering Performance tuning Parallel environment Cluster information center has more (also explains error codes!) Adaptive Computing/Cluster Resources MOAB workload manager TORQUE resource manager
Tutorials SciNet User Tutorial Parallel Scientific Computing Workshop, SciNet, Aug 2009: Slides /Video IBM AIX Workshop, SciNet, Nov 2008 IBM MPI Workshop, SciNet, Feb 2009 IBM Compiler Workshop, SciNet, Feb 2009 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 NVidia archived courses for GPGPU Programming LLNL MPI Tutorial: This was the basis for the MPI workshop at SciNet. 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.
What's New On The Wiki July 2010: Added an Intel Whitepaper on Floating Point Consistency to the Manual Section (Northrup 13 July) Tips for running the climate modelling code CCSM4 on the TCS from the Peltier group (Guido 11 July) How to apply file access control to specific members of your group (Pinto 7 July) More tips on using GAMESS(US) on the GPC from the Fekl group (Mzd 7 July). Explanation of what PolicyViolation means and why your job won't start with one (Ljdursi 1 July) June 2010: Tips for using HyperThreading on the GPC (Rzon) How to trap signals in C, C++ and Fortran (Rzon) Printing to standard output in .bashrc can break lots of things. This and other tips in important .bashrc guidelines (Rzon) Instructions on using the ParaView Visualization Package on GPC (Ljdursi) Tips on using the Vasp code from the Polanyi Group (Imcnab) Updated tips on using Ram Disk on GPC jobs (Rzon) More sophisticated methods to run serial jobs on GPC (Rzon) `What's new' section on the wiki main page (Ljdursi)	User-Supplied Content Share your expertise with the SciNet Community! Running specific codes on SciNet machines Tips for performance or convenience on SciNet machines Running serial batch jobs (including GNU parallel) Using the ramdisk on SciNet's GPC User-space perl modules Packing up large data sets and putting them on HPSS Remote batch