SciNet News October 2010

October 4, 2010 in for_users, newsletter

Added to the wiki in September:

  • Link to the SciNet courses website,
  • How to use the enhanced diskUsage command to get information on quotas and how much your usage has changed over a certain period.
  • TechTalk “Parallel File System and IO” slides.
  • “Intro to SciNet” slides.
  • Slides and source code from 1-day “Intro to Practical Parallel Programming” course.
  • Tips on how to use ramdisk in combination with GAMESS.
  • Updated module information for newly installed software (see below).

System changes:

  • During the Sept 9 shut-down, GPFS file system was upgraded to; Stricter /scratch quotas of 10TB were implemented; check yours with
  • GPC: The quantum chemistry software package NWChem 5.1.1 installed.
  • GPC: CPMD, a Carr-Parinello molecular dynamics package, was installed.
  • GPC: Gromacs 4.5.1 (single precision), a molecular simulation package was installed.
  • GPC: The IntelMPI 3.2 module has been deprecated.

What else happened at SciNet in September?

  • A course web site was set up: Here, users can read about and register for courses given by SciNet.
  • Two “Intro to SciNet” 90 minute classes were given on Sept 3 and 10. More “Intro to SciNet” classes will be given if there is demand.
  • A SNUG meeting with TechTalk on Parallel I/O and the file system was held on Sept 8.
  • A one-day course “Intro to Practical Parallel Programming” was given on Sept 22.
  • A chiller pump failure caused an unexpected system outage on Sept 24.

Coming up:

(Unless otherwise stated, all events take place at the SciNet Headquarters at 256 McCaul St.)

  • The Compute Canada National Resource Allocation Call for Proposals is out. PIs can request computing and storage allocations anywhere in Canada, including SciNet. Proposals must be submitted electronically to Compute Canada on or before November 8, 2010 at 3pm. For more info go to
  • SNUG (SciNet Users Group) meetings are held every second Wednesday of the Month, starting at 12 noon. They will include a half-hour TechTalk, user discussion, and pizza. TechTalk schedule: Wed Oct 13 Version control at SciNet: svn, git, mercurial Wed Nov 10 Debuggers & parallel debugging at SciNet: gdb, ddd, padb Wed Dec 8 Performance & profiling at SciNet: gprof,scalasca,peekperf If you are going to attend, please register at
  • SciNet classes: Wed Oct 6 Parallel I/O (whole day) May 2011 5-day Parallel Programming course. OpenMP, MPI and more will be covered. The aim is for you to leave the course able to start parallelizing your code. Register at There will likely be a fee for the 5-day course to cover course material costs. All other courses and SNUG meetings are free.
  • SciNet is the local UofT site for the Coast-to-Coast seminar series. The fall 2010 theme is “The Marine Environment and Climate Change: Problems and Possible Solutions” Dates: Oct 05, Oct 19, Nov 02, Nov 16, Nov 30. 2:30 to 3:30 EST. More info at
  • 8 Oct-8 Dec Software Carpentry: Software Development for Scientists This free, non-credit course is not being taught by SciNet, but we are involved in it. If you, your colleagues, or your students are interested, please go to for details. This instance of the course is apparently full. Do not dismay! It is all online! If you’d like to take this course at a later date, please let the course administrator know at .