SciNet News September 2010

September 4, 2010 in for_users, newsletter

Added to the wiki in August:

  • SSH keys and SciNet
  • How to find out how much disk space you’re using and how much you have left
  • Hyper-threading with Gromacs
  • Updates and improved SciNet User Tutorial
  • Updated module list
  • SciNet classes announced

System changes:

  • File system: Stricter /scratch quotas (on both space and number of files) will be implemented during the 9 Sept maintenance window. Details to appear.
  • GPC: As per Aug 4, the default intelmpi version was upgraded from version 3 to version 4, and the default intel compiler v11.1 was changed to Update 6 (module intel/
  • GPC: A number of versions of PetSc 3.1 were installed.
  • GPC: OpenSpeedShop v1.9.3.4 was installed.
  • Still working on some file system issues.

Planned down time:

  • All systems will be inaccessible on Sept 9 for maintenance.

Coming up:

All events take place at the SciNet Headquarters at 256 McCaul St.

  • “Intro to SciNet” class – learn how to use SciNet systems in 90 minutes! Even experienced users could get some useful tips out of this class. Choose your date: Fri Sept 3, 2010 at 12 noon – for this first one there’ll be pizza! Fri Sept 10, 2010 at 12 noon. Let us know which one you plan to attend ( Please print out the latest ‘User Tutorial’ and bring it to the class. More sessions will be given throughout the year depending on user interest.
  • SNUG (SciNet Users Group) meetings are held the second Wednesday of each Month, starting at 12 noon. They will include a half-hour TechTalk, user discussion, and pizza. TechTalk schedule: Wed Sept 8 The GPFS File Systems Wed Oct 13 Version control on SciNet – svn, git, mercurial Wed Nov 10 Debuggers & parallel debugging on SciNet – gdb, ddd, padb Wed Dec 8 Performance and profiling on SciNet – gprof, scalasca, peekperf Let us know if your going to attend the Sept. 8 SNUG (
  • SciNet classes: Wed Sept 22 Intro to Parallel Programming (whole day) 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 Let us know which one(s) you are going to attend (! Note: A better registration system for courses will be implemented soon.
  • Other planned classes, depending on interest:
    • Scientific Programming in C++
    • Scientific Programming in Modern Fortran
    • Tools for scientific computing: Makefiles, version control, development environments
    • Visualization Please let us know if you would be interested!
  • SciNet is one of the local seminar locations for the Coast-to-Coast seminar series. The fall 2010 theme is “The Marine Environment and Climate Change: Problems and Possible Solutions” Dates: Sept 21, Oct 05, Oct 19, Nov 02, Nov 16, Nov 30. 2:30 to 3:30 EST. More info at