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What is MPI_MPROBE?

April 15, 2011 at 5:17 pm PST

Here’s some MPI quick-bites for this week:

  • The MPI_MPROBE proposal was voted into MPI-3 a few weeks ago.  Yay! (see this quick slideshow for an explanation of what MPI_MPROBE is)
  • The Hardware Locality project just released hwloc v1.2.  This new version now includes distance metrics between objects in the topology tree.  W00t!
  • Support for large counts looks good for getting passed into MPI-3; it’s up for its first formal reading at the upcoming Forum meeting.
  • The same is true for the new MPI-3 one-sided stuff; it, too, is up for its first formal reading at the upcoming Forum meeting (they haven’t sent around their new PDF yet, but they will within a week or so — stay tuned here for updates).
  • Likewise, the new Fortran-08 bindings are up for their first Forum presentation next meeting.  We solved all of the outstanding Fortran issues with the F77 and F90 bindings… with the possible exception of non-blocking communication code movement.  :-(  That one is still being debated with the Fortran language standardization body — it’s a complicated issue!
  • Finally — the new MPI tools interface chapter is up for a first formal reading, too.

WHEW!

That’s a lot of first formal readings in one meeting…

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Euro MPI 2011 Call for Papers

April 5, 2011 at 8:53 am PST

Euro MPI 2011 has just issued their call for papers (please re-distribute!):

Santorini, Greece, September 18-21, 2011
BACKGROUND AND TOPICS

EuroMPI is the primary meeting where the users and developers of MPI and other message-passing programming environments can interact. The 18th European MPI Users’ Group Meeting will be a forum for the users and developers of MPI, but also welcome hybrid programing models that combine message passing with programming of modern architectures such as multi-core, or accelerators. Through the presentation of contributed papers, poster presentations and invited talks, attendees will have the opportunity to share ideas and experiences to contribute to the improvement and furthering of message-passing and related parallel programming paradigms.

Topics of interest for the meeting include, but are not limited to:

  • Algorithms using the message-passing paradigm
  • Applications in science and engineering based on message-passing
  • User experiences in programming heterogeneous systems using MPI
  • Tools and environments for programming heterogeneous systems using MPI
  • MPI implementation issues and improvements
  • Latest extensions to MPI
  • MPI for high-performance computing, clusters and grid environments
  • New message-passing and hybrid parallel programming paradigms
  • Interaction between message-passing software and hardware
  • Fault tolerance in message-passing programs
  • Performance evaluation of MPI applications
  • Tools and environments for MPI

See the full web site for more information.

Special RCE podcast: Fukushima reactor

March 26, 2011 at 8:00 am PST

Given the seriousness of issues surrounding the Fukushima, Japan reactors, Brock and I decided to reach out through our HPC contacts to find some experts to discuss the situation.  We found Drs. Kim Kearfott and Mike Hartman at the University of Michigan (Dr. Harman is one of Brock’s HPC users at UM); both are on the faculty of the nuclear engineering department at the University of Michigan.

Our conversation with the good Doctors provided a wealth of accurate, easy-to-understand information about what is — and what is not — concerning about Fukushima.

Most people forget that the “E” in “RCE” stands for engineering, so while this podcast topic is a bit outside our normal fare, it is actually within the original charter of the series.

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Trust, but verify: good science

March 25, 2011 at 10:27 am PST

A recent exchange on the Open MPI users’ list turned up a minor bug in our code base.  The bug had to do with how Open MPI reported a settings value through our configuration querying tool (“ompi_info”).

The code using the configuration value in question was doing the Right Things, but the tool was effectively reporting the wrong value.  This led to some confusion on the mailing list, resulting in a bug fix being pushed upstream and the user concluding, “Trust, but verify.”

Very true!

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More on Memory Affinity

March 18, 2011 at 7:35 am PST

There was a great comment chain on my prior post (“Unexpected Linux Memory Migration“) which brought out a number of good points.  Let me clarify a few things from my post:

  • My comments were definitely about HPC types of applications, which are admittedly a small subset of applications that run on Linux.  It is probably a fair statement to say that the OS’s treatment of memory affinity will be just fine for most (non-HPC) applications.
  • Note, however, that Microsoft Windows and Solaris do retain memory affinity information when pages are swapped out.  When the pages are swapped back in, if they were bound to a specific locality before swapping, they are restored to that same locality.  This is why I was a bit surprised by Linux’s behavior.
  • More specifically, Microsoft Windows and Solaris seem to treat memory locality as a binding decision — Linux treats it as a hint.
  • Many (most?) HPC applications are designed not to cause paging.  However, at least some do.  A side point of this blog is that HPC is becoming commoditized — not everyone is out at the bleeding edge (meaning: some people willingly violate the “do not page” HPC mantra and are willing to give up a little performance in exchange for the other benefits that swapping provides).

To be clear, Open MPI has a few cases where it has very specific memory affinity needs that almost certainly fall outside the realm of just about all OS’s default memory placement schemes.  My point is that other applications may also have similar requirements, particularly as core counts are going up, and therefore communication between threads / processes on different cores will become more common.

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