General Project

January 28, 2005

Meeting Minutes - January 28, 2005

Folding@Clusters


  • Poster outline. Hopefully this weekend - Charlie

  • Molecular systems in /cluster/project/molecules are ready to use. nsteps
    = 500, checkpointing, Readme. Still to be done is to remove the other options
    that are causing lots of extra files to be created. Charlie.

  • Major Bugs. See source/TODO for these (review weekly).

  • A2 Release Testing - Running tests on 1 through 4 nodes for about 12 molecular
    systems on bazaar and cairo. So far about 500 or so runs.

    • NFS/Non-NFS - not done.
    • Different Mol types: - done.
    • Platforms: x86/Linux, PPC/Linux, PPC/OSX - done.
    • Number of nodes [2-16] - 1 through 4 nodes currently.
    • Failure and Recovery (with fault tolerance checking) - not done.

      • Look at folding-at-clusters/documentation/index.html
      • Killing lam on non n0 nodes.

    • Matricies

      1. NFS/Non-NFS Platform
      2. Mol. Types + Number of nodes + Platform
      3. Faulure/Recovery + Platform (high number of nodes)



  • SMP testing - Charlie will contact Henry Neeman and get the details
    for access to OSCER's SMP box to JoshH who will do the testing.

  • Less focus on code for the next 2 weeks, work on poster.

  • Review/Update protocol.txt - Revisit after SIAM. Make a phase diagram
    so we can figure-out how to test checkpointing, failure, and recovery
    completely.

  • Cleanup of files on non-NFS systems - Revisit after SIAM.


Numerical Methods


  • Nota bene - This section is unchanged from last week, which was unchanged
    from the week before that, ...

  • Basic MidWife - JoshM

    JohnS will send pointer to JoshM about what is there so far, and what
    needs to happen. [use the folding-at-cluster/testing directory]

  • Extensions to MidWife concept (new program and schema?) that supports
    building FFTW, GROMACS, etc. with particular configure and compiler/linker
    options. Table until next meeting...

  • Literature search - JohnS

    • inverse square root, molecular dynamics, vector
      MT
      Link

      Create a Literature Notes file in CVS
      (numerical-methods/doc/literature-search-notes.txt)

  • Poster outline - Charlie (this weekend)

  • NAMD Report: looking for benchmark molecules, Keep working on how to get
    Charm working - JoshM

Plumbing


  • Cairo image - F@C build problem, F@C run unknown, NAMD no, ganglia no

  • Bazaar image - F@C builds, F@C runs, NAMD no, GAUSSIAN no, ganglia no

  • DVC - results integration - JoshM and Charlie

  • New image notes

    • How to decide if /cluster/... vs locally on each node for a particular
      package? Let's discuss this in more detail after SIAM.

    • Postgres client libraries, binaries, DBI, and DBD::Pg on all client nodes.

    • JoshM will post a software list for us to review and update.

  • NAMD/CHARM - can run binary under OSX but can't install source and build
    under PPC-Linux. JoshM will try building on bazaar.

  • CodeViz stuff is installed on Bazaar /cluster/, JoshM will post instructions.
    Incompatibility between compilers, //tag and graphing. After SIAM.

  • Charlie has had two odd CVS experiences recently, TODO and gromacs. He'll
    look and see what if anything is going wrong here.

  • Cleaned-up DVC file spamming - JoshM.

  • distcc doesn't work with //tag option that GROMACS uses. Don't worry about
    it, distcc is really only useful for BCCD. JoshM.

Other


  • New copy of B-and-T GROMACS poster. After SIAM.

  • Mary Lou changed the plane ticket to have Josh's correct last name.

Posted by charliep at January 28, 2005 09:49 AM
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