Cluster Computing Group

Meeting Minutes - January 21, 2005

Folding@Clusters

• Poster outline. Hopefully this weekend - Charlie

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

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

• A2 Release Testing - Charlie has a simple framework and is running
  tests on 1-4 nodes for about 8 molecular systems on bazaar and cairo. So
  far about 200 or so runs. The only problems that have come-up are either
  known or fixed, at least so far.
  
  
  
  • NFS/Non-NFS
    
  • Different Mol types: All...
    
  • Platforms: x86/Linux, PPC/Linux, PPC/OSX
    
  • Number of nodes [2-16]
    
  • Failure and Recovery - with fault tolerance checking.
    
  • 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.
  
  
• Checkpointing - nxtxout (in number of steps) is the mdp file option
  that controls checkpointing. Charlie will update documentation/README.
  
  
• Cleanup of files on non-NFS systems - Revisit next week.
  

Numerical Methods

• Nota bene - This section is unchanged from last week.

• 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: look for benchmark molecules, Keep working on how to get
  Charm working - JoshM
  

Plumbing

• Cairo image - can't compile GROMACS, haven't tried running F@C. Re-imaging
  is working and is easy. distcc works. ntp working. updated c3 doc with
  version 4 syntax.
  
  
• Bazaar image - isn't imaging yet. JoshM will contact Skylar.
  
  
• Keep Non-NFS nodes [Cairo c13-15, Bazaar will be b13-b15]
  
  New images on Cairo c9-12, and Bazaar b9-12
  
  First test of new Images:
  
  
  
  • Bazaar - F@C, GAUSSIAN, NAMD, ganglia
    
  • Cairo - F@C, NAMD, ganglia
    
  
  
  
• 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/, Josh M will post instructions.
  
  
• Humidity solution on it's way from John Walker. Not sure if it will
  be mounted in the ceiling with the HVAC or in the cluster closet.

• GAUSSIAN on bazaar add to /cluster/

Other

• Poster design meeting - 4p Wednesday
  
  
• The hotel reservations are correct for SIAM CSE 05 now, checkin on Thursday
  and checkout on Tuesday (5 nights). According to Mary Lou the misspelling on
  the airline ticket can only be corrected when we get to the airport. They
  have put a note in the file about it, and we shouldn't have any problems, but
  I think we'll make sure to leave with plenty of time for the airport that day.
  JoshH, if you have a passport bring it.

• IU tour - Yes, JoshH and Charlie will work this out later in the spring.
  

Posted by charliep at January 21, 2005 02:32 PM