Cluster:Todo

(Need a notation for relative priority. Please don't delete anything unless we're updating this during a meeting.)

Current Items (updated September 21, 2005)

• Little-Fe
  • Fossilize BCCD onto Little-Fe, making progress, see BCCD/PPC wiki for details (Kevin and Toby)
  • Measure load with 4 nodes, 2 disk drives, CD drive; order transformer (Charlie)
• LLK (see Cluster:LowLatency for the details)
  • Read the STP paper, emulate his test methodology/program? (Everyone)
  • Is there a 2.6 version of STP? (Only from us.) SGI? (Not likely.) (Skylar)
  • Measure latency in kernel and on wire using either kperf or tp_timer - (Alex and Toby)
    • Test accuracy by loading one of the nodes with CPU and disk traffic (lots)
    • Setup and document this, along with kernel building/loading/starting, so that any of us can make a change and a measurement.
    • Measure packet loss rate at each node and the switches and hopper using SNMP/Cricket (Skylar)
    • Measure bit error rate (Skylar)
    • Use a structure/array for tp_ routines (Alex and Toby)
  • No word from MAGNET on 2.6.x
  • Real time kernels and TCP/IP book _late next week_.
  • Update the list of references, llk.bib (Everyone)
  • Literature search (Skylar, JoshM)
    • Document all sysctls, build options, etc. that effect network performance, particularly latency
    • Look for papers, etc. that discuss network performance/latency under Linux 2.6.x. For each paper write a paragraph describing what's useful, things we should try, etc., a BibTeX entry, put an electronic copy in /cluster/project/llk/references.
• Folding@Clusters
  • Build a 3.1.4 CVS export with instructions and park it in ~pande for Guha (JoshM)
  • Test a range of molecules, clusters, and sizes with Alex's scripts and PBS/Maui (Skylar)
• Plumbing
  • on bazaar: ccache & distcc with wiki howto (Skylar,done)
  • on cairo: distcc (currently installed but not running) with wiki howto (Skylar,done)
  • Nate Bass's problems (JoshM)
• Other
  • Dinner at the Ranch on September 30th (Everyone, including SOs)
  • There may be a student program at the Oberlin Computational Science conference (November 4-6)
  • Merck/AAAS Poster Session. Wednesday October 26th. Folding@Clusters and Little-Fe. We need to remember how to do smallish posters. (JoshM)

Aug 26, 2005 Meeting Minutes

• Charlie, Toby, Alex (3 credits), Kevin (2 credits), Josh, Skylar (3 credits)
• SIAM PP06
  • September 30, 2005 abstracts due, conference is February 22-24.
  • Low Latency Kernel
    • Collect papers, read, discuss next Wednesday. Wiki entry, papers, Beowulf posts, kernel source, in central place. Literature search, scholar.google.com, kernel development How-Tos, kernel mailing list, Beowulf mailing list, Toby to ask.
  • Little-Fe
    • BCCD with scripts to do mods for diskless booting
    • Write-up with pedagogical stuff and curriculum modules (list-packages)
• Other
  • Clean and organize Wiki
  • Clean and organize Recompute/CCG lab

Plumbing

• Get PBS/Maui working on bazaar (done), cairo (done), athena (done), and ACL (done); wiki for usage description, wiki for setup description; node0 exlude lists for startup files or figure-out particular files per machine with SystemImager. Can't get Lori's molecular system to parallelize even outside of PBS/Maui, Josh can give us a pointer to a test suite molecule that will parallelize (Skylar, done)
• Setup Amanda, follow-up with Dan (Skylar)
  • Finish setting up weekly tape backups with AMANDA (Skylar). Stalled on borken tape drive.
• Fiber uplink for bazaar (Charlie)
• Return GBIC module (Alex)
• Cool Athena in the display cabinet
• Construct shelving for Athena
• Figure-out why CVS commit emails don't always appear
• Setup POVray on Athena (Skylar)
• Protect F@C source and molecular systems, open http, ftp?, ssh? at cluster.earlham.edu (JoshM and Skylar)
  • Protect folding-at-clusters/articles/dr-dobbs (Charlie)
  • Can script find-out (environment variable?) where the checkout went so that it can protect those files?
• Updates to http://cluster.earlham.edu
  • add link to cluster wiki page
  • loose rss feed, leave a single link to mt, last mt entry
  • news - siam posters, bccd.cs.uni.edu, others?
  • General and Resources link sets horizontal instead of vertical.
  • Add link to Resources called documents (add static link to last MT entry and link to wiki)
  • Update weatherduck link
  • Add link to wiki doc under tools
  • Update preset query link
  • Overview and Press prose update (Charlie)
• Update speedup and speedup/efficiency within DVT for endnodes (Alex)

LittleFe

• LittleFe's Todo

Folding@Clusters

• Work with Betsy Ward to get the plumbing for F@C setup on the D224 OSX machines. Local user, document the setup with a Wiki entry. Modify run-fatc.pl, command line option to produce raw SQL. (JoshM and Alex)
  • Stalled on NetPIPE capability discovery errors from fatc.
• Console (JoshM)
  • Environment variable called $FATCHOME
  • Command line
  • Sockets to communicate with mother
  • Variable in mother.conf for console port
  • Mother listens and responds to commands on the console port
  • Command list: status [(running|paused|stopped), molecular system, x out of y steps completed, estimated time remaining, # nodes started, # of nodes current], checkpoint, pause, resume, stop.
  • Command line option -nn interval for compact, refreshed display.
  • First version of console has to be supplied with a hostname and port number.
  • Future versions (possibly when we introduce the grandmother) can take a $FATCHOME environment variable that points to a mother.conf file (to get a port number) as a discovery mechanism.
    • Can happen now: status(x out of y, stopped or running), stop
    • After mods to mdrun and F@C updates: status(paused, molecular system, estimated time remaining, nodes started, nodes current), pause, resume, checkpoint
  • Give the console the ability to trigger the checkpoint and quit mechanism.
• Checkpointing hook in GROMACS - change mdrun data structures (checkpoint frequency variable) instead of using SIGUSR1, and which files we are using. Figure-out how we can start, checkpoint, and recover using TPR and TOP files as input (JoshM)
• Develop test canon (Alex and Charlie)
• Document pval_report.pl and compare_walltime.pl (done) in Wiki (headings for each are already under HowTos) (Alex)
• Supervise test runs, non-nfs, a2.7, all molecules, 1-4 nodes, bazaar and cairo, separate table (Alex)
• rerun the following configurations and compare nfs/nonnfs (Alex)
  • bazaar proteasome
  • bazaar villin-urea
  • cairo methanol 1-8 nodes
  • cairo mixed
  • cairo proteasome
  • cairo water 1-8 nodes
  • bazaar water
• Check copyright headers, see Adam's message of March 11, 2005
• Test with PBS/Maui (Skylar)
• Re-write run-fatc to take PBS (no LAM) into account. (Skylar)
• Get PBS to allow unlimited walltime. (Skylar)

Curriculum Modules

• Producing a cluster/distro specific set of modules out of one base unit
• Generating a wiki entry and repository entry from one base unit
• Population ecology module, start by finding what packages are available and making a list. (Skylar)

Recompute

• Setup room in permament configuration.
• Accept next shipment from ECS.

Green Science

• Track down current and archival weather data (wind, temperature, others) for this area, Muncie airport, RP&L, other sources? (Mary)