Cluster:Todo

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

Plumbing

• Get PBS working on bazaar, cairo, athena, and ACL (Skylar)
• Setup WeatherDuck on hopper (Skylar)
  • Problem with some serial ports
• Setup Amanda (Skylar)
• Copy /cluster/old-hopper to tape, give it to charlie (Skylar)
• Fiber uplink for bazaar (Charlie)
• Network lag, monitoring?
• Put Athena in the display cabinet
• Setup Povray on Athena
• Protect F@C source and molecular systems, open http, ftp?, ssh? at cluster.earlham.edu (JoshM and Skylar)
  • post checkout trigger in CVS to change permissions on folding-at-clusters/source
  • add links to cluster wiki
  • loose rss feed, leave a single link to mt, last mt entry
  • news - siam posters, bccd.cs.uni.edu, others?
• Update speedup and speedup/efficiency within DVT for endnodes (Alex)

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. (Alex)
• 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.
  • 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
• Develop test canon (Alex and Charlie)
• Document pval_report.pl and compare_walltime.pl 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

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