Difference between revisions of "Cluster:Todo"

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__NOTOC__
 
__NOTOC__
  
−
== Current Items (updated September 21, 2005)==
+
== Quick Test ==
−
* Little-Fe
+
== Current Items (updated November 9, 2005)==
−
** Fossilize BCCD onto Little-Fe, making progress, see BCCD/PPC wiki for details (Kevin and Toby)
+
=== Little-Fe ===
−
** Measure load with 4 nodes, 2 disk drives, CD drive; order transformer (Charlie)
+
* Liberate BCCD onto Little-Fe, making progress, see BCCD/PPC wiki for details (Kevin and Toby)
−
* LLK (see [[Cluster:LowLatency]] for the details)
+
** Use singularity
−
**  
+
* Send email to Paul about BCCD changes (Toby)
−
** Read the STP paper, emulate his test methodology/program? (Everyone)
+
* Setup archive for list-packages
−
** Is there a 2.6 version of STP? (''Only from us.'')  SGI? (''Not likely.'') (Skylar)
+
* Get test clusters liberated
−
** Measure latency in kernel and on wire using either kperf or tp_timer - (Alex and Toby)
+
* Get qemu or UML working for test environment (Skylar/Kevin)
−
*** Test accuracy by loading one of the nodes with CPU and disk traffic (lots)
+
* Talk about Bugzilla setup for liberation
−
*** 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)
+
=== LLK (see [[Cluster:LowLatency]] for the details) ===
−
*** Measure bit error rate (Skylar)
+
* '''Note:''' migration of this list to bugzilla is in progress; here's the current [http://cluster.earlham.edu/bugzilla/buglist.cgi?query_format=specific&order=relevance+desc&bug_status=__open__&product=llk llk bug list]
−
*** Use a structure/array for tp_ routines (Alex and Toby)
+
* Check Alteon drivers for STP, do they support cairo?
−
** No word from MAGNET on 2.6.x
+
* Find statistics information (Skylar,Alex)
−
** Real time kernels and TCP/IP book _late next week_.
+
* Read the STP paper, emulate his test methodology/program? (Everyone)
−
** Update the list of references, llk.bib (Everyone)
+
* Is there a 2.6 version of STP? (''Only from us.'')  SGI? (''Not likely.'') (Skylar)
−
** Literature search (Skylar, JoshM)
+
* Look at separate socket implementations (Skylar)
−
*** Document all sysctls, build options, etc. that effect network performance, particularly latency
+
* Look at Netpipe calls for STP help (Skylar)
−
*** 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.
+
* Measure latency in kernel and on wire using either kperf or tp_timer - (Alex and Toby)
−
* Folding@Clusters
+
* Investigate tp_timer instabilities (Toby, Alex)
−
** Build a 3.1.4 CVS export with instructions and park it in ~pande for Guha (JoshM)
+
** Test accuracy by loading one of the nodes with CPU and disk traffic (lots)
−
** Test a range of molecules, clusters, and sizes with Alex's scripts and PBS/Maui (Skylar)
+
** 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)
 +
* Figure out linking (AlexL)
 +
=== 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
 
* Plumbing
−
** on bazaar: ccache & distcc with wiki howto (Skylar,''done'')
+
* Figure out how to get poster in one go (Skylar) LaTeX?
−
** on cairo: distcc (currently installed but not running) with wiki howto (Skylar,''done'')
+
* on bazaar: ccache & distcc with wiki howto (Skylar,''done'')
−
** Nate Bass's problems (JoshM)
+
* on cairo: distcc (currently installed but not running) [[Building_the_GIMP|with wiki howto]] (Skylar,''done''). Pull image too (Skylar)
−
* Other
+
* Investigate cairo's network delays. Switches? sshd? Timer reset? IPF? (Skylar, Toby)
−
** Dinner at the Ranch on September 30th (Everyone, including SOs)
+
* Setup testing flows (UDP, ICMP) between hopper and cairo to test latency. (Skylar)
−
** 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 ==
 
== Aug 26, 2005 Meeting Minutes ==
Line 48: Line 53:
  
 
== Plumbing ==
 
== 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)
+
* Whitebord(s) for 4th (Charlie)
−
* Setup Amanda, follow-up with Dan (Skylar)
+
* Change Vijay's password (JoshM)
−
** Finish setting up weekly tape backups with AMANDA (Skylar). Stalled on borken tape drive.
 
 
* Fiber uplink for bazaar (Charlie)
 
* Fiber uplink for bazaar (Charlie)
 
* Return GBIC module (Alex)
 
* Return GBIC module (Alex)
Line 57: Line 61:
 
* Figure-out why CVS commit emails don't always appear
 
* Figure-out why CVS commit emails don't always appear
 
* Setup POVray on Athena (Skylar)
 
* 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
 
* Updates to http://cluster.earlham.edu
 
** add link to cluster wiki page
 
** add link to cluster wiki page
Line 71: Line 72:
 
** Overview and Press prose update (Charlie)
 
** Overview and Press prose update (Charlie)
 
* Update speedup and speedup/efficiency within DVT for endnodes (Alex)
 
* Update speedup and speedup/efficiency within DVT for endnodes (Alex)
 +
* Talk about backup strategies/repartitioning
  
 
== LittleFe ==
 
== LittleFe ==
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== Folding@Clusters ==
 
== 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)
 
* 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)
 
* Develop test canon (Alex and Charlie)

Latest revision as of 14:02, 20 August 2008

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


Quick Test

Current Items (updated November 9, 2005)

Little-Fe

  • Liberate BCCD onto Little-Fe, making progress, see BCCD/PPC wiki for details (Kevin and Toby)
    • Use singularity
  • Send email to Paul about BCCD changes (Toby)
  • Setup archive for list-packages
  • Get test clusters liberated
  • Get qemu or UML working for test environment (Skylar/Kevin)
  • Talk about Bugzilla setup for liberation

LLK (see Cluster:LowLatency for the details)

  • Note: migration of this list to bugzilla is in progress; here's the current llk bug list
  • Check Alteon drivers for STP, do they support cairo?
  • Find statistics information (Skylar,Alex)
  • 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)
  • Look at separate socket implementations (Skylar)
  • Look at Netpipe calls for STP help (Skylar)
  • Measure latency in kernel and on wire using either kperf or tp_timer - (Alex and Toby)
  • Investigate tp_timer instabilities (Toby, Alex)
    • 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)
  • Figure out linking (AlexL)

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
  • Figure out how to get poster in one go (Skylar) LaTeX?
  • on bazaar: ccache & distcc with wiki howto (Skylar,done)
  • on cairo: distcc (currently installed but not running) with wiki howto (Skylar,done). Pull image too (Skylar)
  • Investigate cairo's network delays. Switches? sshd? Timer reset? IPF? (Skylar, Toby)
  • Setup testing flows (UDP, ICMP) between hopper and cairo to test latency. (Skylar)

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

  • Whitebord(s) for 4th (Charlie)
  • Change Vijay's password (JoshM)
  • 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)
  • 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)
  • Talk about backup strategies/repartitioning

LittleFe

Folding@Clusters

  • 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)
Retrieved from "https://wiki.cs.earlham.edu/index.php?title=Cluster:Todo&oldid=5343"