Cluster:Todo - Revision history

Charliep: /* Current Items (updated November 9, 2005) */

2008-08-20T18:02:44Z

Current Items (updated November 9, 2005)

← Older revision		Revision as of 18:02, 20 August 2008
Line 2:		Line 2:
	__NOTOC__		__NOTOC__

			== Quick Test ==
	== Current Items (updated November 9, 2005)==		== Current Items (updated November 9, 2005)==
	=== Little-Fe ===		=== Little-Fe ===

Skylar at 22:05, 8 March 2006

2006-03-08T22:05:57Z

← Older revision		Revision as of 22:05, 8 March 2006
Line 10:		Line 10:
	* Get test clusters liberated		* Get test clusters liberated
	* Get qemu or UML working for test environment (Skylar/Kevin)		* Get qemu or UML working for test environment (Skylar/Kevin)
			* Talk about Bugzilla setup for liberation

	=== LLK (see [[Cluster:LowLatency]] for the details) ===		=== LLK (see [[Cluster:LowLatency]] for the details) ===

Skylar at 17:27, 9 February 2006

2006-02-09T17:27:00Z

← Older revision		Revision as of 17:27, 9 February 2006
Line 9:		Line 9:
	* Setup archive for list-packages		* Setup archive for list-packages
	* Get test clusters liberated		* Get test clusters liberated
			* Get qemu or UML working for test environment (Skylar/Kevin)

	=== LLK (see [[Cluster:LowLatency]] for the details) ===		=== LLK (see [[Cluster:LowLatency]] for the details) ===
Line 25:		Line 26:
	** Measure bit error rate (Skylar)		** Measure bit error rate (Skylar)
	** Use a structure/array for tp_ routines (Alex and Toby)		** Use a structure/array for tp_ routines (Alex and Toby)
			* Figure out linking (AlexL)
	=== Folding@Clusters ===		=== Folding@Clusters ===
	* Build a 3.1.4 CVS export with instructions and park it in ~pande for Guha (JoshM)		* Build a 3.1.4 CVS export with instructions and park it in ~pande for Guha (JoshM)

Skylar at 21:14, 19 January 2006

2006-01-19T21:14:51Z

← Older revision		Revision as of 21:14, 19 January 2006
Line 69:		Line 69:
	** 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 ==

Skylar at 17:43, 16 November 2005

2005-11-16T17:43:29Z

← Older revision		Revision as of 17:43, 16 November 2005
Line 8:		Line 8:
	* Send email to Paul about BCCD changes (Toby)		* Send email to Paul about BCCD changes (Toby)
	* Setup archive for list-packages		* Setup archive for list-packages
			* Get test clusters liberated

	=== LLK (see [[Cluster:LowLatency]] for the details) ===		=== LLK (see [[Cluster:LowLatency]] for the details) ===
	* '''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]		* '''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]
	* Check Alteon drivers for STP, do they support cairo?		* Check Alteon drivers for STP, do they support cairo?
			* Find statistics information (Skylar,Alex)
	* Read the STP paper, emulate his test methodology/program? (Everyone)		* 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)		* Is there a 2.6 version of STP? (''Only from us.'') SGI? (''Not likely.'') (Skylar)
Line 33:		Line 35:
	* Investigate cairo's network delays. Switches? sshd? Timer reset? IPF? (Skylar, Toby)		* 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)		* Setup testing flows (UDP, ICMP) between hopper and cairo to test latency. (Skylar)
	~~=== Other ===~~
	* 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 53:		Line 52:
	* Whitebord(s) for 4th (Charlie)		* Whitebord(s) for 4th (Charlie)
	* Change Vijay's password (JoshM)		* Change Vijay's password (JoshM)
	* Fix '''Watts up?''', possibly battery (Skylar)
	** Actually needs replacing (Charlie)
	* 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)		* Fiber uplink for bazaar (Charlie)
	* Return GBIC module (Alex)		* Return GBIC module (Alex)
Line 63:		Line 58:
	* 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 82:		Line 74:

	== 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)

Charliep at 14:51, 10 November 2005

2005-11-10T14:51:27Z

← Older revision		Revision as of 14:51, 10 November 2005
Line 4:		Line 4:
	== Current Items (updated November 9, 2005)==		== Current Items (updated November 9, 2005)==
	=== Little-Fe ===		=== Little-Fe ===
	* ~~Upgrade firmware on borken LF node (Skylar, ''done'')~~		* Liberate BCCD onto Little-Fe, making progress, see BCCD/PPC wiki for details (Kevin and Toby)
	* Fossilize 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)		* Send email to Paul about BCCD changes (Toby)
	* ~~Return lf2 ''with proper processor~~ for ~~2.6'' (Skylar)~~		* Setup archive for list-packages
	** In Centerville now. 1Z 6E5 329 02 4993 490 8

	=== LLK (see [[Cluster:LowLatency]] for the details) ===		=== LLK (see [[Cluster:LowLatency]] for the details) ===

Skylar at 17:43, 9 November 2005

2005-11-09T17:43:29Z

← Older revision		Revision as of 17:43, 9 November 2005
Line 2:		Line 2:
	__NOTOC__		__NOTOC__

	== Current Items (updated ~~September 28~~, 2005)==		== Current Items (updated November 9, 2005)==
	* Little-Fe		=== Little-Fe ===
	** Upgrade firmware on borken LF node (Skylar)		* Upgrade firmware on borken LF node (Skylar, ''done'')
	** Implement boot-off-zip		* Fossilize BCCD onto Little-Fe, making progress, see BCCD/PPC wiki for details (Kevin and Toby)
	** Fossilize BCCD onto Little-Fe, making progress, see BCCD/PPC wiki for details (Kevin and Toby)		* Send email to Paul about BCCD changes (Toby)
	** Make backup dump of current LittleFe to admin (Kevin)		* Return lf2 ''with proper processor for 2.6'' (Skylar)
	** Measure load with 4 nodes, 2 disk drives, CD drive; order transformer (Charlie)		** In Centerville now. 1Z 6E5 329 02 4993 490 8
	** Send email to Paul about BCCD changes (Toby)
	** Return lf2 ''with proper processor for 2.6'' (Skylar)

	* LLK (see [[Cluster:LowLatency]] for the details)		=== LLK (see [[Cluster:LowLatency]] for the details) ===
	** '''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]		* '''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]
	** Check Alteon drivers for STP, do they support cairo?		* Check Alteon drivers for STP, do they support cairo?
	** Read the STP paper, emulate his test methodology/program? (Everyone)		* 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)		* Is there a 2.6 version of STP? (''Only from us.'') SGI? (''Not likely.'') (Skylar)
	** Look at separate socket implementations (Skylar)		* Look at separate socket implementations (Skylar)
	** Look at Netpipe calls for STP help (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)		* Measure latency in kernel and on wire using either kperf or tp_timer - (Alex and Toby)
	** Investigate tp_timer instabilities (Toby, Alex)		* Investigate tp_timer instabilities (Toby, Alex)
	*** Test accuracy by loading one of the nodes with CPU and disk traffic (lots)		** 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.		** 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 packet loss rate at each node and the switches and hopper using SNMP/Cricket (Skylar)
	*** Measure bit error rate (Skylar)		** Measure bit error rate (Skylar)
	*** Use a structure/array for tp_ routines (Alex and Toby)		** 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_.		=== Folding@Clusters ===
	** Update the list of references, llk.bib (Everyone)		* Build a 3.1.4 CVS export with instructions and park it in ~pande for Guha (JoshM)
	** Literature search (Skylar, JoshM)		* Test a range of molecules, clusters, and sizes with Alex's scripts and PBS/Maui (Skylar)
	*** 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		* Plumbing
	** Figure out how to get poster in one go (Skylar) LaTeX?		* Figure out how to get poster in one go (Skylar) LaTeX?
	** on bazaar: ccache & distcc with wiki howto (Skylar,''done'')		* on bazaar: ccache & distcc with wiki howto (Skylar,''done'')
	** on cairo: distcc (currently installed but not running) [[Building_the_GIMP\|with wiki howto]] (Skylar,''done''). Pull image too (Skylar)		* on cairo: distcc (currently installed but not running) [[Building_the_GIMP\|with wiki howto]] (Skylar,''done''). Pull image too (Skylar)
	** Investigate cairo's network delays. Switches? sshd? Timer reset? (Skylar, Toby)		* 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)		* Setup testing flows (UDP, ICMP) between hopper and cairo to test latency. (Skylar)
	* Other		=== Other ===
	** There may be a student program at the Oberlin Computational Science conference (November 4-6)		* 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)		* 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 ==

Tmcnulty: /* Current Items (updated September 28, 2005) */ move llk todo items to bugzilla

2005-11-07T21:58:35Z

Current Items (updated September 28, 2005): move llk todo items to bugzilla

← Older revision		Revision as of 21:58, 7 November 2005
Line 13:		Line 13:

	* LLK (see [[Cluster:LowLatency]] for the details)		* LLK (see [[Cluster:LowLatency]] for the details)
	** ~~Verify~~&~~validate content, and define high- and low-level benchmarks~~		** '''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]
	** Condense diagram
	** Make diagram vertical (Alex)
	** Make bar lengths relative to size

	** Check Alteon drivers for STP, do they support cairo?		** Check Alteon drivers for STP, do they support cairo?
	** Read the STP paper, emulate his test methodology/program? (Everyone)		** Read the STP paper, emulate his test methodology/program? (Everyone)
Line 24:		Line 20:
	** Look at Netpipe calls for STP help (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)		** Measure latency in kernel and on wire using either kperf or tp_timer - (Alex and Toby)
	** Put together HOWTO using JoshM's diagram and timing structure, with both Netpipe and packgen (Alex, Toby)		** Investigate tp_timer instabilities (Toby, Alex)
	** Use latest Netpipe for packet generation, specify payload, validate (Toby, Alex)
	* Investigate tp_timer instabilities (Toby, Alex)
	*** Test accuracy by loading one of the nodes with CPU and disk traffic (lots)		*** 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.		*** Setup and document this, along with kernel building/loading/starting, so that any of us can make a change and a measurement.

Skylar at 17:44, 2 November 2005

2005-11-02T17:44:45Z

← Older revision		Revision as of 17:44, 2 November 2005
Line 15:		Line 15:
	** Verify&validate content, and define high- and low-level benchmarks		** Verify&validate content, and define high- and low-level benchmarks
	** Condense diagram		** Condense diagram
	** Make diagram vertical		** Make diagram vertical (Alex)
	** Make bar lengths relative to size		** Make bar lengths relative to size

Skylar at 17:38, 2 November 2005

2005-11-02T17:38:31Z

← Older revision		Revision as of 17:38, 2 November 2005
Line 13:		Line 13:

	* LLK (see [[Cluster:LowLatency]] for the details)		* LLK (see [[Cluster:LowLatency]] for the details)
			** Verify&validate content, and define high- and low-level benchmarks
	** Condense diagram		** Condense diagram
	** Make diagram vertical		** Make diagram vertical
Line 41:		Line 42:
	** Test a range of molecules, clusters, and sizes with Alex's scripts and PBS/Maui (Skylar)		** Test a range of molecules, clusters, and sizes with Alex's scripts and PBS/Maui (Skylar)
	* Plumbing		* Plumbing
			** Figure out how to get poster in one go (Skylar) LaTeX?
	** on bazaar: ccache & distcc with wiki howto (Skylar,''done'')		** on bazaar: ccache & distcc with wiki howto (Skylar,''done'')
	** on cairo: distcc (currently installed but not running) [[Building_the_GIMP\|with wiki howto]] (Skylar,''done''). Pull image too (Skylar)		** on cairo: distcc (currently installed but not running) [[Building_the_GIMP\|with wiki howto]] (Skylar,''done''). Pull image too (Skylar)