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Site Admin
Site Admin

Joined: 25 Apr 2002
Posts: 1361
Location: Wigan,uk

PostPosted: Wed 21 Aug, 2002 22:44  Post subject:  Improvements/suggestions Pande Group (AKA to-do list)
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This is merely a start to the to-do list it is not final or prioritise in anyway yet. There is a link here or at the foot of this post which will take you to a thread you can make comments.
EDIT: A second thread was started here

This thread is locked so that it doesn't get messy and difficult for Pande group to navigate. But the link at the foot of the post will take you to an unlocked thread.

Website/Stats Server

  • Show UT as well as PST/PDT in the stats
  • Show On-Time/Late on Server statistics page
  • Both Stats systems should show WU received: Accepted / Rejected, Reason (dup/bad cksum/etc)
  • Reduced points/No points for late WUs (zero value to science!)
  • Website needs better protein info
  • improved stats resolution (Tracking per client-cpu using an ID-replacing alias name)
  • Consistency and Fairness in FAH WU scoring (GAH has been excellent)
  • add team name and WU scores to stats
    WAS: Rank__|__User_______|_______WU for project xxx_____|
    TO BE:Rank__|__User___|__Team_|___WU for project xxx__|__Proj Score____|
  • Get the stats fixed right and fixed for good - - Repeated stats failures (both FAH and GAH)
  • on the personal stats, display what I folded in the last week
  • Info on the download page: should an update be installed over a previous version or uninstall the old version first? Should they wait till the current WU has finished?
  • Can't use & in a user name
  • Add OS to psummary
  • Show a running count of WUs returned, by project and an overall summary
  • Feedback to user on accepted/rejected WUs
  • Enable team stats search by credit range like user stats
  • Track rate of WU returns and No. of active CPUs like the GAH website does
  • Synchronized stats pages
  • Subteam identification
  • Total individual stats across multiple teams and a true individual ranking vs. other individuals
  • Allow page flipping in longer stats pages
  • Provide a counter image that displays "my" score
  • Provide individual stats with a ranking for my total contribution

Better WU selection methods (clearly some are conflicting)

  • Add dead-line information to screen saver. User can decide to continue current protein or abandon it.
  • Use benchmark to send big WU to fast machines / shorter ones to slower machines Goal: Approx 1 WU per day. (User inputs Hrs/wk machine is on.)
  • User selected WUs: [all, all large, all small,long schedule-short WU(for slow machines)]
  • Ask for core preference, such as Tinker or Gromacs
  • Server to adjust assignments based on user history: If ever late, or how early (stored by CPU-ID)
  • Assign "Urgent" WU to fast machines regardless of size - - e.g. the reprocessing of WUs past their deadline
  • Vary the WU selection. (repeated protein = boring)
  • Priority to Science, not user requests - - "KISS" principle, Keep It Simple Stupid - - minimize user selectable options
  • Server monitoring the other 12h of the day (European server site?) Donors, step right up.
  • Unburden upload/download (realtime) servers - - Separate servers to handle WU processing, stats, etc. (batch)
  • Display current time as well as last update time on stats pages (for those in different timezones
  • If a WU is rejected (e.g.-digital signature failure) issue a message in the client
  • Server should never assign huge WUs to slow PCs (Min number of hours per day could be assumed, or if possible, configured) Very slow PCs or ones running very few hours would only get GAH work
  • Download enough work that the client can upload only at specific times
  • A permanent benchmark WU worth zero points (one per core)
  • Balance AS workload. Attempt to contact a random AS. Then try the other one(s). Then try last known good server. Then loop back to AS.
  • Provide a dependable source of SHORT WUs after a reasonable number of retries for the preferred selection
  • Allow donor to select total runtime of WU
  • Send re-issued WUs to specially selected clients

GUI Client / SS Client

  • simple status on mouse-over the tray icon: Show the current operation (Working, Downloading, etc) and percent complete rather than just "[email protected]" (and for Mac)
  • Flash the tray icon when a problem is encountered (e.g.-Core is currently download/sleeping)
  • Add Due-date, Project number, WU Points, & THE DISEASE that the WU relates to.
  • add wireframe and alpha helix visualizations.
  • Add power menu to include links to user stats, teams stats, and log file.
  • allow the networking popup to be covered or minimized.
  • Button to suspend so shutdown/resume loses no work
  • upgrade installer to uninstall existing version, OR loudly document instructions for upgrading an existing version. (I.e. should I uninstall first? What about mid-WU? Make it idiot-proof.)
  • disable opening browser on mouse click in screen-save mode
  • make the web-linked region of the display more obvious
  • give the user solid feedback about the fate of WUs after a server connection
  • Missing client.cfg does not force the -config panel like initial install(resuming a partial WU.)
  • Support for 256 colors
  • Access to parameter-like functions like queueinfo and send x inside GUI
  • Client to download/display personal Stats
  • Elapsed-time of previous frame and start-time of current frame
  • Drop the insignificant ".0" from the percent display
  • The ability to "freeze" GUI to reduce CPU
  • Pause-when-done should be sticky - - until WU is finished, not reset by reboot
  • Change default view to wireframe, not spacefilled (Faster)
  • Manage all command line parameters from inside the GUI
  • Priority boost button or popup
  • A button for send now like "-send all" but in the GUI
  • Change the GAH reported progress from 6000 iterations to 30 sequences
  • Provide a standard protein display rather than individual atoms
  • Suggested GUI improvements including better descriptions and slow rotation
  • Include an OpenGL validation test with the GUI installer
  • Uninstall old client automatically.
  • Screensaver should pause / resume the core rather that stop / start
  • Remove computation/configuration from SS version and have it only display work from another client.
  • Add Connection status indicator to the GUI window

All Clients

  • Compress data before upload (lhz rather than zip, for minimal server load?) - - Optional? e.g.- for dialup only
  • Count-down clock in the Client.
  • Console should accept commands while running (GUI can set/unset Pause-when-done, etc.)
  • Provide a Pause/Unpause function (for overheating, or games)
  • Transportable WUs. (Move to non-internet PC, & return for upload)
  • Add lock files to prevent inadvertently running two clients (or cores) in the same directory
  • Print the project number in the log file (with the run, clone, gen)
  • Additional checkpoints (e.g.- every minute) between frames
  • Provide direct install as a Win Service Also Multple service for SMP
  • Minimize I/O, including Client checking on core (particularly for a LAN mounted disk)
  • Self Reseeding GAH WUs for continuous processing
  • Suspend/resume task (e.g.- for laptops) . . . or . . .
  • More frequent restartable checkpoints (intermediate to frame)
  • Single documented data file for 3rd Pty dvlprs (or add to queue.dat): - Protein name - Number of atoms - Current frame (or percentage) - Total dyn steps - current dyn steps - A link to the science page explaining the protein
  • Improved client checking of core return codes. Bad WU != bad core.
  • To detecting CPU features, use a small piece of code that will run only on the "featured" system. If error, disable that "feature"
  • WAS: - Error: Could not transmit unit 02. Keeping unit in queue.
    TO BE:- Error: Could not transmit unit 02 (PROTEIN NAME, Completed: DATE). Keeping unit in queue.
  • Timestamp on every log line or More Time stamps(particularly on aborted attempts to send or receive)
  • tracking information on all WU: Gromacs & GAH WU need protein/Run/Clone/Gen
  • Logic to allow upload/download once a day - - download multiple WU if needed to keep busy for 24 hrs
  • One console to spawn multiple cores - - one per CPU
  • Loss of power should not disable optimized loops
  • Between WU, order should be (A) Download, (B) Start core, (C) Upload rather than A,C,B. (but "pause" would still be C,Stop)
  • GAH WU don't have run/clone/gen info (or equiv.)
  • GUI client can PAUSE for scan disks, defraggs and Virus Scans, but not console
  • GAH should recognize -verbosity N and skip the 10% log entries
  • Permanent running log of protein, start time/date, completion time/date, and time/date uploaded
  • Enter both a GAH and a FAH team number
  • Better retry interval (for dialup)
  • Multiple language support
  • Use the new Intel compiler
  • To reduce server CPU load, make compression optional. (e.g.- for modem users only, and perhaps for Gromacs only)
  • Send output to a Syslog server
  • Publish checksum values or the core
  • Add a delayed start option so reboot can finish
  • Client should parse the Username for spaces and illegal characters
  • Use the News From Folding line to announce a new client
  • Since the choice is not [NoPref, FAH, GAH] but really a choice of [NoPref, FAH, GAH, AdvMethods] provide the mutually exclusive choices all in one place and eliminate the parameters
  • Provide a user exit to run a program between WUs
  • Improve rotation of previous logs
  • Add machine readable standard date/rev to client
  • Download both deadlines with the WU
  • Add padding to queue.dat so the file is platform independent
  • Write a checkpoint at normal shutdown
  • Add version numbers to the properties of the executable code
  • Add progress counter (to GUI, and ?perhaps? to CLI)
  • Pause the core when certain programs run
  • Anticipatory downloading of next WU
  • Allow FAHlog to grow larger or use one FAHlog(n) per WU
  • Add a timestamp to the shutdown message
  • Display the full path to the folding directory during startup
  • Overlap processing by changing "standard" uploads to the autosend type
  • When set for nonet, client should use autosend if a connection is available.
  • Adjust CPU utilizatioin to limit temperature.
  • Bug: stats count EARLY_UNIT_END as a WU but not the local count

Client - OS Specifics

  • Enable the -service switch in Win9x.
  • boost Linux performance with Windows compiler
  • Standard format for queue.dat, padded in the same way, for all Intel-based platforms, so dual boot Linux/Windows can work on the same WU (Use Cygwin?)
  • Keep track of %CPU and record in log
  • Rename window so that the minimized console shows nn% complete as a pseudo-tooltip
  • Linux suspend if running to avoid latency problems with Oo and a few other programs
  • Add % CPU choice to Linux and OS-X Advanced Config (like Windows)
  • During installation, remove the previous startup shortcut to prevent two copies of the client from starting after an upgrade
  • Provide the WinGUI capabilites in the MacGUI client. e.g.- Context menu choices for Pause when done, Status > queueinfo, etc.
  • Work with Norton Protected Recycle Bin so that thousands of entries of Current.pdb are not stored unless all the files to retore a checkpoint are included
  • Add the option "Ask Before Connect" to the Mac client
  • Add a flag for openbsd elf2olf of cores


  • Thorough Beta test of ALL new features. Unmonitored machines must receive only highly reliable code
  • Call us donators, or donors, NOT users
  • Link the stats to printable citations
  • Add a thank you message to uploads
  • project priorities:
    1) the usefulness of the results
    2) the continuity of stats
    3) in case of problems, keep the users informed!
    4) wishlist from the user-end concerning the client (proxy, firewall support)
    5) to-do list team

Reported Bugs - gathering information

  • Bug causes cursor to be invisible in windowed display (& config window) until client is restarted.
  • GUI conflicts with other graphical programs
  • intermittent bug causes two display windows when opening from systray icon
  • Client should never receive a WU containing a null address. (It's difficult to upload to "http://")
  • Client should never receive a WU pointing to port 0
  • Validate core URL before downloading-or delete bad WU. (See here)
  • Bug: Proxy Config step: accept 'y' and 'n' as well as 'yes' and 'no'
  • Bug: Console config options are not spell-checked, leading to wrong results
  • Bug: GUI minimizes games
  • Core_c9 runs Idle, even though Low is specified
  • Bug:Sometimes WORK doesn't get cleaned out after uploading
  • FAHlog sometimes freezes although work continues
  • Bug? BAD_FRAME_CHECKSUM - - unknown cause
  • GUI reports "Working on _____" with GAH WU
  • GUI messes up XP Tooltips
  • Some firewalls block core downloads but pass WUs
  • Client does not respect the GAH only or FAH only setting
  • WinGUI often fails to redisplay white data in left grey panels (Notably with SiS 315)
  • AddtoARC error should delete WU
  • GUI Right-click menu doesn't disappear until selection is made
  • Windows installer fails if temp contains leftover information from other software installations
  • Security risks in the Mac Screensaver
  • Various screensaver problems
  • Fix Win9x screensaver, or document that it does not exist
  • Encription of proxy password in client.cfg and support for Microsoft NTLM proxy
  • segfault with glibc 2.3.1
  • Stats scripts seem to be interchanged
  • Can run dual SS clients or Console clients or GUI/Console clients(see also "lock file" above)
  • My folding link doesn't work with other browsers

Don't worry about priorities or the order of things for now, I think we just need everything we think important putting together in one place.


John & Bruce

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Vijay Pande
Pande Group
Pande Group

Joined: 25 Apr 2002
Posts: 4510
Location: Stanford University

PostPosted: Sun 01 Sep, 2002 22:32  Post subject:  
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It's great to have this list, esp after its all merged in to Py's first post (w/ the categories).

However, several of the desired features go against each other (eg more frequent checkpointing, but less frequent disk access). We'll have to sort all of that out and see which are the most important things to do first.

I'm right now most concerned about any bugs. I'd like to get that settled before adding any new features. Finally, my philosophy for the client these days are to make it simpler rather than more complex. Suggestions along this line will likely get done first and suggestions which would make it more complex (and therefore increase its potential for bugs or other screwups) are at a lower priority in my mind. I hope everyone will agree with (or at least be understanding of) this general philosophy.


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Site Admin / Owner
Site Admin / Owner

Age: 31
Joined: 24 Apr 2002
Posts: 3308
Location: Abingdon, Oxon

PostPosted: Mon 24 Feb, 2003 23:47  Post subject:  
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trying again
WW Folding For A Cure
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