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Thread: Beta 2 now available - beta testers please update

  1. #1

    Beta 2 now available - beta testers please update

    Ok, I have released an updated beta with all the bugs that have been found so far fixed. If you are helping to beta test, please get the update from the same place as before:

    ftp://ftp.mshri.on.ca/pub/distribfol...ux-i386.tar.gz
    for Linux and
    ftp://ftp.mshri.on.ca/pub/distribfol...beta-win9x.zip

    To install, just overwrite the previous beta or a fresh install with the files in this archive; no other files have changed.

    Please delete filelist.txt as well, if present, to force it to restart at generation zero.

    If you downloaded it recently and are not sure which you got, just look at the readme.txt which should say 'Beta 2' on the first line, if you've got it.

    Please post any further bugs/problems with Beta 2 in THIS thread and I will ignore any further reports in the previous thread, I will assume those are from the old version.

    Thanks for your assistance.
    Last edited by Brian the Fist; 02-21-2003 at 03:23 PM.
    Howard Feldman

  2. #2
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    Okay, this one seems to be working correct. No more data file checksum error. Doesn't seem to be stuck for so long as well.
    Good job.

  3. #3
    Fixer of Broken Things FoBoT's Avatar
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    the new beta2 for windows doesn't ask about the # of files to buffer, the foldit.bat on both of my beta boxes skipped that question
    Use the right tool for the right job!

  4. #4
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    I've tested some (ca. 6) different options under SuSE Linux 8.1 - no error occured up to now.

    Great work!

    If an error occures, I'll post something about it

  5. #5
    Originally posted by FoBoT
    the new beta2 for windows doesn't ask about the # of files to buffer, the foldit.bat on both of my beta boxes skipped that question
    You mean pertaining to the -df option right? As stated in the 'readme.txt', the -df option is now always enabled. This is because it is not needed anymore. The files are a lot smaller than they used to be and the program should never take up TOO much disk space (until someone complains that it does of course ).

    Ok, please try to break this version as much as you can, meanwhile I still have a few small things to add to it. Since it is probably relatively stable now, I will take feature requests and suggestions at this time too - but please keep them simple and useful to many people (not just yourself). As always they will be judged fairly and if deemed worthy, included in the next (and hopefully final) beta.

    P.S. when I change to the next beta, something will change on the server too meaning data from the old beta will not be accepted any longer. In fact that might be a good way to tell when the next beta is ready, if you don't check here often No big deal otherwise.
    Howard Feldman

  6. #6
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    Originally posted by Brian the Fist
    ... Since it is probably relatively stable now, I will take feature requests and suggestions at this time too - but please keep them simple and useful to many people (not just yourself). As always they will be judged fairly and if deemed worthy, included in the next (and hopefully final) beta.
    Perhaps you can add displaying the number of the produced stuctures and the best RMSD of this sequence of generations.
    The best RMSD could be updatet after each generation.
    Although it might be a bit difficult, it might be a good step for monitoring.

  7. #7
    TeAm AnandTech Insidious's Avatar
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    Running WinXP ASCII client at the moment.

    I haven't been able to break it wrt internet disconnects so far

    running other apps. and games doesn't seem to bother it a bit!

    When I shut it down improperly (windows re-start without stopping client first). The next time I ran it, it started over and
    data was apparently lost (I think you said this is normal) After that everything seemed to progress normally!

    KUDOS!

    Will experiment with service install next.

    update: it's running fine as a service for me as well


    For the shallow amoung us, it would be fun if the progress.txt file
    indicated how many "points" were uploaded since client last started. (I don't understand how to correlate the scores on the
    stats site with what I see on my client display/progress.txt.

    -Sid
    Last edited by Insidious; 02-21-2003 at 08:55 PM.
    ~~~~ Just Passin' Through ~~~~

  8. #8
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    Currently been running for 2hrs with no errors so far

    Nicely done
    OCAU Distributed Folding Team Member
    11.5gig DF'ing 24/7
    Idle temp ?? What idle temp ??

  9. #9
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    Will the client be hardcoded to use 5000 for generation 0 and 200 for subsequent generations, or will it be possible for the user to change those values?
    One might want to start out with 10000 to get the best possible structure top start out with.

  10. #10
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    Are there any plans to change the format of progress.txt between the beta and the release of the new client?

    If the format does change, then updating dfGUI would be pointless, but if it doesn't, then starting with the update now would probably be a good idea.

    I do see that Insidious has asked for:

    it would be fun if the progress.txt file indicated how many "points" were uploaded since client last started.
    which would be a format change in progress.txt, so perhaps I should wait to start modifications of the Linux port (of dfGUI, that is) until I hear on whether that's going to happen.

  11. #11
    P4-1.8A,
    256 DDR 333 x2,
    ASUS P4S533,
    gforce4ti-4200 64MB...

    Windows XP Pro (Hong Kong Version)
    __________________________________

    When I shut it down (pressing "Q"), it can resume next time. It seems be no problem until finishing 500th struct.

    When making Gen. 3 Trajectory Distribution, an error occurs.
    [ ][NULL_Caption] FATAL ERROR:
    [012.002] Attempt to insert duplicate residue number into database
    Hit Return

    After pressing "Enter", it displays Abrupt: code = 12

    In error.log,
    FATAL ERROR: [012.002] {trajtools.c, line 2377} Attempt to insert duplicate residue number into database

    When it started over again, the error is still here.
    I have no any idea......

  12. #12
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    Post Argument order issue?

    Software Setup:
    WinXP Pro version 2002

    Hardware:
    Motherboard ASUS A7M-266-D (dual Athlon MP1800+)

    Environment:
    No other instances of the beta2 are running.
    Several IE windows are open.
    Only Winzip8.1 and various hardware drivers are installed.

    Description: Fatal error on every run of foldit.bat (non-service install).


    Steps to Reproduce:
    1)Unzip latest full version of win9x command line client.
    2)Unzip beta (version2) into existing dir overwriting files.
    3)Change the foldtrajlite arguments to the following:
    .\foldtrajlite -f protein -n native -s 10000 -df -p 20

    4)run "foldit.bat"
    5)Error occurs immediately

    Error Description:
    When runnign foldit.bat for the first time the following error message is displayed to the command screen:

    [NULL_Caption] FATAL ERROR: [000.000] Missing/Invalid arguments. For usage, run program, with no arguments.
    Hit Return

    After hitting return the following windows pops up:
    Title: foldtrajlite.exe - Fatal Application Exit
    Message:Abrupt: code = 0
    robi2106

  13. #13

    Arrow

    One point I have not mentioned.
    The parameter of client I ran is -qf -it -rt.

    Without -qf parameter, it seemed be no problems (ran continuously for an hr)


    When minimizing energy of best structure found, my PC cannot run smoothly although the priority of CPU usage of the client is the lowest. (I do not know if it is a problem or not) A bit annoying I felt.

  14. #14
    Beta seems to run smoothly except for one thing...
    As long as the client window has focus it runs like lightning...
    If I click on some other window it nearly stops and proceeds at a snails pace. That isn't the case on the current release.

    OS Win 95 SE
    AMD Athlon 1.466 Mhz

    Nothing was changed... unzipped the new stuff right over the old.

  15. #15
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    Re: Argument order issue?

    Originally posted by robi2106
    .\foldtrajlite -f protein -n native -s 10000 -df -p 20
    There is no -s switch. The client is exiting with a fatal error because you are giving it an invalid switch.

    Run foldtrajlite without any arguments to see a list of valid switches.

  16. #16
    So far with both versions of the beta, the client has been working great for me! The improvement in the accuracy of the protein structure predictor is really amazing. I can actually actually watch my best protein structure progressively improve as I upload additional structures. Instead of merely randomly going down in numbers occassionally, I've actually seen it drop by .01 two uploaded sets in a row. The results definately look encouraging so far. The really interesting question will be how much better the best protein structure prediction will be compared to the previous client with a large enough sample size.
    A member of TSF http://teamstirfry.net/

  17. #17
    ginaguy18p0r
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    This post is GONE.

    Edited by admin for inappropriate content.

  18. #18
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    Re: Argument order issue?

    Originally posted by AMD_is_logical
    There is no -s switch. The client is exiting with a fatal error because you are giving it an invalid switch.

    Run foldtrajlite without any arguments to see a list of valid switches.
    I included that argument because it is listed in the readmefirst.txt that comes with the current full version of the beta (upload frequency control).
    robi2106

  19. #19
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    Re: Re: Argument order issue?

    Originally posted by robi2106
    I included that argument because it is listed in the readmefirst.txt that comes with the current full version of the beta (upload frequency control).
    That is a valid argument with the regular version. With it didn't really matter whether you uploaded 1000 units 10 times or 10000 units once. But with the beta the first generation is just to get a good fold to start with for the succeeding generations, so you no longer have the option to choose how many this is going to be.

  20. #20
    System used: PIII 600, 128MB, Win NT4 Sp6.
    Tested the options -qt -rt + removing .lock file etc without a problem so far.

    Small remark, you get '[]====[]===' output on your screen even when you use the -qt option. This doesn't cause any problem however .

  21. #21
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    enhancements

    1) Client now says what generation it's currently working on which is nice. Better still to list all generations done so far and the best rmsd or energy for each generation. This could replace the ASCII art.

    2) Instead of having each client do 5000 random selections first and then choose the best of their own 5000 to 'drill down on', why not have each client that is connected to the net report its 5000 to your server and have your server assign the structure to explore more?
    That way you could leverage the best of the entire collection as opposed to just the best out of each 5000. Furthermore, this would set up a structure where you could apply some intelligent guidance to the selection process based upon whatever criteria you deem best in the future.

    3) The 'DATA UPLOADED TO SERVER - CONTINUING' message stays on too long in generations after the first.

    Of these, only #2 is really substantive and is also the most difficult to implement. Maybe in a future release...

    ms

  22. #22
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    When minimizing energy of best structure found, my PC cannot run smoothly although the priority of CPU usage of the client is the lowest. (I do not know if it is a problem or not)
    I also had this problem with the client. Running on Win 98se, 650 processor, 256mg ram, with the -qt -rt switches, although I had the client set on high priority. Glad to see it was not just in the low priority setting that this happened.

    This is a problem for people who will run this on boxes that are not dedicated crunchers. There were instances of not being able to open or close applications and severe keyboard lag.

  23. #23
    Team Overclockers UK Mpemba Effect's Avatar
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    Thumbs up Re: enhancements

    This client seem to be very good, haven't been able to break it so far

    One thing though, I do like the funky ascii art but with this client generating huge asciiness all the structures seems to look the same i.e writing over itself filling the entire screen. So it'll be nice to change this to something else maybe, any chance of a really cut down version of the client without any graphical output at all? The majority of us proberbly run it as a service or quietly in the background in linux anyway. I know you can run it in quiet mode, but it's gotta save on some speed over the lengths of time we run the client at?

  24. #24
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    Re: enhancements

    Originally posted by Brian the Roman


    2) Instead of having each client do 5000 random selections first and then choose the best of their own 5000 to 'drill down on', why not have each client that is connected to the net report its 5000 to your server and have your server assign the structure to explore more?
    That way you could leverage the best of the entire collection as opposed to just the best out of each 5000. Furthermore, this would set up a structure where you could apply some intelligent guidance to the selection process based upon whatever criteria you deem best in the future.
    That's funny, I was just about to post the same thing

    The 'Distributed Particle Accelerator Project' uses a similar strategy. You can download a file with the best 250 results so that your own client can directly do computations based on those good results.

    Best 250 FAQ item

    I have the feeling that a similar strategy could be very benificial for DF as well..

  25. #25
    Deleted...
    went back and read about new stuff in 1st beta thread...
    Last edited by TheWeatherMan; 02-22-2003 at 11:30 AM.

  26. #26
    Originally posted by Akkermans
    System used: PIII 600, 128MB, Win NT4 Sp6.
    Tested the options -qt -rt + removing .lock file etc without a problem so far.

    Small remark, you get '[]====[]===' output on your screen even when you use the -qt option. This doesn't cause any problem however .
    I assume you mean during energy minimization, the progress bar?? This should NOT be the case. I'll fix that if its true. It is important that quiet mode has NO output (it can cause problems depending on how people use it).
    Last edited by Brian the Fist; 02-22-2003 at 11:59 AM.
    Howard Feldman

  27. #27
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    Re: Re: enhancements

    Originally posted by Starfish
    That's funny, I was just about to post the same thing

    The 'Distributed Particle Accelerator Project' uses a similar strategy. You can download a file with the best 250 results so that your own client can directly do computations based on those good results.

    Best 250 FAQ item

    I have the feeling that a similar strategy could be very benificial for DF as well..
    Glad someone agrees. Actually I was thinking about this a bit more and you probably wouldn't need the full 5000 from everyone, just the best 100 or so since they're the ones we're really interested in anyway.

    ms

  28. #28

    Re: enhancements

    Originally posted by Brian the Roman
    1) Client now says what generation it's currently working on which is nice. Better still to list all generations done so far and the best rmsd or energy for each generation. This could replace the ASCII art.

    2) Instead of having each client do 5000 random selections first and then choose the best of their own 5000 to 'drill down on', why not have each client that is connected to the net report its 5000 to your server and have your server assign the structure to explore more?
    That way you could leverage the best of the entire collection as opposed to just the best out of each 5000. Furthermore, this would set up a structure where you could apply some intelligent guidance to the selection process based upon whatever criteria you deem best in the future.

    3) The 'DATA UPLOADED TO SERVER - CONTINUING' message stays on too long in generations after the first.

    Of these, only #2 is really substantive and is also the most difficult to implement. Maybe in a future release...

    ms
    2: Im not sure I understand. Why does the server have to pick out of the 5000 instead of the client?? After we've tested the present sampling method on a few proteins, we may change it more to be like a genetic algorithm. I won't go into detail now but I think it'll be a bit similar to your suggestion with some added complexity and randomness.

    3: Can you be more specific? Is it a bug? The length of time it stays on is measured in structures, not real-time, could this be why?
    Howard Feldman

  29. #29
    Originally posted by grobinette
    I also had this problem with the client. Running on Win 98se, 650 processor, 256mg ram, with the -qt -rt switches, although I had the client set on high priority. Glad to see it was not just in the low priority setting that this happened.

    This is a problem for people who will run this on boxes that are not dedicated crunchers. There were instances of not being able to open or close applications and severe keyboard lag.
    I will verify this, but I'm not sure if there is anything I can do about it, as it is a Windows thing. The only difference I can think of is that this part of the code is multithreaded (2 threads, one to do the work, one to update the progress bar) - maybe Windows doesnt handle low priority multi-theads well? Any Microsoft experts out there? Actually, one idea comes to mind, perhaps I need to put a sleep() in the progress bar updating loop or else that might be thrashing the CPU as it basically loops endlessly waiting for the real work to progress. I'll try it out...
    Howard Feldman

  30. #30
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    Re: Re: enhancements

    Originally posted by Brian the Fist
    2: Im not sure I understand. Why does the server have to pick out of the 5000 instead of the client?? After we've tested the present sampling method on a few proteins, we may change it more to be like a genetic algorithm. I won't go into detail now but I think it'll be a bit similar to your suggestion with some added complexity and randomness.
    It's more like:

    1) The client gives its best result(s) to the server
    2) The server does know what the few best results are from ALL work returned by all clients (best results of the entire project phase)

    3) The server gives the best results back as a few extra 'random seeds' (or something like that) to ALL the clients again, so that All clients may benefit from the few best results of a few clients. (giving them a headstart/foundation to work on)

    But I must confess that I don't know if this could be implemented, because I don't know how the 'intelligence' in the beta client works.

    edit: it's more or less a way to 'share intelligence' between clients so that the avg. 'not so smart' client benefits from the 'few bright clients' who returned a great result

  31. #31
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    I'm trying the beta on one of my cluster nodes. These are diskless nodes that use an NFS server. The network activity on that node is *far* higher than with the old client. I estimate it's about 30 times higher (in terms of bytes transfered) than the old client.

    What is all this disk activity? I know it isn't due to the /tmp stuff, as that is on the client's ramdisk. Could it be eliminated by having the client cache whatever it's reading in its RAM? (I'm already using the -rt switch.) The client wasn't doing anything unusual at the time. It was just working on structure 1 of a later generation waiting for enough 3 minute timeouts so that it could proceed.

    I don't think my server can handle such a huge amount of activity on all nodes at once. The best thing would be to fix the client so that it doesn't have so much needless disk activity. (I don't see the need for any disk activity while a structure is being worked on, except for checking the lock file, and if this is from checking the lock file then it is being done several orders of magnetude too often.) If that isn't done, I will need to know what file(s) are involved, then find a way to put them on the client's ramdisk.

  32. #32
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    Originally posted by Brian the Fist
    I will verify this, but I'm not sure if there is anything I can do about it, as it is a Windows thing. The only difference I can think of is that this part of the code is multithreaded (2 threads, one to do the work, one to update the progress bar) - maybe Windows doesnt handle low priority multi-theads well? Any Microsoft experts out there? Actually, one idea comes to mind, perhaps I need to put a sleep() in the progress bar updating loop or else that might be thrashing the CPU as it basically loops endlessly waiting for the real work to progress. I'll try it out...
    Some additional information if you are interested but I was running standard office applications at the times it caused the keyboard lags and/or freezes, Outlook, Norton AV and Word. Nothing out of the ordinary. System resources were still at 76% once everything returned to a "normal" state. The problems were intermittent throughout the folding process, but I could not even control alt delete to stop any processes once it froze the apps.

  33. #33
    Originally posted by Brian the Fist
    I assume you mean during energy minimization, the progress bar?? This should NOT be the case. I'll fix that if its true. It is important that quiet mode has NO output (it can cause problems depending on how people use it).
    This happens indeed with the -qt option during the energy minimization phase and Generating Trajectory Distribution.
    The lenghth is more that the standard Enegry minimazation window size. It can go up to 4 to 5 lines in the DOS box (so
    []==================================================================================================== ==================================================================================================== =============================================[]==================================================================================================== ==================================================================================================== ===================================[]======... etc)

    So you get far more = characters than without the -qt option.
    Last edited by Akkermans; 02-23-2003 at 06:08 AM.

  34. #34
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    So I am seeing a big delay doing certain things in Windows XP. I timed the main application that I run all the time for opening and closing times. I had the client running in a dos box with the -rt switch.

    Open with regular client: 3 seconds
    Open with beta client: 33 seconds
    Close with regular client: 5 seconds
    Close with beta client: 70 seconds

    A also saw this over a year ago when I was trying to run the cli version of seti. It seems like the beta client is willing to give up the cpu but the application never really asks for it. It was the first thing that I checked when I started on this project. Once the application is open it seems to be able to grab the cpu time that it needs.

    I normally run as a service and that is where I first noticed this. I was just running in the dos box because it was faster to set up and I wanted to make sure it was just doing the normal folding part instead of the energy minimization part.

  35. #35
    During the Minimizing energy routine a fatal error occured.

    Windows message:
    FOLDTRAJLITE caused an invalid page fault in
    module <unknown> at 00de:7c004407.
    Registers:
    EAX=00000000 CS=017f EIP=7c004407 EFLGS=00010212
    EBX=a0000000 SS=0187 ESP=08dffe55 EBP=0108dffe
    ECX=00000001 DS=0187 ESI=fc08b4b3 FS=392f
    EDX=089e1e50 ES=0187 EDI=bc08ba97 GS=0000
    Bytes at CS:EIP:

    Stack dump:
    bc08dffe 0008b4b3 b0000000 2008b4b3 0108ba99 60000000 6008ba97 0108ba98 00089100 6a000000 42c19760 f5416a1e 00bf87d3 3fe80000 e0000000 c69ad33c

    OS: Win 98SE
    CPU: AMD 1.466 Ghz
    RAM: 500 Megs PC 133
    Flags used: .\foldtrajlite -f protein -n native -qf -df -it -rt

    Update:
    I restarted the client changing nothing...
    The client started over and promptly crashed after finishing the first part and while the minimzing routines were running.

    I shut down everything, rebooted Windows, and restarted the client.
    At exactly the same point it crashed again.
    Last edited by TheWeatherMan; 02-22-2003 at 07:16 PM.

  36. #36
    TeAm AnandTech Insidious's Avatar
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    That one sounds like the errors I get if I am OC'd more than DF likes.

    DF is the most sensitive app. I run to memory errors, and is usually the first to indicate I am pushing things beyond 100% stable.

    -Sid
    ~~~~ Just Passin' Through ~~~~

  37. #37
    Originally posted by Insidious
    That one sounds like the errors I get if I am OC'd more than DF likes.

    DF is the most sensitive app. I run to memory errors, and is usually the first to indicate I am pushing things beyond 100% stable.

    -Sid
    Well, I might agree with you if the system wasn't stable. It's been running the non-beta version now for nearly 2 weeks... no problem. This version has run fine since yesterday. Also, this machine has run the Stanford Gromacs core which is sensitive to overclocking to the extreme without a problem. I put it back to stock speed and it did exactly the same thing. It's now running a Stanford work unit. I'll wait and see what happens. Thanks for the suggestion.

  38. #38
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    Re: Re: enhancements

    Originally posted by Brian the Fist
    2: Im not sure I understand. Why does the server have to pick out of the 5000 instead of the client?? After we've tested the present sampling method on a few proteins, we may change it more to be like a genetic algorithm. I won't go into detail now but I think it'll be a bit similar to your suggestion with some added complexity and randomness.
    The process as I understand it now is that the client will generate 5000 structures, pick the best one to drill down on in the next generation, and then pick the best one of that generation, etc until 50 generations have been done.
    The weakness in this approach is that each client is limited in its choice of structures to the 5000 it produced at the beginning. If you have 100 people crunching it's very unlikely that the 100 best structures overall will be distributed evenly across the 100 sets of 5000. Rather, some sets of 5000 will actually contain several very good structures while some others will have none. The guy who ends up drilling down on the set that had no good structures to begin with is wasting his time compared to the guy who got lucky and got a good structure. The way to avoid this is to pool the best of the structures crunched by the clients on your server. Then, the server assigns the best structure that has not already been assigned to each client who asks. That way all of the best structures are pooled on the server and every client is drilling down on the best structure available out of the entire pool instead of just its own 5000.

    To be sure I've been clear I'll do this as pseudo code. (sorry if you already understand)

    1) client A crunches 5000 and reports the best 100 structures to the server.
    2) the server assigns the best structure of the 100 to client A to drill down on and marks the structure as 'taken'.
    3) client B crunches 5000 and reports the best 100 to the server.
    4) the server assigns the the best structure out of the 200 excluding those already taken to client B to drill down on and marks that structure as taken.
    5) and so on for the rest of the clients

    The advantage of the above approach is that each client is always crunching the best unique structure available. With the current method some of the best structures found overall are ignored completely simply because they happen to be second best out of 5000.

    looking at this from another perspective, you're not leveraging all of the sampling work done by all of the clients when choosing the best to drill down on. Everyone's on their own which will almost certainly be less effective overall.

    ms

  39. #39
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    Re: Re: enhancements

    Originally posted by Brian the Fist

    3: Can you be more specific? Is it a bug? The length of time it stays on is measured in structures, not real-time, could this be why?
    No it's not a bug. It's just that now that the structures take a minute or so each instead of a second or two, the message stays up about 60 times longer than it used to. It's a minor point

    ms

  40. #40

    Question

    Running in -qf mode, I've noticed that the residue calculation number will "hang" or even fall back in sequence.

    ie., "calculating residue 6x of 96", may fall back to "5x of 96", go back up to "7x of 96" and fall back to "6x of 96". It's currently on #7 generation, but #6 was similar. Is this normal?
    It's like it gets bored and just doodles all over itself.

    WinXP w/AMD 1.4 T-Bird
    -df -qf -it -rt switches

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