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Thread: Folding@Home

  1. - Top - End - #121
    Barbarian in the Playground
     
    Simius's Avatar

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    Default Re: Folding@Home

    Quote Originally Posted by bingo_bob View Post
    Great. Straight from one 5000-frame WU to another 5000-fram WU. Blargh.
    Well, for me the 1500 frame units take longer than the 5000 frame ones. I don't think the frame count matters much for the time it takes to finish a WU.

  2. - Top - End - #122
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    HalfOrcPirate

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    Default Re: Folding@Home

    Giant in the Playground Folding Team Update #9

    In team news this week:
    2 new members have joined our team this week - Colin and The_Mighty_Unknown - Welcome to the team!

    Team member point contributions
    :
    Who has contributed to the team points this week? Here is the list (in alphabetic order):
    _Simius_, adanedhel9, Alarra, Alizhdheg, Amazon, Beaudoin, Bitzeralisis, Colin, e_chuck, Elektro, Exachix, frdougal, gaelbert, Jackie, MaxDibe, Mobius_Stripped, NisseBosseLasse, Phoe, rward30, Samiam303, StupidFatHobbit, tannish2, The_Mighty_Unknown, zargon, ZebTheTroll and ZombieRockStar.
    With the top 10 members in points gained in the last week being:
    1 Alizhdheg
    2 frdougal
    3 Elektro
    4 gaelbert
    5 rward30
    6 ZebTheTroll
    7 Bitzeralisis
    8 adanedhel9
    9 zargon
    10 StupidFatHobbit

    Moving up in team ranks (in the top 20):
    In the top 10: frdougal continues to move up and have jumped up 2 to take the #2 spot!! rward20 moves up into 7th! adanedhel9 moves up into 9th! And zargon returns once again to the top 10 in 10th.
    In the top 20: Elektro moves up 2 into 17th!

    Individual Milestones achieved (in points at 1K, 5K, 10K, etc.):
    20,000 points: Alizhdheg
    10,000 points: Bitzeralisis and frdougal
    Congratulations to all those that have achieved a new milestone!

    Link of the week
    :
    The main web site for the project has been updated: http://folding.stanford.edu/

  3. - Top - End - #123
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    AssassinGuy

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    Default Re: Folding@Home

    Well, I decided to jump on the bandwagon, now that it's a hit. :)

    I chose "JT-GitP" to differentiate me from the other "JT" names out there.

    My first frame should complete in another 5 minutes, at which point, I hope the WU end is estimated more accurately. Right now, it says it'll take 5-1/6 days.

    I've got a dual core A64-4800 w/ 2GB of ram, and don't do much^H^H^H^H anything that taxes even one of them, so I don't notice that one of the cores is now in use, unless I look at the ASUS console.

    ...
    Eh -- only 2 minutes left for the first frame. Let's wait before posting this. :)

    Yay! Now it thinks there's only 2-1/2 days for the work unit to complete! And it got a 2nd frame done there somehow, too.

    And... down to 1-2/3 days. Soon it'll be getting done before I downloaded it!
    Last edited by JT; 2007-10-25 at 12:14 AM.

  4. - Top - End - #124
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    RedWizardGuy

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    Default Re: Folding@Home

    100 Work Units completed! Yay!!

  5. - Top - End - #125
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    HalfOrcPirate

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    Default Re: Folding@Home

    Welcome to the team JT!
    There are several projects that a WU can come from, some go quickly, some take quite a long time. With 2GB, there shouldn't be a problem accepting large projects (they can be up to 150MB is size) if you want.
    For CPU use, folding only uses otherwise unused CPU time.
    Since it seems you are using the windows graphic client, you may need to close the program while you are running 3D apps such as games.
    To use both cores, add a console client or perhaps go to the beta SMP client (although I'd suggest holding off on the SMP client until the new release as it is quite beta)

  6. - Top - End - #126
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    Default Re: Folding@Home

    Quote Originally Posted by Al'izh'dheg View Post
    100 Work Units completed! Yay!!
    Pfft, Zeb has allready done ove 600

    ps. if you're starting to feel too good about yourself, have a look at the teams in the top 100.

  7. - Top - End - #127
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    Default Re: Folding@Home

    Quote Originally Posted by Al'izh'dheg View Post
    100 Work Units completed! Yay!!
    Hm... yes, 100. Clearly.



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  8. - Top - End - #128
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    AssassinGuy

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    Default Re: Folding@Home

    Quote Originally Posted by Zargon View Post
    Welcome to the team JT!
    There are several projects that a WU can come from, some go quickly, some take quite a long time. With 2GB, there shouldn't be a problem accepting large projects (they can be up to 150MB is size) if you want.
    Thanks for the welcome. I didn't know if it was standard to say you'd joined the team, but I didn't want to just show up the next time someone ran stats.

    I configured the program to be pretty much "take what you want"
    It's allowed to give me assignments >5MB, and can take up to 100% of the processor (since I have two cores, it doesn't really matter to me). I didn't up the core priority, because it isn't being interfered with.


    Since it seems you are using the windows graphic client, you may need to close the program while you are running 3D apps such as games.
    To use both cores, add a console client or perhaps go to the beta SMP client (although I'd suggest holding off on the SMP client until the new release as it is quite beta)
    I've got some games, but I've been too busy with real life (and looking for updates to OOTS and Erf) to play them, so it shouldn't be a problem. I should probably install the console client, since I don't tax even the single remaining core. Maybe I'll download the Linux client for my server, too... though that box is a little more important/busy.

    I'd love to add this to my work servers, but I think my employer might be a tish upset if I were to do that.... It'd be cool to have another 70 cores working for the Giant's team, though.

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    RedWizardGuy

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    Default Re: Folding@Home

    Micate, the link you were looking for is: http://fah-web.stanford.edu/awards/cert.php?u=Al'izh'dheg&pts=100&t=wus&bg=3


    :)

    And yes, I realize that my 100 isn't all that big of a deal compared to those who have been around for a lot longer, but it's exciting to me! :)

  10. - Top - End - #130
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    HalfOrcPirate

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    Default Re: Folding@Home

    Too new for anything to be standard here! And I do secretly QUIETLY hope the forum gods will bless us with team upgrades
    Then we could have a formal welcome thread - but until then it's always good to have a hello post!
    In the mean time I'll put together a FAQ thread in the near future (thanks for the suggestion Rawhide!).
    For the stats, yeah... I try to keep them weekly, but sometimes (like last weekend) planets were misaligned and other excuses

    As for games - hmmm... last time I played something heavily was back in the Baldur's gate/Torment days - I tried Oblivion and half-life but after a few hours just didn't get into it and stopped. I just got Fallout 2 (yes, very old) so will try that when I get a bit of time (ha!). I think short quirky games is all I can muster otherwise - Portal is the only recent game I think I'd be interested in (imagine Belkar with the portal gun!)... maybe

    For even a busy computer, the console client with reduced settings (no large projects, idle priority, 80% idle cpu use max) should be able run on it with just about no impact on performance.

    For companies, always need formal (email) permission... unless you own the company! Otherwise who you know is really important. If you or anyone needs some help writing up a brief summary, let me know.
    Last edited by Zargon; 2007-10-25 at 07:37 PM. Reason: reason for editing? because I hit the submit button instead of the preview button...

  11. - Top - End - #131
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    Default Re: Folding@Home

    Right, I've just installed it. My old computer could not have coped with this at all. This one shoul;d do it fine though.
    I now have a blog. Have a look if you wish. It contains those naughty profanities that you won't find here. If you like what you read send me a PM, or if you don't like it. I'd like to know how many people here read it.

    Avatar done by me. If you want one then you clearly have no taste. I'll do one happily. You just have no taste.

  12. - Top - End - #132
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    Default Re: Folding@Home

    Giant in the Playground Folding Team Update #10

    In team news this week:
    3 new members have joined our team for this update - JT-GitP, MacXimus and Morrinn - Welcome to the team!

    Team member point contributions:
    Who has contributed to the team points for this update? Here is the list (in alphabetic order):
    _Simius_, adanedhel9, Alarra, Alizhdheg, Amazon, Beaudoin, Bitzeralisis, Bobnik, e_chuck, Elektro, frdougal, gaelbert, Jackie, JT-GitP, Krursk, MacXimus, MaxDibe, menschenfresser, Micate, Mobius_Stripped, Morrinn, Nemglan, Phoe, rward30, Samiam303, StupidFatHobbit, The_Mighty_Unknown, zargon, ZebTheTroll and ZombieRockStar.
    With the top 10 members in points gained since the last update being:
    1 frdougal
    2 Alizhdheg
    3 Micate
    4 Elektro
    5 Mobius_Stripped
    6 ZebTheTroll
    7 rward30
    8 gaelbert
    9 The_Mighty_Unknown
    10 StupidFatHobbit

    Moving up in team ranks (in the top 20):
    In the top 10: Lots of moves for this update! Mobius_Stripped has moved up to take the #3 spot! ZebTheTroll has moved up into 4th! gaelbert has moved up into 5th! zargon has moved up by 2 and into 8th! And Phoe has also moved up 2 and into the top 10 in 9th!
    In the top 20: Alarra moves up into 12th! Micate has jumped up by 5 into 13th! Elektro has moved up 2 into 15th! And new in the top 20 is StupidFatHobbit that has jumped up by 4 into 19th and e_chuck that has moved up 5 into 20th!

    Individual Milestones achieved (in points at 1K, 5K, 10K, etc.):
    20,000 points: frdougal
    10,000 points: Mobius_Stripped, ZebTheTroll, gaelbert and rward30
    5,000 points: Elektro and Micate
    1,000 points: ZombieRockStar, menschenfresser, The_Mighty_Unknown, Morrinn and MacXimus
    Congratulations to all those that have achieved a new milestone!

  13. - Top - End - #133
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    AssassinGuy

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    Default Re: Folding@Home

    The scope of the project becomes clearer when you've run things for a while, and only scratched the first layer of the outer shell's top coat, in one teensy tiny place.

    Still fun to watch the molecular display.

    Anyone know whether the odd yellowish-green atom (I only saw one, and only in a couple of the shots) is something that's being modeled as the odd/incorrect/defective piece? (This was project 2416_Ribosomething_Cl or ...Na I think, so I'm wondering if it was a chlorine or sodium atom stuck in there.)

  14. - Top - End - #134
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    Default Re: Folding@Home

    It's most likely a sulfur atom. Generally, these are the atoms and their corresponding colors in amino acids:

    black: carbon
    red: oxygen
    blue: nitrogen
    white: hydrogen
    yellow: sulfur

    Sulfur is found in methionine (R-group: -CH2-CH2-S-CH3) and cysteine (R-group: -CH2-SH) - that one is most likely the thiol group of cysteine as methionine is only found at the first position in the protein chain/polypeptide.

    See, I knew that BS in Biochemistry would come in handy someday!
    Last edited by Elektro; 2007-11-01 at 01:10 AM.
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  15. - Top - End - #135
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    Default Re: Folding@Home

    Quote Originally Posted by Elektro View Post
    It's most likely a sulfur atom. Generally, these are the atoms and their corresponding colors in amino acids:

    black: carbon
    red: oxygen
    blue: nitrogen
    white: hydrogen
    yellow: sulfur

    Sulfur is found in methionine (R-group: -CH2-CH2-S-CH3) and cysteine (R-group: -CH2-SH) - that one is most likely the thiol group of cysteine as methionine is only found at the first position in the protein chain/polypeptide.
    Thanks. I was confident of the black (well, dark gray) and white (well, light gray), and was pretty sure that blue and red were, in some order, oxygen and nitrogen (I never got a molecular model kit to play with, though)

    The thing is that I've only seen the one yellowish-green, and only for a while (perspective / frame-size could account for that), so I figured that something that's "normal" wouldn't be so "rare."

    Not that I'm gonna understand a thing about the program/projects, just by looking at pretty displays....

  16. - Top - End - #136
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    Default Re: Folding@Home

    Hmmmm, this project intrigues me. I shall check it out. Hopefully it runs on OS X. Seems alot more meaningful than electric sheep :P

    Edit: And I have installed and joined the GitP group, if it is ok. woot, go little dual core processor with 2 gb RAM.
    Last edited by Soups; 2007-11-01 at 05:33 PM.

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    Default Re: Folding@Home

    Oh, well, I joined too.
    Couldn't stand not folding much longer (geez, I'm studying this kind of crap so ...). With any luck my first frame (...hurray to me...*sigh*) will be ready in about 15' (@Soups: Yeah, DualCore with 2GB Ram sounds about right ;) )

    --
    edit:
    23' 7'' per Frame, at least on this project.
    Last edited by tirsales; 2007-11-01 at 06:45 PM.

  18. - Top - End - #138
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    Default Re: Folding@Home

    Maybe Im special in the head, but I entered the team number, but apparently, im not part of the team. Im running v6 on OS X.

  19. - Top - End - #139
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    Default Re: Folding@Home

    Quote Originally Posted by Soups View Post
    Maybe Im special in the head, but I entered the team number, but apparently, im not part of the team. Im running v6 on OS X.
    Have you completed a work unit yet? I don't think you'll show up until then.

  20. - Top - End - #140
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    Default Re: Folding@Home

    I was reading the FAQ and OS X doesnt get a visual or an idea on what is done unless you refresh the account page (user is : Soups), but i can't really read it. It all looks like gibberish to me.

  21. - Top - End - #141
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    Default Re: Folding@Home

    Quote Originally Posted by JT View Post
    The thing is that I've only seen the one yellowish-green, and only for a while (perspective / frame-size could account for that), so I figured that something that's "normal" wouldn't be so "rare."
    Well, you're only modeling portions of proteins. Probably 20-40 amino acids at a time. It's too hard to do anything else, especially as some multimeric proteins can have thousands of amino acids.

    Methionine is rare. It's unique to the first amino acid position in the chain. You'll only ever have one of those, regardless of how big the protein is. Cysteine is pretty rare too - it's usually found in the active site, which makes sense why you'd see it in the folded "pocket" of the peptide. Most of the amino acids found in a protein (ala, leu, gly) have R-group hydrocarbons, which explains all those grey and white atoms!

    Quote Originally Posted by tirsales View Post
    Oh, well, I joined too.
    Couldn't stand not folding much longer (geez, I'm studying this kind of crap so ...).
    Lernst du Biochimie? Glueck! (du wirst es brauchen )
    Last edited by Elektro; 2007-11-01 at 07:28 PM.
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  22. - Top - End - #142
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    Default Re: Folding@Home

    Quote Originally Posted by Soups View Post
    Maybe Im special in the head, but I entered the team number, but apparently, im not part of the team. Im running v6 on OS X.
    My first WU took 2 days plus a bit to complete. And as was said, I don't know that you should up as part of the team until you've completed a WU that's for that team.
    It also takes a while, after you submit the results, to get the credit to appear. The database is updated multiple times per day, but it is not updated for each and every completion.

    Go to http://folding.stanford.edu/English/Stats and click on the "Donor Stats" link. Then, type your username into the search box and click on the search button.
    You should show up, and your team-number is part of your record. At least, I think it is, even before you complete something.

    As an aside, if you decide to grab the console client (since you have a dual core) to run 2 copies of FAH, please read the info about running it in parallel (you need to configure it as "local" and put it in a different directory, or else it collides with the display client, or with an already existing console client. I screwed up some work that way (lost my work in progress... a miniscule drop in the ocean of total work).


    Another aside... woo hoo! I'm 33 on the team! Look out numbers 27-32... I've got a big WU (I think) that should be complete in 5 hours! Of course, they probably have stuff running too....

  23. - Top - End - #143
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    HalfOrcPirate

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    Default Re: Folding@Home

    Quote Originally Posted by Elektro View Post
    Well, you're only modeling portions of proteins. Probably 20-40 amino acids at a time. It's too hard to do anything else, especially as some multimeric proteins can have thousands of amino acids.
    How many atoms is 20-40 amino acids?
    I took a quick look and saw that many of the SMP projects have over 120,000 atoms and there were other folding projects with over 300,000 atoms. There are also quite a few smaller folding projects (such as those run by the PS3s) with under 1000 atoms. # of atoms & description found at http://fah-web.stanford.edu/psummary.html
    Can look at projects in 3D at http://jmol.sourceforge.net/fah/

  24. - Top - End - #144
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    Default Re: Folding@Home

    I took a quick look and saw that many of the SMP projects have over 120,000 atoms and there were other folding projects with over 300,000 atoms. There are also quite a few smaller folding projects (such as those run by the PS3s) with under 1000 atoms. # of atoms & description found at http://fah-web.stanford.edu/psummary.html
    Wow, you're right. My previous statement was based on what my graphical output looked like. The graphical console must just show a portion of the whole peptide, since my project has 9700 atoms which is about 650 amino acids (average number of atoms per amino acid is about 15). There definitely weren't that many on the screen. Those ones with >10000 or so atoms are multimeric proteins or large protein complexes. Just goes to show I don't know anything about the computer science part of all this.

    Anyone know whether the odd yellowish-green atom (I only saw one, and only in a couple of the shots) is something that's being modeled as the odd/incorrect/defective piece? (This was project 2416_Ribosomething_Cl or ...Na I think, so I'm wondering if it was a chlorine or sodium atom stuck in there.)
    JT, I read your project description and you are right about that being a Na/Cl atom. They're modeling small molecule binding to specific sites on the ribosome and determining loss of function. That yellow atom can't be sulfur, as the ribosome is rRNA, which only contains nitrogen, oxygen, carbon, and hydrogen. It seems strange to model the ribosomal interaction with an ion that is ubiquitous in the cell, but I'm sure they have a good reason.
    "Il nous faut de l'audace, et encore de l'audace, et toujours de l'audace" Georges Jacques Dalton

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  25. - Top - End - #145
    Pixie in the Playground
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    Default Re: Folding@Home

    I was looking over the current team stats and see a new person: steviefool. Out of curiosity, if you don't mind, what kind of setup are you running. 11 WUs in less than a week, and counting! All I have to say is this....WOW, and *drool* over the monster you must have running the client. Like I said, if you don't mind answering, what are the specs of the system you are running on?

  26. - Top - End - #146
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    HalfOrcPirate

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    Default Re: Folding@Home

    Looking at the stats of steviefool at http://fah-web.stanford.edu/cgi-bin/...ame=steviefool, I can see that it appears to be a PS3 as that are the projects being completed. Yes, PS3s do folding very very well on some types of projects!
    e.g. one of the project is 4000 - from the description:
    "A villin headpiece subdomain walks into a bar. "I'd like a 6 M solution of guanidinium hydrochloride, please," it tells the bartender. "My ..."
    http://fah-web.stanford.edu/cgi-bin/fahproject?p=4000

  27. - Top - End - #147
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    Default Re: Folding@Home

    I just wish I didn't have to turn mine off in order to play games. I think it's my vid card, but whenever I try to play a game in full screen mode with this running I get dropped to desktop, even though I don't actually have the FAH display up.
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  28. - Top - End - #148
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    Default Re: Folding@Home

    Quote Originally Posted by Zeb The Troll View Post
    I just wish I didn't have to turn mine off in order to play games. I think it's my vid card, but whenever I try to play a game in full screen mode with this running I get dropped to desktop, even though I don't actually have the FAH display up.
    Have you tried running just the console client? I know when I was running the graphic client I had some issues, but switching over to the console took care of those. Just a suggestion.

  29. - Top - End - #149
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    Default Re: Folding@Home

    Quote Originally Posted by rward30 View Post
    Have you tried running just the console client? I know when I was running the graphic client I had some issues, but switching over to the console took care of those. Just a suggestion.
    *blink* *blink blink* Who did what to whom in which barn?

    I'll have to go back and look but I only remember seeing a Windows client and a Windows beta client. I'll give that a try.
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  30. - Top - End - #150
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    Default Re: Folding@Home

    Quote Originally Posted by Zeb The Troll View Post
    *blink* *blink blink* Who did what to whom in which barn?

    I'll have to go back and look but I only remember seeing a Windows client and a Windows beta client. I'll give that a try.
    If you check way back to post #43 of this thread, Zargon gave some wonderful instructions on how to get the console client going.

    If I knew how to link to the specific post, I'd do that, but I don't, so I won't.

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