What the...?

LeonardoLeonardo Wake up and smell the glaciersEagle River, Alaska Icrontian
edited August 2003 in Folding@Home
heck am I folding? On one of my CPUs I am processing protein "#05". It is taking 60.06 minutes a frame. This is really intense. :eek2: For reference, a 639 usually takes the same CPU about 5.5 minutes. This protein has 200 frames. At his rate, it will take over a week to process! Is something wrong? Should I dump it and download another protein? :scratch:


    edited August 2003
    I don't know, Leo. I have one on one of my machines that's taking almost an hour for each step. That tower hasn't turned in wu yet this week, and is a little more than half way thorugh the steps (500).

    The protein is 373_gnra_pf2_noi

    I'm just letting this one run it's course.
  • ThraxThrax 🐌 Austin, TX Icrontian
    edited August 2003
    Better be worth like...300 points. :shakehead
  • a2jfreaka2jfreak Houston, TX Member
    edited August 2003
    Watch it be worth like 7.
    Thrax said
    Better be worth like...300 points. :shakehead
  • SlickSlick Upstate New York
    edited August 2003
    That kind of stuff happend to me before. Really though, whats the point in folding if you are going to dump units, I mean, its the data you process that counts, the points are just for extra fun.
  • mmonninmmonnin Centreville, VA
    edited August 2003
    Its worth 53.3 points.


    I have done some of those 53.3 pointers and they have never taken that long. I havent done that particular one tho.
  • TBonZTBonZ Ottawa, ON Icrontian
    edited August 2003
    Leo, have you tried rebooting your machine? That frame time is much to large, I think you'll see a difference with a reboot.
  • LeonardoLeonardo Wake up and smell the glaciers Eagle River, Alaska Icrontian
    edited August 2003
    whats the point in folding if you are going to dump units

    That's not my point (pardon the pun). Don't infer from post something that's not there. I thought perhaps something was wrong with the protein coding.

    I'll reboot and see what happens.
  • LeonardoLeonardo Wake up and smell the glaciers Eagle River, Alaska Icrontian
    edited August 2003
    As it turned out, #05 was finished and sent while I was sleeping. Now I'm working #06 and #02 at 9.66 and 9.67min respectively. Both are 50 frame units.
  • Straight_ManStraight_Man Geeky, in my own way Naples, FL Icrontian
    edited August 2003
    What folding is doing is more and more complex followups. The most complex environments with protiens that yeild knowledge from more simplistic runs (faster) are being put in fluid scenearios (sets of fluid specs, not circs that radically change but more complex surroundings). The big complex things are being fed to boxes that are capable of doing slightly less complex code sets hyperfast compared to the benched times on a slower CPU.

    P4s and XP+ CPU boxes fold differently, and the vay they calc vectors (thus where a molecule will settle giving its chemcical and ionic properties) and fluids make this more and more interesting as they can dampen movemement and make molecules gathr different. We are calcing physics (atomic molecular buy atom affinity and likelyhood of building certain things with certain atomics and then molecule formation), especially those with high probability of yeilding something that will be useful. We can let our boxes distributively compute and experiment and this will yeild mountains of data and they then drill into the details that vary by nature of physics to see how molecule builds chenge with circumstance imposed as a scenario.

    The reason WUs are starting to take longer on bigger boxes is they are using smaller capacity boxes to do earlier and smaller general probes. The more big boxes(resource wise) we use the more the team can drill faster into more complex details and the more likely the assignment server is being skewed to give more comlex projects to big-resource and fast computing boxes more complex projects. THIS is the tip of the iceberg, as they need more and more complex scenarios as WU series to drill into details that right now could vary things finer and give more immediately useful knowledge as well as guidance toward what tosses a bad folding fold to not happen-- if a non-human-destructive scenario that prevents a fold that is in cancer by study results that it usually happens results in no fold, then probably that can be worked into a treatment.

    OUR folding network of end nodes can then be used to work on more complex issues about which not much is known and many fast boxes will be needed to isolate variables that could lead to treatment reactions and failure. They need to isolate what could go majorly wrong because of informed consent and also pressure to find working cures by society.

    Collectively, we can take and reduce things to about 1\100th of the human time needed to do it in a lab. In essence, we are a virtual cluster of many thousands of boxes. If you get a hyper big WU that takes long times as a shared instance and want that work result to them even faster, you can shut down the faster running instance and the more complex one will proceed faster as it is tuned for a full P4 or XP+ and is more complex as they drill down. This is why my P4 runs a single instance and takes anything these days-- I want tinker followthroughs in fluid that are too complex for slower machines because my total focus in giving this online box a calc skewed environment for one WU but as complex a one as they choose to devise is totally not points (which are reputation thing) it is pure knowledge gaining as there are cancers killing folks every day.

    Thus, I do not fold in a points oriented team and although I do not want individual competition I also want knowledge results to them. It would take longer away from their work to retune points for fast boxes and re-calc the capabilitise of advanced boxes than leaving things and just working more and more on results, reaching goal by running with the big boxes and worrying less about fine tuning of points which have to be done with scientists familiar with the results(same scientists cannot work two ways and the new building lets them use this project to educate new scientists also which is imho the most valuable snowball effect if those scientists can intergrate results into further exploration possible that is more likely to get very accruate and precision applicable results).

    Look at the bench times for WUs you commonly get, with a standard early WU, take complexity of calcsbeing increased also as more fine details are needed to zero in among probably useful info and expect more complex WUs as more complex ideas are being calced. I would expect, if enough WUs can be calced at once from big boxes, that the results of savings will prove to be results in 1\100th the time as these big boxes can experiment instead of just aggregatively validate preliminary theories that started much earlier as niggles of ideas in high-caliber scinetific minds. More complex units and bigger buildings imply success, BTW, and they are using big boxes to make it less likely that someone will die partly because an existing unknown prevented treatment and no one has the time to waste analyzing what is no longer there in dead tissue after a body ceases to flow its 90 percent fluidic structure around in ever changing fine environmental details.

    My father lost his voice to an unknown, there was one chemical known to kill a very cancerous tumor very close to his spinal column up near brain stem and the doctors could only try a catheter run up through half his body in major vessels to the locality of the because that tumor had to be surrounded by chemical to die and it was too close and too wrapped around things to operate on.

    The unknown was buildup of material on amajor vessel that was just big enough to casue a stroke, that stroke affected muscular control of larynx and also was big enough that he lost partial use of his writing hand and one leg. Father had made his living defending smaller railroads against bigger ones, in three state and one federal court structure. to live he felt he needed a voice. The thing to possibly save had destroyed his best asset other than his mind. Within two months he was dead, inoperable and uncurable, and spent those two months at home.

    I fold to keep that thing from happening to soemone else, I fold for LOVE and not points, and as memorial for a great Christian man. Enough said, and after three plus years I still remember those days and now one minor lack of knowledge casued a problem that caused my father to lose will and to pass on to what I fervently hope is heaven because for the three years prior to that he gave about 20 hours a week to por bono work for charitable organization work and saved charity organizations many thousands even in this county alone adn before that he worshipped God and taught God's word to us kids in ACTIONs and showing us how to logically think as well as helping churches get legally set as non-profits wqhere teh IRS questioned profits fromthings like rummage sales and wanted the rummage sales established as businesses run by churches ($25,000 a year profit from two rummage sales every year for five years runnning tends to make them want to examine how much the rummage sales are like businesses).

    He told the church to show how much it could trace funds to ministries and to charity giving, and helped do so, filed one brief, and the IRS closed the case. That church fed about $1,000,000 a year into charity local and worldwide, and partly replaced a heating plant from a 75 year old boiler to a new very effective one with soem of those "profits". Had he not given them and guided them with both mind and analysis and application of legal knownledge they guess they woudl have spent $9,000 in legal and accounting costs alone for that one brief. He got the problem solved in two weeks. he had done 100 plus like things when he took on more complex cases involving not-for-profit challanges against established charities for 4-5 years.

    This is not boasting, it is a way of showing that one little unkown can hit a man where he is weakest withough warning and that precise knowledge of details makes all the diference between a cur that kills half of those it is supposed to cure versus one that does less harm while curing and cures more proportionately.

    Call this the other side of folding from points. I do not accuse nor put you down, you help a lot, but this is why I am adversely reactive to points organized competitive teams in reasearch-- unless the points are given for contributions which are probably going to be semi-random as to cure finding result by box.
  • edited August 2003
    Leo did EMIII just mess up?
    edited August 2003
    I think Leo was just wondering the same thing I was..
    is the protein running right, or is it hung up somehow.
    I'm not so worried about points, although some competion makes for good fun. For me, the competition aspect is more to spur on other Folders because then the whole team, as well as F@H wins.

    I'm sure Leo has his reasons for why he folds, as do I. I just haven't posted to the "why" thread yet.

    I also understand Ageeks pov.

    But really, it all goes to the good of mankind.

    We Fold for the Cure.. so it's all good.

  • mmonninmmonnin Centreville, VA
    edited August 2003
    Ageek: I have essays shorter than that. I copied it to word and its 1466 words long. Concise it a lil please.
  • EnverexEnverex Worcester, UK Icrontian
    edited August 2003
    mmonnin said
    Ageek: I have essays shorter than that. I copied it to word and its 1466 words long. Concise it a lil please.

    With 46 spelling mistakes (rounding to 1 per word) :banghead:

  • LeonardoLeonardo Wake up and smell the glaciers Eagle River, Alaska Icrontian
    edited August 2003
    Hey guys, lay off Ageek. We all communicate in a different fashion - it's that simple.

    Now to the mulitple points (again, pardon the pun) put forth:

    1) "The reason WUs are starting to take longer on bigger boxes is they are using smaller capacity boxes to do earlier and smaller general probes."

    Well then, it's an honor to be selected for a toughie.

    2) "I think Leo was just wondering the same thing I was..
    is the protein running right, or is it hung up somehow."

    Precisely - thank you.

    3) Motivation for Folding.

    My motivation springs from three things, in the given order: philanthropy, competition and sport, and interest in science.

    Whatever one's motivation for participation in this project, it is a noble endeavor as long as the work units are being processed and returned to Stanford. Love is a wonderful thing; if it is your sole motivation for contribution, I salute you, Sir. The fact of the matter is that human nature (heredity) is, in my opinion, about 80% of our makeup. I've no doubt that if it weren't for the competitive element in the Folding@Home project, contributions would drop at least 50%. If the personal and group competition brings about enthusiasm and generates action, then tapping into human nature for good is a wonderful thing.

    Metaphor: Newegg sells me great products for great prices, with excellent customer support. They have no emotional attachment to me. They compete with thousands of other vendors and have prevailed, because they understand human nature and are truly competitive.

    Ageek - thank you very much for your rich explanation and personal background. (Wordy - yes; but I am guilty of the same charge sometimes.)

    The rest of you - I love you all too! :wave:
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