Posts by Doug Worrall

1) Message boards : Number crunching : Problems with Rosetta version 5.67 (Message 41521)
Posted 27 May 2007 by Profile Doug Worrall
Post:
I have a work unit that seems to be \"almost\" stuck at 97% complete. The % complete has been slowly increasing (by about .4%) over the last two hours. I have work units set to complete in 4 hours, and we are going over 6 with this one. It is wuid=74278854

Yup,
I also have my w/u size set at 2 hours crunch time.The LARGE 1 decoy w/u stop around 10 minute 1 sec.These w/u are great for Rosie, and receive more credit.Have a w/u moving very slowly and at 97.2% done, yes, it will end suddenly.I have graphics disabled for better performance.GL and Happy Crunching.
Here is one here:
http://boinc.bakerlab.org/rosetta/result.php?resultid=82460229
Doug
2) Message boards : Number crunching : Poor Credits for w/u twice the size???? (Message 41427)
Posted 25 May 2007 by Profile Doug Worrall
Post:
Doug, I\'m not sure how much reading you\'ve been doing or how long you\'ve been around these boards, but in a word, the reason why is that other people\'s machines found these tasks were not as great a hurdle as yours did. The raw computational work for each type of task is slightly different. Always highly concenrated on floating point operations, but slightly different.

Your credit issued is based on the credit claims of all those returning results for the same study before you. For the \"short\" ones, your machine found they crunched more easily then your BOINC benchmarks predicted and you were granted more credit then you claimed. For the \"long\" ones, other people\'s machine found them to crunch more easily then their BOINC benchmarks predicted, and they were granted more then they claimed.

There is also variability with a given protein or RNA being studied from model to model, and noone knows ahead of time what a given random starting point will yield. You\'ve only got two of the shorter tasks left in your history. So it is entirely possible that these were unusually high credit for you.

...yes, looking at the rest of your history, you see that the granted credit of about 32 for 13-14,000 seconds of work is abnormally high compared to the rest of your history. ...on the other hand you have one that was granted almost 42 credits for 13,567 seconds of work as well. Another was granted 26 credits for almost exactly same number of seconds.

All of your \"long\" tasks were new RNA studies. And Rhiju has improved some of the energy functions being used in the new release which just came out today. And these types of improvements will help make the crunch times per model more consistent and remove much of the variability. These RNA studies are still very new science, so I\'m sure there is still much to learn about hunting down the best models efficiently.

Thx again MOD Sense,
I am under the suspiscian that at night the w/u are slowing down or something.Yes, I donnot do much reading at the Forums here due to time constraints.Surfing the internet is a Luxury for this 1 BOX, when trying to run Boinc 24-7 and just Rosey.One of the Most important experiments due too the great work being done, I am just guessing when it comes too decoys, but, I believe the 1 decoy w/u are good for Rosey.That is all I wanted too convey, albeit, conveying and Communicating before a morning coffee is not a good idea.
Am happy to receive a used pc that I will fix up and use for surfing,Then this Box can crunch 24-7, without interuption.I know very little about pc,s this used one is a Compact Presario 7469 with Windows 98 installed.Will add RAM and change it over to a Linux based Distro, probably Feisty Dawn from Ubuntu.This Box has PClinuxOS, very fast, clean , and FREE!

\"Happy Crunching ev1\"
Sincerely
Doug
Here is a real different w/u that found http://boinc.bakerlab.org/rosetta/result.php?resultid=81346627WOW
161 decoys with 161 attemts.Find it quite interesting the differences in w/u,s and
deoys found.
3) Message boards : Number crunching : Poor Credits for w/u twice the size???? (Message 41418)
Posted 25 May 2007 by Profile Doug Worrall
Post:
82148954 74000781 25 May 2007 3:55:16 UTC 4 Jun 2007 3:55:16 UTC In Progress Unknown New --- --- ---
82101448 73902364 24 May 2007 21:37:07 UTC 25 May 2007 8:32:58 UTC Over Success Done 21,983.36 40.16 25.24
82074316 73931201 24 May 2007 18:27:54 UTC 25 May 2007 3:55:16 UTC Over Success Done 22,391.50 40.91 25.52
81942999 73809341 24 May 2007 3:30:18 UTC 24 May 2007 18:27:54 UTC Over Success Done 20,748.55 37.91 25.75
81893125 71623280 23 May 2007 21:21:14 UTC 24 May 2007 15:21:13 UTC Over Success Done 20,795.00 37.99 25.67
81834544 73709038 23 May 2007 15:18:45 UTC 24 May 2007 3:30:18 UTC Over Success Done 20,081.49 36.89 24.65
81800874 73678184 23 May 2007 11:39:35 UTC 23 May 2007 21:21:14 UTC Over Success Done 14,023.86 25.76 34.05
81754602 73635627 23 May 2007 6:33:31 UTC 23 May 2007 15:18:45 UTC Over Success Done 13,413.26 24.64 30.03
Hello,
I was told that these BIG w/u would be receiving \"More\" credit due too there length.Yet again last night had another Huge w/u and only turned in 3 yesterday compared to 6 a day.Why are these w/u so large.http://boinc.bakerlab.org/rosetta/result.php?resultid=82101448
This is one of the 1 decoy w/u that take so long, and receive , less credit.I was told these 1 decoy w/u are good for Rosetta, and more credit will be received.
\"Not so\" I am receiveing Lesss credit for a w/u that takes twice the time? Why?

THX

Doug
4) Message boards : Number crunching : Problems with Rosetta version 5.64 (Message 41266)
Posted 21 May 2007 by Profile Doug Worrall
Post:
Yay! For once, my Rosetta workunit checkpointed and resumed OK--it didn\'t lose any CPU time this time around!

Workunit: here

Hopefully this is the way they will all be now. :-| Probably not though.


WTG,
The Link says, \"in Progress\" w/u, but, am sure you copied wrong path.

Am sure all w/u will be successful.GL


\"Happy Crunching\"
5) Message boards : Number crunching : Problems with Rosetta version 5.64 (Message 41234)
Posted 21 May 2007 by Profile Doug Worrall
Post:
I\'m thinking, if we could get some better checkpointing around here, it would be nice. Yes, I know that the WU can only checkpoint at certain points in the model, but for people who don\'t crunch 24/7 (not to mention having other projects that have to share the part of the day that the computer is on), this can be a bit of a problem, at least for the big \"Abinition-relax\" and \"Symmetric Fold And Dock\" workunits that seem to be so common lately. When the model takes up to 3 hours to complete, and the model can\'t be checkpointed very often throughout, you get a problem. Isn\'t there a better way to checkpoint, that allows you to do so at any time?

I was thinking of a way it might be done (although it probably won\'t be feasible, I\'ll say it anyway, in case it helps): You know how if you have your preferences set to leave apps in memory while preempted, if the workunit just pauses, it can sit there, with the entire workunit loaded into memory? I\'m thinking, the Rosetta application can simply save everything it has loaded into memory, to disk, and then when it needs to restore from the checkpoint, it will simply load that back into memory, and restore as if it was restoring from a preempted task left in memory. Would this work at all? If so, then if it could be at all possible to make the application save its contents to disk as described every 5 or 10 minutes, that would be enough to make sure that hours of work are not wasted when a computer needs to be shut down!

Hope this helps--although it probably won\'t (as I am neither a protein expert or a programmer), but maybe it will. :-)


Myself,
Am very happy checkpointing has \"just\" been implimented.Having a Linux Box, I dont shut down for weeks and Months at a time.Therefore no problems.It is so easy to download a Linux Distro/Dual Boot , if you want to save your Widows O.S.
Myself was happy to lose defraging, Viruses,Constant probing of ports, Spy and Mal ware.If you must shut down, click no more work, finish what you have in your que, then reboot if you must.
Doug
6) Message boards : Number crunching : Problems with Rosetta version 5.64 (Message 41127)
Posted 18 May 2007 by Profile Doug Worrall
Post:
LohnesinPR, I am seeing some tasks taking 5+ hours per model on a 3Ghz Pemtium 4. Your machine has less memory, so perhaps doesn\'t get sent this type of task. The difference basically is that the models of many of the current tasks are much larger then they used to be. So the time per model is going up.

The 90% thing is the new estimated runtime. Once you exceed your runtime preference (as configured in your Rosetta preferences) they don\'t really know what % complete to estimate. So they set it to a point that shows you\'ve got about 10 minutes left and reduce exponentially from there.

The results of your crunching are collected at the end of a model. If you look at the graphic, I\'ll bet you will see you are still working on model 1 and that the steps are increasing. So, things are progressing (even if the % completed may not have a good way to indicate that).

If the above is indeed the case, please do this once. Let the task run for even longer. Let\'s say up to 48 hours (on your .5 Ghz CPU). The system is already watching the task for you with it\'s \"watchdog\". If the watchdog sees no progress being made, it will end the task for you. But I think you will find that you finally complete that first model and the task reports back normally.

I for one enjoy seeing these huge and complex RNA structures being studied. It shows that Rosetta has come a long way from just a year ago when tasks with just 30-50 amino acids were still \"interesting\". I hope that once you see that your crunching is indeed working properly you will agree. You will also get much more credit for these long running tasks as well since they take so much longer to complete.

Thank You Mod.Sense Below is w/u large:
http://boinc.bakerlab.org/rosetta/result.php?resultid=80490081
I have had 4 in a row that stop at 10 minutes, and they finish quite quickly after that.These paticular w/u find only 1 decoy, which gives this Project a really good sequence, From what I understand.Am very pleased there are checkpoints now. Was concerned lately and am happy to see this Post.
\"Happy Crunching\"
sluger
7) Message boards : Rosetta@home Science : 10 reasons I crunch R@H and you should too (Message 41033)
Posted 15 May 2007 by Profile Doug Worrall
Post:
I must emulate the sentiments of my fellow crunching colleagues that have stated the 10 reasons before me.

Would like to add some for myself, I crunch for Rosetta because I believe in this project wholeheartedly. Of the many plethora of distributed computing projects available this I believe is the most important. Therefore I have decided to throw my computing might, limited as it may be :), to this project. May God bless your efforts and the cures be found speedily for the terrible afflictions that plague the world today. Long and prosperous life to you all. May it be blessed.

Antony


Wow Antony,
You hit the nail on the head, struck a cord with me \"as you were\".
This experiment, if it can save but, 1 life. It is worth our Collabrative effort.
Sincerely

Doug
8) Message boards : Number crunching : Problems with Rosetta version 5.64 (Message 41001)
Posted 15 May 2007 by Profile Doug Worrall
Post:
Thanks RHIJU,

Just finished another Biggy here:http://boinc.bakerlab.org/rosetta/result.php?resultid=79676296

And it makes me very happy too know that these 1 decoy w/u are actually good for Rosey. Am learning that the checkpoints are working well, quit a session, actually rebooted this actual w/u. and it did not fail.Rosey has come a long way, should take a look at Ralph again soon, after Rosey is no longer the Project of the Month at B.S.
\"Happy Crunching\"
Great work Scientists, and Moderators, and all staff at Rosetta@home
Sincerely
Doug
9) Message boards : Number crunching : \"Large W/U, only 1 \"Decoy\"\"5.64 \"OUCH\" (Message 40959)
Posted 14 May 2007 by Profile Doug Worrall
Post:
Hello,
Have just returned this sucessful, LONG w/u http://boinc.bakerlab.org/rosetta/result.php?resultid=79610297
And have nearly finished another of the same w/u.Running a Linux O.S.Usual w/u find 18 Decoys, with a 10 Decoy found average.These w/u are 1/3 longer too crunch.Usual \"real time\" is 2 1/2 Hour.These W/U.s come in at 4/1/2 clocked Hours.
Have not seen these before, and am wondering, with what I would Guess, are not favorouble for Rosetta, due to the 1 decoy found.And not favorouble to me, due too extra crunching time, and same credit?

Thanks
Happy Crunching For Rosey
Doug
10) Message boards : Number crunching : Problems with Rosetta version 5.64 (Message 40940)
Posted 14 May 2007 by Profile Doug Worrall
Post:
http://boinc.bakerlab.org/rosetta/result.php?resultid=79610297

Hello,
I have not posted in Long time due too Job duties and health.Had this rather \"LARGE\" w/u {url at top of post},that crunched for 4 hours, while finding 1 decoy, from 1 attempt.To me this must be an error,even though it was successful.Maybe I just want too post, and DSy hello to the Staff and say \"Great Job\". all Rosetta w/u have been the mostly, the same size.Some fetching 18 decoys, and average of 10.
Noticed Rosetta had no w/u cued on Friday I beleive. Had 2 crunch \"Another\"
experiment, untill there were more w/u in the Cue.Have not been to the Boards in a Long time.No complaints, hope I have the right thread also.Am running a Linux Distro.

Doug
11) Message boards : Number crunching : What happened with the credits here? (Message 22421)
Posted 13 Aug 2006 by Profile Doug Worrall
Post:

Have a good time away Stan.

Diug. Best wishes
12) Message boards : Number crunching : What happened with the credits here? (Message 22409)
Posted 13 Aug 2006 by Profile Doug Worrall
Post:


Hello,
Thanks Stan,
No, I donnot need a firewall with Linux,too may partitions and stuff.Thiery,hope
you donnot mind the P.M. at home.The difference between linux and windows is
closing,Looking at other results of Linux and Widows Machines , the difference is ninimal.,but not with some of the experiments.I use the einstein app for Linux,and
belive in them, especially us with just one P.C.And farms.
But manipulating credits and benchs is wrong.The Seti app was great also ,but
all the stuff goes on,and, Politics, this is something we do for the better of our Society.\"Boincing\" is a great resource in this world where Money rules, and Heals!
{medically}2 teered Medical,Dohh!Why cannot I reboot a Rosetta Unit?That is why I run Ralph!
All the best to all, and may good come from everything.
Sincerely
Doug*
13) Message boards : Number crunching : What happened with the credits here? (Message 22400)
Posted 13 Aug 2006 by Profile Doug Worrall
Post:
Hey Doug....Appreciate your comments...by the way.. noticed that you are using BOINC 5.4.9, there is an issue with McAfee Virus on that platform

I also noticed on the preceeding thread that they are using a core client called 5.5.0 and getting similiar credits to E @ home...

I will have to ask where that core client is for download as I had not heard of it.....

user stats

Thanks Stan,
I was under the beleif that mcafee Virus ws a Windows problem.That may explain the strange behavior.But never heard of it.Thank-You for informing me.Yup, after reboot,w/u was fubarred.Downloaded another, have quit session, and will reboot again after this note.This time I \"Suspended\" Rosetta in the hopes that may help the problem.Please inform me further of this McaFee Virus?
Sincerely
Doug*
14) Message boards : Number crunching : What happened with the credits here? (Message 22395)
Posted 13 Aug 2006 by Profile Doug Worrall
Post:
Hello Stan,
You are right, this is an exeptinally great experiment with the greatest scientists,crunchers,staff,forum reps,etcc.I know that credits are not an issue with most people.Lots of farms out there, and when you want to \"Compete\" and
not to be able to use your 1 P.C.to send Emails , surf, download songs etc......
So, running Rosetta, which compared to most other experiments ,especially
Einstein.I receive 20 credits for 5000 seconds of work on average.As much as I know this experiment is beneficial too many people, not all that good for 1 P.C. clients crunching 23 hours, and surfing etc, for 1 hour a day.1/2 the credits
of other experiments!I also hope a Linux user can reboot a rosetta w/u without
fubared sesults.Cause I just did,\"even with app saved in memory on your general preferences tab!
Sincerely
Doug*

15) Message boards : Rosetta@home Science : \"large w/u I cannot find on list\" (Message 22386)
Posted 13 Aug 2006 by Profile Doug Worrall
Post:

Hello Rosey crunchers and staff and scientist,
Have been not able to crunch Rosey for a while and am trying again, after Ralph worked well,than ran out of w/u,s.The w/u is 5.25 for Linux
FRA_1368_CASPR_homOO1_6_1368_4_InaOA16NORE
Have finsihed 58.24 minutes with 1.563% with 19:16:24
remaining.If I need to reboot the w/u would start at beginning again and Fubar.Has this been rectified?,or,
if I must reboot \"suspend\" the app first?
Thanking-You in advace
Sincerely
Doug*
16) Message boards : Number crunching : What happened with the credits here? (Message 22385)
Posted 13 Aug 2006 by Profile Doug Worrall
Post:

Wow,
That must be some kind of super computer to have a floating speed ,I cannot understand why someone would cheat.This must be an error.Myself, just reopened my account after Ralph ran out of work.Have a question regarding this HUGE w/u I got for my first-one, will go to the correct thread.Please people, there Boinc
is no place to cheat, that is why this makes no sense.Good-luck Team rechenkraft.net with this issue.This has to be an error, but that is definetly the
most rediculous floating.

Is there cheating regarding this user?

Sincerely
Doug*
17) Message boards : Cafe Rosetta : I\'m a novice^^ (Message 13460)
Posted 11 Apr 2006 by Profile Doug Worrall
Post:
How do I get you to send me that dog? :-)


LOL,
Woof,Woof,Go Rosetta and B.S.Robert.

Sincerely

Sluger*
18) Message boards : Number crunching : Help us solve the 1% bug! (Message 12454)
Posted 21 Mar 2006 by Profile Doug Worrall
Post:
Hello,
I feel embarassed posting the only 1% stuck bug.It,s 4.81_i6 \"FA_RLXpt_h.....\"
yada.It had a problem Downloading also.3 attemepts got \"Timed out\" {error}
Its red anyways.LOL.Not to concerned about 1 w/u but,will subscribe to this
thread and I am able to help-out I will.Just donnot have enough time to read
all these Posts on this Problem.Also lots are running mutliple Boxes and they
are needing the Help with this Bug.
\"Happy Crunching All\"

Sincerely
Doug Sluger Worrall
19) Message boards : Number crunching : \"Concerned my P.C. isnot well\" (Message 11979)
Posted 13 Mar 2006 by Profile Doug Worrall
Post:
20) Message boards : Number crunching : \"Concerned my P.C. isnot well\" (Message 11965)
Posted 13 Mar 2006 by Profile Doug Worrall
Post:
As it stands I only can crunch for 2 experiments now.Somehow I meesed-up the O.V. and Boinc crashe several times.Now to start Boinc,I must go to home.
\"Conquerer\" and hold down CNTL click the run Client go to tools and execute
the shell.Then I have to repeat the same to get the Boinc Manager operational.


As well as I can follow what you\'re having to do to start it, I have to say I\'m not sure what would cause that. How were you starting it before? We\'re you clicking on run_client or were you opening a shell first and typing it in? What does it do when you try to start it the way you used to - does it give you any messages or does it just not start?


All my Malaria w/u failed,but, Einstein and Rosetta still work and am getting better Credits than ever.I may have to do a Complete install of this O.S. Unless you can Delete all Boinc files and reaaply them????


Your benchmarks look better now, so whatever you did there helped a lot. Your floating point went from 378 to 585, and your integer went from 1001 to 1637. That looks much more inline with what other systems like yours seem to report. And that will be why your credits have went up. They seem to have gone from less than 6 credits for 2 hours to just over 9 credits - that looks like a decent improvement for your cpu.

As for the malaria work units failing, that\'s one of the few projects I\'ve never joined so I can\'t offer any suggestions on that one short of letting it download a new malaria executable. The best way to do that is to do a project reset on malaria - don\'t detach, just do the reset. Or if you prefer you can delete the files in the project folder for malaria in your boinc directory - then it will have to download new ones. If you do the project reset, it will keep your client_state file clean as you go whereas deleting the files will trigger an error in boinc which it will then correct by downloading new ones.




Hello,Darren,
Just did a complete install of O.S.My Bench marks and stuff will be different.
Usually would go into quick browser at boot.Click on Boinc then go back in and click on Manager.Yesterday after crashes when I clicked on the manager
it would freeze.{Not Now.}After I crunch all night I will see how things are,
and if my credits are low I will Try that Optimised client Again.
Thanks for being a \"Helper\" Darren,I see you donnot belong to a Team.Maybe
that is the way I should go.
Sincerely
Doug* Will be more informative tommorow after agood nights sleep.Was up all
night trying to fix,but,all looks better anyways.Still have to apply lots through
Symnaptic.Especially the new Opera anf Firefox and Hotplug support.
Sleep well,will chat tommorow Darren
Doug*


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