Posts by Nothing But Idle Time

1) Message boards : Number crunching : Problems with Minirosetta Version 1.67 (Message 61317)
Posted 21 May 2009 by Nothing But Idle Time
Post:
I've experienced 10 compute errors out of the last 22 tasks -- not a good track record. I think this is the most errors I've ever had with a particular version of Rosetta or perhaps it is the tasks themselves.
2) Message boards : Number crunching : Problems with Minirosetta Version 1.67 (Message 61295)
Posted 21 May 2009 by Nothing But Idle Time
Post:
pp_lr6_A_score12_rlbd_1g4i_IGNORE_THE_REST_DECOY_12373_1941_0
Reason: Access Violation (0xc0000005) at address 0x0064D617 read attempt to address 0x00000000

ev_frb_0_8_mike_chosen_cst_hb.t369_.IGNORE_THE_REST.c.25.0.pdb.c.25.0.loop_12435_20_0
Reason: Access Violation (0xc0000005) at address 0x0058AD29 read attempt to address 0x00000008
3) Message boards : Number crunching : Report long-running models here (Message 60895)
Posted 29 Apr 2009 by Nothing But Idle Time
Post:
Maybe if I watched the screen saver and observed how models are generated I might better comprehend the methodology. I just never wanted to waste cpu cycles on it nor visually sate myself with wiggling molecules like some people apparently do. Graphics add nothing to the scientific value.
4) Message boards : Number crunching : Report long-running models here (Message 60886)
Posted 29 Apr 2009 by Nothing But Idle Time
Post:
Adrianxw: My question was more, "Is there scientific benefit from having longer run times?". If the team get more out of 2 x 12 hour units then 4 x 6 then I'd like to know. I don't know enough about their models to answer this myself.
Mod.Sense: The benefit to the science is more based on how many hours of crunching per day you do. Not how many hours per task. But less hits to the servers per day from your machine leaves them free to service more participants with the same server hardware.


I'm curious about the topic that adrianxw raises. Bear with me 'cause I'm no linguist nor writer.

Tasks begin with a seed, some starting point from which models are developed, no? Is this akin to a tree with roots and branches that grow from the seed? The longer the tree lives (task run time) the more roots and branches, no? So based on this it "seems" that a long run time is better, more output based on the one input seed.

No two trees look alike. A different seed leads to different roots and branches and different outcome I guess? So if you run a unique seed for 24 hours you get one set of roots, branches, models. For 12 hours work presumably you get say half as many roots and branches. So if you run a task for 12 hours instead of 24 then how do you uncover/discover those roots and branches that would have been revealed if the task was allowed to run 24 hours?

Also, after a 12-hour run you are assigned a new task of whatever kind with another unique starting seed. So, a participant running 4, 6-hour tasks would likely get 4 different kinds of "proteins to model" with 4 different seeds. While a single task of 24 hours length would produce results for one "protein" study.

Anyway, what I'm trying to convey in a peculiar way is that I don't see how one can compare what is ostensibly achieved from a host running 4x6 tasks, or 1x24 task, or 8x3 tasks, or whatever. I don't see how you can say that it doesn't matter whether you run 1x24 or 4x6, because it seems to me that it does matter. The missing link for me to understand this is the whole concept of a "seed", where it comes from and how it relates from one task to another. That is, if I run a task with a given seed for 12 hours, is there another task sent out with a different seed that ostensibly reveals the information that would have been produced if the first task had run for 24 hours? Or does the project not care about that?

I think people want to know the optimal run time that produces the optimum scientific output. You say it doesn't matter. What needs explaining is how the "seed" concept renders the run time as moot and irrelevant with regard to scientific achievement.

Sorry, wish I could do better.
5) Message boards : Number crunching : Resource Share Obsolete? (Message 60752)
Posted 20 Apr 2009 by Nothing But Idle Time
Post:
Is this work fetch/scheduling idea floated on other project fora or only here? If only here, why? Shouldn't this be on the BOINC fora for generalized discussion or is that like posting republican ideas on a liberal website -- the audience just isn't interested and will rip you to shreds for mentioning it?
6) Message boards : Number crunching : CPU Optimization, GPU utilization: so sad! (Message 60716)
Posted 18 Apr 2009 by Nothing But Idle Time
Post:
To Michael G.R. -- Nobody here wants to denegrate your ideas, we can only provide history as we remember it. If you need answers to questions that nobody in the fora can provide you should plead directly to David Kim and company.
7) Message boards : Number crunching : CPU Optimization, GPU utilization: so sad! (Message 60693)
Posted 17 Apr 2009 by Nothing But Idle Time
Post:
I haven't posted for a long time and suddenly feel the urge to interject my two cents worth. This is my opinion only and is not meant to criticize anyone specifically.

First, optimizing the code is not a new topic and arises over and over. The project team has stated in previous threads that they did not expect any real benefit from SSE/2 optimizations versus just leaving the code as is. I accept their decision whether it is accurate or not. Why can't the public accept this?

People need to differentiate between 1) using a static analytic methodology (referred to in this thread as the "algorithm") to discover protein conformations and thereby medical treatments and 2) testing the algorithm's effectiveness while constantly improving on it's predictive behavior. A static algorithm likely can be expected to be optimized but a constantly changing algorithm IMO is probably not worth optimizing since the optimization could be lost in the next round of improvement.

Second, all the pleading and begging and posturing is based on an assumption that optimizing the Rosetta code will translate directly into saving countless lives sooner. This is a big leap for cause and effect, it's altruistic, wishful thinking not based on known quantities. No good scientific pursuit should be conducted with this kind of thinking. And apparently the project staff does not have the resources of time, money and expertise to do anything other than what they are now. Unless the staff is a bunch of idiots, if there was any substantive gain to be made from optimization one has to believe they would pursue it in their own best interest. We clients reserve the right to offer suggestions but if they are not accepted I don't think we should dwell on it ad nauseum.
8) Message boards : Number crunching : efforts in reviving old users which dont get credits (Message 59362)
Posted 5 Feb 2009 by Nothing But Idle Time
Post:
nothing but idle time: you are one of those who are against everything arent you? i dont know really but i guess other projects are also not 100% error-free...

Please get your facts straight. I never said anywhere in this thread that I was against something. In this case you refer to the effort to "revive" inactive hosts/users. I merely opined on why users become inactive and said previously that your efforts would best be served by trying to get new users and not try to coax back into service folks who have decided not to participate. So in that respect Mod.Sense agrees with me. I have nothing further to say on this topic, but feel free to get in the last word, most people do.
9) Message boards : Number crunching : efforts in reviving old users which dont get credits (Message 59346)
Posted 5 Feb 2009 by Nothing But Idle Time
Post:
@nothing but idle time: i dont know whether you read the news on R@H, but 1.54 is quite stable and has a low error rate...


Well, I don't know whether 1.54 has a low error rate or not, but it still has errors. Otherwise why do we have a thread to report errors for every single version of the app that is produced? We didn't get to Mini version 1.54 or to Rosetta version 5.98 over night; there is a long history that leads up to the 87% inactive hosts. And no doubt there will be v1.55, etc, all with errors of some kind. All I'm saying is that dedicated Rosetta crunchers have a high tolerance for errors while the inactive users probably do not.
10) Message boards : Number crunching : efforts in reviving old users which dont get credits (Message 59337)
Posted 5 Feb 2009 by Nothing But Idle Time
Post:
the second chart written here by feet1st is even better, 87% of all hosts are inactive

This 87% number signifies (IMO) that contributors had bad experiences with Rosetta apps and would not tolerate the persistent error rate. Once they leave there is good chance they won't return. People do love this project's goals, but many have a low tolerance for failed tasks. That's because much of one's contribution is wasted and, further, failing to correct the persistent error rate indicates a lack of appreciation for one's contribution. I do believe many people share this view.
11) Message boards : Number crunching : LHC@home gives BOINC a bad name (Message 59334)
Posted 5 Feb 2009 by Nothing But Idle Time
Post:
I like spirited debate if it concentrates on persuading someone to accept another's POV, not involving debater's personality or mental state.

Since the topic IMO centers around persuading people to contribute to project A vs project B, why not have this discussion on the BOINC fora under the "Project" category. This "debate" does seem out of place here; I do look forward to followup disussion if anything further is to be derived from it.

Side note: I contributed greatly to Cosmology project in it's early stages, but the staff proved to my satisfaction they were incapable of running a project to my satisfaction. I left and haven't returned, though I still have hopes that things will turn around some day.
12) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59151)
Posted 29 Jan 2009 by Nothing But Idle Time
Post:
resultid=224470749

Reason: Access Violation (0xc0000005) at address 0x00467846 read attempt to address 0x11B524C4

This task was running fine but after I suspended it, rebooted my system, and restarted the task it terminated almost immediately with access violation. Maybe restarts don't work very well or something is flakey with my hard drive or system. Having some troubles with access violations on Einstein tasks as well. But I've run memtest86 and prime95 and CHKDSK and none of them indicate any local computer problems. I'm just shaking my head in disgust.
13) Message boards : Number crunching : Report long-running models here (Message 58370)
Posted 2 Jan 2009 by Nothing But Idle Time
Post:
Claimed credit 392.681268578232
Granted credit 37.8765655196635
Thanks for the credit.

People are experiencing similar results. So how can the credit system be working right if there is such a large disparity between claim and grant? I thought the grant was a running average of claims? Apparently too few decoys are being produced. Something smells; and if the smell gets strong enough I will, er... "have to leave the room".



can you post what task that was? with large over runs the credit system gets messed up from what i can tell. i've had stuff that goes 2 hours over limit and returns a lousy credit.

See Rifleman's posts 58332 and 58333 in this thread. I also posted one earlier.
14) Message boards : Number crunching : Report long-running models here (Message 58357)
Posted 2 Jan 2009 by Nothing But Idle Time
Post:
Claimed credit 392.681268578232
Granted credit 37.8765655196635
Thanks for the credit.

People are experiencing similar results. So how can the credit system be working right if there is such a large disparity between claim and grant? I thought the grant was a running average of claims? Apparently too few decoys are being produced. Something smells; and if the smell gets strong enough I will, er... "have to leave the room".
15) Message boards : Number crunching : Report long-running models here (Message 58309)
Posted 31 Dec 2008 by Nothing But Idle Time
Post:
As you can see my chosen runtime is 12 hours but this task ran for 20 hours.
Stealing the sentiment of greg_be "This sucks".

1nkuA_BOINC_MPZN_with_zinc_abrelax_6130_97328_0
Claimed credit 153
Granted credit 76 (benevolent of you)

# cpu_run_time_pref: 43200
======================================================
DONE :: 1 starting structures 71773.1 cpu seconds
This process generated 2 decoys from 2 attempts
======================================================
16) Message boards : Number crunching : efforts in reviving old users which dont get credits (Message 58148)
Posted 24 Dec 2008 by Nothing But Idle Time
Post:
...Leave people alone and let them make whatever choices they want without solicitation.
wheres the problem? i just said "what about getting some volunteers back", not about being "aggressive at solicing support". if you dont like the idea, say that, but dont become unobjective.

I'm being quite objective and giving one point of view that you don't like. Seeking new participants is appropriate but attempting to re-activate (nag) previous participants who have consciously decided NOT to participate can/will be viewed as intruding into one's personal affairs. I would consider this an insult to my intelligence and freedom of action and may in fact be why a previous attempt to solicit participants was met with a cool response.
17) Message boards : Number crunching : efforts in reviving old users which dont get credits (Message 58110)
Posted 22 Dec 2008 by Nothing But Idle Time
Post:
And volunteers by definition must have unencumbered freedom to participate or not at their own discretion for their own reasons.


when you say "please help again", they have unencumbered freedom to participate. as i said, this is for volunteers who forgot rosetta or stopped because of bugs or something like that.

How many people out there are like me and no longer answer the telephone because we are tired of being badgered by the "please give me a handout" calls? If I want to contribute to a charity or other organization I first make the choice to do so and second I proactively seek out a charity/org that fits my goals, afterall, I can't contribute to everyone no matter how deserving they view themselves. And if any charity/org is aggressive at soliciting my support it has a negative effect.

Also, here at Rosetta bugs are a fact of life. People who actively support Rosetta are apparently willing to accept that fact. Others prefer only to support projects that run smoothly. Leave people alone and let them make whatever choices they want without solicitation.
18) Message boards : Number crunching : efforts in reviving old users which dont get credits (Message 58045)
Posted 19 Dec 2008 by Nothing But Idle Time
Post:
Ya know, distributed computing is volunteer work at the participant's expense. And volunteers by definition must have unencumbered freedom to participate or not at their own discretion for their own reasons. Who are we to bother them with our own views and opinions about the level of their participation (even if it is zero) or about the importance of this project (charity) above another.
19) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 57929)
Posted 16 Dec 2008 by Nothing But Idle Time
Post:
After a 1 week hiatus I downloaded v1.47 and 4 tasks. The first task showed a completion time of 12 hours which corresponds to my chosen runtime. The other 3 tasks, all _rlbd_ tasks, showed completion times of only 1 hour. What's up with that? It suggests that the staff provided an estimated task runtime of something like 45 minutes instead of the customary 8 hours.

Because of the 1-hour runtimes BOINC also downloaded additional tasks to fill the cache. Not good.
20) Message boards : Number crunching : I give up! (Message 57864)
Posted 14 Dec 2008 by Nothing But Idle Time
Post:
@rochester
hopefully you can return some day when things stabilize...


I've been with Rosetta since 2005 and today's environment is no more stable than 3 years ago, maybe less so. Stability is cyclic and unpredictable as the project team speeds up new investigations. How many projects also have a test bed like Ralph before realeasing new apps? Despite Ralph we continue to get errors though. I just think everyone would be more tolerant of errors if they were fixed expeditiously. Getting poked once with a needle is painful but tolerable, getting poked repeteadly will invoke violent reaction. Here it means taking ones computer and going elsewhere.


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