Posts by Cesium_133*

1) Message boards : Number crunching : Minirosetta 3.50 (Message 76676)
Posted 1 May 2014 by Profile Cesium_133*
Post:
Guys, I signed up for 47 WU\'s. Two of them aborted as comp errors, 0 file or whatever. The others gummed up my machine so it darn near wouldn\'t run. This sort of thing has happened before to me, and I can\'t suffer it. I\'ll have to detach for now until you can send me something you can guarantee will run as well as the average WU from somewhere else... sorry...
2) Message boards : Cafe Rosetta : Distributed Thinking (Message 64116)
Posted 21 Nov 2009 by Profile Cesium_133*
Post:
Distributed human thinking is what makes things go wrong when you have too many people working on the same thing at the same time. Too many cooks spoiling the soup, so to speak. That\'s what makes DC so great: pure objectivity. All we have to do is come up with a goal and some program code for finding it. The computers involved will do the rest, and without the threat of skewing results or anything like that...

Let\'s spread the word to everyone to hop on the BOINC bandwagon. Then there\'ll be no worry about humans trying to solve problems better left to the computer... :)

3) Message boards : Number crunching : Minirosetta 2.00 (Message 64115)
Posted 21 Nov 2009 by Profile Cesium_133*
Post:
So we\'re up to v2.00 on the Mini. I\'m hoping that we\'re building upon a good foundation and cleaning up problems as we go... not just patching up this problem and that or finding work-arounds. I am very satisfied with the main bulk of the project, the computation... the graphic side isn\'t as important to me, but error creep, as it were, could always happen.

To perfection and no bugs :D
4) Message boards : Number crunching : Minirosetta 1.98 (Message 63859)
Posted 27 Oct 2009 by Profile Cesium_133*
Post:
Not only am I losing houres of crunching time for R@H but all other projects are being affected.


Happened to me too a while back... it\'s why I walked away from Rosetta and went to POEM. Their WU\'s don\'t foul up. I gave Rosetta time to fix their issues, and while my experience hasn\'t been as bad as the last poster, I have had 2-3 comp error aborts. Also, the graphics for 1.98 often won\'t show when prompted, a symptom of troubles generally in the code.

The alternative is to suspend R@H until the problem is fixed.


Managers of R@H, take note of that last line. The original poster, joined by myself, just said a mouthful... we value the use of our flops!
5) Message boards : Number crunching : Minirosetta 1.98 (Message 63803)
Posted 24 Oct 2009 by Profile Cesium_133*
Post:
I\'ll join the chorus on error-halted WU\'s (I assume this is the place to give notice about such things) :

symm_lr8_seq_score12_ss_1.7_rlbd_1npu_IGNORE_THE_REST_DECOY_14923_2726_0

Computation error after 1m 13s...

If this isn\'t the venue to report such glitches, though it seems to be, please let me know :) Incidentally, what % of WU\'s are found to be corrupted/abortive/unfinishable, and can they be rehabilitated for purposes of this project? :)

The inquiring layman\'s mind wishes to know... :)
6) Message boards : Rosetta@home Science : Types of WU\'s and Their Nomenclature (Message 63608)
Posted 5 Oct 2009 by Profile Cesium_133*
Post:
Bugger all, that\'s some advanced microbiology... thanks, Morten, for the direction. Obviously, understanding any useful amount of that is contingent on having a degree in cellular chemistry, organic chemistry, or something similar dealing with high-level biochemistry/biophysiology/biophysics. I\'m just glad I know what tyrosine and tryptophan are.

However, as I don\'t want simply to be a lackey, unaware of what I am really doing to help, I shall start from the beginning and try to get my mind around what all that chemical and molecular jargon means. I know simple stuff about DNA... codons, triplets, mRNA, tRNA, rRNA, and such, so I might be able to become 1/4 conversant in this field...

But I warn everyone... this subject looks pretty ferocious and complex. Be warned... those tentacles coming off the main DNA trunk might sting... :p
7) Message boards : Rosetta@home Science : Types of WU\'s and Their Nomenclature (Message 63606)
Posted 5 Oct 2009 by Profile Cesium_133*
Post:
Seems that Rosetta is working well now, and I\'m glad to be back on board after an absence.

I\'m interested in what the WU codes and abbreviations mean. I know that a fair bit of it is just unit numbering and call-signs as to what researchers should look at and what the WU is doing, but as to...

lr8_combine_smooth_torsion...IGNORE_THE_REST_DECOY,

Rossmann2X3...

symm_lr8... and

histone_loopbuild...,

can anyone explain these WUs\' procedures in reasonably simple terms? They look like football play calls :p I\'ve seen many other codings as well, and if anyone could post them or tell me where to look for an explanation, I\'d be appreciative. I\'m very interested in this kind of thing :)
8) Message boards : Rosetta@home Science : Is Ibercivis now doing some related work? (Message 63593)
Posted 4 Oct 2009 by Profile Cesium_133*
Post:
As with other users, I can\'t read Spanish or Portuguese, so I disengaged from Ibercivis a while back. However, if they are running similar WU\'s, perhaps we could dig up someone who understands one of those languages and get them on board with Rosetta... would avoid duplicate efforts...
9) Message boards : Number crunching : CPU usage (Message 62076)
Posted 3 Jul 2009 by Profile Cesium_133*
Post:
I\'d suggest your issue is closer to home. What do you think it is that makes your machines report this?


My machine (I run 1, with 2 separate CPU\'s, and a friend collaborates with me on my account) isn\'t the problem. Here\'s the thing: I\'ve gone over to POEM. No problems; no hanging such that I must reset BOINC; no discarded, shredded, folded, spindled, mutilated, returned for full refund, or any other kind of program problem. My WU\'s come in, get computed, and go back out. They get reported in 24 hours unless I update first, per BOINC specs. I have no problems.

Thus, whatever it is that makes BOINC, Rosetta, and my CPU\'s not get along, I\'m not sure, and I have little reason to care *shrug*. I love Rosetta and what it does; however, POEM is very important, too. I have contributed to it in the past. It does a lot of what Rosetta does, plus adds a facet of cataloging. Works for me and many others.

I can say this: Rosetta never damaged or messed up any other prog on my laptop, nor did it adversely affect the BOINC client per se (it didn\'t change its coding or cause it not to recognize other projects, e.g.). It just performed substandardly. I can also say: I\'m not the only one presenting with these symptoms. My computer has an issue with x; someone else is complaining about y; and another has trouble with issue z. Read the thread back to yourself. The problems here aren\'t a faulty diode, clocking, or some scheduling or priority conflict. It\'s different WU\'s, different errors. The efficacy of the code is lacking, and depending on what the bugs come into contact with on a system, they\'re manifesting in a plethora of ways. This is 30 years of using computers talking; you feel it after a while, the crux of the problems.

I am a user and user-end whiz kid (36, an old kid). I can\'t program too well, and I\'m not good at reading machine or coding language. I leave it to someone who can do all that to work out the bugs. You ask me what else it could be in my system? I don\'t know. I might not know if the code jumped right out on my screen in a box saying \"This is why Rosetta is not working.\" To guess at it might send those in the know on a fool\'s errand, and I would rather not have that...

My best to the programmers... may they debug their project... :)
10) Message boards : Number crunching : CPU usage (Message 61928)
Posted 25 Jun 2009 by Profile Cesium_133*
Post:
I just don\'t know why you can\'t detach from Rosetta...


I say this totally respectfully, as I am addressing the programmers of Rosetta: it\'s because their programs have more errors in them than the 1985 Los Angeles Dodgers infield. I told you, shoddy code... of course nobody\'s going to know why you can\'t detach... not unless Rosetta will open their source code and present it to the community, preferably compiled -and- decompiled. Otherwise, you\'ll continue to have program cancer, which Rosetta ironically tries to treat :p You\'ve already seen the metastasis in some areas...

Call up Rosetta directly and tell them your issues... they have a damn good concept. It\'s a pity they\'re wasting away time and resources on poor computation coding...
11) Message boards : Number crunching : CPU usage (Message 61911)
Posted 23 Jun 2009 by Profile Cesium_133*
Post:
I only have the problem with the Windows machine. A 3 hour work unit appears to intermittently be taking over 6 hours.


I\'ve had them go 8, 9 hours with no end in sight. Windows? It may not be perfect, but it\'s the BMOC, and you have to work with it. Linux and Apple are not the bad boys on the block... Bill Gate$ and Micro$oft are. Like it or not, that\'s what most of us run, and if interfacing with the OS is Rosetta\'s problem, well, it\'s Rosetta\'s problem... not mine. Again, all the other projects, including POEM, seem to be running great on King Bill\'s Windows...

So why mess about with a prog that doesn\'t cut the mustard?
12) Message boards : Number crunching : CPU usage (Message 61906)
Posted 23 Jun 2009 by Profile Cesium_133*
Post:
Given that we\'ve had to discuss problems with this and that about Rosetta, its interfacing with BOINC, and the ongoing Rosetta Mini fiasco to this extent... in my own famous words, what is going on here?

Are we contributing to research, or are we turning into alpha testers of Rosetta programs that happen to be trying to run projects as an afterthought? This is 2009; there should be, for example, no question about a program\'s compatibility across multiple, modern platforms. Vista, XP, 2000, Linux... someone should have figured this all out long ago and made WU\'s and the project itself watertight in this regard. So Vista is a clunker... well, tough... you want compatibility, make it happen!

Something else: you release a new version of something when it\'s ready. You release an improved version of same when IT\'S ready. Looking at the Mini timetable on its version log thread, I see 4 versions, one after another. They have new features, claim to fix bugs, and on and on. Four of them inside of a couple months! Who\'s throwing this stuff out here? Is it necessary? And why aren\'t the problems with the main module and CPU interface, like calculations ceasing, being addressed? Is someone at Rosetta writing a new line of code and proclaiming, \"New version 1.xx! Eureka, our problems are solved!\"?

We as volunteers deserve better than having to putz around waiting for some new solution du jour to fix the latest bug. We didn\'t sign on to keep re-setting and starting/stopping BOINC just to keep this tin lizzy moving. I don\'t see this dynamic playing itself out anywhere else, and I mentioned in another, earlier post that if this kept up, I would detach...

Which I am. I\'ve gone to POEM and returned the unfinished WU\'s to Rosetta. Someone please let me know when the Rosetta people figure out whatever it is that every other project seems to have... when they can get a program running that actually runs! I haven\'t the time or patience for such imperfections... and my flops agree...

Sorry to have to go, for now... but I want to do crunching without worries, and I by God will. There are plenty of good projects on BOINC that don\'t make you upset due to shoddy coding, which is all this is... I have used computers since 1978. I have seen the effects of bad registries, poor motherboards, lack of memory, and crappy code. This is crappy code, and I won\'t associate myself with it. Let me know when it\'s prudent to return, and why... Cesium...
13) Message boards : Number crunching : Problems with Minirosetta 1.75 (Message 61804)
Posted 17 Jun 2009 by Profile Cesium_133*
Post:
For Rosetta@home, the alpha testing is supposed to be over at Ralph@home. I\'ve seen no clear sign that their beta testing is also, though. Their in-house computers don\'t offer enough capacity for either, but at least for Ralph@home, they ask for volunteers.


Glad they have volunteers. I go for the real thing... give me good stuff to work with, and a program that can do it...

Oh, as to the alpha/beta thing, I was being sarcastic, :) my 1/2-humorous insinuation being that Rosetta sends out programs that haven\'t been properly vetted. I know they have the best of intentions in mind. However, I have never seen this many bugs within the confines of any other BOINC app or project, and I\'ve run 29 at one time or another. It makes me wonder who\'s minding the fort, and if they\'re perhaps a bit eager to release new progs into the wild.

I have the same beef with eBay, whose TurboLister I use... and which has bugs seen in v2.0 (they\'re at v7.2 now). They should get the Mini and all else in order before going with an overhaul. I hear rumblings of that happening, but before they put a v2 out, they should handle all the little dinky things that make 1.xx less than stellar...
14) Message boards : Number crunching : Problems with Minirosetta 1.75 (Message 61775)
Posted 16 Jun 2009 by Profile Cesium_133*
Post:
I don\'t know what decoys or zero size file errors (I can guess on that one, though) or this or that zip file or directory tree are... I\'m a user-end genius and a programming dunce. I can do anything a program is set up for me to do and is not bug-infested in that regard. When it comes to the internal circuitry and source code, though, I am lost... I let someone who\'s good at that kind of thing handle it.

That said, I just want to keep letting my comp do its thing for cancer. I think my profile mentions that, while I have a good mind, there is a lot I don\'t know, including how we could use protein therapy to help cure cancer. I just know it\'s reasonable to assume we can, like we have done with immunotherapy. Something else I have never learned is hardware ins and outs, and another is coding. I can do HTML ok, but I am not good with abstract thought that requires translation to words and committment to paper.

So... I\'ll post any WU\'s that go limp on me, and do my best to stick with you all. Do ask the powers that be, though, to do their bleeping alpha and beta testing in-house as much as possible. I don\'t like the thought of losing one single flop to a bug when it could be the one to find the codon triplet to turn off all reproductive commands in a cancerous cell... or block its angiogenesis...

Serious as, well, cancer about beating cancer... DC and BOINC rock...
15) Message boards : Number crunching : Problems with Minirosetta 1.75 (Message 61741)
Posted 14 Jun 2009 by Profile Cesium_133*
Post:
It looks like 1.75 can have the lockfile problem, too:


Well, it can lockfile this -gives the Spaceballs salute- if it keeps deciding to stop computing on me. I had it do the same thing again, spin its wheels, on 2 WU\'s in the past 24 hours. It pulls this one more time, I\'ll go back to POEM or something similar until the Rosetta people can extricate their heads from you-know-where and devise some code on par with everyone else. This is silly, putting out what looks like an alpha replacement for an already-knackered 1.71... X-(
16) Message boards : Number crunching : Problems with Minirosetta 1.75 (Message 61736)
Posted 14 Jun 2009 by Profile Cesium_133*
Post:
Where can you find such websites giving temperature limits for HP computers? I\'d like to find that information for the two I have.


Now that I look again, I can\'t find the confounded specs :( Though you might wish to start here:

http://www.shopping.hp.com/webapp/shopping/store_access.do?template_type=landing&landing=notebooks

I know I had to look and look the last time...

Wherever you find the info, I doubt it\'ll address the issue of software compatibility or problems along those lines with the dv9700 series...
17) Message boards : Number crunching : Problems with Minirosetta 1.75 (Message 61727)
Posted 13 Jun 2009 by Profile Cesium_133*
Post:
Looks likely to be the same lockfile problem I\'m trying to track down. For more details, see the thread on 1.71 problems.


Whatever a lockfile problem is :) I\'ll read the 1.71 bug thread.

Do you have the Rosetta@home project set to be allowed to use 100% of the CPU time if nothing with a higher priority is trying to use that CPU time? That makes the problem less frequent, but is not recommended on many laptops and on computers that tend to overheat if set to use that much.


All 4 of my projects are set to run at 100% flop utilization. Rosetta has 85% of total CPU time allocated to it, so it\'s the BMOC if it\'s running. Everything else runs less of the time and dependent on when BOINC decides to run something other than Rosetta. Whenever another project is running, it also has 100% CPU access. I have everything set to change between programs every 90 minutes.

I can exploit the CPU like this because I have a good separate heat sink that keeps the drive at 45-48 C, the CPU around 50, and the core and GPU at 77-80. This represents 10-12 C off ordinary temperature for my computer, and is within acceptable parameters according to its website (I run an HP Pavilion 9600 or the like, 2 CPU\'s, actually...)

If you\'re unable to set the CPU time to 100%, you could join me in trying to send in a zipped up collection of the *.txt and *.old files from the BOINC data directory tree every time the problem occurs...


I can set the CPU to 100% and get it to run that way. The rest... are you saying you can prove Oswald did not act alone? Something about a tree on the grassy knoll? And you have the Zapruder film in an old zip file? Nice...

The loss of some time elapsed and percentage of completion is a normal result of restarting from a checkpoint... (it) cleans up the leftover lockfiles from failed workunits that make the problem cascade to any later workunits that try to run in the same slot.


Makes sense that it would have a self-fix algorithm that would work to repair itself on a reset... seems that\'s the way with most programs in modern computing, be they this or Vista. As for what makes a bug propagate, well, I know what the Domino Theory is in the abstract. However, I am a user-end whiz kid, not a programmer by birth. Thanks for the reply :)
18) Message boards : Number crunching : Problems with Minirosetta 1.75 (Message 61721)
Posted 13 Jun 2009 by Profile Cesium_133*
Post:
Had a glitch with a WU just downloaded and running on Mini 1.75... it\'s a similar thing that\'s been plaguing me with other, earlier Mini versions:

lb_dk_ksync__full_hb_t313__IGNORE_THE_REST_12649_620_2

As with some others, it seemed to hang and not compute for a couple of hours while I was away. I turned BOINC off and back on, and it now is working again. It did, however, reset its \"time elapsed\" and \"to completion\" figures to lower values. An earlier, similar issue with another WU also reset the percentage of the job completed to a lower value.

Can someone give me a heads-up as to what demon, devil, or wraith is causing this, and if an exorcism is possible... thx...
19) Message boards : Cafe Rosetta : Personal Milestones (Message 61667)
Posted 11 Jun 2009 by Profile Cesium_133*
Post:
Passed 100,000 cobblestones 7 June 09... I guess that is some sort of victory... do I get lots of karma? :)
20) Message boards : Number crunching : aborting work units (Message 61570)
Posted 4 Jun 2009 by Profile Cesium_133*
Post:
If you would state your intentions it might help people comment on alternative approaches to achieve your goals.


My intentions are to get as many WU\'s assigned to my machine as it can process by the required deadline of each WU. Also, I want such WU\'s to be compliant in quantity and required total crunching time over a given, long period (>= a matter of a few months, at least) with my set %ages for Rosetta et al. Nothing fishy or abusive; just good use of my resources. I know I would finish more discrete WU\'s with Hydrogen than Rosetta, but I want my PC to run Rosetta more, and it\'s doing so... thus, good there...

If the net result is that your machine contacts the project fewer times during the week, it is a net good thing for the project servers.


Granted, though I have yet to figure out the exact algorithm BOINC uses for contacting home -for credit-. Every WU is allowing BOINC to upload its finished data forthwith on completion, as it should, but if a WU finishes closer than a certain amount of time before the deadline, BOINC will report it alone for credit. WU\'s can be running high-priority before this unknown time, though, finish up and report, and queue up on my machine to be either reported manually or called in per the 24-hour default time.

Eventually BOINC is going to figure out that you are getting behind on your climate model, and it is going to devote the time it takes to try and complete that before its deadline.


As it should, yes... I have 3 WU\'s on climate... one due April 2010, the others November 2011. Must be big ones. Over time, I would expect to be assigned WU\'s finishable by their respective deadlines per my allocated resource time.

...(t)he next step is key to your question. Analyze the results of your experiments. When will you start this phase of your research?


Understood. What I\'m getting at is the hour/minute/second precision of the deadlines. Why not just have a given day at 11:59:59 PM all the time? Do the individual projects work off a formula which relies on when they\'re compiled, or sent into the wild? It just seems illogical to have some WU\'s with a deadline 2 minutes later than some others, unless it\'s all automated. Even then, why not use the Easy Button and go to the end of the day? Maybe it\'s too good an idea :)

I sit around thinking of this stuff, btw... I could use a gf... lol... such as the one I have in my pic and sig... :D


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