Posts by Snake Doctor

21) Message boards : Rosetta@home Science : CASP6 revisited. (Message 15652)
Posted 7 May 2006 by Profile Snake Doctor
Post:
I see we are crunching some of the CASP6 proteins again. I was wondering, with the improvements made in the interim, how todays Rosetta results compare to the CASP6 Rosetta at that time?


That would be interesting to see. It would alos be interesting to know for those predictions that were close in CASP6, how many models had to be done verses using todays Rosetta application.
22) Message boards : Rosetta@home Science : Rosetta@home page at Wikipedia (Message 15651)
Posted 7 May 2006 by Profile Snake Doctor
Post:
Today I've added some minor stuff

1/ info about the Baker Lab scientific team (taken the names from http://depts.washington.edu/bakerpg/members.html (it's nice to see so many nationalities, I even noticed a greek name there too).

2/ some info provided here by eberndl about experimental determination of protein structure ("Protein structures are currently solved, very slowly (it can take weeks or even months to figure out how to crystallize a protein for the first time) and at high cost (about $100,000 USD per protein), in the lab by X-ray crystallography or through Nuclear Magnetic Resonance (NMR) experiments.")

Let me know if there are any glaring errors or ommissions (or just go ahead and correct them yourself).

I still need to do the restructuring I mentioned in previous post.

Also, would someone let me know which of the papers in http://depts.washington.edu/~bakerpg/publications.html to include under a "Bibliography" section.

PS: I've no idea how many people read the Wikipedia page (I couldn't find a stats page for individual pages), but I can tell you that my own DC-HOWTO page has been read about 38,000 times (!!!) since I created it in Jan06 and is linked to from over 100 different pages (as I can tell from referrer-log).



You might want to port some of your changes to the Unofficial BOINC wiki. I would be surprised if that is current. That links from the project front page and should be checked for errors.
23) Message boards : Rosetta@home Science : CASP7 to start in April (Message 15650)
Posted 7 May 2006 by Profile Snake Doctor
Post:
could they not pick any hotter months of the year for this? how many of us shut down during the summer, or at least know people that do? just plain stupid.


rosetta did not pick the dates for this. It is done by international agreement. Probably since most of the research is done at universities, they pick the summer because the research teams are not busy teaching at that time.
24) Message boards : Number crunching : Report Problems with Rosetta Version 5.07 (Message 15649)
Posted 7 May 2006 by Profile Snake Doctor
Post:
All three on Mac OS 10.4.6, Dual G4, 1 GB memory. BOINC Ver 5.4.9, Rosetta 5.07.

AB_CASP6_t272__486_1242_0 - this WU Was killed by watchdog.
HBLR_1.0_1dtj_RDFLAGS_473_8871_0 - this WU failed almost on arrival.
HBLR_1.0_1mky_ROT_TRIALS_TRIE_CHECKPOINTS_482_7412_0 - This Wu Failed almost on arrival.
25) Message boards : Number crunching : Report Problems with Rosetta Version 5.07 (Message 15631)
Posted 6 May 2006 by Profile Snake Doctor
Post:
Well I don't get many errors but I have two within just a few moments of each other. Mac g4 Dual, 1GB of memory. It looked like BOINC tried to start running them before they finished downloading.

here and here

the errors were both -
<core_client_version>5.4.9</core_client_version>
<message>
Couldn't start or resume: -146
</message>

26) Questions and Answers : Wish list : Adjustable Size "Buttons" (Message 15598)
Posted 6 May 2006 by Profile Snake Doctor
Post:
this is a BOINC issue not a Rosetta issue. Perhaps you should post it on the BOINC forums.

Regards
Phil
27) Message boards : Rosetta@home Science : 10 reasons I crunch R@H and you should too (Message 15411)
Posted 3 May 2006 by Profile Snake Doctor
Post:
There are a lot of very good reasons for anyone to install BOINC and run Rosetta@home. Besides simply being the best project in the current group of BOINC distributed computing projects, My list would include (in no particular order)-

    1) Possibility of understanding how and why proteins can cause disease
    2) The possibility of discovering new ways to treat serious illness
    3) Advance the general level of human knowledge
    4) Assist in the development of distributed computing and new computing tools applicable to a broad range of research
    5) Increase my own personal knowledge and understanding of biological science
    6) The communication and information flow between the project team and the user community is better at Rosetta than any other project
    7) The project is "alive", and new information is posted all the time to keep people informed about how their computers are being used and where the project is going.
    8) The projects willingness to incorporate user ideas into the project and their responsiveness to users requesting help in the forums
    9) The opportunity to participate in creating the next version of the software by running RALPH@home along side of Rosetta@home.
    10) The project site and Forums are not so different form other BOINC projects that users can't find what they need



This project stands out among other BOINC projects because of the information flow from the project to the users. Many other projects provide no information updates of any kind, but at Rosetta it is actually difficult to keep up with all the new information updates.

On many BOINC projects pleas for help from users are actually ignored. That never happens at Rosetta. When users ask for help on the Forums, it is rarely longer than 30 minutes before a project team member, Moderator, or System Administrator responds to help.

28) Message boards : Rosetta@home Science : Discussion - Reasons to run Rosetta@Home (Message 14961)
Posted 29 Apr 2006 by Profile Snake Doctor
Post:
Why Rosetta gets my crunch time:

1. Cutting edge research!
2. Potential live saving long-term-goals and concrete short-term-goals!
3. Competition in CASP7 with the winning team!
4. Detailed science updates and transparency what's done!
5. Nice and responsive project team!
6. User setable length of Work units!
7. Nice and active community!
8. No outages - work always available!
9. Scientifically renowned project leader!
10. Nice screensaver!

Perhaps we can make a page with serveral such 10 reasons why...



This makes us very happy!! now how do you get these lists out to the general
boinc community?
thanks,
David

Perhaps a periodic news item that reads like a an interview with a rosetta user. The prople could be picked by the project at random to provide comments on the project, that would be posted in the News line on the fornt page. That feed goes out to all the teams.
29) Message boards : Rosetta@home Science : Concerns: Will someone (i.e. BigPharma) make money out of my CPU time? (Message 14747)
Posted 27 Apr 2006 by Profile Snake Doctor
Post:
Drug companies can patent more than just the active element in a product. The inerts and other things in the product make for a unique formulation that is what gets patented. So just because the active element is public, does not mean that they would not be able to make, patent, and profit from a particular product. Aspirin is a perfect example. The stuff can be found in the bark of willow trees, but companies seem to make a wide variety of aspirin based products, and do so at a profit.

Regards
Phil
30) Questions and Answers : Preferences : General Preferences: Doesn't obey max up/down rates (Message 14568)
Posted 25 Apr 2006 by Profile Snake Doctor
Post:
I also have a similar issue wher I have set in the preferences to hide the computers and they are still shown in my profile. It seem the website doesn't obey the program settings very well. Maybe the management should contact SETI@Home or one of the other larger projects for some technical assistance before I yank the program from my PC's for security reasons.


As to the original question. You also have to set your local BOINC Maneger to "Run Based On Preferences".
If you fail to do that it will ignore your preferences.


As to the display computers. You will always be able to view your own computers. The hide function keeps OTHER USERS from viewing them (though I don't know why anyone would want to do that other people cannot help you if they cant see your computers)

So the only way for you to test if they can be seen would be to go to somplace like BOINCSynergy stats site, register, add this project into you preferences there and see if your computers are shown as hidden when it updates your stats.

Or you could just take my word for the fact that when I try to look at your computers they are in fact hidden.

So the server is working just fine.
31) Questions and Answers : Windows : can upload only to 16.73kb (Message 14567)
Posted 25 Apr 2006 by Profile Snake Doctor
Post:
Does the system download ok? It looks like it might be dropping the connection somehow.
32) Message boards : Cafe Rosetta : Team Jesus (Message 14339)
Posted 22 Apr 2006 by Profile Snake Doctor
Post:
You mean some topics have exlamation marks next to them?

They've been stickied, usually by a mod, so they stay at the top of the page.
I think thats what you meant.. ??



Actually the exclamation marks are the ones that float up the listing based on users voting this up using the rating icons at the bottom of each post.

The stickies are always at the top of the forum pages and have a different icon.
33) Message boards : Cafe Rosetta : Personal Milestones (Message 14338)
Posted 22 Apr 2006 by Profile Snake Doctor
Post:
I can see 100,000 looking VERY large in the windshield It won't be long now. Less than 400 to go.
34) Message boards : Number crunching : Report stuck & aborted WU here please - II (Message 14267)
Posted 21 Apr 2006 by Profile Snake Doctor
Post:
ANother HUGE ammount of CPU time wasted!!!! ...



Jose,

Your time is not wasted. Look at This post. From this statement the results are used and you will be granted credit.

So perhaps not so much ARGH but more like AHHH!

Regards
Phil
35) Questions and Answers : Wish list : Merge computers in view list... (Message 14233)
Posted 21 Apr 2006 by Profile Snake Doctor
Post:
Currently the merge function is turned off. It is expected it will be turned on again in a few weeks. Merging was causing some problems with server performance. It is a BOINC issue and there is a fix coming.

Regards
Phil
36) Message boards : Rosetta@home Science : rosetta client changelogs? (Message 14221)
Posted 21 Apr 2006 by Profile Snake Doctor
Post:
I believe you must be looking at a WU from Ralph (the beta test of each upcoming Rosetta release). There is some info on the boards there. Great stuff coming!

...nope! Just checked the Rosetta applications page and it shows v5.01, this means it's here already!!!

...and to answer your NEXT question... unless you're having specific problems with Rosetta on your PC, go ahead and crunch the 4.98 WUs.


No "XS" is right Rosy just went to 5.01!! Great news for the Windoze folks (sorry Mac guy). So now maybe we can get down and crunch some serious proteins.

I have never seen a Release log for Rosy, but it would be a VERY nice and welcome addition. A lot of people would like to know what is going on when they get a new release.

Regards
Phil
37) Message boards : Number crunching : Report stuck & aborted WU here please - II (Message 14157)
Posted 20 Apr 2006 by Profile Snake Doctor
Post:
As a personal asside I might point out that the usefulness of your posting is directly related to the information you provide concerning the problem. Could you at least provide a link to the result ID so the problem can be examined?[/color][/b]


Ok after spending the last 1.5 Hrs looking I found it
Note the time sent and the time sent back over 104 that meens this job was on it's 3rd loop 48 + 48 + 7 Now look at the granted points 8.25156419314919
for for a job that ran for 104 Hrs
Now you can see why I was saying your Auto abort and your granting due credit is not working And the Real need to find a way to purge BAD WU's from the Rosetta Servers and the members clients.
It is unfaire for Rosetta to make us members pay the bills to purge the system of your Bad WU's
...

What is unfair is for people to bash the developers and the people who are trying to help you and others with the issues. The errors are frustrating for everyone most of all the project people. While I am sure it may be difficult for you to manage certain aspects of your farm if things aren't perfect, you built the farm. The work and expense is just part of what is required if you plan to run it.

While you have made it very clear that the 30 or so credits you may have lost on this WU should be the single most important thing in the universe to the project, just try to get ANY of the credits for a failed work unit on ANY of the other projects. (and yes ALL projects have failed WUs) The Rosy people are doing what they can on the credit issue, and it is a lot more than what you get from other venues. But there are other things going on right now, so they only do it once a week.

Why don't you just post the error, with sufficient information to help them fix the problem without all the bashing of the project people. It has already been explained that BOINC does not allow the project to remove WUs from your system and why. The only project that does this at all is CPDN and they are using a highly modified version of the BOINC client to do it. This project uses the standard BOINC package for everything, including the results pages. If you are having a problem with BOINC you should post the issue on the BOINC development site.

As for looking up the links to your results, have you tried bookmarking a separate page in your browser for each machine? It is very easy to do. That way you can isolate the results by machine, and monitor them individually if something comes up. That should help you find things. Also, if you reduce your connection interval and increase your time setting you will have fewer WUs to look through.
38) Message boards : Cafe Rosetta : Moderator contact thread archive (Message 13991)
Posted 18 Apr 2006 by Profile Snake Doctor
Post:

...
Yes it is spill over and you have just proved my point to Angus where he has deliberately spammed threads for the only fact that they were closed by the thread author. Thank you!

There have been more supporting evidence but this was the original post. Since the acct name was just recently changed you'll have IP info to go with it. Admin can check the weblogs against both accounts. As I have said previously you can delete this whenever you want as it was meant only for you mods.


"Misfit"
It occurs to me that this sort of thing might be handled better by using the mod9 e-mail contact. Especially since, as was noted, the wanky ID has not even posted here. If what you say is true, this sort of discussion will only serve to provide yet another opportunity for a flame war.

In my experience with his posting, he does not need much encouragement to set him off, and he certainly does not need to be provided the opportunity that this discussion provides him to spout off. From what I have seen, the Mods probably already know there is a problem anyway. Note his thread attacking the Rosie Mods for some supposed power grab, when in fact it was a CPDN mod.
39) Message boards : Rosetta@home Science : Information on Rosetta@home for the BBC (Message 13861)
Posted 15 Apr 2006 by Profile Snake Doctor
Post:
The thing that puts people off of CPDN most has nothing to do with downloads, uploads or bandwidth. The problem with CPDN is the level of dedication it requires. To complete a single model requires at least a month on a fast dedicated machine. Moreover, the models fail frequently, and do so after people have spend hundreds of hours running them. Most of the discussions on forums and Team sites from people who have left CPDN mention specifically the failing model wasting their CPU time as the reason they left the project.

Personally I left when they decided not to support Mac platforms. For me this was a matter of principal. I have a number Windows machines available to me and could apply them to any project, but I will not support a project that does not support the standard platforms supported by BOINC.

I think we can assume that people who sign up for BOINC projects have already demonstrated a level of commitment to the concept of DC. Part of that commitment is downloading the project and the WUs. While the landing page might mention the bandwidth required to load and run the project, I would not make a big deal out of that. If people connect and later find that the bandwidth requirement is beyond their level of commitment, then they have the option of disconnecting.

The Rosetta time setting if properly used can reduce the loading of WUs to a factor far less than other BOINC projects when measured over time.

I say invite the people in and let them decide if they want to stay. The big issue the project needs to worry about is fixing the last of the bugs, not compressing files. Most people will run the application if it will run without errors.
40) Message boards : Number crunching : Odd wu/wu behaviour? (Message 13706)
Posted 14 Apr 2006 by Profile Snake Doctor
Post:
17128664 seemed to be going wrong. It was still under 2% finished after more then an hour of crunching. It was moving, because I'd noticed it at 1.87% and later saw it had crawled to 1.9%, so not a 1% issue.

Thing is, next time I looked at it, ~5 minutes later, it was complate and ready to report. Note despite a 7200 seconds preference, it ran for a lot less.


The WU will start at 1%. Then there will be small increments as the WU goes through several stages of the first model (less than 1% total). After each model a larger jump in percentage is made based on how many models the rosetta app thinks it can do. If it doesn't think it can fit another model in without running too far over, the percent will jump directly to 100%.

That is the correct answer.


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