Posts by rbpeake

1) Message boards : Rosetta@home Science : What is a "Decoy"? (Message 53693)
Posted 14 Jun 2008 by Profile rbpeake
Post:
This is probably quite a basic question, but I found no reference to it.....

1. For the results we return, what is the difference between a "starting structure" [always just one returned], and a "decoy" [multiple ones returned per run]?

2. Is the starting structure a basically stable structure, and then the decoys are results of "fine-tuning" the starting structure to get an even lower energy?

3. And lets say there was no limit on run time, would there be an almost endless number of decoys for each starting structure?

4. And why not allow run times of longer than a day, in order to generate the maximum number of decoys?

Thanks!
2) Message boards : Cafe Rosetta : New Protein Folding Project on BOINC...POEM@home (Message 47831)
Posted 18 Oct 2007 by Profile rbpeake
Post:
Just forget it, I am out of here.

That wrong opinion is not related in any way to Rosetta, so perhaps you might consider reconsidering because your action is against the project which is innocent. Just imho.
3) Message boards : Cafe Rosetta : New Protein Folding Project on BOINC...POEM@home (Message 47815)
Posted 17 Oct 2007 by Profile rbpeake
Post:
Brand new protein folding project, with this group having used Rosetta it would appear.
4) Message boards : Number crunching : Best Computer Features for Crunching (Message 47003)
Posted 26 Sep 2007 by Profile rbpeake
Post:
I always fail to see the "wait 3 months because the XXX...", because in 3 months the same will be said of the XXX+!.

Propose an economic system from readily available components today...

Good point! I have been waiting and waiting, but part of that is because my AMD Athlon 1.2GH is still running OK and I overclock it about 12%. But it is almost 8 years old, although I have put more RAM into it to keep it young! ;)

That being said, I will seriously be in the market to buy a new system at the beginning of 2008, and am thinking perhaps a quad core Penryn.....I must make the leap! ;)
5) Message boards : Number crunching : Discussion of Rosetta memory requirements (Message 46925)
Posted 24 Sep 2007 by Profile rbpeake
Post:
i dont really think thats a good way of thinking, it probs is going to mean you should buy 2 2048 sticks, ur willing to pay for that?

Depends what I want to do and how much I am willing to pay for it, I guess. If I like crunching memory intensive BOINC applications on all 4 cores, then I guess I would need to unless I want to slow my machine down, or limit crunching to maybe 2 cores and not 4. :)
6) Message boards : Number crunching : Please Add Opt-Out Option for Beta Workunits (Message 46874)
Posted 24 Sep 2007 by Profile rbpeake
Post:
...How can that possibly be adequate testing? Less than 24 hours? Get real.

Sounds like a judgment call that went bad...

Hopefully this will be remembered in the future, but to their credit, I think they were onto the problem pretty quickly with the bad CAPRI units (although admittedly there should not have been a problem that was let loose onto Rosetta in the first place! ;)
7) Message boards : Number crunching : Discussion of Rosetta memory requirements (Message 46872)
Posted 24 Sep 2007 by Profile rbpeake
Post:
...My solution was to buy another stick of RAM for $40. :)

I am thinking of buying my first multi-core machine soon, and thanks for the heads-up that every individual core really needs as much memory as a single core machine does. That being said, if I decide to get a 4-core machine, I should probably up the ante and buy 4GB of RAM as well!
8) Message boards : Rosetta@home Science : ferredoxin-like WUs (Message 46802)
Posted 22 Sep 2007 by Profile rbpeake
Post:
Just so you are aware of it, the moderators are not in a position to address such scientific questions, nor to update the active work units log, nor to create a page with work unit progress etc. The knowledge, databases and skills required to do that are all within BakerLab.

May we respectfully suggest that the moderators pass this request along to the Baker Lab people, so they can address it as they see fit. Thanks! :)
9) Message boards : Rosetta@home Science : Help me explain the science behind Rosetta@home! (Message 46801)
Posted 22 Sep 2007 by Profile rbpeake
Post:
I recently learned about some of the different types of mathematics used in computational chemistry. It seems there is a branch of computational chemistry that uses deterministic methods, and another that uses probabilistic methods, and each has its use depending on what you want to do and the problem at hand!

I found it extremely fascinating, and so perhaps a subtopic explaining computational chemistry methods and how and which are used by Rosetta I think would be very interesting! :)
10) Message boards : Rosetta@home Science : ferredoxin-like WUs (Message 46777)
Posted 22 Sep 2007 by Profile rbpeake
Post:
These new WUs sound interesting, what are they used for?..

For the moderators, this comment of course goes hand in hand with the comments about updating on a regular basis the Active Work Units Log thread. ;)
11) Message boards : Number crunching : TFlops (Message 38130)
Posted 22 Mar 2007 by Profile rbpeake
Post:
....Here is a link to a graph (third one down) which shows the number of ACTIVE hosts on Rosetta:
http://www.boincstats.com/stats/project_graph.php?pr=rosetta&view=hosts
The graph seems to illustrait that the project is large enough now that you will have to attract 100s of new users each day just to break-even with the ones that leave.

Over time though, hopefully, more and more people will realize that these are worthy projects and they will do great things for mankind.


That is an interesting observation, the project seems to reach a certain state of equilibrium. Seems like other projects have a similar experience, of course, which makes sense. Just to maintain equilibrium is a worthy goal, and hopefully with news, publicity, the You Tube promotional piece, etc., the equilibrium can be kicked up a few notches! :)
12) Message boards : Number crunching : Report problems with Rosetta version 5.36 (Message 30508)
Posted 2 Nov 2006 by Profile rbpeake
Post:
This one ran more than 30 minutes over my 8 hour preference, which is very unusual. I aborted it.

Here it is.

13) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (2) (Message 23529)
Posted 19 Aug 2006 by Profile rbpeake
Post:
Yes, some excerpts from the Grid Computing conference would be very interesting and much appreciated! :)
14) Message boards : Number crunching : New credit system now being tested at RALPH@home (Message 22088)
Posted 9 Aug 2006 by Profile rbpeake
Post:
Just curious. Would Rosetta's total project points have to be separated as well? How would this display on Rosetta's Serverstats "Total Credits" and how would Boinc Stats be affected? I assume that "Boinc Stats" reporting would still show only total credits.

I am probably getting too complicated, but given the difference of opinions here maybe it is worth at least floating this idea:

Have two playing fields: One would be to leave the existing credits as is and the new credit system would build on that (Call this Option A); and the second option (Option B) would be an option for the user to switch to the level playing field while keeping the old credits as an historical record, much as rcofell suggests below.

I realize then you would really have two credit systems for the same project, but whichever one felt more comfortable with is the one that one could choose.

Just a thought...
15) Message boards : Number crunching : New credit system now being tested at RALPH@home (Message 22084)
Posted 9 Aug 2006 by Profile rbpeake
Post:
Why should the users who have been using stock managers, clients and stock-clocked machines have to start at 0? It's not wise to punish the innocent.

I agree! I am proud of the honest effort I have put into obtaining my score, and to lose it through no fault of my own would be very frustrating. These many months for naught! I would probably go to another project where I would not be "cancelled". :)
16) Message boards : Number crunching : 5.5.10 Is troubled (Message 22003)
Posted 8 Aug 2006 by Profile rbpeake
Post:
5.5.11 for windows is now up!
17) Message boards : Number crunching : 5.5.10 Is troubled (Message 21910)
Posted 5 Aug 2006 by Profile rbpeake
Post:
I read your post, Tony, after I had switched my PC at work yesterday over to 5.5.10. Fortunately, the problem does not seem to be effecting my two machines, so thank goodness it is not a universal problem. Whew! :)

But I hope they release 5.5.11 soon!
18) Message boards : Cafe Rosetta : Moderator contact thread archive (Message 18396)
Posted 10 Jun 2006 by Profile rbpeake
Post:
...The only problems I can see are related to the short deadlines for CASP. If the machine is really slow, you might want to run it with the shortest time setting (1 or 2 hours) so it can meet the deadlines.
I think you mean to say to run at a longer time setting, since it will take a slow machine a long time to even do one variant. If the setting is left at 1 or 2 hours, the user should be aware that the runs will probably last longer because the software will not quit until one variant is achieved.
19) Message boards : Number crunching : Report Problems with Rosetta Version 5.22 (Message 18306)
Posted 9 Jun 2006 by Profile rbpeake
Post:
I get the following report with the new 5.22:

Result ID 23395831
Name t306__CASP7_JUMPRELAX_SAVE_ALL_OUT_BARCODE_hom001__656_21236_0
Workunit 19711334
Created 8 Jun 2006 22:11:53 UTC
Sent 8 Jun 2006 23:44:52 UTC
Received 9 Jun 2006 11:22:33 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x0)
Computer ID 246538
Report deadline 15 Jun 2006 23:44:52 UTC
CPU time 21089.578125
stderr out <core_client_version>5.3.12.tx36</core_client_version>
<stderr_txt>
# random seed: 1831515
# cpu_run_time_pref: 21600
# DONE :: 1 starting structures built 21 (nstruct) times
# This process generated 21 decoys from 21 attempts


BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...

</stderr_txt>


Validate state Valid
Claimed credit 71.993372528454
Granted credit 71.993372528454
application version 5.22

In other post I have see that someone also reported that Watchdog has shutting down the process.

Regards,
Ricardo

This is a normal shutdown for a successfully completed workunit.

The note regarding the watchdog is just to identify that now that the work unit has finished, the watchdog function is being closed down as well.
20) Message boards : Cafe Rosetta : Request from a journalist (Message 17633)
Posted 5 Jun 2006 by Profile rbpeake
Post:
The national version of my story went out today, so it should be in papers and on Web sites around the nation tomorrow morning.
Donna

Great news! Thanks for the update!


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