Posts by darkpella

1) Message boards : Number crunching : Minirosetta 2.00 (Message 64232)
Posted 26 Nov 2009 by darkpella
Post:
I'm also seeing a considerable number of WUs with errors similar to those posted by others recently.

.....


Similar here with the following WUs:
299885240
299643164
299547442
298811740

stderr is slightly different though. stderr from my WUs is like:
<core_client_version>6.6.38</core_client_version>
<![CDATA[
<message>
Funzione non corretta. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
[2009-11-24 9:22: 6:] :: BOINC:: Initializing ... ok.
[2009-11-24 9:22: 6:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
Loaded options.... ok
Processed options.... ok
Initializing random generators... ok
Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/yfsong_lr8_combine_smooth_torsion_it00_rama06_A.zip
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/lr8_1shf.out.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Fullatom mode ..
ERROR: Value of inactive option accessed: -score:dun08_dir


</stderr_txt>
]]>


while the one from some of bruce's WUs is like:
<core_client_version>6.10.18</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
[2009-11-25 13:11: 0:] :: BOINC:: Initializing ... ok.
[2009-11-25 13:11: 0:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
Loaded options.... ok
Processed options.... ok
Initializing random generators... ok
Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/sel_core_1.0_low200_beta_low200_nostart.broker_corebuild.t313_.olange.boinc_files.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.

ERROR: res1 != res2
ERROR:: Exit from: ....srccorekinematicsFoldTree.cc line: 2342
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


</stderr_txt>
]]>
2) Message boards : Number crunching : Problems with web site (Message 49208)
Posted 29 Nov 2007 by darkpella
Post:
Hi,

guess this doesn't belong right here but, as you will see, I got no chance to post it where it belongs..

In the last couple of days RALPH is totally unreachable: can't report WU that were already uploaded, cant upload newly finished WUs, cant' fetch scheduler list, can't access website itself...

Any idea about what's going on and how long this will last?

Bye

darkpella
3) Message boards : Rosetta@home Science : Help me explain the science behind Rosetta@home! (Message 45543)
Posted 28 Aug 2007 by darkpella
Post:
Hi,

I do have two points I could not really understand in the explanation I found here about what rosetta basically does.

In this page, if I understood it right, it is told that, starting from one point in the trajectory (current "accepted" configuration) Rosetta will try to move a bit some part of the amino-acid chain in a random manner and then decide whether this new configuration can become the new "accepted" one based on the energy of this "trial" configuration. If so, the "trial" becomes the new "accepted" configuation and the process starts again modifying this new "accepted" configuration", otherwise the old "accepted" configuration is modified again in a different way to get a new "trial" one, the energy of which is then calculated to see whether this new "trial" can be taken as the new "accepted" and so on.
The subsequent "accepted" configurations form a trajecory. Rosetta keeps track of what the lowest energy "accepted" configuration found along the trajecory is, then, when the trajecory calculation end, takes this lowest energy configuration as the best prediction for that trajectory. 5 to 20 trajectories are calculated for each WU and lowest energy configuration found among them all is returned as the best prediction for that particular WU.

Now the points I don't get are:

  • What criteria is used to decide whether the energy of the "trial" configuartion is right to make a new "accepted" one? It can not be simply that its energy is lower than the one of the "accepted" configuration it was obtained from, since otherwise the energy would be always reducing, hence the last "accepted" configuration would always be the lowest energy one, which is not what happens.
  • How does Rosetta decide that the calculation of a particular trajectory has come to an end? For the same reason as before it can not be that it has found a local minimum


Bye

darkpella

4) Message boards : Rosetta@home Science : CASP7 T0363 top predictions posted (Message 28491)
Posted 25 Sep 2006 by darkpella
Post:
From the front page.
----------------------------
Sep 25, 2006A
The predicted model from Rosetta@home for CASP7 target T0363 and the users whose computers generated the lowest energy models have been posted on the top predictions page.

....

Comparison of native structure (blue) and template (red) based prediction (green) with Rosetta@home, 1.65 Angstroms over 47 residues.

.....


Hi,
I noticed that the comparison in this picture is made among 3 different structures:
1. Native (green) structure, as published by CASP I guess, letting no questions arise about whre it comes from and why it takes part to this comparison.
2. Lowest energy (blue) R@H prediction, hence R@H best guess for the protein structure, also letting no basic questions arise.
3. A template (red) structure, the origin of which is not very clear to me... could someone tell me where this structure comes froma, and what should it add to the comparison between the native (or, better, CASP-published) structure and the R@H best guess one?

Thanks

darkpella
5) Message boards : Rosetta@home Science : Lowest energy structure and distance to true structure (Message 27572)
Posted 19 Sep 2006 by darkpella
Post:
Hi darkpella,

RMSD means "Root mean square deviation". It goes like this:

- Overlay both structures and measure the distances between calculated position and true position
- Square all distances
- divide the sum of all these squares by the number of all atoms
- take the square root of the result

Here is the formula explained in the Wikipedia.

(In fact you will find the closest match of both structures by first overlaying them roughly and calculating the RMSD. Then you optimize that until the lowest RMSD is reached which is your final value.)


Guess the optimization is done against the 6 DOF of a rigid body in the 3D space, ain't it?



After all we know natural protein folding does pursue the lowest energy structure. All structures of known proteins that were tested with Rosetta are at least somewhere near the energetic minimum and not in quite another theater. If Rosetta would work perfectly there would be a match of the lowest energy structure and the lowest RMSD structure.

Or almost a match, I guess there will always be little deviations, as you cannot measure all factors involved with absolute precision. There is still a lot of empirism in it as far as I understand it like Temperature effects or the effect of mineral concentrations in our cells' plasma.

In addition to that it is well possible that the protein structures as e.g. found in crystals are a little distorted due to packing effects and energetic differences between the surrounding in the crystal and in a living cell.

And finally the accuracy of the measured protein structures is limited, they mostly are known to something like 1 or 1.5 Angstroms if they are real good structures. In other words: you may find the almost true structure by simulation but still have an RMSD of 1 Angstrom in comparison to the otherwise determined structure because it is just wrong by that amount at average.


My aerodynamics teacher at college always told that, when experiments don't agree with predictions, it might be that predictions are wrong or that experiments are wrong (or both). Guess that's the case...


But above all that: Rosetta is currently under development and is still collecting information as to what current algorithms are best suited and what future algorithms might look like. There has never been as much computing power for it as there is today, so one might say that that field of research is still in its infancy.

To sum it up: if Rosetta did the job perfectly, then CASP would be unnecessary. We'd then have THE tool already and everybody would use that instead of trying to design their own one.



I'll let my PC go on crunching for R@H then (and for Predictor@Home either, as soon as they get back with their new prediction scheme)

Thanks for the explanation!

Bye

darkpella
6) Message boards : Rosetta@home Science : Lowest energy structure and distance to true structure (Message 27555)
Posted 19 Sep 2006 by darkpella
Post:
Hi,

I had a look at the top prediction page (http://boinc.bakerlab.org/rosetta/rah_top_predictions.php) and a pair of questions arose:

1. How is distance of a predicted structure to the true structure calculated (i.e. what does RMSD stand for)?
2. I noticed that the lowet energy structure and the lowets distance to true structure one are never the same . Does this mean that natural protein folding does not pursue lowest energy? What pursues R@H then? How can one possibly choose which prediction is the most accurate one among the many ones that come in, if the lowest energy criterion is not the right one?

bye you all!

darkpella
7) Message boards : Number crunching : Question on results of latest CASP (Message 27549)
Posted 19 Sep 2006 by darkpella
Post:
Hi,

does anyone know wether and where the results of the latest CASP can be found to see how R@H performed?

I read a messaage through RSS on R@H newsboard stating that the native protein structers of latest CASP proteins were eginning to be released, but didn't hear anything more about it therefater.

Bye you all

darkpella



You can try CASP7

BTW the official results will be announced at the 7th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction meeting to be held at Asilomar Conference Center, Pacific Grove, CA on November 26-30, 2006

Two shots, two kills, very good.
Thanks a lot for your prompt reply!

darkpella
8) Message boards : Number crunching : Question on results of latest CASP (Message 27544)
Posted 19 Sep 2006 by darkpella
Post:
Hi,

does anyone know wether and where the results of the latest CASP can be found to see how R@H performed?

I read a messaage through RSS on R@H newsboard stating that the native protein structers of latest CASP proteins were eginning to be released, but didn't hear anything more about it therefater.

Bye you all

darkpella
9) Message boards : Cafe Rosetta : Dr. Baker's plea... (Message 21203)
Posted 26 Jul 2006 by darkpella
Post:
Hi Dr. Baker,
on July 15 you asked the crunching community to increase the CPU % devoted to R@H for a couple of weeks, since a lot of CASPs were due in a short time.
Since the 2 weeks are coming to an end, I would like to know whether R@H will (likely) meet the delivery deadline for those CASPs.
By the way, could you notice any increase in resources devoted to R@H?

Apart from them, a small poll:
- Did you (crucnchers) read DB's request? (I did ;)
- Did you actually increase R@H resource share? to what extent? (I prevented all other BOINC-projects from getting new tasks).

That's all folks!
darkpella
10) Message boards : Number crunching : David, how's it going with the CASP due? (Message 21202)
Posted 26 Jul 2006 by darkpella
Post:
Hi David,
on July 15 you asked the crunching community to increase the CPU % devoted to R@H for a couple of weeks, since a lot of CASPs were due in a short time.
Since the 2 weeks are coming to an end, I would like to know whether R@H will (likely) meet the delivery deadline for those CASPs.
By the way, could you notice any increase in resources devoted to R@H?

Apart from them, a small poll:
- Did you (crucnchers) read DB's request? (I did ;)
- Did you actually increase R@H resource share? to what extent? (I prevented all other BOINC-projects from getting new tasks).

That's all folks!
darkpella

11) Questions and Answers : Windows : Not getting any further workunit (Message 12607)
Posted 24 Mar 2006 by darkpella
Post:
Hello,
Since some days I'm not getting any further workunit from any boinc project.
I got Boinc 5.2.13 on Win2k Pro and subscribed the following projects:
BBC Climate Change Experiment
rosetta@home
boincsimap
climateprediction.net
Einstein @home
LHC@home
QMC@home
SETI@home
SZTAKI Desktop Grid

I try updating these projects and/or rebooting, scheduler requests (when I update) succeed, but no new workunit is downloaded.
The only project running now is climateprediction.net, since it doesn't often require new workunits to work on.

Any idea about what the problem is?

Thanks darkpella






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