Posts by Christoph

1) Message boards : Number crunching : Minirosetta 3.14 (Message 70656)
Posted 28 Jun 2011 by Christoph
Post:
With the three stuck workunits I have at the moment, I can confirm that they seem to get stuck right after a checkpoint, maybe even at the checkpoint itself.

The three workunits are:
http://boinc.bakerlab.org/rosetta/result.php?resultid=432501911, last checkpoint: 8:38:03, cpu time: 8:38:04
http://boinc.bakerlab.org/rosetta/result.php?resultid=432531601, last checkpoint: 8:25:02, cpu time: 8:25:03
http://boinc.bakerlab.org/rosetta/result.php?resultid=432552233, last checkpoint: 6:24:59, cpu time: 6:24:59

I used Process Explorer to take a look at the threads and call stacks of one of those and posted them here, hope they are somewhat helpful.

Then I noticed that one of the threads is in suspended state, manually resumed it and the WU continued fine without problems. This has worked for all three workunits that I've tested. Looks to me like the worker thread isn't resumed after a checkpoint was done.
2) Message boards : Rosetta@home Science : Rosetta Active Workunit Log (Message 69904)
Posted 27 Mar 2011 by Christoph
Post:
Just wanted to add that the screensaver is actually capable of showing a small description of what the workunit is doing. This had been used a while when that feature was added to Rosetta, but I haven't seen any workunit that used this the last two years or so.
3) Message boards : Number crunching : Protein name in the graphics (Message 61089)
Posted 10 May 2009 by Christoph
Post:
Good idea! Currently you can get the PDB id by looking at the workunit name. For example "lr8_fast18_score12_rlbd_1acf_IGNORE_THE_REST_DECOY_11814_1264" works on 1acf.
4) Message boards : Number crunching : Certificate - small thing but makes lots of fun :) (Message 60777)
Posted 22 Apr 2009 by Christoph
Post:
http://boinc.bakerlab.org/rosetta/cert1.php ;)
5) Message boards : Rosetta@home Science : IGNORE_THE_REST (Message 58248)
Posted 30 Dec 2008 by Christoph
Post:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=2729
6) Message boards : Number crunching : Screen Saver question (Message 57627)
Posted 5 Dec 2008 by Christoph
Post:
I've never seen so many "red" dots before.

Is this normal?

It's a very small protien. That's why Rosetta was able to compute so much models in 2,5 hours.
7) Message boards : Number crunching : Problems with Rosetta 5.95 (Message 51959)
Posted 15 Mar 2008 by Christoph
Post:
It's simply amazing how a new release can be a minor bug fix on Ralph,
The Ralph executable has been updated to 5.95. This version fixes a small bug in the previous version.

but when it gets to Rosetta (after only 6 days of testing) it is a major change in process.

The previous version on Rosetta@home was 5.93 and with 5.94 they released that new feature.
8) Message boards : Rosetta@home Science : Energy and RMSD box (Message 51757)
Posted 2 Mar 2008 by Christoph
Post:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1754&nowrap=true#26632
9) Message boards : Number crunching : Memory Usage in Beta 5.80 (Message 46366)
Posted 16 Sep 2007 by Christoph
Post:
http://boinc.bakerlab.org/rosetta/result.php?resultid=105599697
Upload = 14 Mb
OMG !!!!!!!!

Weird. This one created 1630 models and he got more than 560 credits for 1 workunit!
10) Message boards : Number crunching : German: Boinc Error, tasks overdue (Message 45995)
Posted 11 Sep 2007 by Christoph
Post:
Hi pool, Wilkommen bei Rosetta@home! :)

Die Fehlermeldung bedeutet eigentlich, dass das Abgabelimit der Workunit um 26 Tage überschritten wurde, und du deswegen möglicherweise keine Credits dafür gutgeschrieben bekommst. Das Limit liegt derzeit bei 10 (oder warens 14?) Tagen, d.h. du musst deine Workunit innerhalb von 10 oder 14 Tagen zum Server zurückliefern. Aber da du ja erst seit gestern dabei bist, kann das nicht ganz korrekt sein. Auf die schnelle fällt mir nur ein, deine Computeruhr zu überprüfen, ob die richtig stimmt (ansonsten mal mit nem Zeitserver synchronisieren oder so).
11) Message boards : Rosetta@home Science : Graphics show dark when roatating molecular structure (Message 44215)
Posted 25 Jul 2007 by Christoph
Post:
I suggested they keep the orientation of the virtual sun fixed so that it is always the same in all the boxes.

I agree.

What about showing this light source in the other display modes too? It would probably slow down the graphics a bit, but I think it would look really nice.
12) Message boards : Number crunching : lookup_account.xml - cleartext acckey? (Message 43344)
Posted 7 Jul 2007 by Christoph
Post:
Every encryption can be decrypted, except if the encryption key is not stored on your disk. That is, you have to enter everytime the password when you start BOINC. And even then, one could read the password out of the memory.
13) Message boards : Number crunching : Anybody ever have this happen? (Message 41763)
Posted 2 Jun 2007 by Christoph
Post:
Hi Rob,

this is absolutely normal. BOINC downloaded a new workunit because your first one would be finished in a few minutes. Then the second one started crunching, the first one stopped. You don't have to do anything, BOINC does everything for you. ;) You could manually set "No new work" and stop the second workunit, and you'll see that the first one will continue.

EDIT: Too late. :/
14) Message boards : Number crunching : Stop or pause BOINC at next checkpoint. (Message 41303)
Posted 22 May 2007 by Christoph
Post:
Hi christoph

I've just run the util on a PC that i'm setting up. Only problem is the exe is looking for BOINC in c:program filesboinc while mine's installed to h:boinc

Any chance you could make it configurable?

cheers!
Danny

Hi,

it's already configurable! (run "sacp.exe /?")

Make sure you specify the path to client_state.xml (in your BOINC directory) if sacp.exe can't find it.


sacp.exe /P "H:BOINCclient_state.xml" /R ...

But it seems the app is still very buggy, especially when a workunit finishes. I'm trying to sort out this problem.
15) Message boards : Rosetta@home Science : Suggestions for improvement thread (Message 41301)
Posted 22 May 2007 by Christoph
Post:
How much processing power does calculating the RMSD for every possible 'structure' use? Wouldn't it be more efficient to just calculate the RMSD for the lowest energy structure of each model? (the only one that actually gets submitted)

Yes, it would be more efficient, but then you wouldn't have a RMSD graph in the screensaver and you couldn't compare the energy with the RMSD.

Here are my suggestions:
- It would be great if you could extend the current WU explanation in the screensaver to show the RCSB protein id, the sequence length and the full protein name (the one shown on each RCSB protein page)
- As Admin already suggested, perhaps you could show the the lowest RMSD and Energy in the screensaver (perhaps in brackets after the current value)
- As far as I know, the best structure of each model (shown in the plot as red dots) isn't shown in the screensaver, when the app restarts from a checkpoint. Perhaps you could save this information at a checkpoint.
16) Message boards : Rosetta@home Science : Recent proteins look cool (Message 40944)
Posted 14 May 2007 by Christoph
Post:
They are just bigger proteins, not really something new.
17) Message boards : Rosetta@home Science : CREDIT what is this for? (Message 40767)
Posted 12 May 2007 by Christoph
Post:
What are credits?

What's RAC?
18) Message boards : Number crunching : Optimum CPU Run Time (Message 40364)
Posted 5 May 2007 by Christoph
Post:
does it make any difference for the project whether I crunch (let's say) 3 wus with 4 hour runtime, or just one wu with 12 hours runtime per day?


Really the scientific result is the same. And the credit would be the same as well. The main difference is bandwidth, and number of results, and what is easy for you to manage with getting new work etc. Even if you have a full-time high bandwidth internet connection, there's really no reason to download 3 times as many tasks.

So go with the runtime that suits your situation. And keep in mind that you can designate a different runtime for different BOINC locations too. So you can tailor each machine if you have more then one.
* Suppose 100 WUs for one protein are sent out, everybody crunches just a single model. You'll get a chart of 100 models.

* However if everybody crunches 100 Models, you'll get 10000 models for that proetin, that would be far more precise!

If you set your WU runtime to 2 hours, your computer will generate x models for 1 protein. If you set it to 1 hours, your computer will generate in the same time x/2 models for 2 proteins, and so on.. It doesn't matter which runtime you select, the computation power is always the same.

19) Message boards : Rosetta@home Science : Where we are and where we are going. (Message 40084)
Posted 30 Apr 2007 by Christoph
Post:
You can find more information about the protein computed in your WUs by entering the identifier of the protein in the search box on the website of the RCSB PDB.
The identifier is always included in the WU name. For example:
FRA_a009_STRUCTURAL_GENOMICS_hom001_4_a009_4_1o6eA_IGNORE_THE_REST_190_1637_14
Hope that helps.
20) Message boards : Number crunching : Stop or pause BOINC at next checkpoint. (Message 39154)
Posted 8 Apr 2007 by Christoph
Post:
I've written a little tool, called stopatcheckpoint :P. You can download it here. You can start the batch file to shutdown your computer if the result 0 checkpoints. Feel free to edit the batch file and replace the shutdown with something other. You get the result id for any running workunit by calling "sacp.exe" without parameters. Make sure you specify the path to client_state.xml (in your BOINC directory) if sacp.exe can't find it. There are a few other options, just call "sacp.exe /?" and a little help is shown.


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