Posts by NJMHoffmann

21) Message boards : Number crunching : Report Problems with Rosetta Version 5.25 (Message 22408)
Posted 13 Aug 2006 by NJMHoffmann
Post:
Rosetta 5.25 writes its checkpoints before calculating, if it shouldn't stop now. With the actual betas of boinc this leads to the funny situation, that boinc waits for a checkpoint to switch task - sees the checkpoint - switches task - and Rosetta sits there with 100% done, till the other projects got their share, before the result is uploaded.

Norbert
22) Message boards : Number crunching : Lost 2h of work (Message 17762)
Posted 6 Jun 2006 by NJMHoffmann
Post:
Rosetta does checkpoint often. On my machine usually between 5 and 20 minutes but that might take longer on slow computers and on certain WUs.

E.g some ofthe t296__CASP_ABINITIO_SAVE_ALL_OUT workunits here have their first checkpoint after about 90-120 min. (2200+ AMD, 2400 INTEL)

Norbert
23) Message boards : Rosetta@home Science : Abort t283? (Message 17547)
Posted 2 Jun 2006 by NJMHoffmann
Post:
Please don't delete any jobs until the deadlines posted on the CASP website have been reached. For t283 we are continuing to do runs in hopes of finding still lower energy solutions. thanks, David

So t284 (haven't seen any of that) and t287 could (should?) be deleted? I have a y287 here with a deadline of june, 7th. Delete or crunch?

Norbert
24) Message boards : Rosetta@home Science : Abort t283? (Message 17536)
Posted 2 Jun 2006 by NJMHoffmann
Post:
Results from robots are already available.

I looked in Prediction receiving status and didn't find anything for BAKER-ROSETTADOM (is that what we crunch for?) now that 2 targets reached their deadline.

Norbert
25) Message boards : Rosetta@home Science : Abort t283? (Message 17531)
Posted 2 Jun 2006 by NJMHoffmann
Post:
We will submit these lowest energy structures for T283 this week


Does this mean t283 is done, and we should abort the remaining workunits on t283 to move on to the other problems?

When (and where) can we read about the first results at the CASP website?

Norbert
26) Message boards : Number crunching : users who run off-line are impacted by shorter deadlines (Message 17445)
Posted 31 May 2006 by NJMHoffmann
Post:
The __server__ ought to have recognized this, and not have downloaded so many WUs to my system.

This bug of the (server-side-)scheduler makes it (near) impossible for the user to set queue length and ressource share to values, that make the user and the project happy.

Norbert

(And then there is the bug at the users, that set their queue length near the deadline. This is only possible, if the host is connected to several projects and EDF can postpone some WUs.)
27) Message boards : Number crunching : users who run off-line are impacted by shorter deadlines (Message 17244)
Posted 27 May 2006 by NJMHoffmann
Post:
(But I really wish BOINC had the option to enable, 'finish job through to the end' rather than this swithing thing, there is loads of time to finish these shorter deadline jobs)

When the BOINC client will sometime be rewritten to match the specs (see: Client scheduling policies, CPU scheduling policies 6.), it will only start a new WU for the same project if the deadline is too near.

Norbert
28) Message boards : Number crunching : users who run off-line are impacted by shorter deadlines (Message 16999)
Posted 24 May 2006 by NJMHoffmann
Post:
Perhaps it is possible to set a deadline of min(14 days, days till needed for CASP). So some (most?) of the deadlines will still be 14 days.

Norbert
29) Message boards : Number crunching : Report Problems with Rosetta Version 5.16 I (Message 16873)
Posted 22 May 2006 by NJMHoffmann
Post:
What settings do you feel are not being respected by the current (improved) checkpointing?

I would interpret the setting "write to disk at most..." as: After a checkpoint wait for x seconds before a new checkpoint and then do it as soon as possible.

Norbert
30) Message boards : Number crunching : Report Problems with Rosetta Version 5.16 I (Message 16864)
Posted 22 May 2006 by NJMHoffmann
Post:
You are already using the version that has had checkpoints added. Originally the checkpoints only were done at the end of a full model. Now they are every ~20 min.

It's much better now and we loose less work with this shorter checkpoint interval. But if it is possible to insert checkpoints, why not respect the user settings?

Norbert
31) Message boards : Number crunching : Improvements to Rosetta@home based on user feedback (Message 16843)
Posted 22 May 2006 by NJMHoffmann
Post:
Actually there are a number of dates that are pertinent depending on the catagory of CASP in which a project submits its results. The dates you are seeing are for server predictions. The predictions that Rosetta is working on are in a different category. The reporting dates they are using have already taken into account the dates the project needs in order to meet the CASP deadlines for the category in which they will submit their results.

Are you shure? The CASP-website says the release date for the structure will be at the 4th of June.

Norbert

Edit: Just saw the answer of David Baker.
32) Message boards : Number crunching : Report Problems with Rosetta Version 5.16 I (Message 16589)
Posted 18 May 2006 by NJMHoffmann
Post:
With Rosetta 5.16 (and earlier) I see at the begin of the "relax"-phase the text "Accepted Energy" written into the low-energy-frame. The text is streched during the first steps until it is moved outside of the window. Hopefully the clipping of the graphics routines prevent bad sideeffects.

Norbert

What type of Work Unit is running just ahead of the CASP work. If it is a work unit that has a known structure, you could just be seeing image retention on the monitor.

I'm running only CASP-WUs at the moment. And it happens at the 2nd etc. model too.

Norbert
33) Message boards : Number crunching : Report Problems with Rosetta Version 5.16 I (Message 16558)
Posted 18 May 2006 by NJMHoffmann
Post:
With Rosetta 5.16 (and earlier) I see at the begin of the "relax"-phase the text "Accepted Energy" written into the low-energy-frame. The text is streched during the first steps until it is moved outside of the window. Hopefully the clipping of the graphics routines prevent bad sideeffects.

Norbert
34) Message boards : Number crunching : Report Problems with Rosetta Version 5.13 (Message 16411)
Posted 16 May 2006 by NJMHoffmann
Post:
I am still a little confused. Does the time to completion decrease after each checkpoint or does it decrease after each completion of a model?

The time to completion decrease happens only, when the percent completed is recalculated. For now this is done only when a model is finished. I would like a recalculation at every checkpoint (that should be possible).

Norbert
35) Message boards : Number crunching : Any Xtra Credit for Protein of the Day? (Message 12212)
Posted 18 Mar 2006 by NJMHoffmann
Post:
I was thinking most people would be against this, but lets hear some opinons. Yes/no, how much, how often?

No. Extra credits at a project is not better than cheating clients. Send a nice certificat to the user.

Norbert
36) Message boards : Number crunching : RAC cheats, is this a problem (Message 12210)
Posted 18 Mar 2006 by NJMHoffmann
Post:

This is why a total focus on RAC alone gives a poor measure of actual system performance.

You are right for RAC. But the reported invented benchmark results are really a pain. I think the way to go is an official (and only accepted) calibrating boinc client and calibrated projects(!). That would stop some of the discussions about cheaters. Plus: the projects had to "hunt" for crunchers with relevance of their science and not with "here you get more credits per minute".

Norbert
37) Message boards : Number crunching : Progress updating every 2% (Message 10745)
Posted 14 Feb 2006 by NJMHoffmann
Post:
When what BoincView logs is the truth, then those WUs even write checkpoints while the percent done does not change. (Even more often than is allowed by the preferences :-)

Norbert
38) Message boards : Number crunching : @ Dave Baker (Deadlines causes EDF) (Message 10201)
Posted 29 Jan 2006 by NJMHoffmann
Post:
I have some machines that are not frequently connected to the Internet so I have my cache set to queue 10 days of work and I sometimes can only connect once a week to upload.

I would let such machines work only on projects with deadlines of 14 days or more. Set the ressource share for Rosetta higer on the other computers.

If the Rosetta team needs the data back earlier, than seldom connected computers can't help. Has nothing to do with "penalize".

Norbert
39) Message boards : Number crunching : Controlling new work (Message 10126)
Posted 28 Jan 2006 by NJMHoffmann
Post:
...(it's the _only_ BOINC project on that system).

But when I connected this time, MORE 7-day-deadline WUs were downloaded -- __despite__ me having specified "no more work". WHY is the rosetta project not giving me control over what work my system does ?
.

It's the boinc client, that decides if a computer needs new work, the Rosetta application is not involved. And (IIRC) if there are no other projects to pull from (or all other projects have no WUs) then work is fetched from NNW-projects.

Norbert
40) Message boards : Rosetta@home Science : Feedback, .. bandwidth usage :-( (Message 8810)
Posted 11 Jan 2006 by NJMHoffmann
Post:
I don't know anything about the application used. So it may be totally nonsence what I write here.

Is it possible to split data the way Einstein does? That is: send one <large_file> (protein data?) and one WU (parameters for the algorithm) at first contact with the user. The next WUs only send new parameters as long as there are WUs for this protein. If all of them are done the next WU will contain the instruction to delete <large_file> and sends <next_large_file>.

Norbert


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