Posts by genes

41) Message boards : Number crunching : Help us solve the 1% bug! (Message 9008)
Posted 14 Jan 2006 by genes
Post:
OK, I've got one: stuck at 1%, 20+ hours of CPU on a P3 1GHz dual, running WinXP SP2, BOINC 5.2.15 client and 4 other BOINC projects (S@H, S@H Enhanced, E@H, and CPDN). I've suspended the WU, stopped BOINC, and I'll run the tests.
----
[edit]
When I ran it from the command prompt, it ran (and is continuing to run) normally. It's at 20% now.

WU name: PRODUCTION_ABINITIO_1iibA_239_573_0

WU link:
http://boinc.bakerlab.org/rosetta/workunit.php?wuid=5159485
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[edit]
The command line that I used:
projects/boinc.bakerlab.org_rosetta/rosetta_4.81_windows_intelx86.exe xx 1iib A -output_silent_gz -silent -increase_cycles 10 -nstruct 10 -constant_seed -jran 1248601
[/edit]

I'm going to stop the command-line app and let it run again normally.
[/edit]
42) Message boards : Rosetta@home Science : Graphics (Message 7709)
Posted 27 Dec 2005 by genes
Post:
Mostly to Jack, regarding the graphics in 4.81. The ability to spin the native form is nice, but a little hard to control, in my humble opinion.

You're doing a rotation, but the center of rotation seems to be a fair distance from the molecule, which means that as I rotate, the molecule tends to swing out of the viewport.

Is there any way you can make the following three points always conincident:

The center of the viewport, the "center" of the molecule, and the center of rotation. That might make things a little more useful.


Please see this thread:

http://boinc.bakerlab.org/rosetta/forum_thread.php?id=755
43) Message boards : Rosetta@home Science : 4.81 allows rotating the protein... anybody try it? (Message 7333)
Posted 23 Dec 2005 by genes
Post:


David Kim is actually the one who put in the rotation, must give him credit. I hope to fix the lines problem and add some other features over the holidays, but no promises.



Well, thanks to David Kim as well! You guys are doing super work, and this really helps the visualization a lot.

The most important thing, of course, is to make sure the errors get sorted out - we can wait for the graphics fixes.

Thanks again :-)
-Gene
44) Message boards : Rosetta@home Science : 4.81 allows rotating the protein... anybody try it? (Message 7328)
Posted 23 Dec 2005 by genes
Post:
I'm glad to see you guys noticed the rotation of the native. It's sort of an documented easter egg until we improve the issues that you saw with the center of rotation. You also might notice that little black outline around the chain doesn't stay in a consistent place and sometimes looks funny. This will be attended too once we are running stably again.


Thank you Jack for the great work! It's nice to have the interactive graphics. Yes I see what you mean about the black outline looking funny at certain angles. Kind of looks like you're rotating a 2-D object in 3-D space, then you're seeing it on-edge (some of the segments, anyway).
45) Message boards : Rosetta@home Science : 4.81 allows rotating the protein... anybody try it? (Message 7166)
Posted 22 Dec 2005 by genes
Post:
I saw in one thread that 4.81 allowed you to rotate the native protein molecule, so I tried the obvious - left-click and drag. And yes! it works!

OK, is it just me or does it seem that the axis of rotation is fixed? No matter where I click, the molecule rotates about the same fixed point. When I get near the orientation that lines it up with the search result, it goes offscreen. I tried right-clicking, holding ctrl, shift, etc., no difference.

Are there other controls I haven't figured out?

46) Message boards : Number crunching : Red Squares in Graphics (Message 5913)
Posted 12 Dec 2005 by genes
Post:
They are actually the lowest energy points found during the "full-atom relax" stages (1 per stage). You won't see any until you've done at least one full-atom relax, or at least 10% complete.
47) Message boards : Number crunching : Screensaver crashing computer (Message 5079)
Posted 4 Dec 2005 by genes
Post:
Here's a link to the ATI thread over at Seti:

http://setiathome.berkeley.edu/forum_thread.php?id=12948

and another one:

http://setiathome.berkeley.edu/forum_thread.php?id=20285

There may be some suggestions there that can help...
48) Message boards : Rosetta@home Science : Graphics (Message 4447)
Posted 27 Nov 2005 by genes
Post:

I thought the new font was a little harder to ready too. But it has the advantage of not requiring the glut32.dll, and also being scalable. So you can make your window larger, and you should be able to see it more clearly.



Seti uses this font, but I think they set it to boldface. That definitely makes it more readable: the i's and l's don't get lost between pixels.

CPDN and Einstein use a different font which doesn't scale, but they space the lines so as to be just barely separate on a small window, and when you make it larger there is a lot of space between the lines. This works as well.

BTW, Thanks!
49) Message boards : Number crunching : Have Graphics Arrived? (Message 4415)
Posted 27 Nov 2005 by genes
Post:
Hi genes,
The display is an Intel 82915g/gv/910gl pci Express Chipset family.(that came directly out of the device manager). I have again tried to get the graphics working, but still no go. I am at a loss.
Thanks also for the link to the thread.


I did a search for your display chipset in this thread:

http://setiathome.berkeley.edu/forum_thread.php?id=12948

Someone _was_ reporting a problem with it. Most of the problems are with ATI, though, as you will see. Have you tried updating the driver?

Can you run any other Boinc projects and see graphics?

[edit] This thread at CPDN mentions an Intel Graphics chip working after updating the driver (it's not your chip, but still...)

http://climateapps2.oucs.ox.ac.uk/cpdnboinc/forum_thread.php?id=2379
[/edit]
50) Message boards : Cafe Rosetta : Screensaver? (Message 4298)
Posted 25 Nov 2005 by genes
Post:
None of the Boinc "screensavers" that I've seen to date are completely free of static components, so they would not qualify as true screensavers as such (except for the Boinc default screensaver, used when a project has no graphics). However, there are three things you can do that will help to insure that your screen doesn't get burned in (some LCD's can get burned in, btw):

1. Enable "go to blank" in the screensaver settings dialog and/or monitor power off.
2. Run more than one Boinc project. Then you will see different graphics from time to time, not always the same one.
3. If you have a multiprocessor computer or one with hyperthreading, allow Boinc to use more than one CPU. Then, Boinc will switch screensaver graphics every 10 minutes while the screensaver is running. (Happens when two graphics-capable projects are running)

[edit] If you are worried about the start button, you can set the task bar to "auto-hide". Then, you get the whole screen for your apps, and the button only shows up when you need it. [/edit]
51) Message boards : Number crunching : Graphics - erroring out (Message 4259)
Posted 25 Nov 2005 by genes
Post:
I had the same thing happen. They are working on eliminating the need to send out glut32.dll with the app, but in the meantime you could just put a copy of it in your system folder.

You can find it here, among other places:
http://www.xmission.com/~nate/glut.html
52) Message boards : Number crunching : Have Graphics Arrived? (Message 4257)
Posted 25 Nov 2005 by genes
Post:
Today I received my first two WU's with graphics. The WU's were distributed to two seperate machines, a n Intel 2.6 ghz celeron, and an Intel Pentium 4 dual core 3.0 ghz. The celeron is displaying the graphics perfectly with no problems. However, the dual core will not display the graphics at all. When the screensaver engages, the screen just goes blank. This happens even when I suspend everything else that is running in BOINC. I cannot start the graphics even if I try to do it manually by clicking on the 'show graphics' button.
...thought you might find that interesting.


Are you running an ATI card on the dual core? Boinc graphics do not run reliably on them. I have a dual core machine at work with an nVidia card in it and the graphics run perfectly (which didn't when I had an ATI)


Also, on a different topic, can you direct me to a page that will explain the screensaver in some detail, along with some of the science involved, so that I can understand what I am looking at. Thanks


They are currently working on a page to explain the graphics, but there is plenty of info in this thread:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=252
53) Message boards : Number crunching : @Admins: quorum of 3 results needed (Message 4256)
Posted 25 Nov 2005 by genes
Post:
I know this may sound simplistic, but, if everybody was running the optimized clients, along with optimized science apps (of course, optimized for every CPU and OS combo), there would be no way to "cheat by optimization", and the projects would get more work done. It's a win-win situation.


I'm sorry but here's a resounding 'NO'. This is a common misconception! At the moment optimized clients just affect benchmarks - they don't change how fast you process a WU - as the rosetta code is not yet open source.

So what that means is that at the moment, 1) some optimized clients geniunely try to even the playing field (ie. linux vs window), and 2) others return grossly inflated benchmark numbers (which can be considered involuntary cheating). Then, 3) there's an even more hardcore group of people who actually spend time modifying the stock or optimized clients with the sole purpose of cheating.

But, at the end of the day, they all return the same science. A WU is a WU, wether it grants the host 10 or 1000000 credits.


This is all an argument for closing up the source to everything, period. And I agree, especially since once the science code is open it is subject to being messed with to the point where it returns erroneous results. Hence actually needing a quorum of three, which this project can live without since the code is not open.
54) Message boards : Number crunching : @Admins: quorum of 3 results needed (Message 4217)
Posted 25 Nov 2005 by genes
Post:
I know this may sound simplistic, but, if everybody was running the optimized clients, along with optimized science apps (of course, optimized for every CPU and OS combo), there would be no way to "cheat by optimization", and the projects would get more work done. It's a win-win situation.

The only problem, of course, is compiling all those optimized versions of things. Funny, though, the people who want them seem to have no problem getting/making them. They should be made available to all, have no drawbacks for running them (i.e. the optimized versions usually have no graphics support), and be supported by the projects. Otherwise, when new versions of the science apps come out, you end up still running your old optimized version, possibly creating erroneous results. [edit] This was seen repeatedly on the Seti Beta project, until the creator of the optimized version of the app himself asked everyone to stop for the good of the project. [/edit]

[edit] See this post -- http://setiweb.ssl.berkeley.edu/beta/forum_thread.php?id=99
[/edit]

I don't run the optimized versions of anything because of that last caveat, and nobody else should either. Only when the project supports them should they be run. There. Go ahead and disagree.
55) Message boards : Rosetta@home Science : Graphics (Message 3858)
Posted 22 Nov 2005 by genes
Post:
Further observations on graphics ;-) -- I let it run as a screensaver for a while, as opposed to "show graphics". On a dual processor machine, it switched back and forth with the graphics of the other running project without a hitch, and no fighting with the screensaver was necessary to regain control of the machine (Think LHC). Great job!
56) Message boards : Rosetta@home Science : Graphics (Message 3852)
Posted 22 Nov 2005 by genes
Post:
Got one, and it just started running! This time it didn't error out like my earlier one -- I put a copy of glut32.dll in my system folder just in case.

This is very cool stuff. You actually get to see the protein moving around, changing shape and settling down to a low energy state! There's a graph along the bottom showing energy, and one up the right side showing RMSD, and the intersection of the two graphs plots a 2-D chart like the ones in the results area of the home page, in addition to two views of the protein shifting around. Really nice stuff!! Everyone's gonna love it.
57) Message boards : Number crunching : Have Graphics Arrived? (Message 3850)
Posted 22 Nov 2005 by genes
Post:
Well, I got another graphics WU (hasn't started yet), and just in case, I put a copy of glut32.dll in my system folder. It can't hurt to have it anyway.
58) Message boards : Number crunching : Have Graphics Arrived? (Message 3816)
Posted 21 Nov 2005 by genes
Post:
Aaack! I got a graphics beta WU, and it errored out! This from the message log:

11/21/2005 12:51:37 PM|rosetta@home|Starting result 1hz7A_abrelaxmode_random_gauss_fix_bb_jitter03_103133_5 using rosetta_graphics_beta version 479
11/21/2005 1:15:38 PM|rosetta@home|Unrecoverable error for result 1hz7A_abrelaxmode_random_gauss_fix_bb_jitter03_103133_5 ( - exit code -1073741515 (0xc0000135))

There was a message box complaining that "glut32.dll" was not found. No mention of this in the log.

I'm running WinXP SP2, and I've got an nVidia FX5950 installed, with nVidia driver version 78.01.
59) Message boards : Number crunching : Have Graphics Arrived? (Message 3771)
Posted 20 Nov 2005 by genes
Post:
None here yet. I just checked my results to see if one might have gotten sent to a machine at work, but nothing there either.
60) Message boards : Rosetta@home Science : Graphics (Message 3467)
Posted 17 Nov 2005 by genes
Post:
Woohoo! Can't wait to see the new graphic WU's! I've upped my Rosetta resource share in anticipation!


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