Report Problems with Rosetta Version 5.16 I

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Message 16412 - Posted: 16 May 2006, 22:40:59 UTC

Rosetta Version 5.16 has been released. Please report any problems in this thread.

The servers may be slow until the new application is distributed.

Version 5.16 has the following features;

(1) We're continuing our efforts to reduce memory usage by typical workunits by rosetta@home. You can expect an even further reduction in memory footprint in our next update.

(2) We're testing a new science mode which uses the sequence and structural information from homologous proteins in an early phase of the simulation, but then returns to the target protein sequence in the final refinement phase. This mode appears to have a larger memory footprint than typical workunits, so we will only send out these jobs to computers that have >1Gb RAM.

(3) Also, we're trying a new feature where at the end of a simulation, Rosetta compares its fold to the predictions made by a dozen other algorithms. (Those predictions are sent to the clients in a compressed format.) Seeing consensus between different algorithms is usually a good sign that a prediction is right.

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Seth Aaronson
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Message 16429 - Posted: 17 May 2006, 4:48:57 UTC - in response to Message 16412.  

It still seems to freeze my machine. This is now my latest error message:

5/16/2006 9:22:21 PM|rosetta@home|Unrecoverable error for result TEST_HOMOLOG_ABRELAX_hom003_1fna__503_50195_0 (Incorrect function. (0x1) - exit code 1 (0x1))

-Seth
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Message 16432 - Posted: 17 May 2006, 8:43:24 UTC

I also have these problems....

2006/5/17 04:20:58|rosetta@home|Unrecoverable error for result CASP_HOMOLOG_ABRELAX_hom001_t287__507_24798_0 ( - exit code -1073741811 (0xc000000d))

2006/5/17 04:35:49|rosetta@home|Unrecoverable error for result T0283_FACONTACTS_hom005_508_16246_0 ( - exit code -1073741811 (0xc000000d))


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Message 16437 - Posted: 17 May 2006, 12:41:58 UTC


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Message 16441 - Posted: 17 May 2006, 13:59:40 UTC

I run the latest boinc, 5.4.9, and lately i get this message that an error occured and it needs to close, so my result list says client error and lots of hours wasted. anyone else have this problem or can help? i run rosetta and seti on it.
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Message 16442 - Posted: 17 May 2006, 14:27:15 UTC
Last modified: 17 May 2006, 14:28:40 UTC

You should use this thread to post your issue(s).

Also, since your computers are hidden, posting the messages from your messages tab will help greatly.
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Message 16451 - Posted: 17 May 2006, 16:47:00 UTC - in response to Message 16442.  

You should use this thread to post your issue(s).

Also, since your computers are hidden, posting the messages from your messages tab will help greatly.


Sounds like a Windows error, so it may not be in the messages tab.

Leo, could you go in to your Rosetta preferences and show your computers. This will just let folks see what operating system you are running, basic system configuration and your WUs. It does not expose you PC to anything on the internet nor bring you any SPAM. But it will help us to better understand what you are describing.

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/
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Seth Aaronson
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Message 16455 - Posted: 17 May 2006, 17:35:23 UTC

I think my problem my be a Windows XP issue.
What is really the problem is that when the Rosetta .exe process throws an error, the Visual Studio JIT debugger catches it on my machine.
I have found a way to turn off the debugger:
http://www.hanselman.com/blog/HowToTurnOffdisableTheNETJITDebuggingDialog.aspx
I'll give it a try even though I think that Rosetta is not a .NET program. I don't really need the debugger anyway.
So, my hope is that after I switch off the debugger, Rosetta will just terminate and perhaps create a stack dump that I could give the Rosetta developers for analysis.

-Seth
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Profile Charles Dennett
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Message 16466 - Posted: 17 May 2006, 18:31:39 UTC
Last modified: 17 May 2006, 18:33:03 UTC

I think there may be a new problem on Windows 98 machines. I am aware of the problem where the RAH application is not reporting CPU time. My old slow Win98SE machine was exhibiting this problem for quite a while. However, I was able to run WUs just fine. I have the WU time set for 1 hour for this machine. However, because it is only a 300 MHz PII, it would take from 1 to maybe 4 hours to do one model. Even though the time was reported as 0, it would stop the WU, call it complete and report it and eventually I'd get some credit. That's all fine with me.

It was like this until 5.12 came along. This machine got a couple of WUs for 5.12:

https://boinc.bakerlab.org/rosetta/result.php?resultid=19784109
https://boinc.bakerlab.org/rosetta/result.php?resultid=19720451

I ended up aborting these manually. One ran for over 12 hours and once for almost 24 hours. Both created many models rather than the usual 1 model. I looked at the graphics to see. This behavior was not the usual for this old slow machine.

Then 5.13 came along because of the problems reported elsewhere with 5.12 and the WUs for 5.13 were back to acting normally (and I use that word loosly here) on this machine - 1 to 4 hours for one model before the WU ended and the results get reported. I did not report it at the time since I figured it was due to 5.12's problems.

Now 5.16 comes along. The first WU for that was running for over 12 hours and had created 12 models before I aborted it. Now the second 5.16 WU has been running for over 8 hours. I think I'll let this one run just to see how long it takes although I don't know if it will ever end by itself. Here is the WU I aborted this morning:

https://boinc.bakerlab.org/rosetta/result.php?resultid=20315583

Another strange this is that the percent complete is slowly creeping up for this WU. It's up to 16.71% right now. (I use the AddOn BoincPHP-GUI to monitor my machines from a web browser so I can see this. What I can't see until I get home is how many models it has done so far.) Usually with one model it goes from 1.04% to 100% with nothing in between.

Oh, and here's the computer:

https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=4381




-Charlie
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Message 16485 - Posted: 17 May 2006, 21:14:00 UTC - in response to Message 16437.  


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Message 16487 - Posted: 17 May 2006, 21:59:01 UTC

I have an issue with screensaver on my notebook. While crunching WU named NO_STRING_RELAX_1mky_ROT_TRIALS_TRIE_CHECKPOINTS_483_958_1 that grey lines that divides screen into parts are randomly changing level of grey and sometimes they disapper for a while. I didn't see it on any other WU before. It is happening in screensaver and also when showing graphics in window.
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Profile Charles Dennett
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Message 16491 - Posted: 17 May 2006, 22:55:12 UTC - in response to Message 16466.  



Another strange this is that the percent complete is slowly creeping up for this WU. It's up to 16.71% right now. (I use the AddOn BoincPHP-GUI to monitor my machines from a web browser so I can see this. What I can't see until I get home is how many models it has done so far.) Usually with one model it goes from 1.04% to 100% with nothing in between.



Just an update. The WU has just over 11 hours of CPU time as measured by the utility wintop. Boinc still see 0 cpu time as is to be expected on this Win98SE machine. It's on model 9. The % done on the graphics window is 26.71017% (yes, that many decimal places) and the %done on the Boinc Manager is 23.38%. Note the difference.

Charlie

-Charlie
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Message 16494 - Posted: 17 May 2006, 23:39:08 UTC - in response to Message 16491.  

The % done on the graphics window is 26.71017% (yes, that many decimal places) and the %done on the Boinc Manager is 23.38%. Note the difference.

Charlie

Charles, that's a boinc issue. If I understand it correctly boinc.scr talks to the boinc.exe(daemon running the app), then the boincmgr.exe (manager) talks to boinc.exe (daemon}. I understand that the (for lack of better words) refresh rate is different so a "lag" is seen.

tony
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Message 16495 - Posted: 17 May 2006, 23:51:42 UTC - in response to Message 16494.  

The % done on the graphics window is 26.71017% (yes, that many decimal places) and the %done on the Boinc Manager is 23.38%. Note the difference.

Charlie

Charles, that's a boinc issue. If I understand it correctly boinc.scr talks to the boinc.exe(daemon running the app), then the boincmgr.exe (manager) talks to boinc.exe (daemon}. I understand that the (for lack of better words) refresh rate is different so a "lag" is seen.

tony


Tony,

Thanks for the reply. I don't use the screen saver. I just hit the graphics button on the boinc manager whenever I want to see the graphics and then dismiss the window when I'm done. I've never noticed this behavior before. I also have another W2K machine in the house running boinc that does not exhibit this behavior.

Oh well, my main machine is a Linux box. I'm much more comfortable with that. These Windows machine are a couple of old ones I had around the house. The w2k one only has 128 MB of memory and it's running RAH just fine.

Charlie


-Charlie
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Message 16496 - Posted: 18 May 2006, 0:11:11 UTC

Result 20512608 has Exit status -1073741811 (0xc000000d) ... watchdog has killed it.

BTW thanks for watchdog, it helps.
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Message 16501 - Posted: 18 May 2006, 0:37:23 UTC - in response to Message 16491.  



Another strange this is that the percent complete is slowly creeping up for this WU. It's up to 16.71% right now. (I use the AddOn BoincPHP-GUI to monitor my machines from a web browser so I can see this. What I can't see until I get home is how many models it has done so far.) Usually with one model it goes from 1.04% to 100% with nothing in between.



Just an update. The WU has just over 11 hours of CPU time as measured by the utility wintop. Boinc still see 0 cpu time as is to be expected on this Win98SE machine. It's on model 9. The % done on the graphics window is 26.71017% (yes, that many decimal places) and the %done on the Boinc Manager is 23.38%. Note the difference.

Charlie


Another update. Darn! I stopped the WU after it checkpointed so I could examine the stdout and stderr files. When I started it back up it started counting the time (it's up to 14 minutes now) but the model count did not reset back to 0. It resarted on model 10.

Charlie


-Charlie
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Message 16504 - Posted: 18 May 2006, 0:44:05 UTC

Here's one that went wrong and appears to have goine off half-cocked. I got 5.13 units after this.

https://boinc.bakerlab.org/rosetta/result.php?resultid=20344697
Ian Cundell, St Albans, UK
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Message 16510 - Posted: 18 May 2006, 3:33:25 UTC - in response to Message 16487.  

I have an issue with screensaver on my notebook. While crunching WU named NO_STRING_RELAX_1mky_ROT_TRIALS_TRIE_CHECKPOINTS_483_958_1 that grey lines that divides screen into parts are randomly changing level of grey and sometimes they disapper for a while. I didn't see it on any other WU before. It is happening in screensaver and also when showing graphics in window.


Actually it does that on all the systems and larger Work units as far as I can tell. It seems to be an artifact of the resizing of the larger proteins to fit in the box. It has no effect on the system or the progress of the work. They may adjust it in a future release. In a way it might be a good thing for people who are still using glass CRT's as it will help prevent the lines from burning into the monitor. Those of us using LCD monitors do not have to worry about that any more.

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Seth Aaronson
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Message 16512 - Posted: 18 May 2006, 3:49:06 UTC

Well, it seems that rosetta just doesn't want to run on my machine.

5/17/2006 8:45:08 PM|rosetta@home|Unrecoverable error for result TEST_HOMOLOG_ABRELAX_hom001_1opd__504_54584_0 ( - exit code -1073741811 (0xc000000d))

This really is getting tiresome. Folding@Home is looking so much better. Have you done any collboration with them at all, or are you in competition with them?

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Message 16513 - Posted: 18 May 2006, 4:09:12 UTC
Last modified: 18 May 2006, 4:09:28 UTC

Everything was fine until I opened the graphics from the boinc manager. Watched the graphics for about 20 sec. and:

<core_client_version>5.4.9</core_client_version>
<message>
- exit code -1073741811 (0xc000000d)
</message>
<stderr_txt>
# random seed: 1511346
# cpu_run_time_pref: 14400

</stderr_txt>

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=17137383

Computer is AMD 64 Win XP.

Is this a graphics problem? I've been turning in 5.16 WU's all day with no graphics on and no errors.

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