Report Problems with Rosetta Version 5.13

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Message 15920 - Posted: 11 May 2006, 13:28:05 UTC
Last modified: 12 May 2006, 20:36:30 UTC

Rosetta@Home Version 5.13 has been released!

Please DO NOT abort Work Units from previous versions if they are running well. The science from them is still important to the project. The new software and Work Units for it will download automatically.

This thread is for reporting errors related to Rosetta application version 5.13. When reporting errors please include a link to the results from any related Work Units.

As always, Credit will be awarded for failed Work units on a DAILY Basis.

For errors related to Version 5.07 continue to use this thread.
For errors related to Version 5.12 continue to use this thread.

For information on the new Version and what it is supposed to do see this post.

For a message from Dr. Baker about the work unit runs in preparation for CASP see his journal entry here.

For important project information updates see This Thread (you may subscribe to the thread for e-mail updates)



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Jose

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Message 15928 - Posted: 11 May 2006, 14:48:39 UTC
Last modified: 11 May 2006, 14:49:34 UTC

I reported two WuS in this thread http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1573
This and no other is the root from which a Tyrant springs; when he first appears he is a protector.”
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Message 15937 - Posted: 11 May 2006, 17:03:03 UTC

A third wu concked out with a client error http://boinc.bakerlab.org/rosetta/result.php?resultid=19847593
This and no other is the root from which a Tyrant springs; when he first appears he is a protector.”
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Message 15972 - Posted: 11 May 2006, 23:13:24 UTC

This isn\'t exactly an error but more of a cosmetic thing, but the descriptive text in the graphics doesn\'t wrap to the next line. For my current unit is says, \"This test is looking to see whether we fold evolutionary similar proteins using the same protocol, we are ab\" and it cuts off right in the middle of that last \'b\'.

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Message 15974 - Posted: 12 May 2006, 0:04:09 UTC - in response to Message 15972.  

This isn\'t exactly an error but more of a cosmetic thing, but the descriptive text in the graphics doesn\'t wrap to the next line. For my current unit is says, \"This test is looking to see whether we fold evolutionary similar proteins using the same protocol, we are ab\" and it cuts off right in the middle of that last \'b\'.

I have also seen this. I think Rhiju is still refining the text display for the graphic, so if you see anything else let us know.
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Message 15986 - Posted: 12 May 2006, 2:04:33 UTC

running homo log abrelax homo 002_t283_505_162 . When the progam started i don\'t get space for RSMD on the display







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Message 15990 - Posted: 12 May 2006, 2:19:17 UTC
Last modified: 12 May 2006, 2:20:58 UTC

http://boinc.bakerlab.org/rosetta/result.php?resultid=19946387

http://boinc.bakerlab.org/rosetta/result.php?resultid=19946264
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Message 15994 - Posted: 12 May 2006, 3:03:40 UTC

I just noticed that as with 5.12, my machine is experiencing the same problem that I first reported here. I also noticed that someone else is experiencing the same problem. Perhaps this screen crashing problem is only limited to ATI gpus? I completed a 5.13 work unit on my office computer earlier today with the graphics open the whole time and experienced no screen crashes (it uses an Intel integrated gpu) For further clarification, the screen crashes don\'t happen during full atom relax.

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Message 15996 - Posted: 12 May 2006, 3:10:40 UTC - in response to Message 15994.  

I just noticed that as with 5.12, my machine is experiencing the same problem that I first reported here. I also noticed that someone else is experiencing the same problem. Perhaps this screen crashing problem is only limited to ATI gpus? I completed a 5.13 work unit on my office computer earlier today with the graphics open the whole time and experienced no screen crashes (it uses an Intel integrated gpu) For further clarification, the screen crashes don\'t happen during full atom relax.

You might want to try upgrading your BOINC client to version 5.4.9. See Here.
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Message 16009 - Posted: 12 May 2006, 5:05:05 UTC - in response to Message 15996.  

I just noticed that as with 5.12, my machine is experiencing the same problem that I first reported here. I also noticed that someone else is experiencing the same problem. Perhaps this screen crashing problem is only limited to ATI gpus? I completed a 5.13 work unit on my office computer earlier today with the graphics open the whole time and experienced no screen crashes (it uses an Intel integrated gpu) For further clarification, the screen crashes don\'t happen during full atom relax.

You might want to try upgrading your BOINC client to version 5.4.9. See Here.


I installed BOINC 5.4.9 and the problem still persisted. However, I think I found the cause. If I don\'t attempt to rotate or zoom in/out of the native protein model, my system can make it all the way through without a screen crash. I\'ve been able to replicate this somewhat. Everytime I rotate the model with my mouse even a small amount, a screen crash does happen but a random time afterward. Interesting bug. ;-)

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Message 16023 - Posted: 12 May 2006, 11:54:57 UTC - in response to Message 15986.  

running homo log abrelax homo 002_t283_505_162 . When the progam started i don\'t get space for RSMD on the display

That is because you are modelling a protein from the CASP7 trials. Researchers gave their results for the shape of the proteins to the CASP7 organizers, without publishing it at the moment. Now several groups try to figure the shape f the protein from the amino acid sequence without knowing the shape, which is of course the purpose for which rosetta is made.
So withou the original shape no RMSD can be calculated for your models and thus you do not see see it.
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Message 16056 - Posted: 12 May 2006, 15:22:35 UTC

I think it should be mentioned in the text below models why we don\'t see RMSD. Now it is really confusing for people who don\'t know what\'s going on.

And to say something about Kerwins problem.. few days ago I had problems running one application on computer with ATI Radeon7000 .. after contacting the support staff they told me, that this graphic card model has problems with OpenGL. I had to replace it.
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Message 16065 - Posted: 12 May 2006, 15:47:59 UTC - in response to Message 16056.  
Last modified: 12 May 2006, 15:51:26 UTC

why we don\'t see RMSD.

...I\'ll take a stab at explaining this. The Rosetta project is trying to invent a tool. And SOME of what they want to tool to do, there are already tools that do the same thing. Many of the tests we\'ve run in the past on Rosetta are comparisons of a new Rosetta tool with the existing known tools. RSMD is a measure of how close the current Rosetta version is coming to the results of other known tools.

Think of it this way, if you want to invent a new compass for navigation, you will test it with other available methods of navigation. And so RSMD is sort of like a measure of how far away from your destination your new compass has taken you.

With the CASP, the precise destination is not known by the participants. It is like a rally race, \"drive at 5mph for 3min, then turn left... go 3 miles at 30mph...\" and in order to \"win\", you have to end up at the right location... AND at the proper time! And so there is no existing tool to use for comparison. RSMD is the comparison to the existing tools used to determine protein structures.
If having a DC project with BOINC is of interest to you, with volunteer or cloud computing resources, but have no time for the BOINC learning curve,
use a hosting service that understands BOINC projects: http://DeepSci.com
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Message 16104 - Posted: 12 May 2006, 21:05:47 UTC

i\'ve had no problems with the standard work unites using 5.13. However when i get a clasp7 one it has a problem that crashes and exites. This only happens when the screensaver comes on. if i stop it from coming on it finishes with no problems at all. but if i see the screensaver for more than a few minutes and it happens. any ideas?
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Message 16106 - Posted: 12 May 2006, 21:21:19 UTC

Every time my new laptop runs a Rosetta workunit, it finished at 100% with a computation error. I also get an error from windows saying that Rosetta 5.13 crashed. Here is the message from BOINC saying the error. - exit code -1073741811 (0xc000000d)
Please help me fix this. I want to run Rosetta but it is not working.

I am running it on an acer TravelMate 4670. You can find the specs on google. It is the faster version with the T2500 processor. I have BOINC only setup to use one processor.
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Message 16108 - Posted: 12 May 2006, 21:24:14 UTC

Also, here is the address where you can look at the workunits and their error messages.
http://boinc.bakerlab.org/rosetta/results.php?hostid=217745
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Message 16110 - Posted: 12 May 2006, 22:58:14 UTC - in response to Message 16104.  

i\'ve had no problems with the standard work unites using 5.13. However when i get a clasp7 one it has a problem that crashes and exites. This only happens when the screensaver comes on. if i stop it from coming on it finishes with no problems at all. but if i see the screensaver for more than a few minutes and it happens. any ideas?

What kind of graphics card are you using?
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Message 16111 - Posted: 12 May 2006, 23:04:55 UTC - in response to Message 16106.  

Every time my new laptop runs a Rosetta workunit, it finished at 100% with a computation error. I also get an error from windows saying that Rosetta 5.13 crashed. Here is the message from BOINC saying the error. - exit code -1073741811 (0xc000000d)
Please help me fix this. I want to run Rosetta but it is not working.

I am running it on an acer TravelMate 4670. You can find the specs on google. It is the faster version with the T2500 processor. I have BOINC only setup to use one processor.

Darin,

I see you are running version 5.2.13 of BOINC. You might want to consider upgrading to version 5.4.9 which is available here. There is a good chance that alone will solve the problem. If not we can have you attach to RALPH where we can diagnose the situation better.

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Message 16112 - Posted: 12 May 2006, 23:08:07 UTC

i\'m currently using a geforce 4600.
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Message 16113 - Posted: 12 May 2006, 23:15:11 UTC - in response to Message 16112.  

i\'m currently using a geforce 4600.

I just read a post from another user who is also a savvy tester for BOINC development. He mentioned that lockups were caused in just the way you describe on older versions of BOINC client software. Today anything older than BOINC version 5.4.9 could have the problem. I did not check your BOINC version number but if you are not running 5.4.9 you might want to consider upgrading. The latest version is available here.
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Message boards : Number crunching : Report Problems with Rosetta Version 5.13



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