Report Problems with Rosetta Version 5.12

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Message 15745 - Posted: 10 May 2006, 2:35:35 UTC
Last modified: 12 May 2006, 20:37:00 UTC

Rosetta@Home Version 5.12 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 5.12. 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 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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Profile David Emigh
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Message 15789 - Posted: 10 May 2006, 15:48:11 UTC

Looks like I'm the first to report an error on v5.12...

Computer ID = 182506

5/10/2006 10:31:38 AM|rosetta@home|Unrecoverable error for result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_1291_0 ( - exit code -1073741811 (0xc000000d))

5/10/2006 10:31:43 AM|rosetta@home|Unrecoverable error for result JUMP_ALLBARCODES_ANTIPARALLEL_1tul__SAVE_ALL_OUT_491_1333_0 ( - exit code -1073741811 (0xc000000d))


Rosie, Rosie, she's our gal,
If she can't do it, no one shall!
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Stu D.
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Message 15796 - Posted: 10 May 2006, 16:21:56 UTC
Last modified: 10 May 2006, 16:23:27 UTC

5/10/2006 12:16:23 PM|rosetta@home|Unrecoverable error for result JUMP_NATIVEBARCODE_ANTIPARALLEL_1tul__SAVE_ALL_OUT_492_877_0 ( - exit code -1073741811 (0xc000000d))
5/10/2006 12:16:19 PM|rosetta@home|Unrecoverable error for result JUMP_ALLBARCODES_ANTIPARALLEL_1tul__SAVE_ALL_OUT_491_4396_0 ( - exit code -1073741811 (0xc000000d))

Computer...175527
Stu
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Message 15834 - Posted: 10 May 2006, 20:36:21 UTC
Last modified: 10 May 2006, 20:40:13 UTC

5/10/2006 4:32:33 PM|rosetta@home|Unrecoverable error for result JUMP_ALLBARCODES_ANTIPARALLEL_1tul__SAVE_ALL_OUT_491_9050_0 ( - exit code -1073741811 (0xc000000d))
5/10/2006 4:32:38 PM|rosetta@home|Unrecoverable error for result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_7224_0 ( - exit code -1073741811 (0xc000000d))

Computer...175527 AMD x2 3800
No problem like this with prior versions.
Stu
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Message 15845 - Posted: 10 May 2006, 21:53:41 UTC

trying to resume Rosetta@home after the machine was offline for over a month, I
get only errors

2006-05-10 13:13:11 [rosetta@home] execv(../../projects/boinc.bakerlab.org_rosetta/rosetta_5.12_i686-pc-linux-gnu) failed: error -1
2006-05-10 13:13:11 [rosetta@home] Starting result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec452_1.pdb_501_7_0 using rosetta version 512
2006-05-10 13:13:12 [rosetta@home] Unrecoverable error for result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec452_1.pdb_501_7_0 (process exited with code 26 (0x1a))
2006-05-10 13:13:12 [rosetta@home] Unrecoverable error for result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec452_1.pdb_501_7_0 (process exited with code 26 (0x1a))
2006-05-10 13:13:12 [---] request_reschedule_cpus: process exited
2006-05-10 13:13:12 [rosetta@home] Computation for result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec452_1.pdb_501_7_0 finished
2006-05-10 13:13:12 [rosetta@home] Starting result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec320_1.pdb_501_7_0 using rosetta version 512
2006-05-10 13:13:12 [rosetta@home] execv(../../projects/boinc.bakerlab.org_rosetta/rosetta_5.12_i686-pc-linux-gnu) failed: error -1
2006-05-10 13:13:13 [rosetta@home] Unrecoverable error for result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec320_1.pdb_501_7_0 (process exited with code 26 (0x1a))
2006-05-10 13:13:13 [rosetta@home] Unrecoverable error for result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec320_1.pdb_501_7_0 (process exited with code 26 (0x1a))
2006-05-10 13:13:13 [---] request_reschedule_cpus: process exited
2006-05-10 13:13:13 [rosetta@home] Computation for result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec320_1.pdb_501_7_0 finished

For now, I have suspended this project.
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Message 15849 - Posted: 10 May 2006, 22:26:44 UTC - in response to Message 15845.  

trying to resume Rosetta@home after the machine was offline for over a month, I
get only errors

2006-05-10 13:13:11 [rosetta@home] execv(../../projects/boinc.bakerlab.org_rosetta/rosetta_5.12_i686-pc-linux-gnu) failed: error -1
2006-05-10 13:13:11 [rosetta@home] Starting result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec452_1.pdb_501_7_0 using rosetta version 512
...For now, I have suspended this project.


This is a file error related to an open file. Since you have been offline for a while try resetting the project.

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Message 15854 - Posted: 11 May 2006, 0:20:42 UTC
Last modified: 11 May 2006, 0:51:29 UTC

I was looking at the graphics for 5.12 and suddenly they stopped, the computer froze, my screen went blank and all of a sudden it reappeared with a message from my Catalyst driver stating that the video card was no longer accepting commands from the driver and that it had to be reset. Once this error message popped up, everything went back to normal, graphics and all.

I'm using an ATI X850 XT. This is the second time this happened. It also happened with a result using 5.07 with the same outcome.

Edit:
I continued watching the graphics and it happened again, but this time 4 in a row a few seconds apart. By the fourth time, the video card stopped responding and the driver reverted to software rendering. At this point I chose to restart my machine. This happened 4.70% into JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_4697_0

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Message 15858 - Posted: 11 May 2006, 0:44:54 UTC - in response to Message 15854.  

I was looking at the graphics for 5.12 and suddenly they stopped, the computer froze, my screen went blank and all of a sudden it reappeared with a message from my Catalyst driver stating that the video card was no longer accepting commands from the driver and that it had to be reset. Once this error message popped up, everything went back to normal, graphics and all.

I'm using an ATI X850 XT. This is the second time this happened. It also happened with a result using 5.07 with the same outcome.


This is very interesting and the first time I have seen a report of this behavior. There is another thread here with a discussion of memory and graphics software issues. You should add this report to that thread as well as it may be a related issue.

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Message 15952 - Posted: 11 May 2006, 19:33:26 UTC - in response to Message 15849.  

trying to resume Rosetta@home after the machine was offline for over a month, I
get only errors

2006-05-10 13:13:11 [rosetta@home] execv(../../projects/boinc.bakerlab.org_rosetta/rosetta_5.12_i686-pc-linux-gnu) failed: error -1
2006-05-10 13:13:11 [rosetta@home] Starting result HOMO_7486_h008_1_LOOPRLX_IGNORE_THE_REST7486h008_dec452_1.pdb_501_7_0 using rosetta version 512
...For now, I have suspended this project.


This is a file error related to an open file. Since you have been offline for a while try resetting the project.


I reset this project and it upgraded itself to version 5.13 which seems to be
running fine so far.
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Message 15954 - Posted: 11 May 2006, 19:37:52 UTC

JUMP_ALLBARCODES_ANTIPARALLEL_1tul__SAVE_ALL_OUT_491_23413_0

https://boinc.bakerlab.org/rosetta/result.php?resultid=19786764

Got to 100% and then just sat there, and sat there, and ...

Got an interesting error though: *** glibc detected *** corrupted double-linked list: 0x0b4af0f8 ***

dag
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Message 15955 - Posted: 11 May 2006, 19:51:21 UTC - in response to Message 15954.  

JUMP_ALLBARCODES_ANTIPARALLEL_1tul__SAVE_ALL_OUT_491_23413_0

https://boinc.bakerlab.org/rosetta/result.php?resultid=19786764

Got to 100% and then just sat there, and sat there, and ...

Got an interesting error though: *** glibc detected *** corrupted double-linked list: 0x0b4af0f8 ***

Well you should get full credit tonight (check the result display for the Work Unit not your Work units list display).

But that message bothers me a bit. It could be caused by two or three things. The most serious would be a disk problem on your hard disk. Keep an eye on your system and see if you have any more of these.

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Message 16116 - Posted: 13 May 2006, 0:25:04 UTC
Last modified: 13 May 2006, 0:29:21 UTC

this compter
16420818
16420797
16420710

BOINC ver 5.4.9
Win XP home sp2 3.00 GHz 1GB RAM



12/05/2006 11:28:04 AM||Suspending network activity - user request - running CPU benchmarks
12/05/2006 11:28:06 AM||Running CPU benchmarks
12/05/2006 11:29:05 AM||Benchmark results:
12/05/2006 11:29:05 AM|| Number of CPUs: 2
12/05/2006 11:29:05 AM|| 1311 floating point MIPS (Whetstone) per CPU
12/05/2006 11:29:05 AM|| 1209 integer MIPS (Dhrystone) per CPU
12/05/2006 11:29:05 AM||Finished CPU benchmarks
12/05/2006 11:29:06 AM|rosetta@home|Resuming task JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16829_0 using rosetta version 512
12/05/2006 11:29:06 AM|rosetta@home|Resuming task JUMP_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16802_0 using rosetta version 512
12/05/2006 11:29:06 AM||Resuming computation
12/05/2006 11:29:06 AM||Rescheduling CPU: Resuming computation
12/05/2006 12:58:06 PM|rosetta@home|Aborting task JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16829_0: exceeded disk limit: 101397335.000000 > 100000000.000000
12/05/2006 12:58:06 PM|rosetta@home|Unrecoverable error for result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16829_0 (Maximum disk usage exceeded)

12/05/2006 12:58:06 PM|rosetta@home|Deferring scheduler requests for 1 minutes and 0 seconds
12/05/2006 12:58:08 PM||Rescheduling CPU: application exited
12/05/2006 12:58:08 PM|rosetta@home|Computation for task JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16829_0 finished
12/05/2006 12:58:08 PM|rosetta@home|Starting task JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16836_0 using rosetta version 512
12/05/2006 1:38:25 PM||Rescheduling CPU: application exited
12/05/2006 1:38:25 PM|rosetta@home|Computation for task JUMP_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16802_0 finished
12/05/2006 1:38:25 PM|rosetta@home|Starting task JUMP_ALLBARCODES_ANTIPARALLEL_1tul__SAVE_ALL_OUT_491_16837_0 using rosetta version 512
12/05/2006 9:28:15 PM|rosetta@home|Aborting task JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16836_0: exceeded disk limit: 100258025.000000 > 100000000.000000
12/05/2006 9:28:15 PM|rosetta@home|Unrecoverable error for result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16836_0 (Maximum disk usage exceeded)

12/05/2006 9:28:15 PM|rosetta@home|Deferring scheduler requests for 1 minutes and 0 seconds
12/05/2006 9:28:17 PM||Rescheduling CPU: application exited
12/05/2006 9:28:17 PM|rosetta@home|Computation for task JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16836_0 finished
12/05/2006 9:28:17 PM|rosetta@home|Starting task JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16800_0 using rosetta version 512
13/05/2006 7:38:36 AM|rosetta@home|Aborting task JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16800_0: exceeded disk limit: 102689604.000000 > 100000000.000000
13/05/2006 7:38:36 AM|rosetta@home|Unrecoverable error for result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16800_0 (Maximum disk usage exceeded)

13/05/2006 7:38:36 AM|rosetta@home|Deferring scheduler requests for 1 minutes and 0 seconds
13/05/2006 7:38:38 AM||Rescheduling CPU: application exited
13/05/2006 7:38:38 AM|rosetta@home|Computation for task JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16800_0 finished
13/05/2006 7:38:38 AM|rosetta@home|Starting task JUMP_ALLBARCODES_ANTIPARALLEL_1tul__SAVE_ALL_OUT_491_16815_0 using rosetta version 512


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Message 16124 - Posted: 13 May 2006, 1:22:02 UTC - in response to Message 16116.  
Last modified: 13 May 2006, 1:32:07 UTC

this compter
16420818
16420797
16420710

BOINC ver 5.4.9
Win XP home sp2 3.00 GHz 1GB RAM
...


Hugo,

You are currently working with Rosetta version 5.12. There is a problem in the BOINC API that causes the errors you are seeing. They will stop as soon as you get Rosetta Version 5.13.

Version 5.12 was only available for about 4 hours, but it seems your queue filled up with Work units during that time. If you reset the project you will get the new version. If you have Work you have not started, suspend those work units and let those you have started complete before you do the rest so you will not loose the time. Then when all the active work unit have been reported, do the reset. That should load version 5.13 and fix the problem

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Message 16141 - Posted: 13 May 2006, 5:24:59 UTC

I've also got an error with 5.12 for "exceeded disk limit". This is on a Gentoo Linux system, so the windows debug code shouldn't be the problem.

Sat May 13 00:41:08 2006|rosetta@home|Aborting result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16783_0: exceeded disk limit: 103092700.000000 > 100000000.000000
Sat May 13 00:41:08 2006|rosetta@home|Unrecoverable error for result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16783_0 (Maximum disk usage exceeded)
Sat May 13 00:41:09 2006||request_reschedule_cpus: process exited
Sat May 13 00:41:09 2006|rosetta@home|Computation for result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16783_0 finished


It's this work unit, which is my only 5.12 work unit - the next is 5.13.



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Message 16142 - Posted: 13 May 2006, 5:39:45 UTC - in response to Message 16141.  
Last modified: 13 May 2006, 5:42:53 UTC

I've also got an error with 5.12 for "exceeded disk limit". This is on a Gentoo Linux system, so the windows debug code shouldn't be the problem.

Sat May 13 00:41:08 2006|rosetta@home|Aborting result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16783_0: exceeded disk limit: 103092700.000000 > 100000000.000000
Sat May 13 00:41:08 2006|rosetta@home|Unrecoverable error for result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16783_0 (Maximum disk usage exceeded)
Sat May 13 00:41:09 2006||request_reschedule_cpus: process exited
Sat May 13 00:41:09 2006|rosetta@home|Computation for result JUMP_CLOSE_CHAINBREAK_ALLBARCODE_1q7sA_SAVE_ALL_OUT_493_16783_0 finished


It's this work unit, which is my only 5.12 work unit - the next is 5.13.


Actually the debug issue was in 5.12 and was a conflict with BOINC. While more prominent in windows machines we also saw it on some linux machines as well. If you are clear of 5.12 work units, that should end the problem. 5.13 and up should be ok.


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Message 16229 - Posted: 14 May 2006, 5:59:06 UTC

I still have a Version 5.12 work unit suspended in my queue until I finish crunching workunits for LHC. Should I abort this workunit?
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Message 16232 - Posted: 14 May 2006, 6:10:50 UTC - in response to Message 16229.  

I still have a Version 5.12 work unit suspended in my queue until I finish crunching workunits for LHC. Should I abort this workunit?

Not if you can run it in time to report the result. No matter what happens you will get credit, so I would let it loose to run.
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Message 16348 - Posted: 16 May 2006, 0:02:15 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=19754192

checkpoint CPU time: 28235.070000
current CPU time: 28241.740000
fraction done: 1.000000


https://boinc.bakerlab.org/rosetta/result.php?resultid=19771884

checkpoint CPU time: 28621.150000
current CPU time: 28626.950000
fraction done: 1.000000

Both of these are JUMP_ALLBARCODES_* workunits and are the first real problems I've noticed since the recent rosetta updates included the watchdog. These differed from past errors in 2 ways, firstly fraction done is exactly 1.00 although checkpoints have been written & both of these were completely frozen (2 different linux servers), now when I say frozen I mean not even the cpu time was increasing unlike the old stuck wu's of past rosetta versions. Anyway the result urls both show glibc errors which is a first out of both of these servers to the best of my knowledge and since both the wu's are JUMP_ALLBARCODES_* I figure this is not a coincidence.

I manually aborted both in the end, since I dont cache wu's time sent shows both of these wu's have been stuck for 5 days each.

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Message 16352 - Posted: 16 May 2006, 1:11:16 UTC - in response to Message 16348.  

https://boinc.bakerlab.org/rosetta/result.php?resultid=19754192

checkpoint CPU time: 28235.070000
current CPU time: 28241.740000
fraction done: 1.000000


https://boinc.bakerlab.org/rosetta/result.php?resultid=19771884

checkpoint CPU time: 28621.150000
current CPU time: 28626.950000
fraction done: 1.000000

Both of these are JUMP_ALLBARCODES_* workunits and are the first real problems I've noticed since the recent rosetta updates included the watchdog. These differed from past errors in 2 ways, firstly fraction done is exactly 1.00 although checkpoints have been written & both of these were completely frozen (2 different linux servers), now when I say frozen I mean not even the cpu time was increasing unlike the old stuck wu's of past rosetta versions. Anyway the result urls both show glibc errors which is a first out of both of these servers to the best of my knowledge and since both the wu's are JUMP_ALLBARCODES_* I figure this is not a coincidence.

I manually aborted both in the end, since I dont cache wu's time sent shows both of these wu's have been stuck for 5 days each.

Well you won't likely see any more of these with the new version.
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