Bug reports for Ralph 5.14

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Rhiju
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Message 1596 - Posted: 12 May 2006, 19:02:45 UTC

Please post bugs in 5.14. A few comments:

(1) The \"phantom chain\" or \"broken chain\" that appear in some workunits are OK -- they\'re new science modes we\'re testing that either focus on specific parts of the protein or rearrange the protein topology to better sample long-range contacts.

(2) The debugger messages (which caused slowdowns for some users with 5.10-5.12, and were removed in 5.13)
have been put back into ralph. But they\'re not on by default. We\'ll ask Rom to post here and fill you in on how to turn them on.

(3) 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.

(4) We\'re also continuing our efforts to reduce memory usage by rosetta/ralph!



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dainenyu

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Message 1598 - Posted: 12 May 2006, 21:28:46 UTC - in response to Message 1596.  
Last modified: 12 May 2006, 21:30:06 UTC

Downloaded 6 WUs, all failed immediately, giving message

5/12/2006 5:41:23 PM|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom023_1fna__509_8_0 (Incorrect function. (0x1) - exit code 1 (0x1))
5/12/2006 5:41:29 PM|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom028_1fna__509_6_0 (Incorrect function. (0x1) - exit code 1 (0x1))
5/12/2006 5:41:38 PM|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom009_1fna__509_5_0 (Incorrect function. (0x1) - exit code 1 (0x1))
5/12/2006 5:41:38 PM|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom009_1fna__509_7_0 (Incorrect function. (0x1) - exit code 1 (0x1))
5/12/2006 5:41:40 PM|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom009_1fna__509_10_0 (Incorrect function. (0x1) - exit code 1 (0x1))
5/12/2006 5:41:44 PM|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom029_1fna__509_7_0 (Incorrect function. (0x1) - exit code 1 (0x1))

WU numbers are 97527, 97483, 97460, 97440, 97430, 97382.

Edit: stderr out reads
<core_client_version>5.4.9</core_client_version>
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
ERROR:: Exit at: .\\map_sequence.cc line:495

</stderr_txt>

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Message 1599 - Posted: 12 May 2006, 21:45:54 UTC

I upgraded to the latest stable release of the BOINC client (5.4.9 for Mac OS X) and now I\'m getting immediate failures:

Fri May 12 16:47:16 2006|ralph@home|Starting task MAPRELAX_TEST_hom018_1fna__509_7_0 using rosetta_beta version 514
Fri May 12 16:47:18 2006|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom018_1fna__509_7_0 (process exited with code 1 (0x1))

Fri May 12 16:48:28 2006|ralph@home|Starting task MAPRELAX_TEST_hom001_1fna__509_11_0 using rosetta_beta version 514
Fri May 12 16:48:30 2006|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom001_1fna__509_11_0 (process exited with code 1 (0x1))

Fri May 12 16:53:20 2006|ralph@home|Starting task MAPRELAX_TEST_hom003_1fna__509_13_0 using rosetta_beta version 514
Fri May 12 16:53:22 2006|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom003_1fna__509_13_0 (process exited with code 1 (0x1))

Fri May 12 16:57:32 2006|ralph@home|Starting task MAPRELAX_TEST_hom022_1fna__509_10_0 using rosetta_beta version 514
Fri May 12 16:57:34 2006|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom022_1fna__509_10_0 (process exited with code 1 (0x1))

Fri May 12 17:01:47 2006|ralph@home|Starting task MAPRELAX_TEST_hom013_1fna__509_11_0 using rosetta_beta version 514
Fri May 12 17:01:50 2006|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom013_1fna__509_11_0 (process exited with code 1 (0x1))

Fri May 12 17:05:50 2006|ralph@home|Starting task MAPRELAX_TEST_hom028_1fna__509_12_0 using rosetta_beta version 514
Fri May 12 17:05:53 2006|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom028_1fna__509_12_0 (process exited with code 1 (0x1))
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Message 1600 - Posted: 12 May 2006, 22:45:00 UTC
Last modified: 12 May 2006, 22:50:03 UTC

I wanted my Seti Beta 5.14 WU finished, so I suspended the 5.14 Ralph WU, which apparently killed it (or what?)

http://ralph.bakerlab.org/workunit.php?wuid=97405

Result: http://ralph.bakerlab.org/result.php?resultid=111703

From my log:

5/13/2006 12:57:29 AM|SETI@home|Restarting task 01mr99aa.26277.31696.309670.3.101_1 using setiathome_enhanced version 512
5/13/2006 12:57:29 AM|SETI@home Beta Test|Pausing task 05au01ab.24507.112.847158.3.93_6 (removed from memory)
5/13/2006 12:58:58 AM||Rescheduling CPU: result suspended, resumed or aborted by user
5/13/2006 12:58:58 AM|SETI@home|Pausing task 01mr99aa.26277.31696.309670.3.101_1 (removed from memory)
5/13/2006 12:58:58 AM|ralph@home|Starting task MAPRELAX_TEST_hom003_1fna__509_6_0 using rosetta_beta version 514
5/13/2006 12:59:01 AM||Rescheduling CPU: result suspended, resumed or aborted by user
5/13/2006 12:59:02 AM|rosetta@home|Restarting task TEST_HOMOLOG_ABRELAX_hom003_1fna__503_12404_0 using rosetta version 513
5/13/2006 12:59:02 AM|ralph@home|Pausing task MAPRELAX_TEST_hom003_1fna__509_6_0 (removed from memory)
5/13/2006 12:59:03 AM|ralph@home|Unrecoverable error for result MAPRELAX_TEST_hom003_1fna__509_6_0 (Forkert funktion. (0x1) - exit code 1 (0x1))
5/13/2006 12:59:03 AM|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
5/13/2006 12:59:03 AM||Rescheduling CPU: application exited
5/13/2006 12:59:03 AM|ralph@home|Computation for task MAPRELAX_TEST_hom003_1fna__509_6_0 finished

5/13/2006 12:59:06 AM||Rescheduling CPU: result suspended, resumed or aborted by user
5/13/2006 12:59:06 AM|LHC@home|Restarting task wfeb1A_v6s4vvnom_mqx__19__64.258_59.268__4_6__6__75_1_sixvf_boinc202329_1 using sixtrack version 467
5/13/2006 12:59:06 AM|rosetta@home|Pausing task TEST_HOMOLOG_ABRELAX_hom003_1fna__503_12404_0 (removed from memory)
5/13/2006 12:59:09 AM||Rescheduling CPU: result suspended, resumed or aborted by user
5/13/2006 12:59:10 AM|LHC@home|Pausing task wfeb1A_v6s4vvnom_mqx__19__64.258_59.268__4_6__6__75_1_sixvf_boinc202329_1 (removed from memory)
5/13/2006 12:59:10 AM|LHC@home|Starting task wfeb1A_v6s4vvnom_mqx__3__64.265_59.275__10_12__6__55_1_sixvf_boinc181092_5 using sixtrack version 467
5/13/2006 12:59:14 AM||Rescheduling CPU: result suspended, resumed or aborted by user
5/13/2006 12:59:15 AM|SETI@home Beta Test|Restarting task 05au01ab.24507.112.847158.3.93_6 using setiathome_enhanced version 514
5/13/2006 12:59:15 AM|LHC@home|Pausing task wfeb1A_v6s4vvnom_mqx__3__64.265_59.275__10_12__6__55_1_sixvf_boinc181092_5 (removed from memory)
5/13/2006 12:59:15 AM|SETI@home Beta Test|Sending scheduler request to http://setiboinc.ssl.berkeley.edu/beta_cgi/cgi
5/13/2006 12:59:15 AM|SETI@home Beta Test|Reason: To fetch work
5/13/2006 12:59:15 AM|SETI@home Beta Test|Requesting 3994 seconds of new work
5/13/2006 12:59:20 AM|SETI@home Beta Test|Scheduler request succeeded
5/13/2006 12:59:22 AM|SETI@home Beta Test|Started download of file 01jn01aa.7728.12640.709662.3.121
5/13/2006 12:59:35 AM|SETI@home Beta Test|Finished download of file 01jn01aa.7728.12640.709662.3.121
5/13/2006 12:59:35 AM|SETI@home Beta Test|Throughput 29497 bytes/sec
5/13/2006 12:59:36 AM||Rescheduling CPU: files downloaded
5/13/2006 12:59:56 AM|ralph@home|Sending scheduler request to http://ralph.bakerlab.org/ralph_cgi/cgi
5/13/2006 12:59:56 AM|ralph@home|Reason: Requested by user
5/13/2006 12:59:56 AM|ralph@home|Reporting 1 tasks
5/13/2006 1:00:01 AM|ralph@home|Scheduler request succeeded






[color=navy][b]"I'm trying to maintain a shred of dignity in this world." - Me[/b][/color]

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Message 1601 - Posted: 12 May 2006, 22:59:10 UTC
Last modified: 12 May 2006, 23:00:28 UTC

Had the same error using BOINC V5.4.9, WU aborted immediately, reporting this error:

Unrecoverable error for result MAPRELAX_TEST_hom007_1fna__510_3_0 (Unzulässige Funktion. (0x1) - exit code 1 (0x1))

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Message 1605 - Posted: 13 May 2006, 1:50:16 UTC - in response to Message 1601.  
Last modified: 13 May 2006, 2:13:35 UTC

Had the same error using BOINC V5.4.9, WU aborted immediately, reporting this error:

Unrecoverable error for result MAPRELAX_TEST_hom007_1fna__510_3_0 (Unzul�ssige Funktion. (0x1) - exit code 1 (0x1))

ALL of these groups of errors look like a bad batch of Work Units. I have over 20 on each of my machines as well. I will bring this to Rhiju\'s attantion.

EDIT: Rhiju is \"commuting\" at the moment but I am advised that as I expected this is a bad batch of Work Units. Rhiju says to let you know-
\"A new batch has been queued up. These should pass through very quickly. Sorry for the inconvience.\"

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Message 1606 - Posted: 13 May 2006, 3:26:49 UTC - in response to Message 1605.  

EDIT: Rhiju is \"commuting\" at the moment but I am advised that as I expected this is a bad batch of Work Units. Rhiju says to let you know-
\"A new batch has been queued up. These should pass through very quickly. Sorry for the inconvience.\"[/b]


I\'ve got a couple of the new WUs (HOMOLOG_ABRELAX_hom*) and they seem to be running fine, almost an hour in.
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Message 1607 - Posted: 13 May 2006, 4:00:07 UTC
Last modified: 13 May 2006, 4:10:24 UTC

Fetched a new WU, this time it started w/o error.
RMSD is missing, I assume that it should be like that, because the native graphic is missing, too...

This causes the RMSD/Lowest Energy graphic to vanish, only a single red spot at the left edge is displayed.
And the description text is a bit too long.
(display end at \"has very close seque\")

So nothing serious, everything else works fine, even the graphics!

Accepted Energy is now below -216 for the second model.
Seems like the stranding algorithm improvements work fine.

Virtual memory load is about 132 MB, no clue what it was before...

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Message 1608 - Posted: 13 May 2006, 4:33:26 UTC - in response to Message 1607.  
Last modified: 13 May 2006, 5:04:05 UTC

Fetched a new WU, this time it started w/o error.
RMSD is missing, I assume that it should be like that, because the native graphic is missing, too...

This causes the RMSD/Lowest Energy graphic to vanish, only a single red spot at the left edge is displayed.
And the description text is a bit too long.
(display end at \"has very close seque\")

So nothing serious, everything else works fine, even the graphics!

Accepted Energy is now below -216 for the second model.
Seems like the stranding algorithm improvements work fine.

Virtual memory load is about 132 MB, no clue what it was before...


All of the CASP7 target Work Units will have this display type. All that you describe is normal (except the long text overrun). Since they do not know the structure, they do not have the RMSD value, the Natural structure, or any other comparative information so it cannot be displayed. Because the RMSD is unknown, this forces the value to zero and the red dots all display at what would be the zero point of the RMSD graph (to the left of the box). As close as they can get to the graphic we all are familiar with is to show the accepted and lowest energy shapes as they occur. Rhiju has said they will work on the text overrun.

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Message 1609 - Posted: 13 May 2006, 9:11:40 UTC
Last modified: 13 May 2006, 9:45:03 UTC

OS : WindowsXP Professional x64 Edition
CPU : Intel PentiumD 920 (2.80GHz)
Used RAM : approx. 115MB x2 at max. / 1GB
Graphic card: nVidia GeForce6600GT 128MB
BOINC version : the newest, 5.4.9

Work tasks - OK before closed
Graphic - OK

They worked fine without error at first. However, once BOINC client has been closed and restarted, the taskes which were being done more than half started from the beginning. Is it an error, or due to my preference of RALPH?

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Message 1610 - Posted: 13 May 2006, 11:38:13 UTC
Last modified: 13 May 2006, 11:39:40 UTC

In case anyone missed this on the Rosetta board, here is an interesting thought on why the debugger code might have been causing the many page faults.

Rosetta Post
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Message 1611 - Posted: 13 May 2006, 12:40:35 UTC - in response to Message 1610.  
Last modified: 13 May 2006, 12:51:39 UTC

In case anyone missed this on the Rosetta board, here is an interesting thought on why the debugger code might have been causing the many page faults.

Rosetta Post



So I think it would be useful, if all the guys with the \'hanging/slow\' machines post here what cpu type they got (HT/dual core/single core)!

If the error occures only there, it would help the developers a lot!
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Message 1613 - Posted: 13 May 2006, 15:01:19 UTC - in response to Message 1609.  

OS : WindowsXP Professional x64 Edition
CPU : Intel PentiumD 920 (2.80GHz)
Used RAM : approx. 115MB x2 at max. / 1GB
Graphic card: nVidia GeForce6600GT 128MB
BOINC version : the newest, 5.4.9

Work tasks - OK before closed
Graphic - OK

They worked fine without error at first. However, once BOINC client has been closed and restarted, the taskes which were being done more than half started from the beginning. Is it an error, or due to my preference of RALPH?

[color=darkred]If the work units start, and then you stop BOINC before about 25-40 min of processing, or in any case before the percent complete is more than 1.4%, when you restart BOINC they will start from zero. [color]
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Message 1614 - Posted: 13 May 2006, 15:18:04 UTC - in response to Message 1613.  
Last modified: 13 May 2006, 15:18:29 UTC

...They worked fine without error at first. However, once BOINC client has been closed and restarted, the taskes which were being done more than half started from the beginning. Is it an error, or due to my preference of RALPH?

If the work units start, and then you stop BOINC before about 25-40 min of processing, or in any case before the percent complete is more than 1.4%, when you restart BOINC they will start from zero.


Is it an unavoidable thing or an error with just this version?

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Message 1615 - Posted: 13 May 2006, 20:50:11 UTC - in response to Message 1605.  

Hi: I wanted to quickly apologize for the batch of bad WU\'s yesterday on ralph. Thanks for your patience! Its actually a new scientific mode in Rosetta, and I think I know why the WUs were failing on ralph. Will be testing the fix later today.

Had the same error using BOINC V5.4.9, WU aborted immediately, reporting this error:

Unrecoverable error for result MAPRELAX_TEST_hom007_1fna__510_3_0 (Unzul�ssige Funktion. (0x1) - exit code 1 (0x1))

ALL of these groups of errors look like a bad batch of Work Units. I have over 20 on each of my machines as well. I will bring this to Rhiju\'s attantion.

EDIT: Rhiju is \"commuting\" at the moment but I am advised that as I expected this is a bad batch of Work Units. Rhiju says to let you know-
\"A new batch has been queued up. These should pass through very quickly. Sorry for the inconvience.\"


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