Bug Report for Ralph 5.29

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Chu
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Message 2331 - Posted: 7 Oct 2006, 1:56:58 UTC

Ralph has been updated to 5.29. In this version, we mainly address two problems seen in 5.28 update.
1. fix a problem of job errors when application is supended, removed fromm memory and restarted again.
2. fix (hopefully) the widely observed \"File Handle Exception\" eorros when full_atom graphic is turned on and off.
Users are expected to see in the \"Searching\" box that when \"Searching_Backbone\" is on, only backbone is drawn and when \"Searching_all_atom\" is on, backbone plus sidechains are drawn. Sidechain flickering is turnned off in this update as it might also be responsible for the \"File Handle Exception\" error.
Please report bugs in this post.
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idlorj

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Message 2332 - Posted: 7 Oct 2006, 2:13:19 UTC

I have received the following error one all of the workunit for at least one of my computers.

10/6/2006 7:07:48 PM|ralph@home|Computation for task IDL_RLX_NT_t292_CASP7_hom001_1_1332_3_2 finished
10/6/2006 7:07:48 PM|ralph@home|Starting task IDL_RLX_NT_t349_CASP7_hom001_1_1332_3_1 using rosetta_beta version 529
10/6/2006 7:07:49 PM|ralph@home|Unrecoverable error for result IDL_RLX_NT_t292_CASP7_hom001_1_1332_3_2 (<file_xfer_error> <file_name>IDL_RLX_NT_t292_CASP7_hom001_1_1332_3_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)
10/6/2006 7:08:19 PM||Rescheduling CPU: application exited
10/6/2006 7:08:19 PM|ralph@home|Computation for task IDL_RLX_NT_t349_CASP7_hom001_1_1332_3_1 finished
10/6/2006 7:08:19 PM|rosetta@home|Resuming task 1a68__BOINC_FILTERS_ABRELAX_SAVE_ALL_OUT_frags83__1252_13983_0 using rosetta version 525
10/6/2006 7:08:20 PM|ralph@home|Unrecoverable error for result IDL_RLX_NT_t349_CASP7_hom001_1_1332_3_1 (<file_xfer_error> <file_name>IDL_RLX_NT_t349_CASP7_hom001_1_1332_3_1_0</file_name> <error_code>-161</error_code></file_xfer_error>)
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Buffalo Bill

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Message 2333 - Posted: 7 Oct 2006, 2:40:36 UTC
Last modified: 7 Oct 2006, 2:46:51 UTC

ERROR:: Unable to determine sequence length from pdb file

These two WU\'s were the only ones attempted. Both failed:

280817
280818

Bill

EDIT: Tried 2 more on AMD and 2 on Celeron box. All failed with same error.
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bdrcca

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Message 2334 - Posted: 7 Oct 2006, 2:46:41 UTC - in response to Message 2332.  
Last modified: 7 Oct 2006, 3:07:09 UTC

Received the same error on all IDL_RLX_NT workunits.
280746
280690
280648
280553

</stderr_txt>
<message>
<file_xfer_error>
<file_name>IDL_RLX_NT_t385_CASP7_hom001_1_1332_5_1_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>


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bdrcca

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Message 2335 - Posted: 7 Oct 2006, 3:10:14 UTC
Last modified: 7 Oct 2006, 3:03:45 UTC

And another - seems to be just the IDL_RLX_NT
workunits.
281173

bdrcca
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Norman_RKN

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Message 2337 - Posted: 7 Oct 2006, 5:11:23 UTC

07.10.2006 07:05:52|ralph@home|Unrecoverable error for result IDL_RLX_NT_t348_CASP7_hom001_1_1332_9_2 (<file_xfer_error> <file_name>IDL_RLX_NT_t348_CASP7_hom001_1_1332_9_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)

282112



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Profile anders n

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Message 2338 - Posted: 7 Oct 2006, 6:30:51 UTC

ERROR:: Unable to determine sequence length from pdb file

On all my computers.

Anders n

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Profile Inais
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Message 2339 - Posted: 7 Oct 2006, 6:57:09 UTC

WU 247902 - Client/Computing error

07.10.2006 08:47:47|ralph@home|Unrecoverable error for result IDL_RLX_NT_t288_CASP7_hom001_1_1332_1_1 (<file_xfer_error> <file_name>IDL_RLX_NT_t288_CASP7_hom001_1_1332_1_1_0</file_name> <error_code>-161</error_code></file_xfer_error>)


Biba - Inais.
I wish I can fly like a bird in the sky
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Profile KSMarksPsych
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Message 2340 - Posted: 7 Oct 2006, 11:40:08 UTC

Got 2 overnight with the above reported error.

<core_client_version>5.4.11</core_client_version>
<stderr_txt>
ERROR:: Unable to determine sequence length from pdb file
======================================================
DONE :: 1 starting structures built 5 (nstruct) times
This process generated 0 decoys from 0 attempts
1 starting pdbs were skipped
======================================================


BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...

</stderr_txt>
<message>
<file_xfer_error>
<file_name>IDL_RLX_NT_t293_CASP7_hom001_1_1332_10_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>




Errored out in 18 and 20 seconds.
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Profile paul and kirsty yates
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Message 2341 - Posted: 7 Oct 2006, 11:56:28 UTC
Last modified: 7 Oct 2006, 11:41:09 UTC

got 4 over the past 2 days
this one
this one
this one
and this one
3 unhandled exeptions
and 1 Unable to determine sequence length from pdb file

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Pieface

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Message 2344 - Posted: 7 Oct 2006, 14:44:08 UTC

Like everyone else I guess, on 5.29 I am getting a slew of the PDB errors on IDX_RLX_NT_* WU\'s (and one FRA_T374_) but occasionally getting a good run on a DOCK_* or 1WHO_* or 5CROA_* type.
I wasn\'t getting any work for a while as the errors had put my daily wu number down in the weeds, but i\'m starting to get some new work now.
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John Lewis Highsmith

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Message 2345 - Posted: 7 Oct 2006, 15:44:09 UTC

Have another:

10/7/2006 9:30:27 AM|ralph@home|Starting task IDL_RLX_NT_t384_CASP7_hom001_1_1332_6_0 using rosetta_beta version 529

10/7/2006 9:31:55 AM|ralph@home|Computation for task IDL_RLX_NT_t384_CASP7_hom001_1_1332_6_0 finished


10/7/2006 9:31:57 AM|ralph@home|Unrecoverable error for result IDL_RLX_NT_t384_CASP7_hom001_1_1332_6_0 (<file_xfer_error> <file_name>IDL_RLX_NT_t384_CASP7_hom001_1_1332_6_0_0</file_name> <error_code>-161</error_code></file_xfer_error>)

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Leffe

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Message 2346 - Posted: 7 Oct 2006, 16:50:01 UTC


got 2 of these...and still 7 wu left

07/10/2006 16:41:01||Rescheduling CPU: application exited
07/10/2006 16:41:01|ralph@home|Computation for task 1utg__BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_15_0 finished
07/10/2006 16:41:01|ralph@home|Starting task IDL_RLX_NT_t347_CASP7_hom001_1_1332_10_2 using rosetta_beta version 529
07/10/2006 16:41:03|ralph@home|Started upload of file 1utg__BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_15_0_0
07/10/2006 16:41:16|ralph@home|Finished upload of file 1utg__BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_15_0_0
07/10/2006 16:41:16|ralph@home|Throughput 1674 bytes/sec
07/10/2006 16:41:33||Rescheduling CPU: application exited
07/10/2006 16:41:33|ralph@home|Computation for task IDL_RLX_NT_t347_CASP7_hom001_1_1332_10_2 finished
07/10/2006 16:41:33|ralph@home|Resuming task 256bA_BOINC_ABRELAX_SAVE_ALL_OUT_truess__1329_12_1 using rosetta_beta version 529
07/10/2006 16:41:34|ralph@home|Unrecoverable error for result IDL_RLX_NT_t347_CASP7_hom001_1_1332_10_2 (<file_xfer_error> <file_name>IDL_RLX_NT_t347_CASP7_hom001_1_1332_10_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)
07/10/2006 16:41:34|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
07/10/2006 17:23:02||Rescheduling CPU: application exited
07/10/2006 17:23:02|ralph@home|Computation for task 256bA_BOINC_ABRELAX_SAVE_ALL_OUT_truess__1329_12_1 finished
07/10/2006 17:23:03|ralph@home|Starting task 1enh__BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_15_0 using rosetta_beta version 529
07/10/2006 17:23:05|ralph@home|Started upload of file 256bA_BOINC_ABRELAX_SAVE_ALL_OUT_truess__1329_12_1_0
07/10/2006 17:23:16|ralph@home|Finished upload of file 256bA_BOINC_ABRELAX_SAVE_ALL_OUT_truess__1329_12_1_0
07/10/2006 17:23:16|ralph@home|Throughput 1328 bytes/sec
07/10/2006 18:20:19||Rescheduling CPU: application exited
07/10/2006 18:20:19|ralph@home|Computation for task 1enh__BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_15_0 finished
07/10/2006 18:20:19|ralph@home|Starting task IDL_RLX_NT_t326_CASP7_hom001_1_1332_8_2 using rosetta_beta version 529
07/10/2006 18:20:21|ralph@home|Started upload of file 1enh__BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_15_0_0
07/10/2006 18:20:30|ralph@home|Finished upload of file 1enh__BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_15_0_0
07/10/2006 18:20:30|ralph@home|Throughput 2774 bytes/sec
07/10/2006 18:20:51||Rescheduling CPU: application exited
07/10/2006 18:20:51|ralph@home|Computation for task IDL_RLX_NT_t326_CASP7_hom001_1_1332_8_2 finished
07/10/2006 18:20:51|ralph@home|Starting task 1fkb__BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_15_0 using rosetta_beta version 529
07/10/2006 18:20:52|ralph@home|Unrecoverable error for result IDL_RLX_NT_t326_CASP7_hom001_1_1332_8_2 (<file_xfer_error> <file_name>IDL_RLX_NT_t326_CASP7_hom001_1_1332_8_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)
07/10/2006 18:20:52|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
07/10/2006 18:54:22||Rescheduling CPU: application exited

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Chu
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Message 2349 - Posted: 7 Oct 2006, 23:51:35 UTC

ERRORS from IDL_RLX WUs are probably due to some missing files or logic errors in Rosetta code (bqian will look into that). So far the rate of \"Unhandle File Exception\" errors is much lower than that for App.5.28. We will watch closely other erros reported here. Thank everyone for help!
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Message 2356 - Posted: 8 Oct 2006, 19:03:24 UTC
Last modified: 8 Oct 2006, 18:49:14 UTC

Still getting some unable to determine sequence length from PDB on those IDL_RLX and IDX_RLX guys, but now they are coming out as 0x0 and 0x1 client errors which i guess is better as we don\'t get the long de-bug info dump. Here are a couple I have seen recently:
RESID 282626
and
RESID 284283

a new one for me is:
RESID 283018
which died with a 0x1 and the message:
ERROR:: Unable to determine sequence length from pdb file
ERROR:: Exit at: .\\pose.cc line:1513


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