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Bug Report for Ralph 5.29

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Message boards : RALPH@home bug list : 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.

    idlorj

    Joined: Feb 16 06
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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>)

      Buffalo Bill

      Joined: May 13 06
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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.
        ____________

        bdrcca

        Joined: Sep 24 06
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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>


          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

            Norman_RKN

            Joined: Mar 26 06
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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



              ____________

              Profile anders n

              Joined: Feb 16 06
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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

                ____________

                Profile Inais
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                Joined: Jul 30 06
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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

                  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.

                    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

                      ____________

                      Pieface

                      Joined: Feb 16 06
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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.
                        ____________

                        John Lewis Highsmith

                        Joined: Mar 1 06
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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>)

                          ____________

                          Leffe

                          Joined: Feb 19 06
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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

                            ____________

                            Chu
                            Forum moderator
                            Project developer
                            Project scientist

                            Joined: Sep 26 06
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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!

                              Pieface

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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


                                Message boards : RALPH@home bug list : Bug Report for Ralph 5.29


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