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Bug report for Rosetta version 5.97

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Message boards : RALPH@home bug list : Bug report for Rosetta version 5.97

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Profile dekim
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Message 4126 - Posted 21 Jun 2008 3:24:47 UTC

    Please post any 5.97 bugs here. This version is identical to 5.96 but includes a fix for a rare infinite loop in the boinc api. \"The dreaded t405 issue\".
    ____________

    Jipsu

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    Message 4128 - Posted 21 Jun 2008 12:18:55 UTC

      This stderr might be interesting, it still was a success though.

      http://ralph.bakerlab.org/result.php?resultid=1045195

      John Hunt
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      Message 4129 - Posted 21 Jun 2008 12:29:22 UTC

        Computation (client) error -

        http://ralph.bakerlab.org/result.php?resultid=1045289

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        Profile Conan
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        Message 4131 - Posted 21 Jun 2008 13:55:03 UTC

          Old \"t405\" is still raising it\'s ugly head, see this result

          <core_client_version>5.10.21</core_client_version>
          <![CDATA[
          <message>
          process exited with code 193 (0xc1, -63)
          </message>
          <stderr_txt>
          Graphics are disabled due to configuration...
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          # cpu_run_time_pref: 21600
          # random seed: 1176122
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          Unrecognized XML in parse_init_data_file: fraction_done_update_period
          Skipping: 1.000000
          Skipping: /fraction_done_update_period
          ======================================================
          DONE :: 1 starting structures 20983.1 cpu seconds
          This process generated 11 decoys from 11 attempts
          ======================================================


          BOINC :: Watchdog shutting down...
          BOINC :: BOINC support services shutting down...
          called boinc_finish
          *** glibc detected *** free(): invalid next size (normal): 0x0959bb58 ***
          SIGABRT: abort called
          Stack trace (19 frames):
          [0x8e1b51f]
          [0x8e15eac]
          [0xb7f6b420]
          [0x8e87104]
          [0x8e9c06f]
          [0x8ea10d5]
          [0x8ea13b3]
          [0x8e71d61]
          [0x8e73789]
          [0x8070d59]
          [0x87cdb6a]
          [0x8e8764f]
          [0x8e17abc]
          [0x8e17bc7]
          [0x86290f2]
          [0x8768b46]
          [0x8768c66]
          [0x8e80044]
          [0x8048111]

          Exiting...

          </stderr_txt>
          ]]>

          Validate state Invalid
          ____________

          Pepo
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          Message 4132 - Posted 21 Jun 2008 14:58:27 UTC

            Last modified: 21 Jun 2008 15:00:55 UTC

            Linux Boinc 6.2.4, t419N_autoalign_IGNORE_THE_REST_renumbered_4388_2_1: \"Maximum disk usage exceeded\". And a lot of

            Unrecognized XML in parse_init_data_file: fraction_done_update_period
            Skipping: 1.000000
            Skipping: /fraction_done_update_period

            in the stderr_txt.

            Peter

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            Message 4133 - Posted 21 Jun 2008 16:52:03 UTC

              You can ignore the unrecognized XML parse output in stderr.txt. There is still a possibility of getting access violations with the t405 jobs. We have to track down and fix the cause. What we are really concerned about is fixing the client stalling issue. This is a really bad problem since without any information sent back from the client, we can\'t determine the status of tasks and obviously a stalled client is a very bad situation.
              ____________

              Profile David Emigh
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              Message 4137 - Posted 22 Jun 2008 13:56:07 UTC

                Last modified: 22 Jun 2008 13:59:38 UTC

                This one threw a \"Compute Error\" at 0 seconds:

                t419N_autoalign_IGNORE_THE_REST_renumbered_4293_3_1

                The error message was:

                Maximum disk usage exceeded

                ____________
                RALPH and Rosie sittin' in a tree,
                F - O - L - D - I - N - G!

                Pepo
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                Message 4139 - Posted 23 Jun 2008 21:01:28 UTC - in response to Message 4133.

                  There is still a possibility of getting access violations with the t405 jobs. We have to track down and fix the cause. What we are really concerned about is fixing the client stalling issue. This is a really bad problem since without any information sent back from the client, we can\'t determine the status of tasks and obviously a stalled client is a very bad situation.

                  If my tasks will stall again (as some already did in the past), what files from my slot/project folders would interest you?

                  Peter

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                  Message 4141 - Posted 24 Jun 2008 10:44:30 UTC

                    My G5 got a computation error on t419N_autoalign_IGNORE_THE_REST_renumbered_4320_3:
                    exit status 1 (0x1), “Unable to determine sequence length from pdb file”.

                    Profile Conan
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                    Message 4142 - Posted 24 Jun 2008 11:53:39 UTC

                      > Another \"t405\" errored WU, see this WU. It has the same error as the one I reported previously.
                      ____________

                      Path7

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                      Message 4143 - Posted 24 Jun 2008 19:05:54 UTC

                        Last modified: 24 Jun 2008 19:20:33 UTC

                        Hello all,
                        Running Ubuntu 7.10 x86 the next WU errored with a -177 (0xffffffffffffff4f) error:
                        t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2
                        While the stderr out gives a: ERROR:: Unable to determine sequence length from pdb file
                        from Boinc messages I find:
                        di 24 jun 2008 20:22:51 CEST|ralph@home|Aborting task t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2: exceeded disk limit: 569.28MB > 476.84MB
                        di 24 jun 2008 20:22:52 CEST|ralph@home|Computation for task t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2 finished
                        di 24 jun 2008 20:22:52 CEST|ralph@home|Output file t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2_0 for task t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2 absent
                        note: di is short for Tuesday.

                        Edit: Boinc disk usage is limited to 2.16 GB.

                        Have a nice day,
                        Path7.

                        Pepo
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                        Message 4144 - Posted 24 Jun 2008 21:35:08 UTC - in response to Message 4143.

                          t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2
                          di 24 jun 2008 20:22:51 CEST|ralph@home|Aborting task t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2: exceeded disk limit: 569.28MB > 476.84MB

                          The t419N_autoalign_IGNORE_THE_REST_renumbered_4406_8_1: \"Maximum disk usage exceeded\". The same happened to all 3 wingmen (Mac, Linux, Vista).

                          Peter

                          Message boards : RALPH@home bug list : Bug report for Rosetta version 5.97


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