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Bug reports for Ralph 5.37 through 5.40

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Message boards : RALPH@home bug list : Bug reports for Ralph 5.37 through 5.40

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Chu
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Message 2452 - Posted 4 Nov 2006 0:36:17 UTC

    If all goes well with this update, we\'ll probably update the main application on Monday. Look for some interesting new workunits with multiple copies of a protein -- these are attempt to simulate fibril formation.

    Pieface

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    Message 2453 - Posted 4 Nov 2006 3:15:12 UTC

      Hmmm. here\'s one I haven\'t seen before:

      resid 312317

      <core_client_version>5.4.11</core_client_version>
      <message>
      The system cannot find the path specified. (0x3) - exit code 3 (0x3)
      </message>
      <stderr_txt>
      # random seed: 2872198
      # cpu_run_time_pref: 14400

      </stderr_txt>

      Profile anders n

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      Message 2454 - Posted 4 Nov 2006 7:06:55 UTC

        This one died just when it was about to start working.

        (I was looking at grafics)

        http://ralph.bakerlab.org/result.php?resultid=312289

        Anders n
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        Profile anders n

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        Message 2455 - Posted 4 Nov 2006 7:09:41 UTC

          This one never got past 31 sek.

          Did that 5 times then died.

          Same thing with looking at grafics as not looking at it.

          http://ralph.bakerlab.org/result.php?resultid=312654

          Anders n
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          Message 2456 - Posted 4 Nov 2006 8:20:25 UTC

            Problems with this one too
            ____________

            Profile anders n

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            Message 2457 - Posted 4 Nov 2006 8:33:24 UTC - in response to Message 2455.

              This one never got past 31 sek.

              Did that 5 times then died.

              Same thing with looking at grafics as not looking at it.

              http://ralph.bakerlab.org/result.php?resultid=312654

              Anders n



              And 2 more 36 sek this time.

              http://ralph.bakerlab.org/result.php?resultid=313537
              http://ralph.bakerlab.org/result.php?resultid=313538

              Anders n
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              Pepo
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              Message 2458 - Posted 4 Nov 2006 9:29:13 UTC

                Last modified: 4 Nov 2006 10:16:46 UTC

                This one (Linux) did not get past 0 seconds too:

                <message>
                process exited with code 1 (0x1)
                </message>
                <stderr_txt>
                Graphics are disabled due to configuration...
                ERROR:: Exit at: read_paths.cc line:346
                </stderr_txt>

                Peter

                bdrcca

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                Message 2459 - Posted 4 Nov 2006 10:20:53 UTC

                  Incorrect dsolv found.
                  313368

                  input_etable: reading etable... dsolv
                  input_etable: WARNING etable types don\'t match!
                  expected dsolv,606 got dsolv,721

                  </stderr_txt>
                  <message>
                  <file_xfer_error>
                  <file_name>1n0u__ETABLE_TEST_ABRELAX_rhh13sm6__1452_16_1_0</file_name>
                  <error_code>-161</error_code>
                  </file_xfer_error>

                  </message>



                  bdrcca

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                  Message 2460 - Posted 4 Nov 2006 10:35:57 UTC - in response to Message 2459.

                    Different machine.Same error message-Incorrect dsolv found.
                    312850
                    312926

                    input_etable: reading etable... dsolv
                    input_etable: WARNING etable types don\'t match!
                    expected dsolv,606 got dsolv,721
                    </stderr_txt>
                    <message>
                    <file_xfer_error>
                    <file_name>1dcj__ETABLE_TEST_ABRELAX_rhh13sm6__1451_1_1_0</file_name>
                    <error_code>-161</error_code>
                    </file_xfer_error>

                    </message>
                    -------------------------------------------------------------------------------
                    </stderr_txt>
                    <message>
                    <file_xfer_error>
                    <file_name>1ogw__ETABLE_TEST_ABRELAX_rhh13sm6__1451_13_0_0</file_name>
                    <error_code>-161</error_code>
                    </file_xfer_error>

                    </message>




                    Snorre

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                    Message 2461 - Posted 4 Nov 2006 11:12:37 UTC

                      04/11/2006 13:08:45|ralph@home|Unrecoverable error for result FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000007_0.pdb_1449_5_0 (Systemet finner ikke angitt bane. (0x3) - exit code 3 (0x3))

                      (System can\'t find specified path.)

                      Running on a WinXP SP2, AMD X2 4600+. Every single WU I\'ve recieved are like this.

                      Pepo
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                      Message 2462 - Posted 4 Nov 2006 12:57:29 UTC

                        Last modified: 4 Nov 2006 13:45:15 UTC

                        Few more failing after few seconds.

                        This one (Linux) went 75 seconds, then
                        process exited with code 131 (0x83)
                        # random seed: 2872049
                        terminate called after throwing an instance of \'std::bad_alloc\'
                        what(): St9bad_alloc
                        SIGABRT: abort called
                        Stack trace (20 frames):
                        [0x89f7e63]
                        [0x8a0ff1c]
                        [0x8a76008]
                        [0x8a764c4]
                        [0x8a6423b]
                        [0x8a6183d]
                        [0x8a61872]
                        [0x8a614a3]
                        [0x8a60fac]
                        [0x8a63321]
                        [0x808c7c0]
                        [0x8537af8]
                        [0x8544946]
                        [0x8549a04]
                        [0x854bb47]
                        [0x880f59e]
                        [0x84597ef]
                        [0x856b5d1]
                        [0x8a6f404]
                        [0x8048111]

                        Exiting...

                        Another one (WinXP) after 105 seconds produced a readable stack trace of all threads and a list of modules (BOINC Windows Runtime Debugger). It\'s a bit large, I\'ll keep a copy of it.

                        Peter

                        John Lewis Highsmith

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                        Message 2463 - Posted 4 Nov 2006 14:22:27 UTC

                          Here are 2 more:
                          1)
                          11/4/2006 5:03:43 AM|ralph@home|Restarting task 1dcj__ETABLE_TEST_ABRELAX_rhh13sm6__1452_8_1 using rosetta_beta version 537

                          11/4/2006 5:03:45 AM|ralph@home|Computation for task 1dcj__ETABLE_TEST_ABRELAX_rhh13sm6__1452_8_1 finished

                          11/4/2006 5:03:46 AM|ralph@home|Unrecoverable error for result 1dcj__ETABLE_TEST_ABRELAX_rhh13sm6__1452_8_1 (<file_xfer_error> <file_name>1dcj__ETABLE_TEST_ABRELAX_rhh13sm6__1452_8_1_0</file_name> <error_code>-161</error_code></file_xfer_error>)


                          2)
                          11/4/2006 7:21:25 AM|ralph@home|Starting task FRA_t364_CASP7_hom001_4_IGNORE_THE_RESTt364_1_S_00001_0000007_0.pdb_1454_13_1 using rosetta_beta version 537

                          11/4/2006 7:21:27 AM|ralph@home|Unrecoverable error for result FRA_t364_CASP7_hom001_4_IGNORE_THE_RESTt364_1_S_00001_0000007_0.pdb_1454_13_1 (Incorrect function. (0x1) - exit code 1 (0x1))

                          ____________

                          Pieface

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                          Message 2464 - Posted 5 Nov 2006 2:27:35 UTC

                            Whoopee.... I just had one go thru to completion (first one today):

                            Resid 314118

                            I hope that\'s a sign that we\'re over this rough spot!!!

                            Profile [B^S] Gamma^Ray

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                            Message 2465 - Posted 6 Nov 2006 7:27:26 UTC

                              Might be just my machine today, But on the new 5.38, I notice with the screen saver maximized, I can\'t really see much if any of the very bottom text (The URL, And the Accepted Energy). Its fine if its not max though.

                              5.4.11/6600GT/XP
                              ____________

                              Profile Krzychu P.

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                              Message 2466 - Posted 6 Nov 2006 7:29:56 UTC

                                I get:

                                2006-11-06 09:23:07|ralph@home|Unrecoverable error for result DOC_1STF_p1_fa_relax_from_native_1462_4_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                <core_client_version>5.6.5</core_client_version>
                                <![CDATA[
                                <message>
                                Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                </message>
                                <stderr_txt>
                                # random seed: 2870558
                                ABORT: bad to aa_rotno_to_packedrotno
                                aa,rot1/2/3/4: GLN 14 3 1 0 0
                                chi no 3 nchi 3 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                ERROR:: Exit at: .\\rotamer_functions.cc line:1509

                                </stderr_txt>
                                ]]>

                                and I get the message in new window about runtime error C++
                                ____________

                                Profile anders n

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                                Message 2467 - Posted 6 Nov 2006 9:55:46 UTC

                                  file_xfer_error

                                  On this wu

                                  http://ralph.bakerlab.org/result.php?resultid=314846

                                  Anders n
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                                  Message 2468 - Posted 6 Nov 2006 11:04:07 UTC

                                    Problems with this wu , but fingers crossed all others seem to be completing ok.
                                    ____________

                                    Profile Conan
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                                    Message 2469 - Posted 6 Nov 2006 11:09:51 UTC

                                      >> Here is one that stayed at 1.01% for over 2 hours before changing and died at about 3.5 hours

                                      http://ralph.bakerlab.org/result.php?resultid=314538

                                      12336.282599
                                      stderr out

                                      <core_client_version>5.2.14</core_client_version>
                                      <stderr_txt>
                                      Graphics are disabled due to configuration...
                                      # random seed: 2870606
                                      # cpu_run_time_pref: 21600
                                      ======================================================
                                      DONE :: 1 starting structures built 1 (nstruct) times
                                      This process generated 1 decoys from 1 attempts
                                      0 starting pdbs were skipped
                                      ======================================================


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

                                      </stderr_txt>
                                      <message><file_xfer_error>
                                      <file_name>DOC_1MAH_p1_fa_relax_from_native_1462_1_0_0</file_name>
                                      <error_code>-161</error_code>
                                      <error_message></error_message>
                                      </file_xfer_error>

                                      Had another one stay at 1.01% for about the same amount of time but is now at 43.81% and still going after 4.45 hours.
                                      This is on 5.38.
                                      ____________

                                      Profile Krzychu P.

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                                      Message 2470 - Posted 6 Nov 2006 13:51:06 UTC

                                        I get message in new small window:

                                        \"Microsoft Visual C++ Runtime Library

                                        Runtime Error!

                                        Program: ...ralph.bakerlab.org\\rosetta_beta_5.38_windows_intelx86.exe

                                        This application has requested the Runtime to terminate it in an unusual way.
                                        Please contact the application\'s support team for more information.\"

                                        2006-11-06 15:54:10|ralph@home|Unrecoverable error for result FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000008_0.pdb_1449_4_2 (System nie może odnaleźć określonej ścieżki. (0x3) - exit code 3 (0x3))

                                        [This mean: System nie może odnaleźć określonej ścieżki <=> System can\'t find specified path]

                                        <core_client_version>5.6.5</core_client_version>
                                        <![CDATA[
                                        <message>
                                        System nie może odnaleźć określonej ścieżki. (0x3) - exit code 3 (0x3)
                                        </message>
                                        <stderr_txt>
                                        # random seed: 2872053

                                        </stderr_txt>
                                        ]]>



                                        ____________

                                        Profile Conan
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                                        Message 2471 - Posted 6 Nov 2006 14:04:07 UTC - in response to Message 2469.

                                          >> Here is one that stayed at 1.01% for over 2 hours before changing and died at about 3.5 hours

                                          http://ralph.bakerlab.org/result.php?resultid=314538

                                          12336.282599
                                          stderr out

                                          <core_client_version>5.2.14</core_client_version>
                                          <stderr_txt>
                                          Graphics are disabled due to configuration...
                                          # random seed: 2870606
                                          # cpu_run_time_pref: 21600
                                          ======================================================
                                          DONE :: 1 starting structures built 1 (nstruct) times
                                          This process generated 1 decoys from 1 attempts
                                          0 starting pdbs were skipped
                                          ======================================================


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

                                          </stderr_txt>
                                          <message><file_xfer_error>
                                          <file_name>DOC_1MAH_p1_fa_relax_from_native_1462_1_0_0</file_name>
                                          <error_code>-161</error_code>
                                          <error_message></error_message>
                                          </file_xfer_error>

                                          Had another one stay at 1.01% for about the same amount of time but is now at 43.81% and still going after 4.45 hours.
                                          This is on 5.38.


                                          >>> And here are another couple
                                          http://ralph.bakerlab.org/result.php?resultid=314540
                                          http://ralph.bakerlab.org/result.php?resultid=314539

                                          result 314540 gave:-
                                          CPU time 21455.314296
                                          stderr out

                                          <core_client_version>5.2.14</core_client_version>
                                          <stderr_txt>
                                          Graphics are disabled due to configuration...
                                          # random seed: 2870596
                                          # cpu_run_time_pref: 21600
                                          ======================================================
                                          DONE :: 1 starting structures built 25 (nstruct) times
                                          This process generated 25 decoys from 25 attempts
                                          0 starting pdbs were skipped
                                          ======================================================


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

                                          </stderr_txt>
                                          <message><file_xfer_error>
                                          <file_name>DOC_1MEL_p1_fa_relax_from_native_1462_1_0_0</file_name>
                                          <error_code>-161</error_code>
                                          <error_message></error_message>
                                          </file_xfer_error>

                                          And result 314539 was the same except for 2 decoys and <file_name>DOC_1MDA_p1_fa_relax_from_native_1462_1_0_0</file>

                                          Again this 5.38. Stayed at 1.00% for about 1 hour 35 minutes then went to 1.01% till past 2 hours, jumps to 43.81% and then errors out around the 5 hour mark or near completion.
                                          I am watching another 2 at the moment doing the same thing, so I will probably have more fail.
                                          ____________

                                          Profile feet1st

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                                          Message 2472 - Posted 6 Nov 2006 14:40:43 UTC

                                            Last modified: 6 Nov 2006 15:29:07 UTC

                                            Not sure what to make of this. Two 5.37 WUs ran over the weekend. PC was up and running all weekend. I\'ve got 24hr runtime preference on Ralph. Both seem to have failed after running for 2 days, but CPU time shows as 00:01:23 and :25 for these.

                                            312611
                                            312612

                                            Here\'s the messages, which shows you the entire timeline:

                                            11/4/2006 12:09:31 AM|ralph@home|Sending scheduler request to http://ralph.bakerlab.org/ralph_cgi/cgi
                                            11/4/2006 12:09:31 AM|ralph@home|Reason: To fetch work
                                            11/4/2006 12:09:31 AM|ralph@home|Requesting 207360 seconds of new work
                                            11/4/2006 12:09:36 AM|ralph@home|Scheduler request succeeded
                                            11/4/2006 12:09:38 AM|ralph@home|Started download of file rosetta_beta_5.37_windows_intelx86.exe
                                            11/4/2006 12:09:38 AM|ralph@home|Started download of file hom001_aat364_03_05.200_v1_3.gz
                                            11/4/2006 12:09:41 AM|ralph@home|Finished download of file hom001_aat364_03_05.200_v1_3.gz
                                            11/4/2006 12:09:41 AM|ralph@home|Throughput 728542 bytes/sec
                                            11/4/2006 12:09:41 AM|ralph@home|Started download of file hom001_aat364_09_05.200_v1_3.gz
                                            11/4/2006 12:09:46 AM|ralph@home|Finished download of file hom001_aat364_09_05.200_v1_3.gz
                                            11/4/2006 12:09:46 AM|ralph@home|Throughput 904946 bytes/sec
                                            11/4/2006 12:09:46 AM|ralph@home|Started download of file hom001_t364_.fasta.gz
                                            11/4/2006 12:09:47 AM|ralph@home|Finished download of file hom001_t364_.fasta.gz
                                            11/4/2006 12:09:47 AM|ralph@home|Throughput 1127 bytes/sec
                                            11/4/2006 12:09:47 AM|ralph@home|Started download of file t364_1_S_00001_0000007_0.pdb.gz
                                            11/4/2006 12:09:48 AM|ralph@home|Finished download of file rosetta_beta_5.37_windows_intelx86.exe
                                            11/4/2006 12:09:48 AM|ralph@home|Throughput 925633 bytes/sec
                                            11/4/2006 12:09:48 AM|ralph@home|Finished download of file t364_1_S_00001_0000007_0.pdb.gz
                                            11/4/2006 12:09:48 AM|ralph@home|Throughput 98559 bytes/sec
                                            11/4/2006 12:09:48 AM|ralph@home|Started download of file t364_loopfile.gz
                                            11/4/2006 12:09:48 AM|ralph@home|Started download of file paths_200_t364.txt
                                            11/4/2006 12:09:50 AM|ralph@home|Finished download of file t364_loopfile.gz
                                            11/4/2006 12:09:50 AM|ralph@home|Throughput 413 bytes/sec
                                            11/4/2006 12:09:50 AM|ralph@home|Finished download of file paths_200_t364.txt
                                            11/4/2006 12:09:50 AM|ralph@home|Throughput 9097 bytes/sec
                                            11/4/2006 12:09:50 AM|ralph@home|Started download of file t364_1_S_00001_0000008_0.pdb.gz
                                            11/4/2006 12:09:51 AM||Rescheduling CPU: files downloaded
                                            11/4/2006 12:09:51 AM|ralph@home|Finished download of file t364_1_S_00001_0000008_0.pdb.gz
                                            11/4/2006 12:09:51 AM|ralph@home|Throughput 99307 bytes/sec
                                            11/4/2006 12:09:51 AM||Using earliest-deadline-first scheduling because computer is overcommitted.
                                            11/4/2006 12:09:51 AM|rosetta@home|Pausing task FRA_t368_HOMOENVLOOPRLX_hom001_11_t368_11_dec01IGNORE_THE_REST_3_1329_45_0 (left in memory)
                                            11/4/2006 12:09:51 AM|ralph@home|Starting task FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000007_0.pdb_1447_3_2 using rosetta_beta version 537
                                            11/4/2006 12:09:51 AM||Suspending work fetch because computer is overcommitted.
                                            11/4/2006 12:09:52 AM||Rescheduling CPU: files downloaded
                                            11/4/2006 12:09:52 AM|rosetta@home|Pausing task BENCH_ABRELAX_SAVE_ALL_OUT_1iibA_BARCODE_R85_filters_1328_358_0 (left in memory)
                                            11/4/2006 12:09:52 AM|ralph@home|Starting task FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000008_0.pdb_1447_3_2 using rosetta_beta version 537
                                            11/4/2006 7:00:00 AM||Suspending network activity - time of day
                                            11/4/2006 7:00:00 PM||Resuming network activity
                                            11/4/2006 11:48:10 PM|rosetta@home|Sending scheduler request to http://boinc.bakerlab.org/rosetta_cgi/cgi
                                            11/4/2006 11:48:10 PM|rosetta@home|Reason: To report completed tasks
                                            11/4/2006 11:48:10 PM|rosetta@home|Reporting 2 tasks
                                            11/4/2006 11:48:15 PM|rosetta@home|Scheduler request succeeded
                                            11/5/2006 7:00:00 AM||Suspending network activity - time of day
                                            11/5/2006 7:00:00 PM||Resuming network activity
                                            11/6/2006 7:00:00 AM||Suspending network activity - time of day
                                            11/6/2006 9:00:58 AM|ralph@home|Unrecoverable error for result FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000007_0.pdb_1447_3_2 ( - exit code -529697949 (0xe06d7363))
                                            11/6/2006 9:00:58 AM|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
                                            11/6/2006 9:00:58 AM||Rescheduling CPU: application exited
                                            11/6/2006 9:00:58 AM|ralph@home|Computation for task FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000007_0.pdb_1447_3_2 finished
                                            11/6/2006 9:00:58 AM|rosetta@home|Resuming task BENCH_ABRELAX_SAVE_ALL_OUT_1iibA_BARCODE_R85_filters_1328_358_0 using rosetta version 536
                                            11/6/2006 9:01:12 AM|ralph@home|Unrecoverable error for result FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000008_0.pdb_1447_3_2 ( - exit code -529697949 (0xe06d7363))
                                            11/6/2006 9:01:12 AM|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
                                            11/6/2006 9:01:14 AM||Rescheduling CPU: application exited
                                            11/6/2006 9:01:14 AM|ralph@home|Computation for task FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000008_0.pdb_1447_3_2 finished
                                            11/6/2006 9:01:14 AM|rosetta@home|Resuming task FRA_t368_HOMOENVLOOPRLX_hom001_11_t368_11_dec01IGNORE_THE_REST_3_1329_45_0 using rosetta version 536


                                            ____________

                                            Profile anders n

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                                            Message 2473 - Posted 6 Nov 2006 14:44:48 UTC - in response to Message 2467.

                                              file_xfer_error

                                              On this wu

                                              http://ralph.bakerlab.org/result.php?resultid=314846

                                              Anders n



                                              One more.

                                              http://ralph.bakerlab.org/result.php?resultid=314848

                                              Anders n
                                              ____________

                                              wraith

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                                              Message 2474 - Posted 6 Nov 2006 14:45:53 UTC

                                                Last modified: 6 Nov 2006 15:34:20 UTC

                                                This one ran for 4 hours and hung at 100%.. , but, could not be preempted... (in run state with no activity).

                                                I stopped and started BOINC and the W.U. restarted from 0.0 .... no checkpointing at all... Unfortunately, this restart lost the stdout/stderr files. I am allowing the unit to rerun in hopes of catching the out/error files on the next glitch.

                                                http://ralph.bakerlab.org/result.php?resultid=314941



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                                                Message 2475 - Posted 6 Nov 2006 16:07:38 UTC

                                                  I should also point out, when I returned to my PC, I had a message prompt from my ZoneAlarm firewall telling me that Rosetta Beta v5.37 was trying to use the internet and should I allow it... I wasn\'t here to respond, and so I presume it timed out.

                                                  ...is there any way to force this debug communication attempt? So I could get a given version of the application setup in the firewall BEFORE a error causes it to try to use the net?
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                                                  Message 2476 - Posted 6 Nov 2006 16:29:18 UTC

                                                    Thank you all for the help. We have already noticed that there are a lot of failures with error code -161 for the newly updated application 5.38. We are investigating the cause for it now...

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                                                    Message 2477 - Posted 6 Nov 2006 16:56:49 UTC

                                                      Last modified: 6 Nov 2006 17:44:34 UTC

                                                      V5.38 WU 315376 just crashed on my other machine. I just HAPPENED to be enlarging the native structure shown at the time of failure, so that was the first I\'d brought up the graphic for this WU, rotated the lowest energy, then enlarged native and then crash and burn.

                                                      exit code -1073741819
                                                      24hr RT preference.
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                                                      Message 2478 - Posted 6 Nov 2006 17:40:19 UTC - in response to Message 2477.

                                                        Hi feet1st. That is really helpful. We have seen that error message ( in the debugging output) for quite a few times but no luck in finding a clue of what is the cause for that. Now for your reporting, we at least know it is somehow related to the graphic and I think it will help us a lot to investigate the real cause.

                                                        V5.38 WU 315376 just crashed on my other machine. I just HAPPENED to be enlarging the native structure shown at the time of failure, so that was the first I\'d brought up the graphic for this WU, rotated the lowest energy, then enlarged native and then crash and burn.

                                                        exit code -1073741819
                                                        24hr RT preference.

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                                                        Message 2479 - Posted 6 Nov 2006 18:51:16 UTC


                                                          got 1 error:


                                                          06/11/2006 18:37:32|ralph@home|Computation for task fibril_abeta40_test1_1463_63_0 finished
                                                          06/11/2006 18:37:32|Spinhenge@home|Starting task fullerene2_4353_0 using metropolis version 242
                                                          06/11/2006 18:37:33|ralph@home|Unrecoverable error for result fibril_abeta40_test1_1463_63_0 (<file_xfer_error> <file_name>fibril_abeta40_test1_1463_63_0_0</file_name> <error_code>-161</error_code></file_xfer_error>)

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                                                          Message 2480 - Posted 6 Nov 2006 19:19:33 UTC

                                                            Error: Result

                                                            11/5/2006 9:10:01 PM|NanoHive@Home|Project is down
                                                            11/6/2006 12:47:28 PM|ralph@home|Sending scheduler request: To fetch work
                                                            11/6/2006 12:47:28 PM|ralph@home|Requesting 591 seconds of new work
                                                            11/6/2006 12:47:33 PM|ralph@home|Scheduler RPC succeeded [server version 505]
                                                            11/6/2006 12:47:33 PM|ralph@home|No work from project
                                                            11/6/2006 12:57:34 PM|ralph@home|Sending scheduler request: To fetch work
                                                            11/6/2006 12:57:34 PM|ralph@home|Requesting 296 seconds of new work
                                                            11/6/2006 12:57:39 PM|ralph@home|Scheduler RPC succeeded [server version 505]
                                                            11/6/2006 1:00:22 PM|ralph@home|Computation for task fibril_abeta40_test1_1463_20_1 finished
                                                            11/6/2006 1:00:22 PM||Starting fibril_abeta40_test1_1463_134_1
                                                            11/6/2006 1:00:22 PM|ralph@home|Starting task fibril_abeta40_test1_1463_134_1 using rosetta_beta version 538
                                                            11/6/2006 1:00:24 PM|ralph@home|Unrecoverable error for result fibril_abeta40_test1_1463_20_1 (<file_xfer_error> <file_name>fibril_abeta40_test1_1463_20_1_0</file_name> <error_code>-161</error_code></file_xfer_error>)
                                                            11/6/2006 1:17:12 PM|rosetta@home|Computation for task DOC_1CGI_R061030_st_model_06_1352_838_0 finished
                                                            11/6/2006 1:17:12 PM||Starting DOC_1CGI_R061030_st_model_07_1352_963_0
                                                            11/6/2006 1:17:12 PM|rosetta@home|Starting task DOC_1CGI_R061030_st_model_07_1352_963_0 using rosetta version 536
                                                            11/6/2006 1:17:14 PM|rosetta@home|Started upload of file DOC_1CGI_R061030_st_model_06_1352_838_0_0
                                                            11/6/2006 1:17:22 PM|rosetta@home|Finished upload of file DOC_1CGI_R061030_st_model_06_1352_838_0_0


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                                                            Message 2481 - Posted 6 Nov 2006 19:30:28 UTC

                                                              2006-11-06 21:03:29|ralph@home|Unrecoverable error for result FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000005_0.pdb_1447_1_2 (System nie może odnaleźć określonej ścieżki. (0x3) - exit code 3 (0x3))

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                                                              Message 2482 - Posted 6 Nov 2006 19:39:33 UTC

                                                                11/6/2006 2:35:31 PM|ralph@home|Unrecoverable error for result FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000007_0.pdb_1447_10_2 (The system cannot find the path specified. (0x3) - exit code 3 (0x3))

                                                                11/6/2006 2:35:31 PM|ralph@home|Computation for task FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000007_0.pdb_1447_10_2 finished
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                                                                Message 2483 - Posted 6 Nov 2006 19:52:38 UTC

                                                                  Error: Result


                                                                  11/6/2006 1:47:17 PM|ralph@home|Computation for task fibril_abeta40_test1_1463_134_1 finished
                                                                  11/6/2006 1:47:18 PM|ralph@home|Unrecoverable error for result fibril_abeta40_test1_1463_134_1 (<file_xfer_error> <file_name>fibril_abeta40_test1_1463_134_1_0</file_name> <error_code>-161</error_code></file_xfer_error>)
                                                                  11/6/2006 1:47:18 PM|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
                                                                  11/6/2006 1:48:22 PM|ralph@home|Sending scheduler request: Requested by user
                                                                  11/6/2006 1:48:22 PM|ralph@home|Reporting 1 tasks
                                                                  11/6/2006 1:48:27 PM|ralph@home|Scheduler RPC succeeded [server version 505]

                                                                  ____________


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                                                                  Message 2484 - Posted 6 Nov 2006 21:24:08 UTC

                                                                    May I ask? I hope a good description can be written for when 5.38 comes to Rosetta... WHY is \"...outputting structures with non-ideal backbone and sidehchain geometries\" an improvement? I know, useful to the science... please explain more, on the surface it sounds to a layperson like a step backwards. Also, what impact will this have on the user experience? Will it mean we\'ll see larger upload sizes on results?
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                                                                    Message 2485 - Posted 6 Nov 2006 21:47:32 UTC

                                                                      >>> The following workunits, whilst running till completion and finished, only produced 2 Decoys in over 5 hours each. In both cases they stayed at 1.00% for about 1 1/2 hours then went to 1.01% for possibly another 2 hours or more before finishing:-

                                                                      http://ralph.bakerlab.org/result.php?resultid=314543
                                                                      http://ralph.bakerlab.org/result.php?resultid=314542

                                                                      Ralph 5.38.
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                                                                      Message 2486 - Posted 6 Nov 2006 23:52:11 UTC

                                                                        It looks like all of the 5.38 tasks I have gotten have crashed. The output on the web page for mine is similar to what is already posted in this thread. One thing I have to add is that on a dual-core machine it was using ~98% of the CPU instead of the ~49% that it should have been.
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                                                                        Message 2487 - Posted 7 Nov 2006 0:12:42 UTC - in response to Message 2485.

                                                                          >>> The following workunits, whilst running till completion and finished, only produced 2 Decoys in over 5 hours each. In both cases they stayed at 1.00% for about 1 1/2 hours then went to 1.01% for possibly another 2 hours or more before finishing:-

                                                                          http://ralph.bakerlab.org/result.php?resultid=314543
                                                                          http://ralph.bakerlab.org/result.php?resultid=314542

                                                                          Ralph 5.38.



                                                                          Another 3 have failed
                                                                          http://ralph.bakerlab.org/result.php?resultid=314545
                                                                          http://ralph.bakerlab.org/result.php?resultid=314601
                                                                          http://ralph.bakerlab.org/result.php?resultid=314602

                                                                          All 3 were minutes from completion with all doing more than 21100 seconds (runtime preference is 21600 seconds or 6 hours), when they errored out.
                                                                          Workunit 314602 did 184 Decoys yet I am told it is invalid.
                                                                          All had \"error code -161\" and were \"file_xfer_error\".
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                                                                          Message 2488 - Posted 7 Nov 2006 2:03:05 UTC

                                                                            Here are 4 (1x 5.38 & 3x 5.37)

                                                                            http://ralph.bakerlab.org/result.php?resultid=315272

                                                                            5.38

                                                                            </stderr_txt>
                                                                            <message>
                                                                            <file_xfer_error>
                                                                            <file_name>DOC_1STF_p2_fa_relax_from_native_1462_4_1_0</file_name>
                                                                            <error_code>-161</error_code>
                                                                            </file_xfer_error>

                                                                            </message>

                                                                            http://ralph.bakerlab.org/result.php?resultid=313951

                                                                            5.37

                                                                            <core_client_version>5.4.11</core_client_version>
                                                                            <message>
                                                                            The system cannot find the path specified. (0x3) - exit code 3 (0x3)
                                                                            </message>
                                                                            <stderr_txt>
                                                                            # random seed: 2872068
                                                                            # cpu_run_time_pref: 21600

                                                                            </stderr_txt>

                                                                            http://ralph.bakerlab.org/result.php?resultid=313010

                                                                            5.37

                                                                            <core_client_version>5.4.11</core_client_version>
                                                                            <stderr_txt>
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            Too many restarts with no progress. Keep application in memory while preempted.
                                                                            ======================================================
                                                                            DONE :: 0 starting structures built 29 (nstruct) times
                                                                            This process generated 0 decoys from 0 attempts
                                                                            ======================================================


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

                                                                            </stderr_txt>
                                                                            <message>
                                                                            <file_xfer_error>
                                                                            <file_name>1ogw__ETABLE_TEST_ABRELAX_rhh13sm6__1452_10_0_0</file_name>
                                                                            <error_code>-161</error_code>
                                                                            </file_xfer_error>

                                                                            </message>

                                                                            http://ralph.bakerlab.org/result.php?resultid=313009

                                                                            5.37

                                                                            core_client_version>5.4.11</core_client_version>
                                                                            <stderr_txt>
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            input_etable: reading etable... dsolv
                                                                            input_etable: WARNING etable types don\'t match!
                                                                            expected dsolv,606 got dsolv,721
                                                                            Too many restarts with no progress. Keep application in memory while preempted.
                                                                            ======================================================
                                                                            DONE :: 0 starting structures built 29 (nstruct) times
                                                                            This process generated 0 decoys from 0 attempts
                                                                            ======================================================


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

                                                                            </stderr_txt>
                                                                            <message>
                                                                            <file_xfer_error>
                                                                            <file_name>1n0u__ETABLE_TEST_ABRELAX_rhh13sm6__1452_10_0_0</file_name>
                                                                            <error_code>-161</error_code>
                                                                            </file_xfer_error>

                                                                            </message>
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                                                                            Message 2489 - Posted 7 Nov 2006 2:07:47 UTC

                                                                              Last modified: 7 Nov 2006 2:55:28 UTC

                                                                              Last three WUs returned crashed with the following errors:

                                                                              07/11/2006 02:02:28|ralph@home|Unrecoverable error for result fibril_abeta40_test1_1463_152_0 (<file_xfer_error> <file_name>fibril_abeta40_test1_1463_152_0_0</file_name> <error_code>-161</error_code></file_xfer_error>)
                                                                              http://ralph.bakerlab.org/result.php?resultid=315577

                                                                              07/11/2006 02:05:54|ralph@home|Unrecoverable error for result fibril_abeta40_test1_1463_133_1 (<file_xfer_error> <file_name>fibril_abeta40_test1_1463_133_1_0</file_name> <error_code>-161</error_code></file_xfer_error>)
                                                                              http://ralph.bakerlab.org/result.php?resultid=315723

                                                                              07/11/2006 03:02:54|ralph@home|Unrecoverable error for result DOC_1BTH_p2_fa_relax_from_native_1462_1_2 (<file_xfer_error> <file_name>DOC_1BTH_p2_fa_relax_from_native_1462_1_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)
                                                                              http://ralph.bakerlab.org/result.php?resultid=315833

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                                                                              Message 2490 - Posted 7 Nov 2006 2:49:59 UTC - in response to Message 2474.

                                                                                This one ran for 4 hours and hung at 100%.. , but, could not be preempted... (in run state with no activity).

                                                                                I stopped and started BOINC and the W.U. restarted from 0.0 .... no checkpointing at all... Unfortunately, this restart lost the stdout/stderr files. I am allowing the unit to rerun in hopes of catching the out/error files on the next glitch.

                                                                                http://ralph.bakerlab.org/result.php?resultid=314941


                                                                                Here is a capture of the second STDOUT...
                                                                                http://web.hotiron.net/boinc/ralph/314941/stdout.txt

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                                                                                Message 2492 - Posted 7 Nov 2006 3:42:29 UTC

                                                                                  Had some -161\'s:
                                                                                  resultid=317218
                                                                                  resultid=317217
                                                                                  resultid=315313

                                                                                  a couple of \"incorrect function\" results:
                                                                                  resultid=315015
                                                                                  resultid=315012

                                                                                  Here\'s a couple with a big dump:
                                                                                  resultid=315014
                                                                                  resultid=315010

                                                                                  and a \"downloading\" one:
                                                                                  resultid=314488

                                                                                  At least a few of these died while screensaver graphics were running. In general, I come back to the machine and see a different project\'s screensaver frozen on the screen, but it isn\'t running. The screensaver cannot be exited, but I can get the machine back with ctrl-alt-del. I look at task manager and see a Ralph WU\'s process listed, but using no CPU time. If I kill it, the screensaver graphics disappear and I get control of the machine back. The Ralph WU\'s status changes to \"Computation error\" and that\'s that.

                                                                                  That being said, the very latest one (resultid=317218, a -161 error) happened while I was using the machine and no graphics were being displayed.

                                                                                  Still have a couple of 5.38\'s left, no 5.39\'s yet.

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                                                                                  Message 2493 - Posted 7 Nov 2006 5:58:05 UTC - in response to Message 2484.

                                                                                    Sure, I am happy to answer that. A normal output file for Rosetta models contain for each atom the xyz position coordinates and some other necessary information. This file is just too large for BOINC application as there will be thousands and thousands of such files to be handled. Therefore, Rosetta uses a clever trick to compress the output which is called \"silent_output\". Under this mode, only the variables ( or degrees of freedom ) in the simulation is being output and these are normally the backbone and sidechain torsion angles ( phi, psi and chi ). By this means, the size of output file can be reduced by at least 30 fold. However, this requires us to reconstruct from these silent out files the normal rosetta output model files (with xyz positions in it) and to do so there is a critical assumption taken that a chemical covalent bond which connect any two atoms has a \'ideal\" value for its length. Similarly, the angle composed by any three connected atom has its own ideal value too. So taking these ideal values together with phi/psi/chi angles, we are able to restore the positions for all the atoms in the protein model and we often refer the structure with \"ideal\" bond lengths and angles as \"idealized structure\". For the ab initio prediction, the output model is always \"idealized\" as it is folded with \"ideal\" geometry and an optimal set of phi/psi/chi angles.

                                                                                    However, there are also some other important tests which requires starting from experimentally solved protein structures (native structures). Normally the bond geometries in these structures have a little bit different values from the ideal ones ( the ideal values are computed as an average over a large distribution of these value from experimental structures ). So in order to run these tests on BOINC, we need to add new functions to allow us to reconstruct protein models from non-idealized bond geometries and phi/psi/chi angles. On the client side, there is almost nothing changed except that the silent output file has one number for each residue which indicates whether it has ideal bonds or non-ideal bonds. The file size increase is very trivial with this new feature, but it opens the door for us to do large-scale tests on the experimentally sovled structures to understand better what are the features for these structures and how we can make Rosetta model more like those native structures.

                                                                                    Hopefully this answers your question.

                                                                                    May I ask? I hope a good description can be written for when 5.38 comes to Rosetta... WHY is \"...outputting structures with non-ideal backbone and sidehchain geometries\" an improvement? I know, useful to the science... please explain more, on the surface it sounds to a layperson like a step backwards. Also, what impact will this have on the user experience? Will it mean we\'ll see larger upload sizes on results?

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                                                                                    Message 2494 - Posted 7 Nov 2006 16:57:35 UTC

                                                                                      Thanks for the description... now try for something the size of your new release annoucement. I\'d suggest focus on last two sentences. Not sure how the ideal compares to the native myself, so wasn\'t sure how to reword. But basically just focus on the question \"How does this new feature help advance the science of Rosetta?\"... and state only minor change to upload file size.
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                                                                                      Message 2495 - Posted 7 Nov 2006 17:00:45 UTC

                                                                                        Last modified: 7 Nov 2006 17:47:37 UTC

                                                                                        Graphic on v5.38 this 1vls wu and this 2ci2I WU doesn\'t function properly. In order to rotate the native structure, you have to click in the low energy box.
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                                                                                        Message 2496 - Posted 7 Nov 2006 18:45:44 UTC


                                                                                          here\'s 1 more:

                                                                                          07/11/2006 21:07:38|ralph@home|Starting task fibril_abeta40_test1_1463_122_0 using rosetta_beta version 538
                                                                                          07/11/2006 21:07:38||Suspending work fetch because computer is overcommitted.
                                                                                          07/11/2006 21:42:56||Allowing work fetch again.
                                                                                          07/11/2006 21:43:00|Predictor @ Home|Sending scheduler request to http://predictor.scripps.edu/predictor_cgi/cgi
                                                                                          07/11/2006 21:43:00|Predictor @ Home|Reason: To fetch work
                                                                                          07/11/2006 21:43:00|Predictor @ Home|Requesting 86400 seconds of new work
                                                                                          07/11/2006 21:43:00||Rescheduling CPU: application exited
                                                                                          07/11/2006 21:43:00|ralph@home|Computation for task fibril_abeta40_test1_1463_122_0 finished
                                                                                          07/11/2006 21:43:00||Resuming round-robin CPU scheduling.
                                                                                          07/11/2006 21:43:00|Einstein@Home|Starting task h1_1250.0_S5R1__1329_S5R1a_1 using einstein_S5R1 version 424
                                                                                          07/11/2006 21:43:02|ralph@home|Unrecoverable error for result fibril_abeta40_test1_1463_122_0 (<file_xfer_error> <file_name>fibril_abeta40_test1_1463_122_0_0</file_name> <error_code>-161</error_code></file_xfer_error>)
                                                                                          07/11/2006 21:43:02|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds
                                                                                          07/11/2006 21:43:02|Predictor @ Home|Scheduler request succeeded
                                                                                          07/11/2006 21:43:02|Predictor @ Home|No work from project

                                                                                          ____________

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                                                                                          Message 2497 - Posted 7 Nov 2006 20:02:52 UTC

                                                                                            Still getting file transfer errors on 5.39:

                                                                                            RESID 319463

                                                                                            </stderr_txt>
                                                                                            <message>
                                                                                            <file_xfer_error>
                                                                                            <file_name>DOC_1CHO_p2_fa_relax_from_native_1462_4_1_0</file_name>
                                                                                            <error_code>-161</error_code>
                                                                                            </file_xfer_error>

                                                                                            </message>

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                                                                                            Message 2498 - Posted 7 Nov 2006 21:07:03 UTC

                                                                                              another one:

                                                                                              Result:
                                                                                              http://ralph.bakerlab.org/result.php?resultid=319535

                                                                                              Wu:
                                                                                              http://ralph.bakerlab.org/workunit.php?wuid=277224

                                                                                              <file_name>fibril_abeta40_test1_1463_172_2_0</file_name>
                                                                                              <error_code>-161</error_code>

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                                                                                              Message 2499 - Posted 7 Nov 2006 21:51:53 UTC

                                                                                                Last modified: 7 Nov 2006 22:39:02 UTC

                                                                                                I\'ve got one as well:
                                                                                                BOINC messages:

                                                                                                Die 07 Nov 2006 21:25:01 CET|ralph@home|Resuming task fibril_abeta40_test1_1463_19_2 using rosetta_beta version 538
                                                                                                Die 07 Nov 2006 23:14:51 CET|ralph@home|Computation for task fibril_abeta40_test1_1463_19_2 finished
                                                                                                Die 07 Nov 2006 23:14:52 CET|ralph@home|Unrecoverable error for result fibril_abeta40_test1_1463_19_2 (<file_xfer_error> <file_name>fibril_abeta40_test1_1463_19_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)
                                                                                                Die 07 Nov 2006 23:14:52 CET|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds


                                                                                                From the stderr.txt:
                                                                                                </stderr_txt>
                                                                                                <message>
                                                                                                <file_xfer_error>
                                                                                                <file_name>fibril_abeta40_test1_1463_19_2_0</file_name>
                                                                                                <error_code>-161</error_code>
                                                                                                </file_xfer_error>

                                                                                                </message>


                                                                                                As you can see, all other Wus failed as well.
                                                                                                ____________
                                                                                                Gruesse vom Saenger

                                                                                                For questions about Boinc look in the BOINC-Wiki

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                                                                                                Message 2502 - Posted 8 Nov 2006 0:09:57 UTC

                                                                                                  >> A few more with the \"error -161\" and \"file_xfer_error\"

                                                                                                  http://ralph.bakerlab.org/result.php?resultid=314519 31 decoys
                                                                                                  http://ralph.bakerlab.org/result.php?resultid=314520 6 decoys
                                                                                                  http://ralph.bakerlab.org/result.php?resultid=314523 10 decoys
                                                                                                  http://ralph.bakerlab.org/result.php?resultid=314524 6 decoys
                                                                                                  http://ralph.bakerlab.org/result.php?resultid=314525 2 decoys
                                                                                                  http://ralph.bakerlab.org/result.php?resultid=314553 5 decoys

                                                                                                  My preference is set to 6 hours or 21600 seconds and all these workunits processed for between 18696.36 to 21488.33 seconds, showing that they were within minutes of completion when they failed.
                                                                                                  Is the problem something to do with completing the data, finalising the data in the file then preparing to upload that data?
                                                                                                  I have seen this error crop up from about version 5.28, so not new just more prevalent.

                                                                                                  Also this workunit
                                                                                                  http://ralph.bakerlab.org/result.php?resultid=314522
                                                                                                  completed, producing 11 decoys but had a very low credit given compared to other successful results on the same computer (5.72 c/h, usual is 12 c/h plus), any reason for this?

                                                                                                  All unit are 5.38.
                                                                                                  ____________

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                                                                                                  Message 2503 - Posted 8 Nov 2006 1:34:15 UTC

                                                                                                    Thank you all for the help. We are sorry that the file transfer bug was not completely fixed in 5.39 and that we had several updates in the last several days. The bug is very sneaky that it is only hit by a special combination of command line flags and only for some protein targets under some certain conditions, which makes local debugging difficult. Anyway, we believe this should be completely fixed in 5.40 as shown by our local preliminary test. We will put more tests on RALPH soon to confirm the fix. Thanks again for the patience and the generous support!

                                                                                                    Leffe

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                                                                                                    Message 2505 - Posted 8 Nov 2006 9:21:47 UTC

                                                                                                      got a screensaver lockdown, only restart cured the problem

                                                                                                      08/11/2006 12:16:37|ralph@home|Resuming task 1n0u__BOINC_POSE_ABRELAX_VARY_ALL_BOND_ANGLES_VARY_ALL_BOND_DISTANCES_NEWRELAXFLAGS__1473_8_0 using rosetta_beta version 540

                                                                                                      ____________

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                                                                                                      Message 2506 - Posted 8 Nov 2006 9:56:35 UTC

                                                                                                        I get:

                                                                                                        2006-11-08 12:01:17|ralph@home|Unrecoverable error for result 1dtj__BOINC_POSE_ABRELAX_VARY_ALL_BOND_ANGLES_VARY_ALL_BOND_DISTANCES_NEWRELAXFLAGS__1473_8_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                        <core_client_version>5.6.5</core_client_version>
                                                                                                        <![CDATA[
                                                                                                        <message>
                                                                                                        Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                        </message>
                                                                                                        <stderr_txt>
                                                                                                        # random seed: 2854769
                                                                                                        # cpu_run_time_pref: 3600
                                                                                                        ABORT: bad to aa_rotno_to_packedrotno
                                                                                                        aa,rot1/2/3/4: MET 11 3 0 0 0
                                                                                                        chi no 2 nchi 3 aav 2 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                        ERROR:: Exit at: .\\rotamer_functions.cc line:1509

                                                                                                        </stderr_txt>
                                                                                                        ]]>
                                                                                                        ____________

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                                                                                                        Message 2507 - Posted 8 Nov 2006 13:54:54 UTC - in response to Message 2462.

                                                                                                          Another one 5.37 (WinXP) after 105 seconds produced a readable stack trace of all threads and a list of modules (BOINC Windows Runtime Debugger). It\'s a bit large, I\'ll keep a copy of it.

                                                                                                          Among 5 successfully crunched 5.40\'s, crunched silently overnight, there was one failed resultid=320612 after 2:30 min runtime, exit code -529697949 (0xe06d7363), again with extensive debugging output.

                                                                                                          Peter

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                                                                                                          Message 2508 - Posted 8 Nov 2006 14:31:15 UTC

                                                                                                            Another -161 file_xfer_error:

                                                                                                            2006-11-07 12:56:43 [ralph@home] Unrecoverable error for result
                                                                                                            DOC_1JHL_p2_fa_relax_from_native_1462_3_1 (<file_xfer_error>

                                                                                                            resultid=315657

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                                                                                                            Message 2509 - Posted 8 Nov 2006 17:01:55 UTC

                                                                                                              Validation errors: 322305, 321713,

                                                                                                              Computation error: 319459
                                                                                                              ____________


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                                                                                                              Message 2510 - Posted 8 Nov 2006 20:10:06 UTC - in response to Message 2507.

                                                                                                                Sweet -- that debug output will be useful. We love it when the app \"loads the PDB symbols\". I\'m letting Bin know; I bet he can debug this quickly.

                                                                                                                Another one 5.37 (WinXP) after 105 seconds produced a readable stack trace of all threads and a list of modules (BOINC Windows Runtime Debugger). It\'s a bit large, I\'ll keep a copy of it.

                                                                                                                Among 5 successfully crunched 5.40\'s, crunched silently overnight, there was one failed resultid=320612 after 2:30 min runtime, exit code -529697949 (0xe06d7363), again with extensive debugging output.

                                                                                                                Peter


                                                                                                                ____________

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                                                                                                                Message 2511 - Posted 8 Nov 2006 20:18:56 UTC - in response to Message 2509.

                                                                                                                  Chu and David K. have tracked down the source of the validation errors, and are working on the fix. Its just for the \"fibril\" workunits.

                                                                                                                  Validation errors: 322305, 321713,

                                                                                                                  Computation error: 319459


                                                                                                                  ____________

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                                                                                                                  Message 2512 - Posted 8 Nov 2006 22:42:52 UTC - in response to Message 2470.

                                                                                                                    I get message in new small window:
                                                                                                                    \"Microsoft Visual C++ Runtime Library
                                                                                                                    Runtime Error!
                                                                                                                    Program: ...ralph.bakerlab.org\\rosetta_beta_5.38_windows_intelx86.exe
                                                                                                                    This application has requested the Runtime to terminate it in an unusual way.
                                                                                                                    Please contact the application\'s support team for more information.\"
                                                                                                                    I got the same error yesterday and today from v5.40. WinXP, US English system, other stuff running, not in screensaver mode. Not sure what other diagnostic info I can provide or where it comes from. HTH, Good luck.

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                                                                                                                    Message 2513 - Posted 9 Nov 2006 0:49:16 UTC

                                                                                                                      Computation Error: 323402
                                                                                                                      ____________


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                                                                                                                      Message 2514 - Posted 9 Nov 2006 2:28:24 UTC

                                                                                                                        Last modified: 9 Nov 2006 3:15:54 UTC

                                                                                                                        Got this watchdog timeout: resultid=323419 with debugging info.


                                                                                                                        ____________

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                                                                                                                        Message 2516 - Posted 9 Nov 2006 11:44:56 UTC

                                                                                                                          http://img146.imageshack.us/my.php?image=rosettasu7.gif

                                                                                                                          Is this alright?
                                                                                                                          ____________

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                                                                                                                          Message 2517 - Posted 9 Nov 2006 11:56:05 UTC - in response to Message 2516.

                                                                                                                            http://img146.imageshack.us/my.php?image=rosettasu7.gif

                                                                                                                            Is this alright?


                                                                                                                            I had the same on my current WU

                                                                                                                            FRA_t362_HOMOENV_CENRLXhom001_8_t362_6_1z54A_IGNORE_THE_REST_266_1369_8_0 using rosetta version 536

                                                                                                                            with normal rosetta not ralph

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                                                                                                                            Message 2520 - Posted 9 Nov 2006 16:45:36 UTC

                                                                                                                              Itay / Wiesi: Both of you are reporting V5.36, where there are detached segments floating off the backbone of the native structure. Have you seen this on the higher versions? I think they\'ve fixed that one.
                                                                                                                              ____________

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                                                                                                                              Message 2522 - Posted 9 Nov 2006 18:49:24 UTC

                                                                                                                                the current version for rosetta@home is V5.36

                                                                                                                                if you mean if I have seen it on ralph 5.40 or so then nope ...
                                                                                                                                that was the first time i saw that

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                                                                                                                                Message 2524 - Posted 9 Nov 2006 22:53:25 UTC

                                                                                                                                  My computer just threw a runtime error by Microsoft Visual C++ for RALPH:

                                                                                                                                  \"This application (RALPH) has requested the Runtime to terminate it in an unusual way\"

                                                                                                                                  Do you need anything from me?

                                                                                                                                  Tim
                                                                                                                                  ____________


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                                                                                                                                  Message 2525 - Posted 9 Nov 2006 22:56:16 UTC

                                                                                                                                    Also just had a Computation Error.
                                                                                                                                    ____________


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                                                                                                                                    Message 2526 - Posted 9 Nov 2006 23:24:12 UTC

                                                                                                                                      I also had a C++ runtime error message and

                                                                                                                                      11/9/2006 6:58:02 PM|ralph@home|Starting task FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000005_0.pdb_1449_14_3 using rosetta_beta version 540

                                                                                                                                      11/9/2006 7:12:35 PM|ralph@home|Unrecoverable error for result FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000005_0.pdb_1449_14_3 (The system cannot find the path specified. (0x3) - exit code 3 (0x3))

                                                                                                                                      11/9/2006 7:12:36 PM|ralph@home|Computation for task FRA_t364_CASP7_hom001_1_IGNORE_THE_RESTt364_1_S_00001_0000005_0.pdb_1449_14_3 finished

                                                                                                                                      ____________

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                                                                                                                                      Message 2527 - Posted 10 Nov 2006 12:15:09 UTC

                                                                                                                                        i got some strange visual c++ runtime error about ralph wanting to shutdown unusually (didn\'t pay too much attention, sorry).
                                                                                                                                        http://ralph.bakerlab.org/result.php?resultid=323137

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                                                                                                                                        Message 2528 - Posted 10 Nov 2006 12:17:31 UTC

                                                                                                                                          Last modified: 10 Nov 2006 13:04:26 UTC

                                                                                                                                          sorry, double post

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                                                                                                                                          Message 2529 - Posted 10 Nov 2006 16:02:43 UTC

                                                                                                                                            Only one bad 5.40 wu to report so far.
                                                                                                                                            ____________

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                                                                                                                                            Message 2530 - Posted 11 Nov 2006 3:27:52 UTC

                                                                                                                                              I\'m currently running a beta 5.40 file and it is running the same as the last 3-4 versions:

                                                                                                                                              A) Only shows a progress of 1.000% until finished.
                                                                                                                                              B) Only counts up for time remaining until completion.

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                                                                                                                                              Message 2532 - Posted 11 Nov 2006 14:28:57 UTC

                                                                                                                                                The grafics on this WU is not in the \"boxes\" for the first

                                                                                                                                                30000 steps or so.

                                                                                                                                                http://ralph.bakerlab.org/result.php?resultid=324350

                                                                                                                                                Anders n
                                                                                                                                                ____________

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                                                                                                                                                Message 2533 - Posted 11 Nov 2006 18:15:10 UTC - in response to Message 2532.

                                                                                                                                                  The grafics on this WU is not in the \"boxes\" for the first

                                                                                                                                                  30000 steps or so.

                                                                                                                                                  http://ralph.bakerlab.org/result.php?resultid=324350

                                                                                                                                                  Anders n



                                                                                                                                                  Update

                                                                                                                                                  It is only when it starts an even Model number ex 2,12,50.

                                                                                                                                                  Anders n


                                                                                                                                                  ____________

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                                                                                                                                                  Message 2538 - Posted 16 Nov 2006 16:49:29 UTC

                                                                                                                                                    FRA_2rio_RIO2_hom002_6_2rio_6_1a06__IGNORE_THE_REST_10_1499_12_0


                                                                                                                                                    WARNING! error deleting file .\\aa2rio.out

                                                                                                                                                    Chu
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                                                                                                                                                    Message 2539 - Posted 16 Nov 2006 23:26:00 UTC - in response to Message 2538.

                                                                                                                                                      We finally got time tracking down this harmless but confusing \"warning\" output. It is due to a problem of not closing a file stream properly after opening it. The fix will be included in the next update.

                                                                                                                                                      FRA_2rio_RIO2_hom002_6_2rio_6_1a06__IGNORE_THE_REST_10_1499_12_0


                                                                                                                                                      WARNING! error deleting file .\\aa2rio.out

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                                                                                                                                                      Message 2540 - Posted 17 Nov 2006 12:24:16 UTC

                                                                                                                                                        Last modified: 17 Nov 2006 13:11:00 UTC

                                                                                                                                                        Pepo wrote:
                                                                                                                                                        Also the version 5.36 is checkpointing after reaching 100% (instead of reporting the result) and then being preempted by other apps afterwards (possibly for a longer time, because of negative STD).

                                                                                                                                                        Also the version 5.40 is checkpointing after reaching 100% (instead of reporting the result) and then being preempted by other apps afterwards (possibly for a longer time, if there is too negative STD).

                                                                                                                                                        Actually it happened on Rosetta, not here, but I assume the responsible code is the same.

                                                                                                                                                        Peter

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                                                                                                                                                        Message 2548 - Posted 21 Nov 2006 7:17:28 UTC

                                                                                                                                                          I get before a moment:

                                                                                                                                                          2006-11-21 09:18:03|ralph@home|Unrecoverable error for result 1agr_1_NMRREF_1_1agr_1_idid_model_09_0001IGNORE_THE_REST_idl_1507_27_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))


                                                                                                                                                          <core_client_version>5.6.5</core_client_version>
                                                                                                                                                          <![CDATA[
                                                                                                                                                          <message>
                                                                                                                                                          Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                                                                          </message>
                                                                                                                                                          <stderr_txt>
                                                                                                                                                          # random seed: 2848069
                                                                                                                                                          sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                                                                                                          sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
                                                                                                                                                          ABORT: bad to aa_rotno_to_packedrotno
                                                                                                                                                          aa,rot1/2/3/4: LEU 10 3 0 0 0
                                                                                                                                                          chi no 2 nchi 2 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
                                                                                                                                                          ERROR:: Exit at: .\\rotamer_functions.cc line:1509
                                                                                                                                                          ____________

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                                                                                                                                                          Message 2552 - Posted 23 Nov 2006 10:11:44 UTC

                                                                                                                                                            One more:

                                                                                                                                                            2006-11-23 12:14:34|ralph@home|Unrecoverable error for result CAPRI_11_U1H2_GLOBAL_DOCKING_1510_39_2 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                                                                            <core_client_version>5.6.5</core_client_version>
                                                                                                                                                            <![CDATA[
                                                                                                                                                            <message>
                                                                                                                                                            Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                                                                            </message>
                                                                                                                                                            <stderr_txt>
                                                                                                                                                            ERROR:: Exit at: .\\docking.cc line:1825

                                                                                                                                                            Even it didn\'t begin to compute :(

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                                                                                                                                                            Message 2553 - Posted 23 Nov 2006 16:14:52 UTC - in response to Message 2540.

                                                                                                                                                              that has been fixed in current Rosetta code repository and will be included in the next ralph release.

                                                                                                                                                              Pepo wrote:
                                                                                                                                                              Also the version 5.36 is checkpointing after reaching 100% (instead of reporting the result) and then being preempted by other apps afterwards (possibly for a longer time, because of negative STD).

                                                                                                                                                              Also the version 5.40 is checkpointing after reaching 100% (instead of reporting the result) and then being preempted by other apps afterwards (possibly for a longer time, if there is too negative STD).

                                                                                                                                                              Actually it happened on Rosetta, not here, but I assume the responsible code is the same.

                                                                                                                                                              Peter

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                                                                                                                                                              Message 2554 - Posted 23 Nov 2006 16:16:58 UTC - in response to Message 2552.

                                                                                                                                                                Thanks. that WU is problematic.

                                                                                                                                                                One more:

                                                                                                                                                                2006-11-23 12:14:34|ralph@home|Unrecoverable error for result CAPRI_11_U1H2_GLOBAL_DOCKING_1510_39_2 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

                                                                                                                                                                <core_client_version>5.6.5</core_client_version>
                                                                                                                                                                <![CDATA[
                                                                                                                                                                <message>
                                                                                                                                                                Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
                                                                                                                                                                </message>
                                                                                                                                                                <stderr_txt>
                                                                                                                                                                ERROR:: Exit at: .\\docking.cc line:1825

                                                                                                                                                                Even it didn\'t begin to compute :(

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                                                                                                                                                                Message 2555 - Posted 23 Nov 2006 19:25:23 UTC

                                                                                                                                                                  Here\'s another one of those capri_i1 guys, same error:

                                                                                                                                                                  resid 330118

                                                                                                                                                                  \'\' ERROR:: Exit at: .\\docking.cc line:1825 \'\'
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                                                                                                                                                                  Message 2556 - Posted 24 Nov 2006 23:23:53 UTC

                                                                                                                                                                    All but two of my capri wu\'s have crashed at rotamer_functions.cc
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                                                                                                                                                                    Message 2557 - Posted 26 Nov 2006 12:47:10 UTC

                                                                                                                                                                      Here\'s another one.
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                                                                                                                                                                      Message boards : RALPH@home bug list : Bug reports for Ralph 5.37 through 5.40


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