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Bug reports for 5.49-5.51

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Message boards : RALPH@home bug list : Bug reports for 5.49-5.51

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Rhiju
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Message 2811 - Posted 3 Mar 2007 5:49:54 UTC

    Let us know what you think with 5.49! We want to really carefully test the new graphics and new RNA modes before going to Rosetta@home. Your feedback will help greatly.
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    Christoph

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    Message 2812 - Posted 3 Mar 2007 10:59:52 UTC

      Could someone make a screenshot of the new graphics please, I\'m too lazy to attach my computer ;)

      [AF>EDLS>BIOMED] Heyoka

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      Message 2813 - Posted 3 Mar 2007 11:25:30 UTC - in response to Message 2812.

        Could someone make a screenshot of the new graphics please, I\'m too lazy to attach my computer ;)



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        alexpoon

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        Message 2814 - Posted 3 Mar 2007 16:10:32 UTC

          I find that the wu cannot come to an end!
          When my wu is at the last model.After finished, the cpu time restored to the time that start the last model

          Christoph

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          Message 2815 - Posted 3 Mar 2007 18:32:37 UTC

            Last modified: 3 Mar 2007 18:33:19 UTC

            Wierd

            ...
            03.03.2007 14:59:32|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:08:51|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no \'finished\' file
            03.03.2007 15:08:51|ralph@home|If this happens repeatedly you may need to reset the project.
            03.03.2007 15:08:51|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:20:17|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no \'finished\' file
            03.03.2007 15:20:17|ralph@home|If this happens repeatedly you may need to reset the project.
            03.03.2007 15:20:17|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:25:42|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no \'finished\' file
            03.03.2007 15:25:42|ralph@home|If this happens repeatedly you may need to reset the project.
            03.03.2007 15:25:42|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:31:13|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no \'finished\' file
            03.03.2007 15:31:13|ralph@home|If this happens repeatedly you may need to reset the project.
            03.03.2007 15:31:13|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:31:47|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no \'finished\' file
            03.03.2007 15:31:47|ralph@home|If this happens repeatedly you may need to reset the project.
            03.03.2007 15:31:47|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:32:22|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no \'finished\' file
            03.03.2007 15:32:22|ralph@home|If this happens repeatedly you may need to reset the project.
            03.03.2007 15:32:22|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:33:32|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no \'finished\' file
            03.03.2007 15:33:32|ralph@home|If this happens repeatedly you may need to reset the project.
            03.03.2007 15:33:32|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:34:18|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no \'finished\' file
            03.03.2007 15:34:18|ralph@home|If this happens repeatedly you may need to reset the project.
            03.03.2007 15:34:18|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:35:05|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no \'finished\' file
            03.03.2007 15:35:05|ralph@home|If this happens repeatedly you may need to reset the project.
            03.03.2007 15:35:05|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
            03.03.2007 15:35:11|ralph@home|Computation for task 1l2x_RNA_TEST_SUBMIT_1805_518_0 finished

            Pieface

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            Message 2816 - Posted 3 Mar 2007 19:52:24 UTC

              Hmmm I had one of those like christoph:

              ((first several restarts deleted))

              3/3/2007 1:27:21 PM|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_262_1 exited with zero status but no \'finished\' file
              3/3/2007 1:27:21 PM|ralph@home|If this happens repeatedly you may need to reset the project.
              3/3/2007 1:27:21 PM|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_262_1 using rosetta_beta version 549
              3/3/2007 1:27:24 PM|ralph@home|Computation for task 1l2x_RNA_TEST_SUBMIT_1805_262_1 finished
              3/3/2007 1:27:24 PM|SETI@home|Resuming task 08dc03ab.11085.22034.379824.3.27_3 using setiathome_enhanced version 515
              3/3/2007 1:27:26 PM|ralph@home|[file_xfer] Started upload of file 1l2x_RNA_TEST_SUBMIT_1805_262_1_0
              3/3/2007 1:27:35 PM|ralph@home|[file_xfer] Finished upload of file 1l2x_RNA_TEST_SUBMIT_1805_262_1_0
              3/3/2007 1:27:35 PM|ralph@home|[file_xfer] Throughput 31748 bytes/sec

              But it looks like it validated alright?

              resid 443594


              Rhiju
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              Message 2817 - Posted 3 Mar 2007 21:33:07 UTC - in response to Message 2816.

                Hi Pieface and Christoph: Thanks for the posts.

                I think I know what the problem is -- forgot to put a silly \"boinc_finish\" call at the end of the new RNA mode. I\'ll get this fixed in the next update. Despite this problem, the results appear to be coming back fine!


                Hmmm I had one of those like christoph:

                ((first several restarts deleted))

                3/3/2007 1:27:21 PM|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_262_1 exited with zero status but no \'finished\' file
                3/3/2007 1:27:21 PM|ralph@home|If this happens repeatedly you may need to reset the project.
                3/3/2007 1:27:21 PM|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_262_1 using rosetta_beta version 549
                3/3/2007 1:27:24 PM|ralph@home|Computation for task 1l2x_RNA_TEST_SUBMIT_1805_262_1 finished
                3/3/2007 1:27:24 PM|SETI@home|Resuming task 08dc03ab.11085.22034.379824.3.27_3 using setiathome_enhanced version 515
                3/3/2007 1:27:26 PM|ralph@home|[file_xfer] Started upload of file 1l2x_RNA_TEST_SUBMIT_1805_262_1_0
                3/3/2007 1:27:35 PM|ralph@home|[file_xfer] Finished upload of file 1l2x_RNA_TEST_SUBMIT_1805_262_1_0
                3/3/2007 1:27:35 PM|ralph@home|[file_xfer] Throughput 31748 bytes/sec

                But it looks like it validated alright?

                resid 443594




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                Profile anders n

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                Message 2818 - Posted 4 Mar 2007 7:01:13 UTC

                  Whith 5.50 I get SIGBUS: bus error like this one.

                  http://ralph.bakerlab.org/result.php?resultid=444448

                  Anders n

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                  alexpoon

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                  Message 2819 - Posted 4 Mar 2007 7:27:48 UTC

                    Last modified: 4 Mar 2007 7:31:24 UTC

                    I got this message
                    4/3/2007|ralph@home|Reason: Unrecoverable error for result 1qwa__BOINC_RNA_ABINITIO__1808_2_1 ( - exit code -1073741819 (0xc0000005))



                    edit:I see that I received this file
                    4/3/2007 |ralph@home|[file_xfer] Started download of file casp7.description.shorter.txt

                    Will it cause to the error?

                    gamer007

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                    Message 2820 - Posted 4 Mar 2007 7:33:48 UTC

                      03/03/2007 10:23:24 PM|ralph@home|Starting 1kka__BOINC_RNA_ABINITIO__1808_5_0
                      03/03/2007 10:23:24 PM|ralph@home|Starting task 1kka__BOINC_RNA_ABINITIO__1808_5_0 using rosetta_beta version 550
                      03/03/2007 10:24:19 PM|ralph@home|Computation for task 1kka__BOINC_RNA_ABINITIO__1808_5_0 finished
                      03/03/2007 10:24:19 PM|ralph@home|Output file 1kka__BOINC_RNA_ABINITIO__1808_5_0_0 for task 1kka__BOINC_RNA_ABINITIO__1808_5_0 absent

                      Site says it only ran for 2 seconds and got an error.
                      444237
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                      Message 2821 - Posted 4 Mar 2007 12:14:28 UTC

                        Last modified: 4 Mar 2007 12:15:13 UTC

                        Result

                        Host



                        3/4/2007 1:06:14 AM|ralph@home|Starting 1a4d__BOINC_RNA_ABINITIO__1808_2_0
                        3/4/2007 1:06:14 AM|ralph@home|[cpu_sched] Starting 1a4d__BOINC_RNA_ABINITIO__1808_2_0 (initial)
                        3/4/2007 1:06:15 AM|ralph@home|[task_debug] task_state=EXECUTING for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 from start
                        3/4/2007 1:06:15 AM|ralph@home|Starting task 1a4d__BOINC_RNA_ABINITIO__1808_2_0 using rosetta_beta version 550
                        3/4/2007 1:06:56 AM|ralph@home|[task_debug] Process for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 exited
                        3/4/2007 1:06:56 AM|ralph@home|[task_debug] task_state=EXITED for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 from handle_exited_app
                        3/4/2007 1:06:56 AM|ralph@home|Deferring communication for 1 min 0 sec
                        3/4/2007 1:06:56 AM|ralph@home|Reason: Unrecoverable error for result 1a4d__BOINC_RNA_ABINITIO__1808_2_0 ( - exit code -1073741819 (0xc0000005))
                        3/4/2007 1:06:56 AM|ralph@home|[task_debug] result state=COMPUTE_ERROR for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 from CS::report_result_error
                        3/4/2007 1:06:56 AM|ralph@home|[task_debug] Process for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 exited
                        3/4/2007 1:06:56 AM|ralph@home|[task_debug] exit code -1073741819 (0xc0000005):
                        3/4/2007 1:06:56 AM|ralph@home|Computation for task 1a4d__BOINC_RNA_ABINITIO__1808_2_0 finished
                        3/4/2007 1:06:56 AM|ralph@home|Output file 1a4d__BOINC_RNA_ABINITIO__1808_2_0_0 for task 1a4d__BOINC_RNA_ABINITIO__1808_2_0 absent
                        3/4/2007 1:06:56 AM|ralph@home|[task_debug] result state=COMPUTE_ERROR for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 from CS::app_finished

                        ____________
                        Kathryn :o)
                        The BOINC FAQ Service
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                        More BOINC information than you can shake a stick of RAM at.

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                        Message 2822 - Posted 4 Mar 2007 18:50:27 UTC

                          Got a bunch of errors with 5.50, but I was away yesterday, so I haven\'t seen them run yet...

                          resultid=444352
                          resultid=444488
                          resultid=444516
                          resultid=444519
                          resultid=444547
                          resultid=444580
                          resultid=444591

                          All of them are access violations, and they only ran for a few seconds.

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                          [B^S] sTrey
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                          Message 2823 - Posted 4 Mar 2007 18:56:10 UTC

                            Another access violation result.

                            Rhiju
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                            Message 2824 - Posted 4 Mar 2007 20:40:27 UTC - in response to Message 2823.

                              Hi all: I\'m looking into these -- basically all the RNA workunits failed with this app, which is actually a good thing, since it should make finding the bug easy. Sorry for the errors!

                              Another access violation result.


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                              Rhiju
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                              Message 2825 - Posted 4 Mar 2007 22:28:55 UTC - in response to Message 2824.

                                I think I found the bug -- its a simple one, and doesn\'t require a new app, just a fix in my workunit. Sending out some jobs again! Thanks for posting.

                                Hi all: I\'m looking into these -- basically all the RNA workunits failed with this app, which is actually a good thing, since it should make finding the bug easy. Sorry for the errors!

                                Another access violation result.



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                                Phil

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                                Message 2826 - Posted 5 Mar 2007 1:41:19 UTC

                                  Woah, Just had success with my first 5.50 unit!

                                  Not bad seeing as I only gave 192MB memory and a 900MHz celeron.

                                  genes
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                                  Message 2827 - Posted 5 Mar 2007 3:15:32 UTC

                                    Last modified: 5 Mar 2007 3:19:42 UTC

                                    Couple more errors, this time not Access Violations, but code 1 \"Incorrect function\".

                                    resultid=445073
                                    resultid=445076

                                    I did have two finish successfully, though.

                                    Note: All of these errors occurred on machines that were sitting undisturbed, so no graphics were running. I have graphics enabled, but only for an hour, then blank.

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                                    Profile anders n

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                                    Message 2828 - Posted 5 Mar 2007 5:12:54 UTC

                                      Last modified: 5 Mar 2007 5:13:27 UTC

                                      Something is strange with these Wu-s.

                                      Look at this text from the result page.

                                      -2931.657911
                                      -stderr out <core_client_version>5.8.15</core_client_version>
                                      -<![CDATA[
                                      -<stderr_txt>
                                      -# random seed: 2725014
                                      -# cpu_run_time_pref: 14400
                                      -======================================================
                                      -DONE :: 1 starting structures built 30 (nstruct) times
                                      -This process generated 0 decoys from 0 attempts


                                      Run time 2931 - pref. time 14400

                                      0 decoys from 0 attempts


                                      http://ralph.bakerlab.org/result.php?resultid=445590
                                      Anders n

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                                      Message 2830 - Posted 5 Mar 2007 9:37:25 UTC

                                        Last modified: 5 Mar 2007 9:38:37 UTC

                                        Lots of errors, all RNA WU\'s,

                                        Error code 131. SIGSEGV (Segmetation Violations)

                                        http://ralph.bakerlab.org/result.php?resultid=445159 1esy_BOINC_RNA
                                        http://ralph.bakerlab.org/result.php?resultid=444524 1xjr_BOINC_RNA
                                        http://ralph.bakerlab.org/result.php?resultid=444526 1esy
                                        http://ralph.bakerlab.org/result.php?resultid=444752 1kka

                                        Exit Code:ERROR:Exit at: pose_rna.cc line:868

                                        http://ralph.bakerlab.org/result.php?resultid=445226 1fkaA_BOINC_RNA
                                        http://ralph.bakerlab.org/result.php?resultid=445229 1fkaA
                                        http://ralph.bakerlab.org/result.php?resultid=445239 1fkaA
                                        http://ralph.bakerlab.org/result.php?resultid=445240 1fkaA
                                        http://ralph.bakerlab.org/result.php?resultid=445219 1fkaA
                                        http://ralph.bakerlab.org/result.php?resultid=445221 1fkaA
                                        http://ralph.bakerlab.org/result.php?resultid=445276 1fkaA
                                        http://ralph.bakerlab.org/result.php?resultid=445279 1fkaA

                                        Exit Code:ERROR:Exit at: read_paths.cc line:351

                                        http://ralph.bakerlab.org/result.php?resultid=445304 1ehzA_BOINC_RNA
                                        http://ralph.bakerlab.org/result.php?resultid=445305 1gidA
                                        http://ralph.bakerlab.org/result.php?resultid=445745 1gidA
                                        http://ralph.bakerlab.org/result.php?resultid=444730 1gidA
                                        http://ralph.bakerlab.org/result.php?resultid=444731 1gidA
                                        http://ralph.bakerlab.org/result.php?resultid=445058 1gidA
                                        http://ralph.bakerlab.org/result.php?resultid=445059 1ehzA
                                        http://ralph.bakerlab.org/result.php?resultid=445093 1gidA
                                        http://ralph.bakerlab.org/result.php?resultid=445321 1gidA
                                        http://ralph.bakerlab.org/result.php?resultid=445322 1ehzA
                                        http://ralph.bakerlab.org/result.php?resultid=444312 1gidA
                                        http://ralph.bakerlab.org/result.php?resultid=444437 1ehzA
                                        http://ralph.bakerlab.org/result.php?resultid=444438 1gidA

                                        Validate Errors

                                        http://ralph.bakerlab.org/result.php?resultid=444851 1qwa_BOINC_RNA
                                        http://ralph.bakerlab.org/result.php?resultid=444937 1zih
                                        http://ralph.bakerlab.org/result.php?resultid=445547 1fkaA
                                        http://ralph.bakerlab.org/result.php?resultid=445028 1kka

                                        Exit Code -1073741819 Access Violation

                                        http://ralph.bakerlab.org/result.php?resultid=444313 1a4d_BOINC_RNA
                                        http://ralph.bakerlab.org/result.php?resultid=444341 1q9a
                                        http://ralph.bakerlab.org/result.php?resultid=444394 1zih
                                        http://ralph.bakerlab.org/result.php?resultid=444678 1xjr

                                        Later today a couple of the 1gidA workunits did actually run.
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                                        Message 2831 - Posted 5 Mar 2007 16:18:45 UTC

                                          This Wu was atleast at step 1.000.000 when it timed out!

                                          http://ralph.bakerlab.org/result.php?resultid=444991

                                          Anders n
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                                          Message 2832 - Posted 5 Mar 2007 18:43:06 UTC - in response to Message 2831.

                                            Yea, that\'s a big one -- I better not send it out again!

                                            I\'m tracking down a few other RNA workunits that have crashed. On the whole, things are looking good, though I\'ll probably need to run more tests, and do another app update this week.

                                            This Wu was atleast at step 1.000.000 when it timed out!

                                            http://ralph.bakerlab.org/result.php?resultid=444991

                                            Anders n


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                                            Message 2833 - Posted 5 Mar 2007 19:34:28 UTC

                                              process exited with code 1 (0x1)


                                              On all my new Wu-s like this one.

                                              http://ralph.bakerlab.org/result.php?resultid=446166

                                              Anders n
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                                              Message 2834 - Posted 5 Mar 2007 20:31:01 UTC - in response to Message 2833.

                                                Thanks for continuing to post. It took a little effort to find this last bug in this set of new WUs -- I had to trap it on my laptop and read the stdout.txt. I think I fixed it, so I\'m sending out a few new jobs.

                                                process exited with code 1 (0x1)


                                                On all my new Wu-s like this one.

                                                http://ralph.bakerlab.org/result.php?resultid=446166

                                                Anders n


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                                                Message 2835 - Posted 6 Mar 2007 3:11:51 UTC

                                                  Wow! The graphics are awesome! (not a bug) :-)

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                                                  Message 2836 - Posted 6 Mar 2007 4:17:24 UTC - in response to Message 2828.

                                                    Last modified: 6 Mar 2007 4:18:35 UTC

                                                    Something is strange with these Wu-s.

                                                    0 decoys from 0 attempts

                                                    Me too... v5.50, 0 decoys and yet exactly 30 nstructs, just as \"anders n\", and it appears to have run for the standard 10,000 seconds rather then my 24hr preference.
                                                    http://ralph.bakerlab.org/result.php?resultid=445489

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                                                    Message 2837 - Posted 6 Mar 2007 13:03:40 UTC - in response to Message 2832.

                                                      Yea, that\'s a big one -- I better not send it out again!


                                                      No problem with me to send it again. :)

                                                      If possibel the big ones should be sent to the \"faster\" computers.

                                                      Anders n

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                                                      Message 2839 - Posted 7 Mar 2007 6:35:04 UTC

                                                        - Unhandled Exception Record -
                                                        Reason: Access Violation (0xc0000005) at address 0x008F2D4C read attempt to address 0x00000E51

                                                        On a number fo Wu-s

                                                        Like this one.

                                                        http://ralph.bakerlab.org/result.php?resultid=450894

                                                        Anders n

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                                                        Message 2840 - Posted 7 Mar 2007 7:13:52 UTC

                                                          Out of seven WUs run under ver 5.50 so far, I\'ve had three rapid failures within seconds of the run starting:

                                                          Two \"Incorrect function. (0x1) - exit code 1 (0x1)\" - 445054 and 446305

                                                          One access violation, which may have occurred when I tried to show graphics - 450818


                                                          j2satx

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                                                          Message 2841 - Posted 7 Mar 2007 11:59:38 UTC

                                                            Computer Project Date ID Message
                                                            6100M902 ralph@home 3/7/2007 4:52:11 AM 518 Reason: Unrecoverable error for result DOCKING_1rhj_SYMM_11rhj_1_d.s036_bigrun.out.85_1826_4_1 (process exited with code 131 (0x83))

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                                                            Michael Stoeter

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                                                            Message 2842 - Posted 7 Mar 2007 13:50:28 UTC

                                                              Last modified: 7 Mar 2007 13:53:44 UTC

                                                              From my last 47 WU ends 41 WU with Error
                                                              Exit status -1073741819 (0xffffffffc0000005)

                                                              http://ralph.bakerlab.org/workunit.php?wuid=398542
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                                                              Message 2843 - Posted 7 Mar 2007 18:10:08 UTC

                                                                Another very rapid access violation in 5.50, this time without any attempt to view the graphics when the WU started: 451729

                                                                Half the WUs my machine has processed under 5.50 have now failed within seconds of starting. The \"incorrect function\" errors with the first two ab-initio RNA folding WUs seem to have stopped, but both of the access violation errors today have been with DOCKING_1rhj_SYMM_11rhj_1_d.s036_bigrun.out. units.

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                                                                Message 2844 - Posted 7 Mar 2007 22:19:40 UTC

                                                                  Hi, the jobs named DOCK_SYMM unraveled a bug in the 5.50 release and all fail shortly after they appear. This problem will be fixed in the next release and no more jobs causing this problem will be submitted. Sorry for the inconvenience!

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                                                                  Message 2845 - Posted 8 Mar 2007 1:57:17 UTC

                                                                    Last modified: 8 Mar 2007 1:57:41 UTC

                                                                    One comment on the graphics. As a new model begins, the graphic shows the strand and gradually scales down during the first few steps... as that happens, the text in the box scales down as well. With the DOC and HINGE WUs, those text labels (Searching, Low Energy, Native...) can get PRETTY small.
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                                                                    Michael.L

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                                                                    Message 2846 - Posted 8 Mar 2007 22:50:22 UTC

                                                                      Last modified: 8 Mar 2007 22:51:12 UTC

                                                                      08/03/2007 22:46:10|ralph@home|Unrecoverable error for result 1ywz_1_NMRREF_1_1ywz_1_idid_model_12IGNORE_THE_REST_idl_1831_8_0 ( - exit code -1073741819 (0xc0000005))

                                                                      WU ran for only 48 seconds before failing.

                                                                      i think the new graphics are great, no problems.

                                                                      Michael.L

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                                                                      Message 2847 - Posted 9 Mar 2007 0:11:16 UTC

                                                                        Last modified: 9 Mar 2007 0:13:24 UTC

                                                                        08/03/2007 23:47:48|ralph@home|Unrecoverable error for result 1ywz_1_NMRREF_1_1ywz_1_idid_model_11IGNORE_THE_REST_idl_1831_8_0 ( - exit code -1073741819 (0xc0000005))

                                                                        08/03/2007 23:58:39|ralph@home|Unrecoverable error for result 1ywz_1_NMRREF_1_1ywz_1_idid_model_01IGNORE_THE_REST_idl_1831_2_2 ( - exit code -1073741819 (0xc0000005))

                                                                        The above two ran for about 46 and 47 seconds each

                                                                        Michael.L

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                                                                        Message 2848 - Posted 9 Mar 2007 0:15:43 UTC

                                                                          Last modified: 9 Mar 2007 0:20:30 UTC

                                                                          Sends feet1st my spare reading glasses.

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                                                                          Message 2849 - Posted 9 Mar 2007 16:47:56 UTC

                                                                            Last modified: 9 Mar 2007 16:48:38 UTC

                                                                            My last two wu\'s, one last night one this morning, both errored out almost immediately with:
                                                                            - exit code -1073741819 (0xc0000005)
                                                                            ERROR:: Unable to determine sequence length from pdb file

                                                                            454165
                                                                            453634

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                                                                            Message 2850 - Posted 10 Mar 2007 2:40:23 UTC

                                                                              Some more access violations...

                                                                              453604
                                                                              453706
                                                                              453803
                                                                              454246

                                                                              none of them ran longer than 2 minutes.

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                                                                              Thomas Leibold

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                                                                              Message 2851 - Posted 10 Mar 2007 4:26:52 UTC

                                                                                Last modified: 10 Mar 2007 4:27:40 UTC

                                                                                400678

                                                                                400776

                                                                                400748

                                                                                On the same workunits that windows users are getting \"exit code -1073741819 (0xc0000005)\" and \"- Unhandled Exception Record - Reason: Access Violation (0xc0000005)\" I\'m getting on Linux \"process exited with code 131 (0x83)\" and a segmentation violation:

                                                                                ERROR:: Unable to determine sequence length from pdb file
                                                                                # random seed: 2719130
                                                                                SIGSEGV: segmentation violation
                                                                                Stack trace (13 frames):
                                                                                [0x8b95623]
                                                                                [0x8bb146c]
                                                                                [0xffffe420]
                                                                                [0x8857337]
                                                                                [0x861bad6]
                                                                                [0x8620366]
                                                                                [0x86222e3]
                                                                                [0x8973172]
                                                                                [0x8529c73]
                                                                                [0x8641c32]
                                                                                [0x8641cdc]
                                                                                [0x8c10a94]
                                                                                [0x8048111]

                                                                                Exiting...

                                                                                RickH

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                                                                                Message 2852 - Posted 10 Mar 2007 4:40:21 UTC

                                                                                  Last modified: 10 Mar 2007 4:59:43 UTC

                                                                                  Just noticed WU ID 400842, DOC_1DFJ_R070309_pose_b_pert_fixbb_score12_1832_6 has been stuck doing no work for over an hour, while the RALPH science app repeatedly tries to directly connect to 207.46.212.122:80 for some reason.

                                                                                  I don\'t know why a science app would be directly using the internet connection instead of letting BOINC handle the file transfers like usual, but it\'s not a good idea. My software firewall (Comodo) is set to require individual app-by-app approval for internet access (to prevent trojans from phoning home), and since rosetta_beta_5.50_windows_intelx86.exe is not on the approved list, it keeps denying the program\'s access and the app is apparently stuck spinning its wheels. Currently at 20+ access errors logged and counting, repeated every 4 minutes or so.

                                                                                  I could of course approve the app for internet access, but that won\'t work long term, since soon enough it\'ll be upgraded to rosetta_beta_5.51... and the game will start all over again. Even if I wanted to do this, each app upgrade will result in hours of wasted CPU time waiting for me to notice each new version\'s approval request popups, along with filling up the firewall\'s access list with dozens of sequential app names. Blech.

                                                                                  I guess I\'ll have to approve this one, since it\'s either that or abort it, but 5.51 needs to either not require direct internet access, or at least fail gracefully if it\'s denied.

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                                                                                  Message 2853 - Posted 10 Mar 2007 4:50:06 UTC

                                                                                    Last modified: 10 Mar 2007 4:52:06 UTC

                                                                                    Figures. I just approved the internet access, and it immediately crashes with the 0xC0000005 fault that\'s going around. Oh, well.

                                                                                    454295

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                                                                                    Message 2854 - Posted 10 Mar 2007 5:53:29 UTC - in response to Message 2852.

                                                                                      ...why a science app would be directly using the internet connection instead of letting BOINC handle the file transfers...


                                                                                      See discussion here: http://boinc.bakerlab.org/forum_thread.php?id=1755&nowrap=true#32219

                                                                                      I could of course approve the app for internet access, but that won\'t work long term, since soon enough it\'ll be upgraded to rosetta_beta_5.51... and the game will start all over again.


                                                                                      Yep. The good news, if you want to call it that, is that the task had failed prior to the firewall challenge. So, the application not being approved in the firewall is not what caused it to fail.
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                                                                                      Message 2855 - Posted 10 Mar 2007 11:59:57 UTC

                                                                                        Oh, I see. What a pain. My firewall doesn\'t support app name wildcards, and there\'s no way to proactively say \"any app that wants to connect to x.y.z.t is allowed, even if you\'ve never heard of it before.\" The app approval seems to be implemented as a separate layer; first the app is checked to see if it\'s allowed to use the internet at all, then if so, the packets are run through the packet-level rules as they go out.

                                                                                        It looks like I\'m stuck with losing many hours of CPU time the first time any new version of the science app aborts, along with it stuffing the error log and approval list full of spam. Argh.

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                                                                                        Message 2857 - Posted 12 Mar 2007 7:16:02 UTC - in response to Message 2851.

                                                                                          Last modified: 12 Mar 2007 7:17:12 UTC

                                                                                          I\'ve contacted Vatsan -- hopefully he\'ll reply about what\'s wrong with these workunits tomorrow.
                                                                                          In the meanwhile, application is updated to 5.51! Not many changes this time, just a very slight fix to allow us to send out symmettric docking work units when we don\'t really know the native structure.


                                                                                          400678

                                                                                          400776

                                                                                          400748

                                                                                          On the same workunits that windows users are getting \"exit code -1073741819 (0xc0000005)\" and \"- Unhandled Exception Record - Reason: Access Violation (0xc0000005)\" I\'m getting on Linux \"process exited with code 131 (0x83)\" and a segmentation violation:

                                                                                          ERROR:: Unable to determine sequence length from pdb file
                                                                                          # random seed: 2719130
                                                                                          SIGSEGV: segmentation violation
                                                                                          Stack trace (13 frames):
                                                                                          [0x8b95623]
                                                                                          [0x8bb146c]
                                                                                          [0xffffe420]
                                                                                          [0x8857337]
                                                                                          [0x861bad6]
                                                                                          [0x8620366]
                                                                                          [0x86222e3]
                                                                                          [0x8973172]
                                                                                          [0x8529c73]
                                                                                          [0x8641c32]
                                                                                          [0x8641cdc]
                                                                                          [0x8c10a94]
                                                                                          [0x8048111]

                                                                                          Exiting...


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                                                                                          Message 2858 - Posted 12 Mar 2007 7:35:15 UTC

                                                                                            Faulty WU, exit code 131

                                                                                            http://ralph.bakerlab.org/workunit.php?wuid=400654
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                                                                                            Message 2859 - Posted 12 Mar 2007 17:41:38 UTC

                                                                                              WU : 40678, 40776 etc I am sorry the WUs crashed. I tested the jobs on my desktop before sending it out to Ralph. There was a small error in renumbering the sequence number in the PDB structure. It ran on my desktop despite this discrepancy. I\'ve fixed it and resubmitted the jobs and they ran cleanly. Sorry for the inconvenience.

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                                                                                              Message 2860 - Posted 12 Mar 2007 19:46:33 UTC

                                                                                                Very short runtime in 5.51 for an abinitio RNA WU that generated 0 decoys from 0 attempts, followed by a validation error

                                                                                                http://ralph.bakerlab.org/result.php?resultid=456095

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                                                                                                Message 2861 - Posted 14 Mar 2007 2:38:00 UTC

                                                                                                  Last modified: 14 Mar 2007 2:41:08 UTC

                                                                                                  This result has been running for close to 6 hours, is still racking up cpu time and says it\'s at 1%. My preference settings are for 4 hours. I just suspended it and I have to reboot for a Windows Update. If it doesn\'t seem more sane after that I\'ll abort it, unless advised to let it run.

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                                                                                                  Message 2862 - Posted 14 Mar 2007 4:17:28 UTC - in response to Message 2861.

                                                                                                    No, it looks like a lot of users have not been able to return results for the WU due to timeouts. I\'m sending some out again that require less computation, let\'s see how those go.

                                                                                                    This result has been running for close to 6 hours, is still racking up cpu time and says it\'s at 1%. My preference settings are for 4 hours. I just suspended it and I have to reboot for a Windows Update. If it doesn\'t seem more sane after that I\'ll abort it, unless advised to let it run.


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                                                                                                    Message 2863 - Posted 14 Mar 2007 9:17:46 UTC

                                                                                                      This workunit has been running for three hours and is stil initializing. It seems to be running fine with almost 5 million steps calculated and moving graphs of folding rna. But I am worried about the lack of progress.

                                                                                                      Jorn
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                                                                                                      Message 2864 - Posted 14 Mar 2007 14:40:52 UTC

                                                                                                        You might wanna check this wu type: 1xjr__BOINC_INCREASE_CYCLES_RNA_ABINITIO-1xjr_-_1843_13_0. It might generate an infinite loop...I mean it runs for over 1 hour and a half (in my prefs I\'ve selected 1 h target time), and it\'s at step no. 1700000 while the stage still states \"initializing\"....I\'m gonna abort it now.

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                                                                                                        Message 2865 - Posted 14 Mar 2007 19:04:16 UTC - in response to Message 2864.

                                                                                                          Thanks for posting. There was a definite problem with an early round of these workunits. Now, most of these workunits have now been returning fine, but I\'ll make sure.

                                                                                                          [BTW, I\'m fixing the \"Initializing...\" bug, and it will go out on the next application update.]

                                                                                                          You might wanna check this wu type: 1xjr__BOINC_INCREASE_CYCLES_RNA_ABINITIO-1xjr_-_1843_13_0. It might generate an infinite loop...I mean it runs for over 1 hour and a half (in my prefs I\'ve selected 1 h target time), and it\'s at step no. 1700000 while the stage still states \"initializing\"....I\'m gonna abort it now.


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