RALPH@home

Bug report for Minirosetta version 1.29

  UW Seal
 
[ Home ] [ Join ] [ About ] [ Participants ] [ Community ] [ Statistics ]
  [ login/out ]


Advanced search

Message boards : RALPH@home bug list : Bug report for Minirosetta version 1.29

AuthorMessage
Profile dekim
Forum moderator
Project administrator
Project developer
Project scientist

Joined: Jan 20 06
Posts: 210
ID: 1
Credit: 411,458
RAC: 2,027
Message 4127 - Posted 21 Jun 2008 3:27:17 UTC

    Please post any bugs/issues here regarding minirosetta version 1.29. This version includes a fix in the boinc api which prevents a rare infinite loop. It also includes a fix to the minirosetta database clean up code.
    ____________

    Profile dekim
    Forum moderator
    Project administrator
    Project developer
    Project scientist

    Joined: Jan 20 06
    Posts: 210
    ID: 1
    Credit: 411,458
    RAC: 2,027
    Message 4134 - Posted 21 Jun 2008 16:54:46 UTC

      can anyone confirm that this version is successfully deleting old minirosetta_database files? or report any issues.
      ____________

      Profile David Emigh
      Avatar

      Joined: Jan 6 08
      Posts: 27
      ID: 3934
      Credit: 26,482
      RAC: 0
      Message 4135 - Posted 21 Jun 2008 18:21:42 UTC

        None of my crunchers has yet been assigned a 1.29 workunit.

        I will be sure to report as soon as I see that I have finished one.
        ____________
        RALPH and Rosie sittin' in a tree,
        F - O - L - D - I - N - G!

        Azurrio

        Joined: Jun 27 07
        Posts: 12
        ID: 3239
        Credit: 8,020
        RAC: 0
        Message 4136 - Posted 22 Jun 2008 9:19:22 UTC

          It is a bit hard to report any possible issues with this app since there aren\'t any WUs to test it with...

          Profile dekim
          Forum moderator
          Project administrator
          Project developer
          Project scientist

          Joined: Jan 20 06
          Posts: 210
          ID: 1
          Credit: 411,458
          RAC: 2,027
          Message 4138 - Posted 23 Jun 2008 18:42:07 UTC

            We submitted a bunch of t405 tasks. We don\'t want to flood the queue with these tests since we need to keep it open for production CASP targets.
            ____________

            Jipsu

            Joined: Mar 11 08
            Posts: 26
            ID: 4117
            Credit: 76,448
            RAC: 0
            Message 4140 - Posted 24 Jun 2008 10:43:47 UTC

              Yes it is deleting old minirosetta_database files. This is from stderr.txt windows xp sp3.

              Unrecognized XML in parse_init_data_file: fraction_done_update_period
              Skipping: 1.000000
              Skipping: /fraction_done_update_period
              Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev20412.zip
              Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev20940.zip
              Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev21566.zip
              Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev22619.zip
              # cpu_run_time_pref: 86400

              Jipsu

              Joined: Mar 11 08
              Posts: 26
              ID: 4117
              Credit: 76,448
              RAC: 0
              Message 4146 - Posted 25 Jun 2008 5:02:58 UTC - in response to Message 4140.

                Last modified: 25 Jun 2008 5:04:55 UTC

                Yes it is deleting old minirosetta_database files. This is from stderr.txt windows xp sp3.

                Unrecognized XML in parse_init_data_file: fraction_done_update_period
                Skipping: 1.000000
                Skipping: /fraction_done_update_period
                Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev20412.zip
                Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev20940.zip
                Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev21566.zip
                Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev22619.zip
                # cpu_run_time_pref: 86400


                Ok now this is strange, rebooted my computer, which means rebooting boinc and it downloaded all the minirosetta_database files again. They will most likely get deleted again when I get a new 1.29 task, but is it supposed to do that?

                6/25/2008 7:56:02 AM||Starting BOINC client version 5.10.45 for windows_intelx86
                6/25/2008 7:56:02 AM||log flags: task, file_xfer, sched_ops
                6/25/2008 7:56:02 AM||Libraries: libcurl/7.18.0 OpenSSL/0.9.8e zlib/1.2.3
                6/25/2008 7:56:02 AM||Data directory: C:\\Program Files\\BOINC
                6/25/2008 7:56:03 AM||Processor: 2 GenuineIntel Intel(R) Core(TM)2 Duo CPU T7500 @ 2.20GHz [x86 Family 6 Model 15 Stepping 10]
                6/25/2008 7:56:03 AM||Processor features: fpu tsc sse sse2 mmx
                6/25/2008 7:56:03 AM||OS: Microsoft Windows XP: Professional Edition, Service Pack 3, (05.01.2600.00)
                6/25/2008 7:56:03 AM||Memory: 1.97 GB physical, 3.79 GB virtual
                6/25/2008 7:56:03 AM||Disk: 25.00 GB total, 13.65 GB free
                6/25/2008 7:56:03 AM||Local time is UTC +3 hours
                6/25/2008 7:56:04 AM|rosetta@home|URL: http://boinc.bakerlab.org/rosetta/; Computer ID: 766606; location: (none); project prefs: default
                6/25/2008 7:56:04 AM|ralph@home|URL: http://ralph.bakerlab.org/; Computer ID: 12866; location: (none); project prefs: default
                6/25/2008 7:56:04 AM||General prefs: from rosetta@home (last modified 13-May-2008 21:19:57)
                6/25/2008 7:56:04 AM||Host location: none
                6/25/2008 7:56:04 AM||General prefs: using your defaults
                6/25/2008 7:56:04 AM||Preferences limit memory usage when active to 1510.67MB
                6/25/2008 7:56:04 AM||Preferences limit memory usage when idle to 1510.67MB
                6/25/2008 7:56:04 AM||Preferences limit disk usage to 12.50GB
                6/25/2008 7:56:05 AM||file projects/ralph.bakerlab.org/minirosetta_database_rev20940.zip not found
                6/25/2008 7:56:05 AM||file projects/ralph.bakerlab.org/minirosetta_database_rev21566.zip not found
                6/25/2008 7:56:05 AM||file projects/ralph.bakerlab.org/minirosetta_database_rev20412.zip not found
                6/25/2008 7:56:05 AM||file projects/ralph.bakerlab.org/minirosetta_database_rev22619.zip not found

                6/25/2008 7:56:05 AM|rosetta@home|Restarting task rb_06_23_11701_20993_T0467_IGNORE_THE_REST_09_16_4103_89_0 using minirosetta version 128
                6/25/2008 7:56:05 AM|ralph@home|Restarting task h001b_BOINC_CASP8_ABRELAX_RANGE_t443_IGNORE_THE_REST-S25-10-S3-7--h001b-_4561_35_0 using minirosetta version 129
                6/25/2008 7:56:06 AM|ralph@home|Started download of minirosetta_database_rev20940.zip
                6/25/2008 7:56:06 AM|ralph@home|Started download of minirosetta_database_rev21566.zip
                6/25/2008 7:56:49 AM|ralph@home|Finished download of minirosetta_database_rev20940.zip
                6/25/2008 7:56:49 AM|ralph@home|Started download of minirosetta_database_rev20412.zip
                6/25/2008 7:56:54 AM|ralph@home|Finished download of minirosetta_database_rev21566.zip
                6/25/2008 7:56:54 AM|ralph@home|Started download of minirosetta_database_rev22619.zip

                6/25/2008 7:56:56 AM|rosetta@home|Computation for task rb_06_23_11701_20993_T0467_IGNORE_THE_REST_09_16_4103_89_0 finished
                6/25/2008 7:56:56 AM|ralph@home|Sending scheduler request: To fetch work. Requesting 1 seconds of work, reporting 0 completed tasks
                6/25/2008 7:56:58 AM|rosetta@home|Started upload of rb_06_23_11701_20993_T0467_IGNORE_THE_REST_09_16_4103_89_0_0
                6/25/2008 7:57:01 AM|ralph@home|Computation for task h001b_BOINC_CASP8_ABRELAX_RANGE_t443_IGNORE_THE_REST-S25-10-S3-7--h001b-_4561_35_0 finished
                6/25/2008 7:57:02 AM|ralph@home|Scheduler request succeeded: got 0 new tasks
                6/25/2008 7:57:03 AM|ralph@home|Started upload of h001b_BOINC_CASP8_ABRELAX_RANGE_t443_IGNORE_THE_REST-S25-10-S3-7--h001b-_4561_35_0_0
                6/25/2008 7:57:07 AM|rosetta@home|Sending scheduler request: To fetch work. Requesting 2 seconds of work, reporting 1 completed tasks
                6/25/2008 7:57:08 AM|rosetta@home|Finished upload of rb_06_23_11701_20993_T0467_IGNORE_THE_REST_09_16_4103_89_0_0
                6/25/2008 7:57:10 AM|ralph@home|Finished upload of h001b_BOINC_CASP8_ABRELAX_RANGE_t443_IGNORE_THE_REST-S25-10-S3-7--h001b-_4561_35_0_0
                6/25/2008 7:57:13 AM|rosetta@home|Scheduler request succeeded: got 1 new tasks
                6/25/2008 7:57:15 AM|rosetta@home|Started download of rb_06_24_11702_20999_T0468_t000_.psipred_ss2
                6/25/2008 7:57:15 AM|rosetta@home|Started download of rb_06_24_11702_20999_T0468_t000_.fasta
                6/25/2008 7:57:16 AM|rosetta@home|Finished download of rb_06_24_11702_20999_T0468_t000_.psipred_ss2
                6/25/2008 7:57:16 AM|rosetta@home|Finished download of rb_06_24_11702_20999_T0468_t000_.fasta
                6/25/2008 7:57:16 AM|rosetta@home|Started download of rb_06_24_11702_20999_T0468_aat000_03_05.200_v1_3.gz
                6/25/2008 7:57:16 AM|rosetta@home|Started download of rb_06_24_11702_20999_T0468_aat000_05_05.200_v1_3.gz
                6/25/2008 7:57:20 AM|rosetta@home|Finished download of rb_06_24_11702_20999_T0468_aat000_03_05.200_v1_3.gz
                6/25/2008 7:57:20 AM|rosetta@home|Started download of rb_06_24_11702_20999_T0468_aat000_10_05.200_v1_3.gz
                6/25/2008 7:57:25 AM|rosetta@home|Finished download of rb_06_24_11702_20999_T0468_aat000_10_05.200_v1_3.gz
                6/25/2008 7:57:27 AM|rosetta@home|Finished download of rb_06_24_11702_20999_T0468_aat000_05_05.200_v1_3.gz
                6/25/2008 7:57:28 AM|rosetta@home|Starting rb_06_24_11702_20999_T0468_IGNORE_THE_REST_05_10_4109_130_0
                6/25/2008 7:57:28 AM|rosetta@home|Starting task rb_06_24_11702_20999_T0468_IGNORE_THE_REST_05_10_4109_130_0 using minirosetta version 128
                6/25/2008 7:57:40 AM|ralph@home|Finished download of minirosetta_database_rev20412.zip
                6/25/2008 7:58:12 AM|ralph@home|Finished download of minirosetta_database_rev22619.zip

                Path7

                Joined: Feb 11 08
                Posts: 56
                ID: 4036
                Credit: 4,974
                RAC: 0
                Message 4147 - Posted 25 Jun 2008 20:05:23 UTC

                  Mini 1.29 deletes old database files old db files downloaded again after reboot.

                  Hello all,
                  Just as Jipsu mentioned above, the minirosetta 1.29 did remove the old database files on my Ubuntu 7.10 x86, Boinc 5.10.45 as it supposed to do.
                  However, after rebooting my PC (and restarting Boinc) Boinc did download 3 old data base files:
                  minirosetta_database_rev20940.zip
                  minirosetta_database_rev21566.zip
                  minirosetta_database_rev22619.zip

                  After all the total effect: Disk usage Ralph@home went from (about) 123 MB to 92 MB right now.

                  Last but not least:
                  The WU: 5croA_JUMPRELAX_NAT_NEWFRAG_SAVE_ALL_OUT-5croA-_4568_4_0
                  with application Minirosetta 1.29 crunched fine.

                  Have a nice day,
                  Path7.

                  Pepo
                  Avatar

                  Joined: Sep 8 06
                  Posts: 104
                  ID: 1812
                  Credit: 36,890
                  RAC: 0
                  Message 4148 - Posted 25 Jun 2008 21:20:11 UTC - in response to Message 4147.

                    Mini 1.29 deletes old database files old db files downloaded again after reboot.

                    Obviously they\'re still being kept listed in client_state.xml... then it is not enough to just delete them.

                    Peter

                    Path7

                    Joined: Feb 11 08
                    Posts: 56
                    ID: 4036
                    Credit: 4,974
                    RAC: 0
                    Message 4149 - Posted 25 Jun 2008 21:32:34 UTC - in response to Message 4147.

                      Last modified: 25 Jun 2008 21:40:18 UTC

                      However, after rebooting my PC (and restarting Boinc) Boinc did download 3 old data base files:
                      minirosetta_database_rev20940.zip
                      minirosetta_database_rev21566.zip
                      minirosetta_database_rev22619.zip

                      Edit:
                      Sorry I overlooked 1 database file, actually Boinc downloaded 4 old database files;
                      including: minirosetta_database_rev20412.zip

                      @ Pepo: Thanks for your thoughts, I guess you\'re right.

                      Have a nice day,
                      Path7.

                      Profile dekim
                      Forum moderator
                      Project administrator
                      Project developer
                      Project scientist

                      Joined: Jan 20 06
                      Posts: 210
                      ID: 1
                      Credit: 411,458
                      RAC: 2,027
                      Message 4151 - Posted 26 Jun 2008 20:44:38 UTC

                        okay, I was worried this might happen. I\'ll have to look into this. Thanks for the heads up.
                        ____________

                        Profile ChertseyAl
                        Avatar

                        Joined: May 20 07
                        Posts: 3
                        ID: 3114
                        Credit: 51,074
                        RAC: 0
                        Message 4155 - Posted 3 Jul 2008 10:10:48 UTC - in response to Message 4127.

                          Please post any bugs/issues here regarding minirosetta version 1.29.


                          Don\'t know if you are interested in these, but I had a few of them over night. Here\'s a sample one:

                          03/07/2008 10:43:28|ralph@home|Starting 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1
                          03/07/2008 10:43:34|ralph@home|Starting task 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1 using minirosetta version 129
                          03/07/2008 10:43:36|ralph@home|Computation for task 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1 finished
                          03/07/2008 10:43:36|ralph@home|Output file 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1_0 for task 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1 absent

                          http://ralph.bakerlab.org/workunit.php?wuid=928656
                          http://ralph.bakerlab.org/result.php?resultid=1050853

                          Al.

                          JordanWeber

                          Joined: May 9 08
                          Posts: 2
                          ID: 4290
                          Credit: 12,774
                          RAC: 0
                          Message 4157 - Posted 3 Jul 2008 13:55:16 UTC

                            1050267 Task was aborted because it never started and never accumulated cpu time (this was on all night overnight). I\'ve been reporting this bug since at least mini 1.25. I was told from Rosetta@home boards to come here and help test mini. Since your guidelines say don\'t abort tasks, and since there\'s no way for the tasks to even start, I still had no choice but to abort.

                            AdeB
                            Avatar

                            Joined: Dec 22 07
                            Posts: 61
                            ID: 3888
                            Credit: 102,300
                            RAC: 159
                            Message 4158 - Posted 3 Jul 2008 20:15:25 UTC

                              Last modified: 3 Jul 2008 20:22:02 UTC

                              Error in resultid=1050453

                              stderr out:
                              <core_client_version>5.10.45</core_client_version>
                              <![CDATA[
                              <message>
                              process exited with code 1 (0x1, -255)
                              </message>
                              <stderr_txt>
                              Unrecognized XML in parse_init_data_file: fraction_done_update_period
                              Skipping: 1.000000
                              Skipping: /fraction_done_update_period
                              ERROR: Option matching -fragdate not found in command line top-level context

                              </stderr_txt>
                              ]]>

                              Azurrio

                              Joined: Jun 27 07
                              Posts: 12
                              ID: 3239
                              Credit: 8,020
                              RAC: 0
                              Message 4159 - Posted 4 Jul 2008 7:32:29 UTC

                                Three compute erros, each with 0 seconds of computing time.
                                WU1
                                WU2
                                WU3

                                Message boards : RALPH@home bug list : Bug report for Minirosetta version 1.29


                                Home | Join | About | Participants | Community | Statistics

                                Copyright © 2017 University of Washington

                                Last Modified: 20 Nov 2008 19:41:56 UTC
                                Back to top ^