RALPH@home

Minirosetta 2.14

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


Advanced search

Message boards : RALPH@home bug list : Minirosetta 2.14

AuthorMessage
Profile Conan
Avatar

Joined: Feb 16 06
Posts: 344
ID: 145
Credit: 1,310,876
RAC: 5
Message 5147 - Posted 24 May 2010 22:18:15 UTC

    Posts for this series of work units were being posted under thread "Minirosetta 2.12" so I thought I would create one for the current series of work units.

    On WU 1831281
    Had this error

    ERROR: Cannot open patchdock file: 1fAc_2odh.patchdock
    ERROR:: Exit from: src/protocols/ProteinInterfaceDesign/read_patchdock.cc line: 101
    BOINC:: Error reading and gzipping output datafile: default.out
    called boinc_finish

    ____________

    Profile Conan
    Avatar

    Joined: Feb 16 06
    Posts: 344
    ID: 145
    Credit: 1,310,876
    RAC: 5
    Message 5149 - Posted 27 May 2010 8:34:10 UTC

      Had this WU 1834847 that reached 86.402% completion sometime between 6 and 7 hours run time, it was still at 86.402% after 19 hours 21 minutes so I aborted it.
      If I have read the slot directory right then it did 167 checkpoints but just did not progress.

      My preferences are set for 6 hours so the WU should of timed out for taking so long, if it still had not finished the first decoy then the WU has a problem.
      ____________

      Profile Conan
      Avatar

      Joined: Feb 16 06
      Posts: 344
      ID: 145
      Credit: 1,310,876
      RAC: 5
      Message 5150 - Posted 28 May 2010 0:46:36 UTC

        ERROR: ERROR: FragmentIO: could not open file myoglobin.frag9.rosetta.tab
        ERROR:: Exit from: ..\..\src\core\fragment\FragmentIO.cc line: 258
        BOINC:: Error reading and gzipping output datafile: default.out

        On This WU

        ____________

        Profile apohawk
        Avatar

        Joined: Dec 1 09
        Posts: 5
        ID: 12957
        Credit: 111,792
        RAC: 0
        Message 5151 - Posted 28 May 2010 5:59:45 UTC - in response to Message 5150.

          parvalbumin_redo_targets_CONTROL_BOINC_abrelax.score12.fastrelax.v1_SAVE_ALL_OUT_14803_2_1
          http://ralph.bakerlab.org/workunit.php?wuid=1631447

          This unit crashed in similiar fashion at both hosts crunching it.

          http://ralph.bakerlab.org/result.php?resultid=1848472


          2010-05-28 07:30:03 ralph@home Output file parvalbumin_redo_targets_CONTROL_BOINC_abrelax.score12.fastrelax.v1_SAVE_ALL_OUT_14803_2_1_0 for task parvalbumin_redo_targets_CONTROL_BOINC_abrelax.score12.fastrelax.v1_SAVE_ALL_OUT_14803_2_1 absent
          # cpu_run_time_pref: 28800
          ======================================================
          DONE :: 50 starting structures 28554.5 cpu seconds
          This process generated 50 decoys from 50 attempts
          ======================================================

          BOINC :: Watchdog shutting down...
          BOINC :: BOINC support services shutting down cleanly ...
          called boinc_finish

          </stderr_txt>
          <message>
          <file_xfer_error>
          <file_name>parvalbumin_redo_targets_CONTROL_BOINC_abrelax.score12.fastrelax.v1_SAVE_ALL_OUT_14803_2_1_0</file_name>
          <error_code>-161</error_code>
          </file_xfer_error>

          </message>
          ]]>
          ____________

          Profile [VENETO] boboviz

          Joined: Apr 9 08
          Posts: 508
          ID: 4205
          Credit: 727,228
          RAC: 146
          Message 5152 - Posted 28 May 2010 20:54:18 UTC - in response to Message 5151.

            1849542


            ERROR: Unable to open weights. Neither ./pcs.weight1.patch nor minirosetta_database\scoring/weights/pcs.weight1.patch.wts_patchexist
            ERROR:: Exit from: ..\..\src\core\scoring\ScoreFunction.cc line: 262
            BOINC:: Error reading and gzipping output datafile: default.out
            called boinc_finish

            Profile Conan
            Avatar

            Joined: Feb 16 06
            Posts: 344
            ID: 145
            Credit: 1,310,876
            RAC: 5
            Message 5153 - Posted 29 May 2010 0:34:50 UTC - in response to Message 5152.

              1849542


              ERROR: Unable to open weights. Neither ./pcs.weight1.patch nor minirosetta_database\scoring/weights/pcs.weight1.patch.wts_patchexist
              ERROR:: Exit from: ..\..\src\core\scoring\ScoreFunction.cc line: 262
              BOINC:: Error reading and gzipping output datafile: default.out
              called boinc_finish



              Same error on 3 work units
              1849128
              1849129
              1849130

              Also had a file transfer error (XFER ERROR)
              on 1848730

              ____________

              Profile Conan
              Avatar

              Joined: Feb 16 06
              Posts: 344
              ID: 145
              Credit: 1,310,876
              RAC: 5
              Message 5154 - Posted 30 May 2010 2:01:41 UTC - in response to Message 5153.

                Last modified: 30 May 2010 2:02:45 UTC

                [quote]1849542


                ERROR: Unable to open weights. Neither ./pcs.weight1.patch nor minirosetta_database\scoring/weights/pcs.weight1.patch.wts_patchexist
                ERROR:: Exit from: ..\..\src\core\scoring\ScoreFunction.cc line: 262
                BOINC:: Error reading and gzipping output datafile: default.out
                called boinc_finish


                Here is another with the same error
                1849490
                ____________

                Divide Overflow

                Joined: Feb 15 06
                Posts: 12
                ID: 6
                Credit: 128,027
                RAC: 0
                Message 5155 - Posted 5 Jun 2010 7:06:43 UTC

                  Completed successfully and validated, but with an odd error message:

                  ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
                  ERROR:: Exit from: ..\..\src\protocols\ProteinInterfaceDesign\movers\PlaceUtils.cc line: 281
                  called boinc_finish

                  http://ralph.bakerlab.org/result.php?resultid=1851904

                  ____________

                  Profile [VENETO] boboviz

                  Joined: Apr 9 08
                  Posts: 508
                  ID: 4205
                  Credit: 727,228
                  RAC: 146
                  Message 5157 - Posted 6 Jun 2010 16:52:24 UTC - in response to Message 5155.

                    Same here:
                    1851619

                    Profile [VENETO] boboviz

                    Joined: Apr 9 08
                    Posts: 508
                    ID: 4205
                    Credit: 727,228
                    RAC: 146
                    Message 5159 - Posted 19 Jul 2010 20:39:10 UTC

                      No work, no debug.... :-)

                      Profile [VENETO] boboviz

                      Joined: Apr 9 08
                      Posts: 508
                      ID: 4205
                      Credit: 727,228
                      RAC: 146
                      Message 5160 - Posted 21 Jul 2010 18:36:39 UTC - in response to Message 5159.

                        No work, no debug.... :-)


                        oh, well....thank you!!

                        Profile EvoDude
                        Avatar

                        Joined: Feb 18 06
                        Posts: 28
                        ID: 527
                        Credit: 639,833
                        RAC: 0
                        Message 5164 - Posted 6 Sep 2010 8:27:59 UTC

                          Another batch of this series and another batch of computation errors!
                          ____________

                          Snagletooth

                          Joined: May 4 07
                          Posts: 65
                          ID: 3020
                          Credit: 112,601
                          RAC: 0
                          Message 5165 - Posted 6 Sep 2010 16:14:23 UTC

                            Last modified: 6 Sep 2010 16:14:58 UTC

                            SAXS-rescore-1eovA__14879_15

                            Mon Sep 6 12:03:24 2010 ralph@home Output file SAXS-rescore-1eovA__14879_15_0_0 for task SAXS-rescore-1eovA__14879_15_0 absent

                            ======================================================
                            DONE :: 1 starting structures 12857.1 cpu seconds
                            This process generated 6 decoys from 6 attempts
                            ======================================================

                            BOINC :: Watchdog shutting down...
                            BOINC :: BOINC support services shutting down cleanly ...
                            called boinc_finish

                            </stderr_txt>
                            <message>
                            <file_xfer_error>
                            <file_name>SAXS-rescore-1eovA__14879_15_0_0</file_name>
                            <error_code>-161</error_code>
                            </file_xfer_error>

                            AdeB
                            Avatar

                            Joined: Dec 22 07
                            Posts: 61
                            ID: 3888
                            Credit: 111,097
                            RAC: 68
                            Message 5166 - Posted 6 Sep 2010 17:39:42 UTC

                              SAXS-rescore-1ks9A__14879_6_1

                              The same error as Snagletooth.

                              ma 06 sep 2010 17:07:49 CEST ralph@home Output file SAXS-rescore-1ks9A__14879_6_1_0 for task SAXS-rescore-1ks9A__14879_6_1 absent

                              stderr out:
                              ======================================================
                              DONE :: 1 starting structures 13314.1 cpu seconds
                              This process generated 9 decoys from 9 attempts
                              ======================================================

                              BOINC :: Watchdog shutting down...
                              BOINC :: BOINC support services shutting down cleanly ...
                              called boinc_finish

                              </stderr_txt>
                              <message>
                              <file_xfer_error>
                              <file_name>SAXS-rescore-1ks9A__14879_6_1_0</file_name>
                              <error_code>-161</error_code>
                              </file_xfer_error>


                              AdeB

                              Profile apohawk
                              Avatar

                              Joined: Dec 1 09
                              Posts: 5
                              ID: 12957
                              Credit: 111,792
                              RAC: 0
                              Message 5167 - Posted 6 Sep 2010 20:31:34 UTC - in response to Message 5166.

                                Last modified: 6 Sep 2010 20:39:16 UTC

                                No luck here either on those "SAXS-rescore".
                                For 13 tasks crunched so far on two machines (1 windows, 1 linux), all 13 got "computation error".

                                <message>
                                <file_xfer_error>
                                <file_name>SAXS-rescore-1tf4B__14879_16_0_0</file_name>
                                <error_code>-161</error_code>
                                </file_xfer_error>

                                </message>


                                For Your Information.

                                EDIT

                                I just saw one WU finish on win7, got to 100% and then this:
                                2010-09-06 22:37:57 ralph@home Output file SAXS-rescore-1mgtA__14879_16_0_0 for task SAXS-rescore-1mgtA__14879_16_0 absent

                                ____________

                                Profile [VENETO] boboviz

                                Joined: Apr 9 08
                                Posts: 508
                                ID: 4205
                                Credit: 727,228
                                RAC: 146
                                Message 5168 - Posted 6 Sep 2010 20:39:20 UTC - in response to Message 5167.

                                  Same here 1906579

                                  mentabelgium

                                  Joined: Nov 28 06
                                  Posts: 1
                                  ID: 2298
                                  Credit: 8,663
                                  RAC: 0
                                  Message 5169 - Posted 7 Sep 2010 6:26:05 UTC

                                    Another one here

                                    AdeB
                                    Avatar

                                    Joined: Dec 22 07
                                    Posts: 61
                                    ID: 3888
                                    Credit: 111,097
                                    RAC: 68
                                    Message 5171 - Posted 7 Sep 2010 7:58:12 UTC

                                      SAXS-rescore-1qfjC__14882_5_0

                                      stderr out:

                                      ERROR: ERROR: Unable to open silent_input file: 'default.out'
                                      ERROR:: Exit from: src/core/io/silent/SilentFileData.cc line: 86
                                      BOINC:: Error reading and gzipping output datafile: default.out
                                      called boinc_finish
                                      Watchdog active.


                                      AdeB

                                      sqweeser

                                      Joined: Jun 19 06
                                      Posts: 5
                                      ID: 1539
                                      Credit: 66,131
                                      RAC: 0
                                      Message 5172 - Posted 7 Sep 2010 8:55:50 UTC

                                        Compute error in WU: SAXS-rescore-1eudA__14881_3_1 with the following error:

                                        ERROR: Option file open failed for: 1eudA-linker_sampler_protocol-saxs-1.0.flags

                                        Profile nenym

                                        Joined: Jan 16 09
                                        Posts: 14
                                        ID: 5145
                                        Credit: 1,007,003
                                        RAC: 0
                                        Message 5173 - Posted 7 Sep 2010 11:56:19 UTC

                                          Last modified: 7 Sep 2010 12:04:49 UTC

                                          All SAXS tasks erroed out

                                          <file_xfer_error>
                                          <file_name>SAXS-rescore-1gcyA__14879_3_0_0</file_name>
                                          <error_code>-161</error_code>
                                          </file_xfer_error>
                                          after finishing wu's (cca 42 000 s).
                                          XP 32bit SAXS-rescore-1bi5A__14879_2_1, SAXS-rescore-1mgtA__14879_12_0
                                          XP 64bit SAXS-rescore-1gcyA__14879_3_0, SAXS-rescore-1d5rA__14879_7_1, SAXS-rescore-1dzfA__14879_15_1

                                          No credit granted.

                                          Profile Conan
                                          Avatar

                                          Joined: Feb 16 06
                                          Posts: 344
                                          ID: 145
                                          Credit: 1,310,876
                                          RAC: 5
                                          Message 5174 - Posted 7 Sep 2010 12:28:10 UTC

                                            Last modified: 7 Sep 2010 12:29:46 UTC

                                            ERROR: ERROR: Unable to open silent_input file: 'default.out'
                                            ERROR:: Exit from: ..\..\src\core\io\silent\SilentFileData.cc line: 86
                                            BOINC:: Error reading and gzipping output datafile: default.out

                                            Had the above error on
                                            1907858
                                            1907812
                                            1907755
                                            1907712
                                            1907941

                                            Had the File XFer Error on
                                            1907101
                                            1907068
                                            1906880
                                            1906866
                                            1907147
                                            1907190
                                            1907193

                                            Had ERROR: Option file open failed for:
                                            1907659
                                            1907584
                                            1907600
                                            1907904

                                            Most work units have been failing but a few recent ones are now running OK.

                                            Thanks
                                            Conan.
                                            ____________

                                            Profile nenym

                                            Joined: Jan 16 09
                                            Posts: 14
                                            ID: 5145
                                            Credit: 1,007,003
                                            RAC: 0
                                            Message 5175 - Posted 7 Sep 2010 17:28:14 UTC - in response to Message 5173.

                                              The last one XP 64bit File Xfer Error
                                              SAXS-rescore-1jpmA__14879_17_1

                                              BigMike
                                              Avatar

                                              Joined: Feb 23 06
                                              Posts: 63
                                              ID: 738
                                              Credit: 58,730
                                              RAC: 0
                                              Message 5176 - Posted 7 Sep 2010 17:37:09 UTC

                                                Last modified: 7 Sep 2010 17:40:38 UTC

                                                Post deleted due to my lack of research before opening my mouth.

                                                =Mike
                                                ____________
                                                Don't believe everything you think.

                                                Profile apohawk
                                                Avatar

                                                Joined: Dec 1 09
                                                Posts: 5
                                                ID: 12957
                                                Credit: 111,792
                                                RAC: 0
                                                Message 5177 - Posted 7 Sep 2010 18:43:58 UTC - in response to Message 5176.

                                                  SAXS batch strikes back. This time with new twist. They end right after the start.
                                                  I got several of those already. No luck for SAXS ;)
                                                  e.g. WU named SAXS-score-1kbwC__14888_2_0 http://ralph.bakerlab.org/result.php?resultid=1912150


                                                  ERROR: Option file open failed for: 1kbwC-linker_sampler_protocol.flags

                                                  ____________

                                                  BigMike
                                                  Avatar

                                                  Joined: Feb 23 06
                                                  Posts: 63
                                                  ID: 738
                                                  Credit: 58,730
                                                  RAC: 0
                                                  Message 5178 - Posted 8 Sep 2010 5:44:12 UTC - in response to Message 5152.

                                                    I also got a weights error and a filexfer error on SAXS WU's.

                                                    =Mike
                                                    ____________
                                                    Don't believe everything you think.

                                                    Profile Conan
                                                    Avatar

                                                    Joined: Feb 16 06
                                                    Posts: 344
                                                    ID: 145
                                                    Credit: 1,310,876
                                                    RAC: 5
                                                    Message 5179 - Posted 8 Sep 2010 12:05:29 UTC

                                                      Some more errors,

                                                      ERROR: Unable to open weights. Neither ./../saxs_cen_patch-1.0 nor minirosetta_database\scoring/weights/../saxs_cen_patch-1.0.wts_patchexist
                                                      ERROR:: Exit from: ..\..\src\core\scoring\ScoreFunction.cc line: 262
                                                      BOINC:: Error reading and gzipping output datafile: default.out

                                                      Had the above error on
                                                      1913600
                                                      1913175
                                                      1913758
                                                      1913909
                                                      1914146
                                                      1914233
                                                      1912897
                                                      1914118
                                                      1914136
                                                      1914137
                                                      1914530

                                                      Also had "file xfer Error" on
                                                      1912783
                                                      1912825

                                                      Hope you are getting to the cause of the errors.

                                                      Conan.












                                                      ____________

                                                      Profile [VENETO] boboviz

                                                      Joined: Apr 9 08
                                                      Posts: 508
                                                      ID: 4205
                                                      Credit: 727,228
                                                      RAC: 146
                                                      Message 5180 - Posted 9 Sep 2010 20:06:18 UTC

                                                        1916074

                                                        Options::adding_options()
                                                        Options::initialize() Check specs.
                                                        Options::initialize() End reached
                                                        ERROR: Option file open failed for: 1knyA-linker_sampler_protocol.flags

                                                        Message boards : RALPH@home bug list : Minirosetta 2.14


                                                        Home | Join | About | Participants | Community | Statistics

                                                        Copyright © 2017 University of Washington

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