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Message boards : RALPH@home bug list : minirosetta 2.17

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Yifan Song

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Message 5203 - Posted 28 Oct 2010 19:03:49 UTC

    This update fixes the memory and invalidation issues from 2 weeks ago.
    please report bugs here.

    Profile [VENETO] boboviz

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    Message 5204 - Posted 30 Oct 2010 18:15:36 UTC

      A lot of wu and no one error.
      It seems to be a good wu version....

      Ironworker16
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      Message 5205 - Posted 1 Nov 2010 2:10:27 UTC

        Last modified: 1 Nov 2010 2:13:40 UTC

        I have some run times over 40 hrs with one work unit at 38% 2 at 7% and 2 at less than 1%. Should I let them continue to run? No matter what the response I receive they will continue to run until I get home tomorrow evening.

        I _ quit

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        Message 5206 - Posted 4 Nov 2010 0:15:26 UTC

          this task Task ID 1976261 Name T0591_AF_rs_stg0_lrlxMultiCst_t000__casp9__aln1_SAVE_ALL_OUT_14996_3920_0 has an elapsed time of 24hrs 7 mins and still 8 hrs run time to go.

          32hrs for a task? Preferences are set for 4hr run time not 32hrs.
          Will let it run, but there is something wrong with the task if it is fouling up Boinc Manager.

          Snagletooth

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          Message 5207 - Posted 4 Nov 2010 14:48:03 UTC - in response to Message 5206.

            Remember that the elapsed time is wall clock time whereas the preference setting is for cpu time. Open the properties window for that particular task to see how much cpu time it has accumulated.

            greg_be, that task completed 4 models in 18418.4 cpu seconds so it appears to have honored your preference of 21600 cpu seconds. If the discrepancy between cpu and elapsed time is dramatically different from from what you are used to seeing then it might be wise to open up task manager (or whatever it's called in Windows) and make sure some new or errant process isn't eating up a bunch of cpu cycles.

            Best,
            Snags



            AdeB
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            Message 5208 - Posted 4 Nov 2010 17:28:17 UTC

              Task: 1978682
              Workunit: t591__boinc_rosetta_cm_loopbuild_threading_cst_relax_wangyr_IGNORE_THE_REST_15010_10

              stderr out:

              ERROR: Option matching -relax:fastrelax_repeats not found in command line top-level context


              AdeB

              Profile [VENETO] boboviz

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              Message 5209 - Posted 4 Nov 2010 20:03:22 UTC - in response to Message 5208.

                Same here on Windows 7:
                1979016
                1979017
                1979018
                1979019
                1979020

                <core_client_version>6.10.58</core_client_version>
                <![CDATA[
                <message>
                Funzione non corretta. (0x1) - exit code 1 (0x1)
                </message>
                <stderr_txt>
                [2010-11- 4 20:26:26:] :: BOINC:: Initializing ... ok.
                [2010-11- 4 20:26:26:] :: BOINC :: boinc_init()
                BOINC:: Setting up shared resources ... ok.
                BOINC:: Setting up semaphores ... ok.
                BOINC:: Updating status ... ok.
                BOINC:: Registering timer callback... ok.
                BOINC:: Worker initialized successfully.
                Registering options..
                Registered extra options.
                Initializing broker options ...
                Registered extra options.
                Initializing core...
                Initializing options.... ok
                Options::initialize()
                Options::adding_options()
                Options::initialize() Check specs.
                Options::initialize() End reached
                ERROR: Option matching -relax:fastrelax_repeats not found in command line top-level context

                Profile [VENETO] boboviz

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                Message 5210 - Posted 5 Nov 2010 6:06:01 UTC

                  New error
                  1980977

                  ERROR: Unable to open atomset file: \work\yfsong\SVN\minirosetta_database\chemical/atom_type_sets/fa_standard//atom_properties.txt
                  ERROR:: Exit from: ..\..\src\core\chemical\AtomTypeSet.cc line: 73
                  BOINC:: Error reading and gzipping output datafile: default.out
                  called boinc_finish

                  Profile [VENETO] boboviz

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                  Message 5211 - Posted 5 Nov 2010 9:06:38 UTC - in response to Message 5210.


                    ERROR: Unable to open atomset file: \work\yfsong\SVN\minirosetta_database\chemical/atom_type_sets/fa_standard//atom_properties.txt
                    ERROR:: Exit from: ..\..\src\core\chemical\AtomTypeSet.cc line: 73
                    BOINC:: Error reading and gzipping output datafile: default.out
                    called boinc_finish


                    Also with windows 7 64-bit, after few seconds:
                    1982643
                    1982730

                    Profile Conan
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                    Message 5212 - Posted 5 Nov 2010 9:12:26 UTC - in response to Message 5211.


                      ERROR: Unable to open atomset file: \work\yfsong\SVN\minirosetta_database\chemical/atom_type_sets/fa_standard//atom_properties.txt
                      ERROR:: Exit from: ..\..\src\core\chemical\AtomTypeSet.cc line: 73
                      BOINC:: Error reading and gzipping output datafile: default.out
                      called boinc_finish


                      Also with windows 7 64-bit, after few seconds:
                      1982643
                      1982730



                      I also get the same error on over 2 pages (40) of work units, all on 2 Windows machines (XP 32 bit).
                      Linux not having the same problem.
                      ____________

                      Profile [VENETO] boboviz

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                      Message 5213 - Posted 5 Nov 2010 10:25:42 UTC - in response to Message 5212.

                        I also get the same error on over 2 pages (40) of work units, all on 2 Windows machines (XP 32 bit). Linux not having the same problem.


                        So, it's a OS problem....

                        Evan

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                        Message 5216 - Posted 6 Nov 2010 10:10:54 UTC

                          PCS_PGR122A_v1.frag_18-51_SAVE_ALL_OUT_15041_1_0
                          This one failed within a few seconds

                          ERROR: First parameter of SVD_Solver constructor MUST be larger than the second parameter
                          ERROR:: Exit from: ..\..\src\numeric\SVD\SVD_Solver.cc line: 202

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                          Message 5217 - Posted 7 Nov 2010 9:42:57 UTC

                            http://ralph.bakerlab.org/result.php?resultid=1979778
                            ERROR: Unable to open atomset file: \work\yfsong\SVN\minirosetta_database\chemical/atom_type_sets/fa_standard//atom_properties.txt
                            ERROR:: Exit from: ..\..\src\core\chemical\AtomTypeSet.cc line: 73
                            BOINC:: Error reading and gzipping output datafile: default.out
                            called boinc_finish


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                            Message 5218 - Posted 7 Nov 2010 9:45:56 UTC - in response to Message 5207.

                              @Snags

                              Changed a preference setting in BOINC.
                              Was switching tasks every 60 mins changed that to every 4hrs to try and get tasks under control. Had 6-8 open in various stages at any one time under old setting.
                              This could account for the bizarre clock time.

                              Snagletooth

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                              Message 5219 - Posted 7 Nov 2010 22:33:27 UTC - in response to Message 5218.

                                @Snags

                                Changed a preference setting in BOINC.
                                Was switching tasks every 60 mins changed that to every 4hrs to try and get tasks under control. Had 6-8 open in various stages at any one time under old setting.
                                This could account for the bizarre clock time.


                                Hey, greg be - I would imagine that having fewer wus in a "waiting to run" status would lessen the reliance on a swap file and thus increase overall efficiency (assuming you've got "leave apps in memory" set to yes). Is that what you were going for? Have the times improved?

                                Best,
                                Snags

                                Profile feet1st

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                                Message 5220 - Posted 11 Nov 2010 1:43:03 UTC

                                  http://ralph.bakerlab.org/result.php?resultid=1989563

                                  ERROR: no convergence in svdcmp

                                  Only ran 44 seconds.
                                  ____________

                                  Profile [VENETO] boboviz

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                                  Message 5221 - Posted 11 Nov 2010 6:26:00 UTC - in response to Message 5210.


                                    ERROR: Unable to open atomset file: \work\yfsong\SVN\minirosetta_database\chemical/atom_type_sets/fa_standard//atom_properties.txt
                                    ERROR:: Exit from: ..\..\src\core\chemical\AtomTypeSet.cc line: 73
                                    BOINC:: Error reading and gzipping output datafile: default.out
                                    called boinc_finish


                                    Same here:
                                    1989656
                                    1989657
                                    1989661

                                    Profile [VENETO] boboviz

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                                    Message 5222 - Posted 11 Nov 2010 6:27:25 UTC - in response to Message 5209.


                                      ERROR: Option matching -relax:fastrelax_repeats not found in command line top-level context


                                      Same here:
                                      1989660

                                      John McLeod VII
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                                      Message 5223 - Posted 20 Nov 2010 3:51:03 UTC

                                        Really long run time. It is currently at 75 hours and 0.266%. The machine is a Windows 7 machine based on a Core i7. What information do you need to help debug this problem.
                                        ____________


                                        BOINC WIKI

                                        Profile feet1st

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                                        Message 5224 - Posted 20 Nov 2010 7:01:13 UTC - in response to Message 5223.

                                          What information do you need to help debug this problem.


                                          I would think they would at least like to know the task name. Was the 75hrs CPU time? Or "elapsed" time? Is the task manager showing it getting CPU?
                                          ____________

                                          Snagletooth

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                                          Message 5225 - Posted 29 Nov 2010 12:32:12 UTC

                                            Validate errors:

                                            lrm_je9o_combined_torsion_dun02_it01_run01_A_rlbn_1utg_IGNORE_THE_REST_NATIVE_NOCON_15096_1

                                            Profile [VENETO] boboviz

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                                            Message 5226 - Posted 30 Nov 2010 6:45:08 UTC - in response to Message 5225.

                                              Validate errors:
                                              lrm_je9o_combined_torsion_dun02_it01_run01_A_rlbn_1utg_IGNORE_THE_REST_NATIVE_NOCON_15096_1


                                              Same here:
                                              1995980
                                              1995982
                                              1995983

                                              AdeB
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                                              Message 5230 - Posted 16 Dec 2010 20:11:53 UTC

                                                task: 2008439

                                                ERROR: Option matching -relax:fastrelax_repeats not found in command line top-level context


                                                AdeB

                                                Profile [VENETO] boboviz

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                                                Message 5234 - Posted 3 Feb 2011 19:16:00 UTC - in response to Message 5230.

                                                  No work means no debug.

                                                  Profile [VENETO] boboviz

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                                                  Message 5237 - Posted 17 Feb 2011 6:29:02 UTC - in response to Message 5234.

                                                    Validate error here:
                                                    2019214

                                                    <core_client_version>6.12.14</core_client_version>
                                                    <![CDATA[
                                                    <stderr_txt>
                                                    [2011- 2-16 21:53:36:] :: BOINC:: Initializing ... ok.
                                                    [2011- 2-16 21:53:36:] :: BOINC :: boinc_init()
                                                    BOINC:: Setting up shared resources ... ok.
                                                    BOINC:: Setting up semaphores ... ok.
                                                    BOINC:: Updating status ... ok.
                                                    BOINC:: Registering timer callback... ok.
                                                    BOINC:: Worker initialized successfully.
                                                    Registering options..
                                                    Registered extra options.
                                                    Initializing broker options ...
                                                    Registered extra options.
                                                    Initializing core...
                                                    Initializing options.... ok
                                                    Options::initialize()
                                                    Options::adding_options()
                                                    Options::initialize() Check specs.
                                                    Options::initialize() End reached
                                                    Loaded options.... ok
                                                    Processed options.... ok
                                                    Initializing random generators... ok
                                                    Initialization complete.
                                                    Initializing options.... ok
                                                    Options::initialize()
                                                    Options::adding_options()
                                                    Options::initialize() Check specs.
                                                    Options::initialize() End reached
                                                    Loaded options.... ok
                                                    Processed options.... ok
                                                    Initializing random generators... ok
                                                    Initialization complete.
                                                    Setting WU description ...
                                                    Unpacking zip data: ../../projects/ralph.bakerlab.org/minirosetta_database_rev39052.zip
                                                    Setting database description ...
                                                    Setting up checkpointing ...
                                                    Setting up graphics native ...
                                                    BOINC:: Worker startup.
                                                    Starting watchdog...
                                                    Watchdog active.
                                                    # cpu_run_time_pref: 7200
                                                    ======================================================
                                                    DONE :: 233 starting structures 7186.86 cpu seconds
                                                    This process generated 233 decoys from 233 attempts
                                                    ======================================================

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

                                                    </stderr_txt>
                                                    ]]>

                                                    Profile [VENETO] boboviz

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                                                    Message 5238 - Posted 5 Mar 2011 10:03:05 UTC

                                                      Version 2.17 was released 28 october...
                                                      When the "2.18" version?? :-)
                                                      Or, if possible, a lot of 2.17???

                                                      Christian R.

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                                                      Message 5241 - Posted 27 Mar 2011 8:10:57 UTC

                                                        my error is: can´t attach shared memory

                                                        Profile [VENETO] boboviz

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                                                        Message 5243 - Posted 27 Mar 2011 19:27:07 UTC - in response to Message 5241.

                                                          my error is: can´t attach shared memory


                                                          This is a server error, not a wu error...

                                                          Message boards : RALPH@home bug list : minirosetta 2.17


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