RALPH@home

Minirosetta 1.81

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


Advanced search

Message boards : RALPH@home bug list : Minirosetta 1.81

AuthorMessage
mtyka
Forum moderator
Project developer
Project scientist

Joined: Mar 19 08
Posts: 79
ID: 4144
Credit: 0
RAC: 0
Message 4865 - Posted 11 Jul 2009 20:33:33 UTC

    Last modified: 11 Jul 2009 20:33:48 UTC

    Supports this Disulfide bonds with encouraging initial results. We're eager to test this on a larger scale.

    http://en.wikipedia.org/wiki/Disulfide_bond

    Also includes bugfixes for some of the issues encountered over on BOINC.

    As always, please post issues here!

    M

    Profile Conan
    Avatar

    Joined: Feb 16 06
    Posts: 344
    ID: 145
    Credit: 1,325,239
    RAC: 792
    Message 4866 - Posted 11 Jul 2009 23:13:02 UTC - in response to Message 4865.

      Supports this Disulfide bonds with encouraging initial results. We're eager to test this on a larger scale.

      http://en.wikipedia.org/wiki/Disulfide_bond

      Also includes bugfixes for some of the issues encountered over on BOINC.

      As always, please post issues here!

      M


      G'Day mtyka,
      Does 1.81 include a fix for the work units that were running for over 4 hours past set preferences before failing due to taking too long to generate 1 decoy ? Like the ones I was reporting in the 1.80 thread.
      ____________

      Profile Conan
      Avatar

      Joined: Feb 16 06
      Posts: 344
      ID: 145
      Credit: 1,325,239
      RAC: 792
      Message 4868 - Posted 12 Jul 2009 8:23:27 UTC

        Errors with 1.81

        <core_client_version>6.4.5</core_client_version>
        <![CDATA[
        <message>
        process exited with code 1 (0x1, -255)
        </message>
        <stderr_txt>
        [2009- 7-12 7:33:46:] :: BOINC:: Initializing ... ok.
        [2009- 7-12 7:33:46:] :: 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.
        Setting WU description ...
        Unpacking zip data: ../../projects/ralph.bakerlab.org/minirosetta_database_rev30680.zip
        Unpacking WU data ...
        Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8_cl1_8.foldcst_chunk_general_cf.t297_.mtyka.boinc_files.zip
        Setting database description ...
        Setting up checkpointing ...
        Setting up graphics native ...
        Setting up folding (abrelax) ...

        ERROR: [ERROR] Unable to open constraints file: t297_.8.cst
        ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 331
        BOINC:: Error reading and gzipping output datafile: default.out
        called boinc_finish

        On this result

        Also had a Validate Error when all appeared OK on This Result

        ____________

        svincent

        Joined: Apr 4 08
        Posts: 34
        ID: 4182
        Credit: 51,768
        RAC: 0
        Message 4870 - Posted 12 Jul 2009 15:41:52 UTC

          This workunit 1541588 on Mac took 5 hours then failed with a Validate error

          BOINC:: Worker startup.
          Starting watchdog...
          Watchdog active.
          Starting work on structure: _1BG2A_2_00001
          BOINC:: CPU time: 18467.3s, 14400s + 3600s[2009- 7-12 2:37:44:] :: BOINC
          Output exists: default.out.gz
          InternalDecoyCount: 0 (GZ)
          0
          Stream information inconsistent.
          Writing W_0000001
          ======================================================
          DONE :: 1 starting structures 18467.3 cpu seconds
          This process generated 1 decoys from 1 attempts
          ======================================================
          called boinc_finish

          </stderr_txt>

          Snagletooth

          Joined: May 4 07
          Posts: 65
          ID: 3020
          Credit: 112,601
          RAC: 0
          Message 4872 - Posted 13 Jul 2009 10:46:16 UTC

            frb_0_8_cl1_5_hb_t297__IGNORE_THE_REST_1FXWF_9_11640_1_1

            ERROR: [ERROR] Unable to open constraints file: t297_.5.cst
            ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 331
            BOINC:: Error reading and gzipping output datafile: default.out

            Evan

            Joined: Dec 23 07
            Posts: 75
            ID: 3893
            Credit: 69,584
            RAC: 0
            Message 4873 - Posted 13 Jul 2009 13:40:42 UTC

              1544975
              http://ralph.bakerlab.org/result.php?resultid=1544975

              1544974
              http://ralph.bakerlab.org/result.php?resultid=1544974

              Errors with both the above. There is a 50% chance it was an operator induced error as they both occurred after I rebooted the computer.

              Billy

              Joined: Jan 29 07
              Posts: 13
              ID: 2592
              Credit: 5,855
              RAC: 0
              Message 4874 - Posted 14 Jul 2009 2:41:06 UTC

                Don't know if it is a bug or not. On my Intel iMac Core Duo, 1.81 is using 444 MB of real memory. This seems high compared to your recommended limit of 512 MB.

                svincent

                Joined: Apr 4 08
                Posts: 34
                ID: 4182
                Credit: 51,768
                RAC: 0
                Message 4875 - Posted 14 Jul 2009 16:17:44 UTC

                  A couple of Validate errors on Mac: both generated 99 decoys in less than 15 minutes.

                  1548638
                  1548639

                  AdeB
                  Avatar

                  Joined: Dec 22 07
                  Posts: 61
                  ID: 3888
                  Credit: 121,238
                  RAC: 465
                  Message 4876 - Posted 14 Jul 2009 16:56:18 UTC

                    Error in task 1543648.

                    Hbond tripped: [2009- 7-13 0:35: 0:]

                    ERROR: dis==0 in pairtermderiv!
                    ERROR:: Exit from: src/core/scoring/methods/PairEnergy.cc line: 334
                    BOINC:: Error reading and gzipping output datafile: default.out
                    called boinc_finish

                    AdeB

                    Billy

                    Joined: Jan 29 07
                    Posts: 13
                    ID: 2592
                    Credit: 5,855
                    RAC: 0
                    Message 4877 - Posted 15 Jul 2009 1:30:28 UTC

                      Last modified: 15 Jul 2009 1:54:26 UTC

                      Task 1554305

                      BOINC:: Worker startup.
                      Starting watchdog...
                      Watchdog active.
                      Starting work on structure: _1BG2A_2_00001
                      BOINC:: CPU time: 18235.1s, 14400s + 3600s[2009- 7-14 19:26:21:] :: BOINC
                      WARNING! cannot get file size for default.out.gz: could not open file.
                      Output exists: default.out.gz Size: -1
                      InternalDecoyCount: 0 (GZ)
                      -----
                      0
                      -----
                      Stream information inconsistent.
                      Writing W_0000001

                      Minirosetta 1.82

                      Valter

                      Joined: Aug 11 08
                      Posts: 3
                      ID: 4571
                      Credit: 95,627
                      RAC: 0
                      Message 4878 - Posted 15 Jul 2009 8:25:32 UTC

                        Hi, everyone.

                        I have a work unit running for 25 hours and at 45.230%. Rosetta Mini 1.81. Should I cancel it or go on running?

                        Thanks and regards,

                        Valter Aguiar
                        Brazil.

                        Evan

                        Joined: Dec 23 07
                        Posts: 75
                        ID: 3893
                        Credit: 69,584
                        RAC: 0
                        Message 4879 - Posted 15 Jul 2009 19:06:57 UTC

                          I am slowly working my way through the frb_0_8_cl_1... work units. No problems so far but I fear the lack of checkpoints will create a few complaints. So far on the long running models I am at aound 4 hours without a checkpoint.

                          AdeB
                          Avatar

                          Joined: Dec 22 07
                          Posts: 61
                          ID: 3888
                          Credit: 121,238
                          RAC: 465
                          Message 4880 - Posted 16 Jul 2009 16:18:23 UTC

                            I never saw this error before:
                            In task 1548231 (frb_0_8_cl1_5_hb_t305__IGNORE_THE_REST_2G59A_7_11642_1_0):

                            <![CDATA[
                            <message>
                            Maximum memory exceeded
                            </message>


                            This is on a PC with 512MB memory, AMD Athlon XP running linux.

                            AdeB

                            Profile Conan
                            Avatar

                            Joined: Feb 16 06
                            Posts: 344
                            ID: 145
                            Credit: 1,325,239
                            RAC: 792
                            Message 4881 - Posted 23 Jul 2009 10:03:49 UTC

                              This is a 1.83 WU error

                              <core_client_version>6.4.7</core_client_version>
                              <![CDATA[
                              <message>
                              Incorrect function. (0x1) - exit code 1 (0x1)
                              </message>
                              <stderr_txt>
                              [2009- 7-23 9:34:44:] :: BOINC:: Initializing ... ok.
                              [2009- 7-23 9:34:44:] :: 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 -detect_disulphides not found in command line top-level context

                              See this WU

                              ____________

                              AdeB
                              Avatar

                              Joined: Dec 22 07
                              Posts: 61
                              ID: 3888
                              Credit: 121,238
                              RAC: 465
                              Message 4882 - Posted 23 Jul 2009 18:09:01 UTC - in response to Message 4881.

                                This is a 1.83 WU error

                                <core_client_version>6.4.7</core_client_version>
                                <![CDATA[
                                <message>
                                Incorrect function. (0x1) - exit code 1 (0x1)
                                </message>
                                <stderr_txt>
                                [2009- 7-23 9:34:44:] :: BOINC:: Initializing ... ok.
                                [2009- 7-23 9:34:44:] :: 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 -detect_disulphides not found in command line top-level context

                                See this WU


                                The same error here

                                AdeB

                                Message boards : RALPH@home bug list : Minirosetta 1.81


                                Home | Join | About | Participants | Community | Statistics

                                Copyright © 2017 University of Washington

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