RALPH@home

minirosetta 2.03

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


Advanced search

Message boards : RALPH@home bug list : minirosetta 2.03

AuthorMessage
mtyka
Forum moderator
Project developer
Project scientist

Joined: Mar 19 08
Posts: 79
ID: 4144
Credit: 0
RAC: 0
Message 5015 - Posted 14 Dec 2009 19:44:37 UTC

    Fixes a stack overflow bug in 2.02.

    Please report issues here :)

    Profile [VENETO] boboviz

    Joined: Apr 9 08
    Posts: 492
    ID: 4205
    Credit: 691,398
    RAC: 620
    Message 5016 - Posted 21 Dec 2009 21:09:34 UTC

      No wu, no debug....

      ANCHULA-MARK
      Avatar

      Joined: Mar 2 08
      Posts: 2
      ID: 4088
      Credit: 100,495
      RAC: 0
      Message 5017 - Posted 22 Dec 2009 2:26:26 UTC

        11 out of 15 died within 30 secs the other 4 are still running @ 10+mins


        Task ID 1686211
        Name homopt1.t369_.t369_.IGNORE_THE_REST.S_00001_0000857_00042.pdb.JOB_13568_1_0
        Workunit 1489861


        ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 147 fold_tree nres: 148
        ERROR:: Exit from: ..\..\src\core\conformation\Conformation.cc line: 234
        BOINC:: Error reading and gzipping output datafile: default.out
        called boinc_finish

        </stderr_txt>
        ]]>
        ____________

        Profile Conan
        Avatar

        Joined: Feb 16 06
        Posts: 344
        ID: 145
        Credit: 1,309,534
        RAC: 0
        Message 5018 - Posted 22 Dec 2009 5:52:01 UTC

          Have so far had 5 fail and 3 succeed.

          Result 1686388 had this error
          ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 147 fold_tree nres: 148
          ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234
          BOINC:: Error reading and gzipping output datafile: default.out

          And results 1687361
          1687351
          1687325
          1687296
          all had the following error

          ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 139 fold_tree nres: 140
          ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234
          BOINC:: Error reading and gzipping output datafile: default.out


          ____________

          Snagletooth

          Joined: May 4 07
          Posts: 65
          ID: 3020
          Credit: 112,601
          RAC: 0
          Message 5019 - Posted 22 Dec 2009 8:10:54 UTC

            homopt1.t369_.t369_.IGNORE_THE_REST.S_00002_0000860_027.pdb.JOB_13568_1
            homopt1.t369_.t369_.IGNORE_THE_REST.S_00002_0000712_020.pdb.JOB_13568_1
            after 19-22 seconds ended with:
            ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 147 fold_tree nres: 148
            ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234
            BOINC:: Error reading and gzipping output datafile: default.out
            called boinc_finish

            homopt1.t331_.t331_.IGNORE_THE_REST.S_00002_0000988_00044.pdb.JOB_13563_1
            ended after 6 seconds with ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 139 fold_tree nres: 140
            ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234
            BOINC:: Error reading and gzipping output datafile: default.out
            called boinc_finish

            homopt1.t368_.t368_.IGNORE_THE_REST.S_00001_0000086_00055.pdb.JOB_13567_1_0 ran successfully completing 11 decoys in 13877 seconds

            homopt1.t313_.t313_.IGNORE_THE_REST.S_00001_0000429_10056.pdb.JOB_13559_1 appears to be crunching successfully, currently working on Model 1 step 4206 after one hour.


            Profile Conan
            Avatar

            Joined: Feb 16 06
            Posts: 344
            ID: 145
            Credit: 1,309,534
            RAC: 0
            Message 5020 - Posted 22 Dec 2009 21:25:36 UTC - in response to Message 5018.

              Have so far had 5 fail and 3 succeed.

              Result 1686388 had this error
              ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 147 fold_tree nres: 148
              ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234
              BOINC:: Error reading and gzipping output datafile: default.out

              And results 1687361
              1687351
              1687325
              1687296
              all had the following error

              ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 139 fold_tree nres: 140
              ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234
              BOINC:: Error reading and gzipping output datafile: default.out


              Have had another 11 fail with a similar error, all exit at the same line (234) only the conformation error varies with a few different numbers.
              They all error after less than 20 minutes.
              ____________

              I _ quit

              Joined: Jan 13 09
              Posts: 44
              ID: 5136
              Credit: 88,562
              RAC: 0
              Message 5022 - Posted 26 Dec 2009 0:54:16 UTC

                6 tasks with the same kind of bugs as listed by the others:

                ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 147 fold_tree nres: 148
                ERROR:: Exit from: ..\..\src\core\conformation\Conformation.cc line: 234
                BOINC:: Error reading and gzipping output datafile: default.out

                http://ralph.bakerlab.org/result.php?resultid=1686083
                http://ralph.bakerlab.org/result.php?resultid=1686082
                http://ralph.bakerlab.org/result.php?resultid=1686077

                and

                ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 154 fold_tree nres: 155
                ERROR:: Exit from: ..\..\src\core\conformation\Conformation.cc line: 234
                BOINC:: Error reading and gzipping output datafile: default.out
                called boinc_finish

                http://ralph.bakerlab.org/result.php?resultid=1686064
                http://ralph.bakerlab.org/result.php?resultid=1686063
                http://ralph.bakerlab.org/result.php?resultid=1686062

                Profile [VENETO] boboviz

                Joined: Apr 9 08
                Posts: 492
                ID: 4205
                Credit: 691,398
                RAC: 620
                Message 5023 - Posted 4 Jan 2010 21:18:20 UTC

                  http://ralph.bakerlab.org/result.php?resultid=1693258

                  ERROR: Cannot open PDB file "native.pdb"
                  ERROR:: Exit from: ..\..\src\core\io\pdb\pose_io.cc line: 170
                  BOINC:: Error reading and gzipping output datafile: default.out
                  called boinc_finish

                  Profile Saenger
                  Avatar

                  Joined: Feb 28 06
                  Posts: 12
                  ID: 861
                  Credit: 44,776
                  RAC: 93
                  Message 5026 - Posted 5 Jan 2010 16:46:35 UTC

                    I got a bunch of errors, but more valids 'til now.

                    Typical error:

                    stderr out

                    <core_client_version>6.10.17</core_client_version>
                    <![CDATA[
                    <message>
                    process exited with code 1 (0x1, -255)
                    </message>
                    <stderr_txt>
                    [2010- 1- 5 2:32: 2:] :: BOINC:: Initializing ... ok.
                    [2010- 1- 5 2:32: 2:] :: 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_rev34260.zip
                    Unpacking WU data ...
                    Unpacking data: ../../projects/ralph.bakerlab.org/job_boinc_t373__loopbuild_threading_tex.boinc.zip
                    Setting database description ...
                    Setting up checkpointing ...
                    Setting up graphics native ...

                    ERROR: Cannot open PDB file "native.pdb"
                    ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 170
                    BOINC:: Error reading and gzipping output datafile: default.out
                    called boinc_finish

                    </stderr_txt>
                    ]]>

                    ____________
                    Gruesse vom Saenger

                    For questions about Boinc look in the BOINC-Wiki

                    ramostol

                    Joined: Mar 29 07
                    Posts: 24
                    ID: 2840
                    Credit: 31,121
                    RAC: 0
                    Message 5028 - Posted 6 Jan 2010 9:58:45 UTC

                      One wu errored out in the recent bunch of tasks:

                      job_boinc_t318__filtered_loopbuild_threading_tex_IGNORE_THE_REST_13730_7_0

                      ERROR: can't find residue type at pos 11in sequence MTQVLVRNGI QAVGDGLTSL IIVGKKSVLK NVTFEGKFKE VAQKFVTDGD SWNSMISRIP ASGRHPLHYE LAHLITVPDASSRGNTPTNA HSIYKELKPI NYPEDTKNVH FVLFAEYPDV LSHVAAIART FCKFSMKTSG IRELNVNIDV VCDKLTNEDAVFLTDLSESV RETARLIDTP ANILTTDALV DEAVKVGNAT GSKITVIRGE ELLKAGFGGI YHVGKAGPTP PAFVVLSHEVPGSTEHIALV GKGVVYDTGG LQIKTKTGMP NMKRDMGGAA GMLEAYSALV KHGFSQTLHA CLCIVENNVS PIANKPDDIIKMLSGKTVEI NNTDAEGRLI LADGVFYAKE TLKATTIFDM ATLTGAQAWL SGRLHGAAMT NDEQLENEII KAGKASGDLVAPMLFAPDLF FGDLKSSIAD MKNSNLGKMD GPPSAVAGLL IGAHIGFGEG LRWLHLDIAA PAEVGDRGTG YGPALFSTLLGKYTSVPMLK Q
                      ERROR:: Exit from: src/core/chemical/util.cc line: 379
                      BOINC:: Error reading and gzipping output datafile: default.out

                      Profile robertmiles

                      Joined: Jan 13 09
                      Posts: 79
                      ID: 5137
                      Credit: 233,290
                      RAC: 1
                      Message 5029 - Posted 6 Jan 2010 15:09:17 UTC

                        One ran about 11 hours instead of the 6 hours I asked for, and produced just one decoy. Appears OK otherwise, though.

                        http://ralph.bakerlab.org/result.php?resultid=1694077

                        Snagletooth

                        Joined: May 4 07
                        Posts: 65
                        ID: 3020
                        Credit: 112,601
                        RAC: 0
                        Message 5031 - Posted 7 Jan 2010 12:59:18 UTC

                          ha_notyr_3gbn_1ksk_6Jan2010_13738_2_0 ran for the full 4 hour preferred runtime to complete 567 decoys. It also ran the 4 hours straight through which is quite unexpected. Checking the current short term debts the new Ralph wu I received almost two hours ago won't begin crunching for at about 3 more hours. Every other wu appears to be switching out as expected which also suggests it may indeed be a case of Ralph not giving way when asked rather that BOINC suddenly ignoring its preferences.

                          Earlier a similarly named wu ha_notyr_3gbn_1osh_6Jan2010_13734_2_0 wrapped things up after completing 100 models in 2719.38 seconds.

                          Snags

                          [B^S]ABoskovich

                          Joined: Feb 22 06
                          Posts: 1
                          ID: 719
                          Credit: 25,774
                          RAC: 9
                          Message 5033 - Posted 7 Jan 2010 19:42:57 UTC

                            I have a wu running 18+ hours showing 5,4% complete. Should I abort?
                            ____________

                            Snagletooth

                            Joined: May 4 07
                            Posts: 65
                            ID: 3020
                            Credit: 112,601
                            RAC: 0
                            Message 5034 - Posted 8 Jan 2010 0:31:56 UTC - in response to Message 5033.

                              I have a wu running 18+ hours showing 5,4% complete. Should I abort?

                              Is that 18 hours of CPU time or wall clock time? (The newer BOINC managers show both.)If CPU time you could try quitting and restarting BOINC (that's quitting the BOINC client not merely closing the manager). Sometimes this gets a stuck WU moving again, sometimes it errors out immediately upon restart; if neither, nothing left to do but abort.

                              coturnix

                              Joined: Jan 5 10
                              Posts: 9
                              ID: 15073
                              Credit: 196,185
                              RAC: 0
                              Message 5035 - Posted 9 Jan 2010 20:06:47 UTC

                                Task: 1703705
                                Workunit: ha_notyr_3gbn_2z84_6Jan2010_13734_1

                                BOINC:: Worker startup.
                                Starting watchdog...
                                Watchdog active.
                                SIGSEGV: segmentation violation

                                Crashed executable name: minirosetta_2.03_i686-apple-darwin
                                built using BOINC library version 6.5.0
                                Machine type Intel 80486 (32-bit executable)
                                System version: Macintosh OS 10.5.8 build 9L30
                                Thu Jan 7 06:48:34 2010

                                Same workunit segfaults on Windows.

                                coturnix

                                Joined: Jan 5 10
                                Posts: 9
                                ID: 15073
                                Credit: 196,185
                                RAC: 0
                                Message 5036 - Posted 9 Jan 2010 20:09:04 UTC

                                  Validate errors:

                                  ha_notyr_3gbn_2img_6Jan2010_13734_2
                                  ha_notyr_3gbn_2fu2_6Jan2010_13734_1

                                  coturnix

                                  Joined: Jan 5 10
                                  Posts: 9
                                  ID: 15073
                                  Credit: 196,185
                                  RAC: 0
                                  Message 5037 - Posted 9 Jan 2010 20:28:00 UTC

                                    Task 1707216 (homopt_cstmc_1.t317_.t317_.IGNORE_THE_REST.S_00006_0000222_090.pdb.JOB_13800_1)
                                    Task 1707217 (homopt_cstmc_1.t317_.t317_.IGNORE_THE_REST.S_00006_0000272_00016.pdb.JOB_13800_1)
                                    Task 1707218 (homopt_cstmc_1.t317_.t317_.IGNORE_THE_REST.S_00006_0000781_045.pdb.JOB_13800_1)

                                    BOINC:: Worker startup.
                                    Starting watchdog...
                                    Watchdog active.
                                    FNAME: native.pdb
                                    FNAME: native.pdb

                                    ERROR: [ERROR] Unable to open constraints file: /work/tex/projects/cm/benchmark/cross_filt/t317_/t317_.aln_list_mike_chosen_bestaln.alns.combined.csts
                                    ERROR:: Exit from: ..\..\src\core\scoring\constraints\ConstraintIO.cc line: 332
                                    BOINC:: Error reading and gzipping output datafile: default.out
                                    called boinc_finish

                                    Snagletooth

                                    Joined: May 4 07
                                    Posts: 65
                                    ID: 3020
                                    Credit: 112,601
                                    RAC: 0
                                    Message 5038 - Posted 9 Jan 2010 22:27:21 UTC

                                      homopt_cstmc_1.t317_.t317_.IGNORE_THE_REST.S_00001_0000752_10003.pdb.JOB_13800_1_0

                                      process exited with code 1 (0x1, -255)

                                      ERROR: [ERROR] Unable to open constraints file: /work/tex/projects/cm/benchmark/cross_filt/t317_/t317_.aln_list_mike_chosen_bestaln.alns.combined.csts
                                      ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 332
                                      BOINC:: Error reading and gzipping output datafile: default.out

                                      Profile Conan
                                      Avatar

                                      Joined: Feb 16 06
                                      Posts: 344
                                      ID: 145
                                      Credit: 1,309,534
                                      RAC: 0
                                      Message 5043 - Posted 21 Jan 2010 5:31:41 UTC

                                        Last modified: 21 Jan 2010 5:34:43 UTC

                                        Had an error on this work unit

                                        1719676

                                        ERROR: [ERROR] Unable to open constraints file: i2240.dist_csts
                                        ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 332
                                        BOINC:: Error reading and gzipping output datafile: default.out
                                        called boinc_finish
                                        ____________

                                        Profile Conan
                                        Avatar

                                        Joined: Feb 16 06
                                        Posts: 344
                                        ID: 145
                                        Credit: 1,309,534
                                        RAC: 0
                                        Message 5045 - Posted 22 Jan 2010 7:29:54 UTC

                                          Last modified: 22 Jan 2010 7:33:37 UTC

                                          A couple of Validate Errors for your perusal

                                          1721498
                                          1721395

                                          I could not see anything wrong with the work units but apparently they don't Validate.
                                          ____________

                                          Message boards : RALPH@home bug list : minirosetta 2.03


                                          Home | Join | About | Participants | Community | Statistics

                                          Copyright © 2017 University of Washington

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