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Message boards : RALPH@home bug list : Minirosetta Beta 3.14

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Profile dekim
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Message 5325 - Posted 15 Jun 2011 4:29:26 UTC

    Please post issues and bugs here. We are particularly interested in excessive disk usage and memory errors. We do expect some jobs to use up to 600-700MB of memory and we'll submit these to higher memory clients. We are also interested in a possible dead lock of the main application and the graphics app where the cpu usage goes to zero for both apps.
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    BigMike
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    Message 5328 - Posted 15 Jun 2011 16:35:46 UTC

      Had one blow up on a sin/cos range error.

      =Mike
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      Message 5329 - Posted 15 Jun 2011 22:29:44 UTC

        thanks for the info. that's a known issue with that type of job.
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        Profile robertmiles

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        Message 5331 - Posted 16 Jun 2011 1:28:51 UTC

          One where BOINC thinks the workunit is still running, but it's using no CPU time at all now:

          http://ralph.bakerlab.org/workunit.php?wuid=1802588

          Elapsed 07:01:04
          48.46% progress and no longer changing
          To completion 06:27:09

          I normally don't have the graphics portion showing, but when I asked for it, it came up solid black.

          Anything special I need to do to send back useful information on why?

          Profile robertmiles

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          Message 5332 - Posted 16 Jun 2011 2:06:23 UTC

            Last modified: 16 Jun 2011 2:08:41 UTC

            A few more details:

            The workunit not using CPU time had a 530 MB maximum working set size.

            Was running in 32-bit mode. Any plans to offer a 64-bit version of this application, even if its main advantage is to help computers like mine that seem to have a limit of around 4 GB on the maximum amount of memory that can be assigned to the entire set of 32-bit programs (BOINC or not) that are in memory at once?

            More memory is installed, but seems useful mainly for 64-bit programs.

            I haven't found a task name for the graphics app. What should I be looking for?

            My other computer also has a 3.14 workunit, running in high priority mode but at least still showing an increasing progress.

            Profile robertmiles

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            Message 5333 - Posted 16 Jun 2011 3:07:41 UTC

              Last modified: 16 Jun 2011 3:20:02 UTC

              I've now found something that might be the graphics application:

              Minirosetta Beta 3.14 - Windows Internet Explorer

              Listed under Applications under Windows Task Manager, not under Processes, and therefore shown without any task name.

              Have not found any way to show the resource usage of anything listed only as an application.

              Total disk usage by all programs about 1 MB per minute, and mainly by system programs.

              Total network usage about 1 MB per minute, mainly by boincmgr.exe and boinc.exe.


              BOINC 6.10.58
              64-bit Vista SP2, with almost all updates offered except Internet Explorer 9


              My other computer has already returned its 3.14 workunit hours sooner than its previous estimated time to completion; already marked as a success. Same versions of BOINC and Windows.

              Profile robertmiles

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              Message 5334 - Posted 16 Jun 2011 4:09:00 UTC

                I've now identified:

                Minirosetta Beta 3.14 - Windows Internet Explorer

                It was the browser window under which I entered the last few messages.


                CPU time at last checkpoint of the faulty workunit: 03:33:00

                CPU time for the workunit: 03:33:15

                Could this indicate a problem with resuming normal operation after checkpoints? I've forgotten just which BOINC project has often been showing workunits stopping any use of CPU time about that soon after a checkpoint lately. Would a separate thread used mainly for checking for such conditions be useful?


                I've added up the memory currently reported as in use by 32-bit programs. About 1.7 GB total, so I don't expect any problem from that.

                Profile robertmiles

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                Message 5335 - Posted 16 Jun 2011 5:01:36 UTC

                  I decided to inspect the list of files in the slot for the failed workunit; it appears that the last file modified there was about 6 hours ago.

                  I also inspected the files lists under minirosetta-database and found that the sections for metal ions do not appear to list aluminum, even though it is connected to the brain damage in one of the later stages of Alzheimer's, or copper, even though the human brain's natural defense against Alzheimer's uses a copper-binding protein. I assume that is not important for this workunit, but how important is it for Rosetta@Home workunits aimed at Alzheimer's?

                  Profile robertmiles

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                  Message 5336 - Posted 16 Jun 2011 7:27:53 UTC

                    Last modified: 16 Jun 2011 7:45:46 UTC

                    Still more:

                    I clicked on the workunit, then Show graphics. Another window, all black inside. I clicked on the X to close that window and got a windows error message for minirosetta_graphics_3.13_windows_x86_64.exe. Details too long to copy, but I used the snipping tool to capture pictures of it.

                    If those details would be useful, how do I send the pictures?

                    Windows Task Manager does not list any program with that name among the programs now running or suspended, and did not when I started this series of messages.

                    Profile dekim
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                    Message 5338 - Posted 16 Jun 2011 20:33:42 UTC

                      robertmiles,

                      Sounds like it might be a dead lock issue. You can manually kill the minirosetta process. We'll look into this further. Let us know if it happens again.
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                      Message 5339 - Posted 17 Jun 2011 0:44:36 UTC - in response to Message 5338.

                        Thanks for replying.

                        Profile [VENETO] boboviz

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                        Message 5343 - Posted 5 Jul 2011 17:59:16 UTC

                          Last modified: 5 Jul 2011 18:00:15 UTC

                          All error after few seconds on win7:

                          2056476
                          2056475
                          2056474
                          2056471
                          2056465


                          ERROR: unrecognized aa LIG
                          ERROR:: Exit from: ..\..\..\src\core\io\pdb\file_data.cc line: 641
                          BOINC:: Error reading and gzipping output datafile: default.out
                          called boinc_finish

                          svincent

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                          Message 5344 - Posted 5 Jul 2011 19:30:21 UTC

                            Failing on Mac also. Slightly different error message


                            ERROR: Cannot open PDB file "2p9hA_suc_0001.pdb"
                            ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 199
                            BOINC:: Error reading and gzipping output datafile: default.out
                            called boinc_finish

                            Task 2056185

                            Rocco Moretti
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                            Message 5345 - Posted 5 Jul 2011 23:20:52 UTC - in response to Message 5343.

                              ERROR: unrecognized aa LIG


                              Sorry about that - there was a file missing from the input files. It should be corrected in newer submissions.

                              ERROR: Cannot open PDB file "2p9hA_suc_0001.pdb"


                              A different input file issue - also should be corrected with newer submissions.

                              --

                              (I will double check my input files before submitting.
                              I will double check my input files before submitting.
                              I will double check my input files before submitting. ...)

                              Profile [VENETO] boboviz

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                              Message 5346 - Posted 6 Jul 2011 5:20:36 UTC - in response to Message 5345.


                                (I will double check my input files before submitting.
                                I will double check my input files before submitting.
                                I will double check my input files before submitting. ...)



                                :-)

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                                Message 5347 - Posted 7 Jul 2011 1:16:42 UTC

                                  Last modified: 7 Jul 2011 1:21:09 UTC

                                  Had this error on 3 of my last few work units

                                  ERROR: unrecognized aa LIG
                                  ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 641
                                  BOINC:: Error reading and gzipping output datafile: default.out
                                  called boinc_finish

                                  See 2056632
                                  2056714
                                  2057573

                                  Also had the following error on another 2 work units

                                  ERROR: Cannot open PDB file "2p9hA_suc_0001.pdb"
                                  ERROR:: Exit from: ..\..\..\src\core\import_pose\import_pose.cc line: 199
                                  BOINC:: Error reading and gzipping output datafile: default.out
                                  called boinc_finish

                                  See 2057602
                                  2057618

                                  Conan
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                                  Message 5348 - Posted 8 Jul 2011 6:32:01 UTC

                                    2058828

                                    ERROR: ERROR: FragmentIO: could not open file frags_w_cs_wt_200.11mers
                                    ERROR:: Exit from: ..\..\..\src\core\fragment\FragmentIO.cc line: 230
                                    BOINC:: Error reading and gzipping output datafile: default.out
                                    called boinc_finish

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                                    Message 5354 - Posted 20 Jul 2011 12:14:10 UTC

                                      Had two errors with the following error code

                                      ERROR: ct == final_atoms
                                      ERROR:: Exit from: ..\..\..\src\core\scoring\rms_util.cc line: 524
                                      BOINC:: Error reading and gzipping output datafile: default.out


                                      On 2078013
                                      and 2078108

                                      Both failed for the resend as well.

                                      Conan
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                                      Message 5355 - Posted 20 Jul 2011 13:18:05 UTC

                                        Same error here 2077145 wingmans unit died also.

                                        ERROR: ct == final_atoms
                                        ERROR:: Exit from: ..\..\..\src\core\scoring\rms_util.cc line: 524
                                        BOINC:: Error reading and gzipping output datafile: default.out
                                        called boinc_finish

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                                        Message 5356 - Posted 20 Jul 2011 13:41:23 UTC

                                          Last modified: 20 Jul 2011 13:59:33 UTC

                                          Anyone having watchdog problems with the cleft.cyca.CYCA... units? I have three all gone past the 12hr target point and bouncing between 9:59 and 10:00 minutes remaining. Longest one is at about 13 hrs 25 mins. Going to let them run this morning to see if they finish on their own.

                                          edit: morning eyes, time for a shower, changed 'deft' to 'cleft'

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                                          Message 5357 - Posted 21 Jul 2011 2:34:52 UTC

                                            Here is another error

                                            ERROR: ERROR: FragmentIO: could not open file frags_w_cs_wt_200.11mers
                                            ERROR:: Exit from: src/core/fragment/FragmentIO.cc line: 230
                                            BOINC:: Error reading and gzipping output datafile: default.out

                                            On 2083601

                                            Conan
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                                            Profile [VENETO] boboviz

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                                            Message 5359 - Posted 22 Jul 2011 21:14:16 UTC

                                              2078238

                                              ERROR: ct == final_atoms
                                              ERROR:: Exit from: ..\..\..\src\core\scoring\rms_util.cc line: 524
                                              BOINC:: Error reading and gzipping output datafile: default.out
                                              called boinc_finish

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                                              Message 5360 - Posted 23 Jul 2011 16:01:00 UTC

                                                Work Units 2081438 and 2081487

                                                Both failed with "Maximum elapsed time exceeded"

                                                Conan

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                                                Profile [VENETO] boboviz

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                                                Message 5361 - Posted 26 Jul 2011 20:09:39 UTC

                                                  2092449

                                                  ERROR: ERROR: FragmentIO: could not open file frags_w_cs_wt_200.11mers
                                                  ERROR:: Exit from: ..\..\..\src\core\fragment\FragmentIO.cc line: 230
                                                  BOINC:: Error reading and gzipping output datafile: default.out
                                                  called boinc_finish

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                                                  Message 5367 - Posted 2 Aug 2011 10:40:46 UTC

                                                    33 failures (complete batch) this morning all failing with 'Client Error'

                                                    http://ralph.bakerlab.org/results.php?userid=527

                                                    Example error:-

                                                    <core_client_version>6.12.33</core_client_version>
                                                    <![CDATA[
                                                    <message>
                                                    Incorrect function. (0x1) - exit code 1 (0x1)
                                                    </message>
                                                    <stderr_txt>
                                                    [2011- 8- 2 10:28:58:] :: BOINC:: Initializing ... ok.
                                                    [2011- 8- 2 10:28:58:] :: 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_rev42272.zip
                                                    Setting database description ...
                                                    Setting up checkpointing ...
                                                    Setting up graphics native ...
                                                    BOINC:: Worker startup.
                                                    Starting watchdog...
                                                    Watchdog active.
                                                    Tag::read - parse error, printing backtrace.

                                                    Tag::read - parse error - file:istream line:5 column:1 - </SFXN5>
                                                    Tag::read - parse error - file:istream line:5 column:1 - ^

                                                    Tag::read - parse error - file:istream line:6 column:1 - </SCOREFXNS>
                                                    Tag::read - parse error - file:istream line:6 column:1 - ^

                                                    Tag::read - parse error - file:istream line:9 column:1 - </FILTERS>
                                                    Tag::read - parse error - file:istream line:9 column:1 - ^

                                                    Tag::read - parse error - file:istream line:13 column:1 - </TASKOPERATIONS>
                                                    Tag::read - parse error - file:istream line:13 column:1 - ^

                                                    Tag::read - parse error - file:istream line:15 column:1 - <FlxbbDesign name=flxbb ncycles=3 sfxn_design=SFXN5 sfxn_relax=SFXN5 SFXN5 clear_all_residues=1 task_operations=limitchi2,layer_allclear_all_residues=0 blueprint="master.blueprint" constraints_NtoC=1.0 />
                                                    Tag::read - parse error - file:istream line:15 column:1 - ^

                                                    Tag::read - parse error - file:istream line:14 column:1 - <MOVERS>
                                                    Tag::read - parse error - file:istream line:14 column:1 - ^

                                                    Tag::read - parse error - file:istream line:1 column:1 - <dock_design>
                                                    Tag::read - parse error - file:istream line:1 column:1 - ^


                                                    ERROR: false
                                                    ERROR:: Exit from: ..\..\..\src\utility\tag\Tag.cc line: 387
                                                    BOINC:: Error reading and gzipping output datafile: default.out
                                                    called boinc_finish

                                                    </stderr_txt>
                                                    ]]>
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                                                    Message 5368 - Posted 2 Aug 2011 17:55:55 UTC - in response to Message 5367.

                                                      Last modified: 2 Aug 2011 17:56:22 UTC

                                                      33 failures (complete batch) this morning all failing with 'Client Error'

                                                      ERROR: false
                                                      ERROR:: Exit from: ..\..\..\src\utility\tag\Tag.cc line: 387
                                                      BOINC:: Error reading and gzipping output datafile: default.out
                                                      called boinc_finish


                                                      Same here after few seconds
                                                      2111200
                                                      and others 30 wus....

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                                                      Message 5371 - Posted 3 Aug 2011 14:09:41 UTC

                                                        Last modified: 3 Aug 2011 14:10:15 UTC

                                                        Yes same Error here as well (although I did a few work units that ran OK).

                                                        Tag::read - parse error, printing backtrace.

                                                        Tag::read - parse error - file:istream line:5 column:1 - </SFXN5>
                                                        Tag::read - parse error - file:istream line:5 column:1 - ^

                                                        Tag::read - parse error - file:istream line:6 column:1 - </SCOREFXNS>
                                                        Tag::read - parse error - file:istream line:6 column:1 - ^

                                                        Tag::read - parse error - file:istream line:9 column:1 - </FILTERS>
                                                        Tag::read - parse error - file:istream line:9 column:1 - ^

                                                        Tag::read - parse error - file:istream line:13 column:1 - </TASKOPERATIONS>
                                                        Tag::read - parse error - file:istream line:13 column:1 - ^

                                                        Tag::read - parse error - file:istream line:15 column:1 - <FlxbbDesign name=flxbb ncycles=3 sfxn_design=SFXN5 sfxn_relax=SFXN5 SFXN5 clear_all_residues=1 task_operations=limitchi2,layer_allclear_all_residues=0 blueprint="master.blueprint" constraints_NtoC=1.0 />
                                                        Tag::read - parse error - file:istream line:15 column:1 - ^

                                                        Tag::read - parse error - file:istream line:14 column:1 - <MOVERS>
                                                        Tag::read - parse error - file:istream line:14 column:1 - ^

                                                        Tag::read - parse error - file:istream line:1 column:1 - <dock_design>
                                                        Tag::read - parse error - file:istream line:1 column:1 - ^


                                                        ERROR: false
                                                        ERROR:: Exit from: ..\..\..\src\utility\tag\Tag.cc line: 387
                                                        BOINC:: Error reading and gzipping output datafile: default.out
                                                        called boinc_finish

                                                        On Work units
                                                        2112936
                                                        2112877
                                                        2112918
                                                        2112933
                                                        2112861
                                                        2112941
                                                        2112898
                                                        2112851
                                                        2112893
                                                        2112934
                                                        2112900
                                                        2112847
                                                        2112940

                                                        Conan
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                                                        svincent

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                                                        Message 5375 - Posted 12 Aug 2011 22:02:53 UTC

                                                          Task 2136909 (3stub_patch_CYCA_1sq2_ProteinInterfaceDesign_11Aug2011_15516_1_0) failed on Mac with a Compute Error.



                                                          SIGPIPE: write on a pipe with no reader
                                                          0 0x00ba68b9 SIGPIPE: write on a pipe with no reader

                                                          etc.

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                                                          Message 5384 - Posted 26 Aug 2011 7:51:22 UTC

                                                            2171363

                                                            Unhandled Exception Detected...

                                                            - Unhandled Exception Record -
                                                            Reason: Access Violation (0xc0000005) at address 0x00996545 read attempt to address 0x00000000

                                                            Engaging BOINC Windows Runtime Debugger...

                                                            ********************
                                                            BOINC Windows Runtime Debugger Version 6.5.0

                                                            Dump Timestamp : 08/26/11 09:15:30
                                                            Install Directory : C:\Programmi\BOINC\
                                                            Data Directory : C:\Documents and Settings\All Users\Dati applicazioni\BOINC
                                                            Project Symstore : http://boinc.bakerlab.org/rosetta/symstore
                                                            Loaded Library : C:\Programmi\BOINC\\dbghelp.dll
                                                            Loaded Library : C:\Programmi\BOINC\\symsrv.dll
                                                            Loaded Library : C:\Programmi\BOINC\\srcsrv.dll
                                                            LoadLibraryA( C:\Programmi\BOINC\\version.dll ): GetLastError = 126
                                                            Loaded Library : version.dll

                                                            </stderr_txt>
                                                            ]]>

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                                                            Message 5387 - Posted 9 Sep 2011 1:07:45 UTC

                                                              Pls check this one out... Ran for 21.5 ksec and looks like it finished fine after 901 decoys, but someone else had already sent in a bad one, so mine was marker as a 'validate error' ???

                                                              2178636

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                                                              Message 5390 - Posted 12 Sep 2011 6:35:16 UTC

                                                                All wu in error:

                                                                2179787
                                                                2179786
                                                                2179786
                                                                etc, etc

                                                                ERROR: in::file::boinc_wu_zip 1uaoA.zip does not exist!
                                                                ERROR:: Exit from: ..\..\..\src\apps\public\boinc\minirosetta.cc line: 167
                                                                BOINC:: Error reading and gzipping output datafile: default.out
                                                                called boinc_finish

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                                                                Message 5391 - Posted 12 Sep 2011 14:26:17 UTC

                                                                  All 80 abrelax ended with client error / compute error

                                                                  Task ID 2179800
                                                                  Name 2WWEA_abrelax_15647_3_0
                                                                  Workunit 1921159
                                                                  Created 12 Sep 2011 5:49:30 UTC
                                                                  Sent 12 Sep 2011 5:52:07 UTC
                                                                  Received 12 Sep 2011 14:18:59 UTC
                                                                  Server state Over
                                                                  Outcome Client error
                                                                  Client state Compute error
                                                                  Exit status 1 (0x1)
                                                                  Computer ID 20656
                                                                  Report deadline 16 Sep 2011 5:52:07 UTC
                                                                  CPU time 2.059213
                                                                  stderr out <core_client_version>6.12.33</core_client_version>
                                                                  <![CDATA[
                                                                  <message>
                                                                  Unzul´┐Żssige Funktion. (0x1) - exit code 1 (0x1)
                                                                  </message>
                                                                  <stderr_txt>
                                                                  [2011- 9-12 15:49:49:] :: BOINC:: Initializing ... ok.
                                                                  [2011- 9-12 15:49:49:] :: 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_rev42272.zip
                                                                  Unpacking WU data ...

                                                                  ERROR: in::file::boinc_wu_zip 1uaoA.zip does not exist!
                                                                  ERROR:: Exit from: ..\..\..\src\apps\public\boinc\minirosetta.cc line: 167
                                                                  BOINC:: Error reading and gzipping output datafile: default.out
                                                                  called boinc_finish

                                                                  </stderr_txt>
                                                                  ]]>


                                                                  Validate state Invalid

                                                                  Profile Conan
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                                                                  Joined: Feb 16 06
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                                                                  Message 5392 - Posted 13 Sep 2011 12:49:27 UTC

                                                                    Had this one fail
                                                                    Result 2185423

                                                                    ERROR: in::file::boinc_wu_zip 1uaoA.zip does not exist!
                                                                    ERROR:: Exit from: ..\..\..\src\apps\public\boinc\minirosetta.cc line: 167
                                                                    BOINC:: Error reading and gzipping output datafile: default.out


                                                                    Conan
                                                                    ____________

                                                                    Profile [VENETO] boboviz

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                                                                    Message 5402 - Posted 31 Oct 2011 15:54:53 UTC

                                                                      Why we are running a lot of 3.14?? Now last version in 3.17.....

                                                                      Profile robertmiles

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                                                                      Message 5407 - Posted 1 Nov 2011 16:35:59 UTC - in response to Message 5402.

                                                                        Last modified: 1 Nov 2011 16:37:00 UTC

                                                                        Could be trying to track down a bug with 3.14 that I saw several times over on Rosetta@Home. If so, something to watch for: Shortly after a checkpoint, the workunit stops using any CPU time at all, WITHOUT telling BOINC it has encountered a problem so that some other workunit can be started instead. If so, the time limit checking cannot run, so the workunit can easily sit there looking like it's running, but not actually doing anything, for many times as long as you've selected for workunits to run.

                                                                        Message boards : RALPH@home bug list : Minirosetta Beta 3.14


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