Posts by svincent

1) Message boards : RALPH@home bug list : Rosetta mini 3.18 (Message 5418) Posted 11 Nov 2011 by svincent Post: Task 2379638 gave a Validate Error, but without anything noteworthy appearing in the log file. Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. ====================================================== DONE :: 1 starting structures 1201 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> Validate state Invalid
2) Message boards : RALPH@home bug list : Minirosetta Beta 3.14 (Message 5375) Posted 12 Aug 2011 by svincent Post: 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.
3) Message boards : RALPH@home bug list : Minirosetta Beta 3.14 (Message 5344) Posted 5 Jul 2011 by svincent Post: 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
4) Message boards : RALPH@home bug list : Minirosetta 3.04 (Message 5266) Posted 30 Apr 2011 by svincent Post: I'm seeing some tasks that have crashed immediately on Mac like this one 2024474 (pred_ECH19_lr19a_228_0001_nh.pdb_15216_3_1) Crashed executable name: minirosetta_3.05_i686-apple-darwin built using BOINC library version 6.5.0 Machine type Intel 80486 (32-bit executable) System version: Macintosh OS 10.6.7 build 10J869 Fri Apr 29 18:26:04 2011 SIGPIPE: write on a pipe with no reader 0 0x0091a119 SIGPIPE: write on a pipe with no reader etc.
5) Message boards : RALPH@home bug list : Minirosetta 3.00 (Message 5258) Posted 5 Apr 2011 by svincent Post: This is quite the memory hog! I don't know if it's the specific workunit (celldivs_RL5_1de2_1h7c_ProteinInterfaceDesign_21Feb2011_15162_1_0) or the new build but memory usage climbed to 1.03MB (real) + 1.32MB (virtual), dragging everything to a halt it seem (Mac).
6) Message boards : RALPH@home bug list : Minirosetta 3.00 (Message 5257) Posted 4 Apr 2011 by svincent Post: The graphics fail in an irreproducible way on Mac OS X 10.6.7. Sometimes the graphics window appears momentarily and then quits: other times it remains blank and hangs.
7) Message boards : RALPH@home bug list : minirosetta 2.05 (Message 5078) Posted 19 Feb 2010 by svincent Post: Some recent failures on Mac OS X 1749862 1749890 1749891 all failed as follows: ERROR: start_res != middle_res ERROR:: Exit from: src/protocols/moves/KinematicMover.cc line: 132 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> 1749898 failed differently SIGPIPE: write on a pipe with no reader 0 0x006e2839 SIGPIPE: write on a pipe with no reader 1 0x00338ace SIGPIPE: write on a pipe with no reader etc.
8) Message boards : RALPH@home bug list : minirosetta 2.05 (Message 5065) Posted 6 Feb 2010 by svincent Post: I have got compute errors on Mac OS X 10.6 for 4 tasks named 1738219 dckCFA_1sq2_3EGN_ppk_0002_foldit_ProteinInterfaceDesign_3Feb2010_14288_1_1 1738220 dckCFA_1sq2_2ODU_ppk_0025_foldit_ProteinInterfaceDesign_3Feb2010_14288_2_1 1738221 dckCFA_1sq2_2OJ4_ppk_0050_ProteinInterfaceDesign_3Feb2010_14288_2_1 1738222 dckCFA_1sq2_3ce7_0044_foldit_ProteinInterfaceDesign_3Feb2010_14288_2_1 All seemed to complete OK but gave an error code at the end. </stderr_txt> <message> <file_xfer_error> <file_name>dckCFA_1sq2_2ODU_ppk_0025_foldit_ProteinInterfaceDesign_3Feb2010_14288_2_1_0</file_name> <error_code>-161</error_code> </file_xfer_error> My wingmen seemed to have similar problems
9) Message boards : RALPH@home bug list : minirosetta 2.01/2.02 (Message 5011) Posted 10 Dec 2009 by svincent Post: I'm seeing my results "disappearing" in the sense that BOINC->Projects->Your results is showing fewer of them. Right now I just see one: yesterday evening there were 2 (both failures as reported above) and I know that several others completed successfully yesterday.
10) Message boards : RALPH@home bug list : minirosetta 2.01/2.02 (Message 5008) Posted 10 Dec 2009 by svincent Post: A couple of failures on Mac OS X 10.6 1681924 lr5_dun08_flat_semirot_A_rlbn_1a8o_SAVE_ALL_OUT_IGNORE_THE_REST_NATIVE_13447_1_0 1681926 lr5_dun08_flat_semirot_A_rlbn_1acf_SAVE_ALL_OUT_IGNORE_THE_REST_NATIVE_13447_1_0 Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords ERROR:: Exit from: src/protocols/relax/ClassicRelax.cc line: 541 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]
11) Message boards : RALPH@home bug list : Minirosetta 1.95 (Message 4945) Posted 28 Aug 2009 by svincent Post: This 1585116 on Mac sat for over an hour apparently initialising ( 0% progress : model 0 step 0) yet it completed OK. I used the Sampler to get a dump of what it was doing while initialising: it's way too big to post here but will Email it if it's of interest. I've had the same issue with a few recent Rosetta@home workunits.
12) Message boards : RALPH@home bug list : Minirosetta 1.95 (Message 4943) Posted 28 Aug 2009 by svincent Post: I'm getting Ralph workunits for 1.95 while Rosetta is at 1.97. How come?
13) Message boards : RALPH@home bug list : minirosetta 1.90 (Message 4898) Posted 31 Jul 2009 by svincent Post: All recent workunits are failing quickly on Mac on file errors 1572293 1572221 (plus some others) Sample output: </stderr_txt> <message> <file_xfer_error> <file_name>1a2p_A_30_S_ddg_predictions_0.3_1_8_local_min_test_sc_min_input_73009__12047_1_0_0</file_name> <error_code>-161</error_code> </file_xfer_error>
14) Message boards : RALPH@home bug list : Minirosetta 1.81 (Message 4875) Posted 14 Jul 2009 by svincent Post: A couple of Validate errors on Mac: both generated 99 decoys in less than 15 minutes. 1548638 1548639
15) Message boards : RALPH@home bug list : Minirosetta 1.81 (Message 4870) Posted 12 Jul 2009 by svincent Post: 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>
16) Message boards : RALPH@home bug list : Minirosetta 1.74/1.75 (Message 4856) Posted 9 Jul 2009 by svincent Post: These tasks all failed on Mac in the same way after nearly an hour. 1534904 1534905 1534906 Watchdog active. Hbond tripped: [2009- 7- 8 20:21:41:] interpolate rotamers bin out of range: MET_p:NtermProteinFull 0 nan -61.3722 178.26 73.8396 22 27 10 11 2147483649 22 0 nan ERROR:: Exit from: src/core/scoring/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh line: 590 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]> We need a new thread for 1.80.
17) Message boards : RALPH@home bug list : minirosetta_1.66 (Message 4814) Posted 5 May 2009 by svincent Post: Crash on 1436972 at end of processing on Mac. Thread 0 Crashed: 0 ...etta_1.66_i686-apple-darwin 0x00f077e3 __ZN7utility7signals9SignalHubIvN4core12conformation7signals16DestructionEventEE11send_signalES5_ + 2015 1 ...etta_1.66_i686-apple-darwin 0x00029f53 __ZN4core12conformation12ConformationD1Ev + 7373 2 ...etta_1.66_i686-apple-darwin 0x0007d2f2 __ZN4core4pose4PoseD1Ev + 4652 3 ...etta_1.66_i686-apple-darwin 0x004ff592 __ZN9protocols3jd214JobDistributor2goEN7utility7pointer10owning_ptrINS_5moves5MoverEEE + 1730 4 ...etta_1.66_i686-apple-darwin 0x00b6a24c __ZN9protocols3jd219BOINCJobDistributor2goEN7utility7pointer10owning_ptrINS_5moves5MoverEEE + 42 5 ...etta_1.66_i686-apple-darwin 0x00126d3d __ZN9protocols8abinitio11Broker_mainEv + 1543 6 ...etta_1.66_i686-apple-darwin 0x00004ba5 _main + 2805
18) Message boards : RALPH@home bug list : minirosetta_1.64 (Message 4811) Posted 3 May 2009 by svincent Post: A couple of failures of version 1.65 (doesn't seem to be a specific thread for it yet) on Mac apparently somewhere in task termination as it seemed to run for a normal length of time. 1436213 1436214 Crashed executable name: minirosetta_1.65_i686-apple-darwin built using BOINC library version 6.5.0 Machine type Intel 80486 (32-bit executable) System version: Macintosh OS 10.4.11 build 8S2167 Sat May 2 20:35:24 2009 Thread 0 Crashed: 0 ...etta_1.65_i686-apple-darwin 0x00edd115 __ZN7utility7signals9SignalHubIvN4core12conformation7signals16DestructionEventEE11send_signalES5_ + 2353 1 ...etta_1.65_i686-apple-darwin 0x00021b39 __ZN4core12conformation12ConformationD1Ev + 7373 2 ...etta_1.65_i686-apple-darwin 0x000784c8 __ZN4core4pose4PoseD1Ev + 4652 3 ...etta_1.65_i686-apple-darwin 0x004fc6a4 __ZN9protocols3jd214JobDistributor2goEN7utility7pointer10owning_ptrINS_5moves5MoverEEE + 1730 4 ...etta_1.65_i686-apple-darwin 0x00b44a7b __ZN9protocols3jd219BOINCJobDistributor2goEN7utility7pointer10owning_ptrINS_5moves5MoverEEE + 41 5 ...etta_1.65_i686-apple-darwin 0x0011fdc1 __ZN9protocols8abinitio11Broker_mainEv + 1543 6 ...etta_1.65_i686-apple-darwin 0x0000469d _main + 2805 7 ...etta_1.65_i686-apple-darwin 0x0000244e __start + 216 8 ...etta_1.65_i686-apple-darwin 0x00002375 start + 41
19) Message boards : RALPH@home bug list : Minirosetta 1.63 (Message 4798) Posted 23 Apr 2009 by svincent Post: Have seen 3 failures on Mac: all failing apparently in the same way. 1428827 1428826 1428824 Thread 0 Crashed: 0 ...etta_1.63_i686-apple-darwin 0x001f43d0 __ZN4core10kinematics8FoldTree10slide_jumpEmmm + 1396 1 ...etta_1.63_i686-apple-darwin 0x007d7be2 __ZN9protocols7docking15DockingProtocol14setup_foldtreeERN4core4pose4PoseE + 4132 2 ...etta_1.63_i686-apple-darwin 0x007d9bf5 __ZN9protocols7docking15DockingProtocol5applyERN4core4pose4PoseE + 5683 3 ...etta_1.63_i686-apple-darwin 0x004312a3 __ZN9protocols22ProteinInterfaceDesign25DockAndRetrieveSidechains5applyERN4core4pose4PoseE + 185 4 ...etta_1.63_i686-apple-darwin 0x003ab845 __ZN9protocols22ProteinInterfaceDesign10DockDesign5applyERN4core4pose4PoseE + 237 5 ...etta_1.63_i686-apple-darwin 0x000ff00a __ZN9protocols22ProteinInterfaceDesign22main_conditional_moverEPFvN7utility7pointer10owning_ptrIN4core4pose4PoseEEERNS3_INS0_10DockDesignEEEEb + 16654 6 ...etta_1.63_i686-apple-darwin 0x00005531 _main + 6985 7 ...etta_1.63_i686-apple-darwin 0x0000228e __start + 216 8 ...etta_1.63_i686-apple-darwin 0x000021b5 start + 41
20) Message boards : RALPH@home bug list : Minirosetta 1.63 (Message 4795) Posted 22 Apr 2009 by svincent Post: This may not be a bug, but I'm seeing some recent tasks generate an unusually large number of decoys. 1428490 for example generated 60 decoys in an hour, which seems excessive.

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