Posts by svincent

21) Message boards : RALPH@home bug list : Minirosetta 1.62 (Message 4792) Posted 21 Apr 2009 by svincent Post: These two tasks failed early on Mac with the same compute error. Other similar docking tasks have worked. 1425894 1425825 ERROR: f.check_fold_tree() ERROR:: Exit from: src/protocols/docking/DockingProtocol.cc line: 232 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]>
22) Message boards : RALPH@home bug list : Minirosetta 1.61 (Message 4783) Posted 16 Apr 2009 by svincent Post: These 3 tasks all (named DvR115G_BOINC_ABINITIO*) crashed almost immediately on Mac in the same routine 1424622 1424561 1423738 Crashed executable name: minirosetta_1.59_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 Thu Apr 16 03:11:08 2009 Thread 0 Crashed: 0 ...etta_1.59_i686-apple-darwin 0x0098727b __ZNK4core7scoring7methods29ResidualDipolarCouplingEnergy16calc_ordermatrixERKmS4_RN9ObjexxFCL8FArray2DIdEERNS5_8FArray1DIdEESB_Rb + 4429 1 ...etta_1.59_i686-apple-darwin 0x00989832 __ZNK4core7scoring7methods29ResidualDipolarCouplingEnergy12eval_dipolarERNS_4pose4PoseE + 1150 2 ...etta_1.59_i686-apple-darwin 0x0098a1aa __ZNK4core7scoring7methods29ResidualDipolarCouplingEnergy21finalize_total_energyERNS_4pose4PoseERKNS0_13ScoreFunctionERNS0_10EMapVectorE + 24 3 ...etta_1.59_i686-apple-darwin 0x00189868 __ZNK4core7scoring13ScoreFunctionclERNS_4pose4PoseE + 4378 4 ...etta_1.59_i686-apple-darwin 0x003285bb __ZN9protocols5moves10MonteCarlo14score_functionERKN4core7scoring13ScoreFunctionE + 129 5 ...etta_1.59_i686-apple-darwin 0x00564535 __ZN9protocols8abinitio15ClassicAbinitio16replace_scorefxnERN4core4pose4PoseENS1_7StageIDEd + 309 6 ...etta_1.59_i686-apple-darwin 0x00563fd9 __ZN9protocols8abinitio15ClassicAbinitio14prepare_stage2ERN4core4pose4PoseE + 51 7 ...etta_1.59_i686-apple-darwin 0x0056fa42 __ZN9protocols8abinitio15ClassicAbinitio5applyERN4core4pose4PoseE + 1774 8 ...etta_1.59_i686-apple-darwin 0x00120d0b __ZN9protocols8abinitio18AbrelaxApplication4foldERN4core4pose4PoseEN7utility7pointer10owning_ptrINS_8ProtocolEEE + 4093 9 ...etta_1.59_i686-apple-darwin 0x001335a7 __ZN9protocols8abinitio18AbrelaxApplication3runEv + 807 10 ...etta_1.59_i686-apple-darwin 0x00003bbb _main + 1395 11 ...etta_1.59_i686-apple-darwin 0x00001eee __start + 216 12 ...etta_1.59_i686-apple-darwin 0x00001e15 start + 41 This one 1424657 (broker_lb_test2_hb_t369__IGNORE_THE_REST_9256_1_1) also crashed after apparent successful completion due to a file error. ====================================================== DONE :: 5 starting structures 3392.47 cpu seconds This process generated 5 decoys from 5 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> <message> <file_xfer_error> <file_name>broker_lb_test2_hb_t369__IGNORE_THE_REST_9256_1_1_0</file_name> <error_code>-161</error_code> </file_xfer_error> </message> ]]>
23) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4774) Posted 15 Apr 2009 by svincent Post: This task crashed on Mac with a segmentation violation. 1421317 Crash log is in the task file: here's the first bit: Thread 0 Crashed: 0 ...etta_1.59_i686-apple-darwin 0x009579fe __ZNK4core7scoring7methods10VDW_Energy19residue_pair_energyERKNS_12conformation7ResidueES6_RKNS_4pose4PoseERKNS0_13ScoreFunctionERNS0_17TwoBodyEMapVectorE + 1534 1 ...etta_1.59_i686-apple-darwin 0x00189b81 __ZNK4core7scoring13ScoreFunctionclERNS_4pose4PoseE + 5171 2 ...etta_1.59_i686-apple-darwin 0x004e9985 __ZN9protocols8abinitio12AbrelaxMover5applyERN4core4pose4PoseE + 5993 3 ...etta_1.59_i686-apple-darwin 0x004d0a99 __ZN9protocols3jd214JobDistributor2goEN7utility7pointer10owning_ptrINS_5moves5MoverEEE + 4041 4 ...etta_1.59_i686-apple-darwin 0x00ace519 __ZN9protocols3jd219BOINCJobDistributor2goEN7utility7pointer10owning_ptrINS_5moves5MoverEEE + 41 5 ...etta_1.59_i686-apple-darwin 0x0010f73c __ZN9protocols8abinitio11Broker_mainEv + 812 6 ...etta_1.59_i686-apple-darwin 0x0000402c _main + 2532 7 ...etta_1.59_i686-apple-darwin 0x00001eee __start + 216 8 ...etta_1.59_i686-apple-darwin 0x00001e15 start + 41
24) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4773) Posted 15 Apr 2009 by svincent Post: These 3 tasks, all named broker_lb_test2_hb*, failed on Mac after apparent successful completion due to some file error. 1421321 1421322 1421323 </stderr_txt> <message> <file_xfer_error> <file_name>broker_lb_test2_hb_t363__IGNORE_THE_REST_9214_1_0_0</file_name> <error_code>-161</error_code> </file_xfer_error>
25) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4760) Posted 27 Mar 2009 by svincent Post: Another unzipping issue with workunit 1223005 on Mac Unpacking zip data: ../../projects/ralph.bakerlab.org/minirosetta_database_rev26003.zip Unpacking WU data ... Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8_el_chosen.foldcst_chunk_general_cf.t325_.mtyka.boinc_files.zip Setting database description ... Setting up checkpointing ... Setting up folding (abrelax) ... ERROR: ERROR: FragmentIO: could not open file aa9mer.1_3.gz ERROR:: Exit from: src/core/fragment/FragmentIO.cc line: 245 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]>
26) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4759) Posted 27 Mar 2009 by svincent Post: This workunit 1223308 gave a Validate Error on Mac: it claimed to generate 99 decoys from 99 attempts in 12 minutes. Seem unlikely. The end of stderr output Starting work on structure: _1UFBA_5_00097 Starting work on structure: _1UFBA_5_00098 Starting work on structure: _1UFBA_5_00099 ====================================================== DONE :: 1 starting structures 782.2 cpu seconds This process generated 99 decoys from 99 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt>
27) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4755) Posted 24 Mar 2009 by svincent Post: More problems on Mac O S X 10.4.11 WU's 1376869,1376870,1376871 failed: see below ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 137 fold_tree nres: 156589050 ERROR:: Exit from: src/core/conformation/Conformation.cc line: 224 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt>
28) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4745) Posted 18 Mar 2009 by svincent Post: Just has a bunch of WU's fail at the start (Mac OS X 10.4.11) all in the same way: sample output below. 1213821 1213853 1213852 1213701 1213693 1213692 1213677 ERROR: [ERROR] Unable to open constraints file: t297_.cst.best.multi ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 330 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish
29) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4742) Posted 17 Mar 2009 by svincent Post: A couple of recent compute errors on Mac OS X 10.4.11 Workunit 1210811 ERROR: Cannot open PDB file "1a17_201.pdb" ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 179 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish Workunit 1210764 RROR: Cannot open PDB file "1ad6_197.pdb" ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 179 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish
30) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4720) Posted 3 Mar 2009 by svincent Post: I've had 4 workunits on Mac OS X 10.4.11 that all failed after apparent successful completion </stderr_txt> <message> <file_xfer_error> <file_name>homobench_natrelax_t312__8094_1_1_0</file_name> <error_code>-161</error_code> </file_xfer_error> Workunit ID's 1170292 1170291 1170290 1170289 It appears in each case, that they had previously been sent to a Windows machine where they failed (as noted by Paul Buck) in the manner shown below, but at the start, not at the end: ERROR: ( vol_a.length() == 2 ) && ( std::isalpha( vol_a[ 0 ] ) ) && ( vol_a[ 1 ] == ':' ) ERROR:: Exit from: ....srcutilityfileFileName.cc line: 41 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish
31) Message boards : RALPH@home bug list : minirosetta v1.55 bug thread (Message 4640) Posted 1 Feb 2009 by svincent Post: I'm seeing the same quirk in progress times that robertmiles and others have already reported. I've got a bunch of tasks with names of the form csttest_1_8_nativecst_harm*, all of which, under Mac OS X 10.4.11, are supposed to take 1 hour approximately to complete. What I'm seeing is that, after say 45 minutes, progress is apparently only 15% complete and there is 1:20:00 left. It's stepping very slowly at this point in a stage called MoverBase+Minimization. Nevertheless the tasks complete in about one hour as they're supposed to.
32) Message boards : RALPH@home bug list : minirosetta v1.55 bug thread (Message 4613) Posted 30 Jan 2009 by svincent Post: Task: 1283328 Workunit: 1117100 Name: testD_cc_1_8_nocst4_hb_t360__IGNORE_THE_REST_2DO9A_7_7074_1_1 OS: Mac OS X 10.4.11 failed at initialization <core_client_version>6.2.18</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> BOINC:: Initializing ... ok. [2009- 1-30 7: 3:49:] :: 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 core... Initializing options.... ok ERROR: Unique best command line context option match not found for -user_tag </stderr_txt> ] (edited for readabilty)
33) Message boards : RALPH@home bug list : Bug Reports for Minirosetta v1.39 (Message 4322) Posted 29 Oct 2008 by svincent Post: Workunit 1035370. Mac OS X 10.4.11 In the Boinc Manager Tasks window the Progress field is stuck permanently at 0% and the CPU time keeps resetting to 0 every 6 minutes or so. In the graphics window : a) the model value is 0. b) The step size is incrementing normally and the graphics look OK. c) As in the Boinc manager window, the % complete field is stuck at 0 and the CPU time resets. d) When the CPU time is reset, the graphics window closes itself.
34) Message boards : RALPH@home bug list : Bug Reports for Rosetta Mini Versions 1.+ (Message 3858) Posted 8 Apr 2008 by svincent Post: Probably not too serious but on the Mac version ( OSX 10.4.11 ) with Mini 1.10 there's a problem with the menu bar. It flashes briefly with some text when you do Show Graphics, then the menu bar goes blank apart from the blue Apple Icon at the left.

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