Mini Rosetta 3.45

Author	Message
Mad_Max Send message Joined: 31 Dec 09 Posts: 209 Credit: 25,983,645 RAC: 14,904	Message 74778 - Posted: 24 Dec 2012, 16:53:30 UTC Last modified: 24 Dec 2012, 16:54:29 UTC Many of CDPK_aa_... WUs in addition to gpaphics app and checkpoints problems fails at start with "ERROR: unrecognized atom_type_name COO" error. Examples (from 3 different computers): CDPK_aa_PfCDPK4_3IGOA_SAVE_ALL_OUT_IGNORE_THE_REST_69298_33_0 CDPK_aa_CpCDPK1_3UPXA_SAVE_ALL_OUT_IGNORE_THE_REST_69197_36_0 CDPK_aa_CpCDPK1_3IGOA_SAVE_ALL_OUT_IGNORE_THE_REST_69178_250_0 CDPK_aa_TgCDPK1_3UPXA_SAVE_ALL_OUT_IGNORE_THE_REST_69407_139_1 ID: 74778 · Rating: 0 · rate: / Reply Quote

P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0	Message 74785 - Posted: 26 Dec 2012, 1:52:18 UTC This one failed after 3sec, not for the first time. CDPK_aa_TgCDPK1_C77Y_3V51A_SAVE_ALL_OUT_IGNORE_THE_REST_69353_111_1 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=501624408 Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev52077.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/input_CDPK_aa_TgCDPK1_C77Y_3V51A_yfsong.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. ERROR: unrecognized atom_type_name Cl ERROR:: Exit from: src/core/chemical/AtomTypeSet.hh line: 110 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ID: 74785 · Rating: 0 · rate: / Reply Quote

P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0	Message 74793 - Posted: 27 Dec 2012, 4:55:21 UTC Another one failed after 4sec. CDPK_aa_EtCDPK_3K21A_SAVE_ALL_OUT_IGNORE_THE_REST_69215_126_1 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=501637340 Initialization complete. Setting WU description ... Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev52077.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/input_CDPK_aa_EtCDPK_3K21A_yfsong.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. ERROR: unrecognized atom_type_name COO ERROR:: Exit from: src/core/chemical/AtomTypeSet.hh line: 110 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ID: 74793 · Rating: 0 · rate: / Reply Quote

m_vw Send message Joined: 10 Aug 08 Posts: 1 Credit: 72,142 RAC: 0	Message 74821 - Posted: 2 Jan 2013, 9:07:13 UTC I just deleted 3 units that where restarting everytime I rebooted my pc.... ID: 74821 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,617,398 RAC: 9,268	Message 74833 - Posted: 3 Jan 2013, 13:10:35 UTC I hope these problems will be fixed with a new version. And, please, test it LARGELY on Ralph, before putting them on Rosetta! ID: 74833 · Rating: 0 · rate: / Reply Quote

P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0	Message 74836 - Posted: 4 Jan 2013, 6:53:02 UTC These buggy tasks are back, giving validate errors. lr_ab_bench_3pu6A_SAVE_ALL_OUT_IGNORE_THE_REST_58289_526_0 # cpu_run_time_pref: 21600 ====================================================== 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 ID: 74836 · Rating: 0 · rate: / Reply Quote

P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0	Message 74863 - Posted: 8 Jan 2013, 6:59:31 UTC Had two of these fail after about 30min, with same type of error. TOR_aa_hybrid_ https://boinc.bakerlab.org/rosetta/workunit.php?wuid=504112775 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=504097935 # cpu_run_time_pref: 21600 SIGSEGV: segmentation violation Stack trace (15 frames): [0xafed447] [0xf778b400] [0xa9ef725] [0xaa5e0b0] [0x88f5846] [0x88feb1d] [0x866dce3] [0x97b619f] [0x97bde49] [0x9979352] [0x99d8ed5] [0x99d6705] [0x80547cc] [0xb07d7e8] [0x8048131] Exiting... </stderr_txt> ]]> ID: 74863 · Rating: 0 · rate: / Reply Quote

Mad_Max Send message Joined: 31 Dec 09 Posts: 209 Credit: 25,983,645 RAC: 14,904	Message 74872 - Posted: 9 Jan 2013, 19:12:49 UTC In all TOR_aa_hybrid_ WUs graphics app (or screesaver app) not working too. Same as on CDPK_aa_ and endo_aa_ WUs. ID: 74872 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,617,398 RAC: 9,268	Message 74878 - Posted: 10 Jan 2013, 15:59:28 UTC - in response to Message 74872. In all TOR_aa_hybrid_ WUs graphics app (or screesaver app) not working too. Same here! ID: 74878 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,617,398 RAC: 9,268	Message 74894 - Posted: 15 Jan 2013, 10:38:02 UTC - in response to Message 74872. In all TOR_aa_hybrid_ WUs graphics app (or screesaver app) not working too. Same as on CDPK_aa_ and endo_aa_ WUs. Same on CDPK_ab_hybrid_ wus (and problems with checkpoint) ID: 74894 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,617,398 RAC: 9,268	Message 74897 - Posted: 15 Jan 2013, 17:08:13 UTC Errors on 556368688 and 556368687 ERROR: unrecognized atom_type_name S ERROR:: Exit from: C:Usersboincsrcrosetta_sourcesrccore/chemical/AtomTypeSet.hh line: 110 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish ID: 74897 · Rating: 0 · rate: / Reply Quote

Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0	Message 74901 - Posted: 15 Jan 2013, 22:20:32 UTC - in response to Message 74897. Errors on 556368688 and 556368687 ERROR: unrecognized atom_type_name S ERROR:: Exit from: C:Usersboincsrcrosetta_sourcesrccore/chemical/AtomTypeSet.hh line: 110 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish Same here on all 3 tasks of this type ID: 74901 · Rating: 0 · rate: / Reply Quote

frederick corse Send message Joined: 7 Oct 05 Posts: 10 Credit: 1,545,999 RAC: 0	Message 74903 - Posted: 16 Jan 2013, 0:04:35 UTC Last modified: 16 Jan 2013, 0:05:10 UTC HELLO I GOT SOME CDPK_ab_hybrid__35575.3mwua.rm-1-101_001 CDPk.ab.hybrid_35577.3mwua.rm-1-101-001 CDPK.ab.hybrid/.3557.3mwua.rm-1-121-0271 they fail at startup same failures as the others . Got another one CDPK_ab_hybrid_35584.3mwua.1245 it ran successful with 2 decoys ID: 74903 · Rating: 0 · rate: / Reply Quote

TJ Send message Joined: 29 Mar 09 Posts: 127 Credit: 4,799,890 RAC: 0	Message 74904 - Posted: 16 Jan 2013, 0:08:13 UTC Indeed all the CDPK_ab_hybrid's I got today are all error out, computation error. When hitting the "Show graphics" button, a black window appears and disappears immediately again. Greetings, TJ. ID: 74904 · Rating: 0 · rate: / Reply Quote

P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0	Message 74906 - Posted: 16 Jan 2013, 5:30:59 UTC This failed after 3sec. CDPK_ab_hybrid_35577.3MWUA.1219_0049_SAVE_ALL_OUT_IGNORE_THE_REST_71159_107_1 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=505597218 Setting WU description ... Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev52077.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/input_CDPK_ab_hybrid_35577.3MWUA.1219_0049_yfsong.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. ERROR: unrecognized atom_type_name F ERROR:: Exit from: src/core/chemical/AtomTypeSet.hh line: 110 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]> ID: 74906 · Rating: 0 · rate: / Reply Quote

frederick corse Send message Joined: 7 Oct 05 Posts: 10 Credit: 1,545,999 RAC: 0	Message 74932 - Posted: 19 Jan 2013, 6:12:41 UTC Hello I got 10 rb_01_18_36313_68791 three of them started up and they failed with error:atom tree:torsion_angle_dof_id_angle range error for message _ ID: 74932 · Rating: 0 · rate: / Reply Quote

P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0	Message 74975 - Posted: 25 Jan 2013, 7:23:48 UTC This failed big time after over 10hrs running, this is just some of it the error goes on for pages please fix/check these tasks before releasing them. rant// I for one am going to abort all of these i get from now on, not going to waste cpu time on them. //end. thanks. hyb_ba_bench_02_3slkB_SAVE_ALL_OUT_IGNORE_THE_REST_72022_836_0 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=507038971 Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 21600 BOINC:: CPU time: 36267.6s, 14400s + 21600s[2013- 1-25 17:59: 7:] :: 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 ====================================================== DONE :: 1 starting structures 36267.6 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== called boinc_finish * glibc detected * ../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.45_x86_64-pc-linux-gnu: double free or corruption (out): 0xcbd00018 *** ======= Backtrace: ========= ID: 74975 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,617,398 RAC: 9,268	Message 74978 - Posted: 25 Jan 2013, 14:29:24 UTC - in response to Message 74975. Last modified: 25 Jan 2013, 15:16:09 UTC hyb_ba_bench_02_3slkB_SAVE_ALL_OUT_IGNORE_THE_REST_72022_836_0 hyb_ba_ wus are nightmares! ID: 74978 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,617,398 RAC: 9,268	Message 74979 - Posted: 25 Jan 2013, 15:16:52 UTC 558342604 ERROR: unrecognized atom_type_name S ERROR:: Exit from: C:Usersboincsrcrosetta_sourcesrccore/chemical/AtomTypeSet.hh line: 110 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish ID: 74979 · Rating: 0 · rate: / Reply Quote

dcdc Send message Joined: 3 Nov 05 Posts: 1831 Credit: 119,617,765 RAC: 11,361	Message 74989 - Posted: 26 Jan 2013, 20:00:17 UTC Last modified: 26 Jan 2013, 20:00:54 UTC Hi All Has everyone seen the post by David Kim requesting debug information regarding the apparent nVidia bug here?: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=6177&nowrap=true#74982 Danny ID: 74989 · Rating: 0 · rate: / Reply Quote