minirosetta 1.80

Author	Message
Yifan Song Send message Joined: 18 May 09 Posts: 13 Credit: 0 RAC: 0	Message 4848 - Posted: 20 Jun 2009, 4:49:32 UTC update on protein-protein docking protocols new rotamer library for test ID: 4848 · Reply Quote

Bernd Vogler Send message Joined: 2 Mar 09 Posts: 1 Credit: 10,396 RAC: 0	Message 4849 - Posted: 20 Jun 2009, 12:02:50 UTC Crunched 4 WUs with Ubuntu 9.04 (32-bit). Everything is O.K. ID: 4849 · Reply Quote

Saenger Send message Joined: 28 Feb 06 Posts: 13 Credit: 67,395 RAC: 0	Message 4851 - Posted: 24 Jun 2009, 17:20:44 UTC Most ran fine, but the last one errored out with this stderr: <core_client_version>6.4.5</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> [2009- 6-24 12:37: 2:] :: BOINC:: Initializing ... ok. [2009- 6-24 12:37: 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_rev30680.zip Unpacking WU data ... Unpacking data: ../../projects/ralph.bakerlab.org/real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.boinc_files.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. ERROR: choice != 0 ERROR:: Exit from: src/protocols/jd2/ShuffleJobDistributor.cc line: 83 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]> This are the messages for the errored WU: Mi 24 Jun 2009 12:36:21 CEST\|ralph@home\|Sending scheduler request: To fetch work. Requesting 4004 seconds of work, reporting 0 completed tasks Mi 24 Jun 2009 12:36:27 CEST\|ralph@home\|Scheduler request completed: got 1 new tasks Mi 24 Jun 2009 12:36:29 CEST\|ralph@home\|Started download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.flags.boinc Mi 24 Jun 2009 12:36:29 CEST\|ralph@home\|Started download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.boinc_files.zip Mi 24 Jun 2009 12:36:30 CEST\|ralph@home\|Finished download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.flags.boinc Mi 24 Jun 2009 12:37:00 CEST\|ralph@home\|Finished download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.boinc_files.zip Mi 24 Jun 2009 12:37:01 CEST\|ralph@home\|Starting real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 Mi 24 Jun 2009 12:37:01 CEST\|ralph@home\|Starting task real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 using minirosetta version 180 Mi 24 Jun 2009 12:37:16 CEST\|ralph@home\|Computation for task real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 finished Mi 24 Jun 2009 12:37:16 CEST\|ralph@home\|Output file real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1_0 for task real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 absent Mi 24 Jun 2009 12:40:32 CEST\|ralph@home\|Sending scheduler request: To fetch work. Requesting 4004 seconds of work, reporting 1 completed tasks Mi 24 Jun 2009 12:40:37 CEST\|ralph@home\|Scheduler request completed: got 0 new tasks My computer ist this. (ubuntu64 on C2Q) Grüße vom Sänger ID: 4851 · Reply Quote

Snagletooth Send message Joined: 4 May 07 Posts: 67 Credit: 134,427 RAC: 0	Message 4852 - Posted: 1 Jul 2009, 2:06:17 UTC Couple of quick errors: BOINC_ABRELAX_1itf_CS_DISTEST_SAVE_ALL_OUT_11247_4_0 ERROR: in::file::boinc_wu_zip /work/rvernon/disulfides/TARGETS/zipfiles/zipfile.1itf.cs.set1.zip does not exist! ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 114 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish BOINC_ABRELAX_1ry3_NN_DISCONTROL_SAVE_ALL_OUT_11248_9_1 ERROR: in::file::boinc_wu_zip /work/rvernon/disulfides/TARGETS/zipfiles/zipfile.1ry3.cs.set1.zip does not exist! ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 114 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish Snags ID: 4852 · Reply Quote

AdeB Send message Joined: 22 Dec 07 Posts: 61 Credit: 161,367 RAC: 0	Message 4853 - Posted: 1 Jul 2009, 15:30:47 UTC - in response to Message 4852. same here: task 1523280 ERROR: in::file::boinc_wu_zip /work/rvernon/disulfides/TARGETS/zipfiles/zipfile.1yl2.cs.set1.zip does not exist! ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 114 BOINC:: Error reading and gzipping output datafile: default.out AdeB ID: 4853 · Reply Quote

lazypug Send message Joined: 15 Jun 08 Posts: 2 Credit: 14,214 RAC: 0	Message 4854 - Posted: 4 Jul 2009, 19:38:35 UTC Last modified: 4 Jul 2009, 20:02:04 UTC Fri 03 Jul 2009 12:09:05 AM EDT\|ralph@home\|Starting 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 Fri 03 Jul 2009 12:09:09 AM EDT\|ralph@home\|Starting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180 Fri 03 Jul 2009 12:12:17 AM EDT\|ralph@home\|Restarting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180 Fri 03 Jul 2009 12:18:33 AM EDT\|ralph@home\|Restarting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180 Fri 03 Jul 2009 12:21:39 AM EDT\|ralph@home\|Restarting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180 This wu kept restarting untill I caught it at Sat 04 Jul 2009 03:14:04 PM EDT\|ralph@home\|Restarting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180 39 hours+ Task ID 1524289 Name 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 Workunit 1350593 Created 30 Jun 2009 23:52:34 UTC Sent 30 Jun 2009 23:59:02 UTC Received 4 Jul 2009 19:20:18 UTC Server state Over Outcome Client error Client state Aborted by user Exit status -197 (0xffffffffffffff3b) Computer ID 18184 Report deadline 4 Jul 2009 23:59:02 UTC CPU time 0 stderr out <core_client_version>6.2.18</core_client_version> <![CDATA[ <message> aborted by user </message> ]]> Validate state Invalid Claimed credit 0 Granted credit 0 application version 1.80 (the next wu did the same thing. rebooted computer and it now wu's working fine) ID: 4854 · Reply Quote

Tim Send message Joined: 5 Apr 08 Posts: 5 Credit: 138,356 RAC: 0	Message 4855 - Posted: 8 Jul 2009, 10:16:01 UTC Aborted picker-L1-sssim-1fkbA_11358_5 after it had run for 29 hours with 49.15% complete. All other similar tasks i ran lasted <4hrs. Needed to free up that core for a Rosetta task :) ID: 4855 · Reply Quote

Snagletooth Send message Joined: 4 May 07 Posts: 67 Credit: 134,427 RAC: 0	Message 4858 - Posted: 9 Jul 2009, 9:11:51 UTC 2 more quick errors about 12 minutes in: frb_0_8__rnd2_aln_list_mike_chosen_bestaln.alns.combined.csts_hb_t362__IGNORE_THE_REST_1Z54A_2_11448_1_0 frb_0_8__rnd2_aln_list_mike_chosen_bestaln.alns.combined.csts_hb_t362__IGNORE_THE_REST_1NJKA_10_11448_1_0 Hbond tripped: [2009- 7- 9 2:41:29:] interpolate rotamers bin out of range: MET_p:NtermProteinFull 0 nan -60.8264 -60.9057 -68.7799 27 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 Snags ID: 4858 · Reply Quote

Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0	Message 4859 - Posted: 9 Jul 2009, 12:11:11 UTC Just had two WUs run for over 10 hours for 1 decoy, my preferences are set for 6 hours. They both wound down to 9 minutes 54 seconds left and sat there getting to 98.38% or thereabouts before failing and granting zero credit. This problem has happened before but I can't find the version that had this problem. See this result and this result both had the following error <core_client_version>5.10.21</core_client_version> <![CDATA[ <stderr_txt> [2009- 7- 9 11:36:19:] :: BOINC:: Initializing ... ok. [2009- 7- 9 11:36:19:] :: 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_rev30680.zip Unpacking WU data ... Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8__rnd2_mike_chosen.intersection_new.csts.foldcst_chunk_general_cf.t286_.mtyka.boinc_files.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... Setting up folding (abrelax) ... Beginning folding (abrelax) ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Starting work on structure: _1BWPA_7_00001 # cpu_run_time_pref: 21600 Hbond tripped: [2009- 7- 9 12: 7:30:] BOINC:: CPU time: 36557.3s, 14400s + 21600s[2009- 7- 9 21:47: 1:] :: BOINC Output exists: default.out.gz InternalDecoyCount: 0 (GZ) ====================================================== DONE :: 1 starting structures 36557.3 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== called boinc_finish </stderr_txt> <message> <file_xfer_error> <file_name>frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t286__IGNORE_THE_REST_1BWPA_7_11514_1_0_0</file_name> <error_code>-161</error_code> </file_xfer_error> ID: 4859 · Reply Quote

nenym Send message Joined: 16 Jan 09 Posts: 14 Credit: 1,007,003 RAC: 0	Message 4861 - Posted: 10 Jul 2009, 9:38:19 UTC Last modified: 10 Jul 2009, 9:47:44 UTC That frb_0_8__rnd2_aln_list_within_4.alns.combined.csts_hb_t293__IGNORE_THE_REST_1WS6A_14_11496_1_0 erroed out. <![CDATA[ <message> Maximum disk usage exceeded </message> <stderr_txt> . . . I have no problem with disk space (aviable for Boinc 67 GB). The same that frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t331__IGNORE_THE_REST_1DNLA_12_11526_1_0 task. Both Win XP x86. ID: 4861 · Reply Quote

Tim Send message Joined: 5 Apr 08 Posts: 5 Credit: 138,356 RAC: 0	Message 4862 - Posted: 10 Jul 2009, 11:51:27 UTC This task error'd lr11_seq_score12_rlbd_1thx_IGNORE_THE_REST_DECOY_11409_1_1 ERROR: ct == final_atoms ERROR:: Exit from: ....srccorescoringrms_util.cc line: 368 BOINC:: Error reading and gzipping output datafile: default.out ID: 4862 · Reply Quote

Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0	Message 4863 - Posted: 10 Jul 2009, 12:31:01 UTC - in response to Message 4859. Just had two WUs run for over 10 hours for 1 decoy, my preferences are set for 6 hours. They both wound down to 9 minutes 54 seconds left and sat there getting to 98.38% or thereabouts before failing and granting zero credit. This problem has happened before but I can't find the version that had this problem. See this result and this result both had the following error <core_client_version>5.10.21</core_client_version> <![CDATA[ <stderr_txt> [2009- 7- 9 11:36:19:] :: BOINC:: Initializing ... ok. [2009- 7- 9 11:36:19:] :: 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_rev30680.zip Unpacking WU data ... Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8__rnd2_mike_chosen.intersection_new.csts.foldcst_chunk_general_cf.t286_.mtyka.boinc_files.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... Setting up folding (abrelax) ... Beginning folding (abrelax) ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Starting work on structure: _1BWPA_7_00001 # cpu_run_time_pref: 21600 Hbond tripped: [2009- 7- 9 12: 7:30:] BOINC:: CPU time: 36557.3s, 14400s + 21600s[2009- 7- 9 21:47: 1:] :: BOINC Output exists: default.out.gz InternalDecoyCount: 0 (GZ) ====================================================== DONE :: 1 starting structures 36557.3 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== called boinc_finish </stderr_txt> <message> <file_xfer_error> <file_name>frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t286__IGNORE_THE_REST_1BWPA_7_11514_1_0_0</file_name> <error_code>-161</error_code> </file_xfer_error> Have had another with exactly the same problem on a different machine, same WU type, frb_0_8_rnd2, also ran for 10 hours before failing (preference is 6 hours) after 1 decoy. This Result ID: 4863 · Reply Quote

Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0	Message 4864 - Posted: 11 Jul 2009, 8:16:18 UTC - in response to Message 4863. Just had two WUs run for over 10 hours for 1 decoy, my preferences are set for 6 hours. They both wound down to 9 minutes 54 seconds left and sat there getting to 98.38% or thereabouts before failing and granting zero credit. This problem has happened before but I can't find the version that had this problem. See this result and this result both had the following error <core_client_version>5.10.21</core_client_version> <![CDATA[ <stderr_txt> [2009- 7- 9 11:36:19:] :: BOINC:: Initializing ... ok. [2009- 7- 9 11:36:19:] :: 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_rev30680.zip Unpacking WU data ... Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8__rnd2_mike_chosen.intersection_new.csts.foldcst_chunk_general_cf.t286_.mtyka.boinc_files.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... Setting up folding (abrelax) ... Beginning folding (abrelax) ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Starting work on structure: _1BWPA_7_00001 # cpu_run_time_pref: 21600 Hbond tripped: [2009- 7- 9 12: 7:30:] BOINC:: CPU time: 36557.3s, 14400s + 21600s[2009- 7- 9 21:47: 1:] :: BOINC Output exists: default.out.gz InternalDecoyCount: 0 (GZ) ====================================================== DONE :: 1 starting structures 36557.3 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== called boinc_finish </stderr_txt> <message> <file_xfer_error> <file_name>frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t286__IGNORE_THE_REST_1BWPA_7_11514_1_0_0</file_name> <error_code>-161</error_code> </file_xfer_error> Have had another with exactly the same problem on a different machine, same WU type, frb_0_8_rnd2, also ran for 10 hours before failing (preference is 6 hours) after 1 decoy. This Result Still another with the same Error, ran for over 10 Hours then errored out, it was another frb_0_8_rnd2 WU See This Result also I aborted another Two work units after they had gone past 6 1/2 hours and only at 66% See This Result and This Result So that is over 62 Hours wasted on 6 WUs, as each only do 1 decoy and then error out with no credit given. ID: 4864 · Reply Quote

Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0	Message 4867 - Posted: 12 Jul 2009, 8:17:50 UTC - in response to Message 4864. Last modified: 12 Jul 2009, 8:31:22 UTC And here is another that ran to 10 hours and then failed after completing 1 decoy See here It's a pity these 10 hour WUs are getting zero credit. ID: 4867 · Reply Quote

Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0	Message 4869 - Posted: 12 Jul 2009, 8:30:20 UTC - in response to Message 4864. Just had two WUs run for over 10 hours for 1 decoy, my preferences are set for 6 hours. They both wound down to 9 minutes 54 seconds left and sat there getting to 98.38% or thereabouts before failing and granting zero credit. This problem has happened before but I can't find the version that had this problem. See this result and this result both had the following error <core_client_version>5.10.21</core_client_version> <![CDATA[ <stderr_txt> [2009- 7- 9 11:36:19:] :: BOINC:: Initializing ... ok. [2009- 7- 9 11:36:19:] :: 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_rev30680.zip Unpacking WU data ... Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8__rnd2_mike_chosen.intersection_new.csts.foldcst_chunk_general_cf.t286_.mtyka.boinc_files.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... Setting up folding (abrelax) ... Beginning folding (abrelax) ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Starting work on structure: _1BWPA_7_00001 # cpu_run_time_pref: 21600 Hbond tripped: [2009- 7- 9 12: 7:30:] BOINC:: CPU time: 36557.3s, 14400s + 21600s[2009- 7- 9 21:47: 1:] :: BOINC Output exists: default.out.gz InternalDecoyCount: 0 (GZ) ====================================================== DONE :: 1 starting structures 36557.3 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== called boinc_finish </stderr_txt> <message> <file_xfer_error> <file_name>frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t286__IGNORE_THE_REST_1BWPA_7_11514_1_0_0</file_name> <error_code>-161</error_code> </file_xfer_error> Have had another with exactly the same problem on a different machine, same WU type, frb_0_8_rnd2, also ran for 10 hours before failing (preference is 6 hours) after 1 decoy. This Result Still another with the same Error, ran for over 10 Hours then errored out, it was another frb_0_8_rnd2 WU See This Result also I aborted another Two work units after they had gone past 6 1/2 hours and only at 66% See This Result and This Result So that is over 62 Hours wasted on 6 WUs, as each only do 1 decoy and then error out with no credit given. Hope I fixed up all the links as I forgot the // ID: 4869 · Reply Quote

Tim Send message Joined: 5 Apr 08 Posts: 5 Credit: 138,356 RAC: 0	Message 4871 - Posted: 13 Jul 2009, 10:26:53 UTC This task ended with ERROR: ct == final_atoms ERROR:: Exit from: ....srccorescoringrms_util.cc line: 368 BOINC:: Error reading and gzipping output datafile: default.out ID: 4871 · Reply Quote