Posts by Ian

1) Message boards : Number crunching : minirosetta 2.17 (Message 70227) Posted 2 May 2011 by Ian_D Post: When I've seen similar error messages, the Norton Internet Security antivirus program was always running in the background (no good way to shut it off other than uninstalling it). Not sure if that's also why I often see the BOINC Manager program lose contact with the rest of BOINC. Do the other people seeing this problem also use Norton Internet Security? Nope, will NOT have Norton on any of my machines.
2) Message boards : Number crunching : minirosetta 2.17 (Message 70214) Posted 2 May 2011 by Ian_D Post: Think I may have "solved" this one and as you so rightly said, it looks like it was a hardware problem. Looking at System info messages I've been getting a lot of intermittent paging problems to one of the hard disks aroud the times of the Reason: Access Violation (0xc0000005) failures Cheers for the steer ! Ian
3) Message boards : Number crunching : minirosetta 2.17 (Message 70205) Posted 1 May 2011 by Ian_D Post: Cheers Greg ! Well guess we will have to wait for the Grad student to wake up and come on duty to fully address you question. I found a little something from the Wiki of Boinc that addresses this issue: Why am I getting a 'Reason: Access Violation (0xc0000005) error'? 1. Change your preferences to leave Rosetta@Home in memory, General Preferences Log in (at General Preferences if you're not already) -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button; also, remember to "update" the BOINC Client Software so that the changes are downloaded. Open the BOINC Manager and select the "Projects Tab", left-click on "Rosetta@home" to select the project, and click the "Update" Button. 2. An error occurred somewhere on the computer, it could have been the BOINC Client Software or the Rosetta@Home Science Application or any programme that your computer was doing at the time. This is not a Rosetta@Home specific error, as far as I am aware it happens, on occasion, in all of the BOINC Powered Projects with all of the Science Applications. Keep Rosetta@Home in memory and ignore this problem if it's not getting out of hand. I'm going to leave it at that....wait for the big experts Yep, task completed after I restarted BOINC - put into snooze , then shutdown and started (in that order) ?? Despite the heartbeat issues, you did complete the task: DONE :: 56 starting structures 14704.5 cpu seconds This process generated 56 decoys from 56 attempts So what's with the following No heartbeat from core client for 30 sec - exiting messages ? Job had been sitting doing NOTHING for 13.5 hours (???) which I noticed and subsequently restarted BOINC. The Windows XP PC concerned is using nVidia onboard graphics (no idea if this has any bearing) http://boinc.bakerlab.org/rosetta/result.php?resultid=419011804 <core_client_version>6.10.58</core_client_version> <![CDATA[ <stderr_txt> [2011- 4-30 2:38:23:] :: BOINC:: Initializing ... ok. [2011- 4-30 2:38:23:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 Unhandled Exception Detected... - Unhandled Exception Record - Reason: Access Violation (0xc0000005) at address 0x7C910F1E read attempt to address 0x00000001 Engaging BOINC Windows Runtime Debugger... [2011- 4-30 21:39:36:] :: BOINC:: Initializing ... ok. [2011- 4-30 21:39:36:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage1 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage2 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage3 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage4_kk_1 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage4_kk_2 ... success! # cpu_run_time_pref: 28800 No heartbeat from core client for 30 sec - exiting [2011- 4-30 22: 6:36:] :: BOINC:: Initializing ... ok. [2011- 4-30 22: 6:36:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage1 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage2 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage3 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage4_kk_1 ... success! # cpu_run_time_pref: 28800 No heartbeat from core client for 30 sec - exiting [2011- 4-30 22: 7:11:] :: BOINC:: Initializing ... ok. [2011- 4-30 22: 7:11:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage1 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage2 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage3 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage4_kk_1 ... success! # cpu_run_time_pref: 28800 Continuing computation from checkpoint: chk_S_00052_FastRelax__chk1_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk2_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk3_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk4_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk5_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk6_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk7_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk8_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk9_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk10_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk11_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk12_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk13_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk14_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk15_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk16_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk17_fa ... success! No heartbeat from core client for 30 sec - exiting [2011- 4-30 22: 8:47:] :: BOINC:: Initializing ... ok. [2011- 4-30 22: 8:47:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 No heartbeat from core client for 30 sec - exiting [2011- 4-30 22:17:41:] :: BOINC:: Initializing ... ok. [2011- 4-30 22:17:41:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 ====================================================== DONE :: 56 starting structures 14704.5 cpu seconds This process generated 56 decoys from 56 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]>
4) Message boards : Number crunching : minirosetta 2.17 (Message 70198) Posted 1 May 2011 by Ian_D Post: Yep, task completed after I restarted BOINC - put into snooze , then shutdown and started (in that order) ?? Despite the heartbeat issues, you did complete the task: DONE :: 56 starting structures 14704.5 cpu seconds This process generated 56 decoys from 56 attempts So what's with the following No heartbeat from core client for 30 sec - exiting messages ? Job had been sitting doing NOTHING for 13.5 hours (???) which I noticed and subsequently restarted BOINC. The Windows XP PC concerned is using nVidia onboard graphics (no idea if this has any bearing) http://boinc.bakerlab.org/rosetta/result.php?resultid=419011804 <core_client_version>6.10.58</core_client_version> <![CDATA[ <stderr_txt> [2011- 4-30 2:38:23:] :: BOINC:: Initializing ... ok. [2011- 4-30 2:38:23:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 Unhandled Exception Detected... - Unhandled Exception Record - Reason: Access Violation (0xc0000005) at address 0x7C910F1E read attempt to address 0x00000001 Engaging BOINC Windows Runtime Debugger... [2011- 4-30 21:39:36:] :: BOINC:: Initializing ... ok. [2011- 4-30 21:39:36:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage1 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage2 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage3 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage4_kk_1 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage4_kk_2 ... success! # cpu_run_time_pref: 28800 No heartbeat from core client for 30 sec - exiting [2011- 4-30 22: 6:36:] :: BOINC:: Initializing ... ok. [2011- 4-30 22: 6:36:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage1 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage2 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage3 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage4_kk_1 ... success! # cpu_run_time_pref: 28800 No heartbeat from core client for 30 sec - exiting [2011- 4-30 22: 7:11:] :: BOINC:: Initializing ... ok. [2011- 4-30 22: 7:11:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage1 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage2 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage3 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage4_kk_1 ... success! # cpu_run_time_pref: 28800 Continuing computation from checkpoint: chk_S_00052_FastRelax__chk1_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk2_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk3_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk4_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk5_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk6_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk7_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk8_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk9_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk10_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk11_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk12_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk13_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk14_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk15_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk16_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk17_fa ... success! No heartbeat from core client for 30 sec - exiting [2011- 4-30 22: 8:47:] :: BOINC:: Initializing ... ok. [2011- 4-30 22: 8:47:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 No heartbeat from core client for 30 sec - exiting [2011- 4-30 22:17:41:] :: BOINC:: Initializing ... ok. [2011- 4-30 22:17:41:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 ====================================================== DONE :: 56 starting structures 14704.5 cpu seconds This process generated 56 decoys from 56 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]>
5) Message boards : Number crunching : minirosetta 2.17 (Message 70186) Posted 30 Apr 2011 by Ian_D Post: So what's with the following No heartbeat from core client for 30 sec - exiting messages ? Job had been sitting doing NOTHING for 13.5 hours (???) which I noticed and subsequently restarted BOINC. The Windows XP PC concerned is using nVidia onboard graphics (no idea if this has any bearing) http://boinc.bakerlab.org/rosetta/result.php?resultid=419011804 <core_client_version>6.10.58</core_client_version> <![CDATA[ <stderr_txt> [2011- 4-30 2:38:23:] :: BOINC:: Initializing ... ok. [2011- 4-30 2:38:23:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 Unhandled Exception Detected... - Unhandled Exception Record - Reason: Access Violation (0xc0000005) at address 0x7C910F1E read attempt to address 0x00000001 Engaging BOINC Windows Runtime Debugger... [2011- 4-30 21:39:36:] :: BOINC:: Initializing ... ok. [2011- 4-30 21:39:36:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage1 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage2 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage3 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage4_kk_1 ... success! Continuing computation from checkpoint: chk_S_00046_FragmentSampler__stage4_kk_2 ... success! # cpu_run_time_pref: 28800 No heartbeat from core client for 30 sec - exiting [2011- 4-30 22: 6:36:] :: BOINC:: Initializing ... ok. [2011- 4-30 22: 6:36:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage1 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage2 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage3 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage4_kk_1 ... success! # cpu_run_time_pref: 28800 No heartbeat from core client for 30 sec - exiting [2011- 4-30 22: 7:11:] :: BOINC:: Initializing ... ok. [2011- 4-30 22: 7:11:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage1 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage2 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage3 ... success! Continuing computation from checkpoint: chk_S_00052_FragmentSampler__stage4_kk_1 ... success! # cpu_run_time_pref: 28800 Continuing computation from checkpoint: chk_S_00052_FastRelax__chk1_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk2_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk3_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk4_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk5_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk6_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk7_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk8_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk9_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk10_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk11_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk12_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk13_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk14_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk15_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk16_fa ... success! Continuing computation from checkpoint: chk_S_00052_FastRelax__chk17_fa ... success! No heartbeat from core client for 30 sec - exiting [2011- 4-30 22: 8:47:] :: BOINC:: Initializing ... ok. [2011- 4-30 22: 8:47:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 No heartbeat from core client for 30 sec - exiting [2011- 4-30 22:17:41:] :: BOINC:: Initializing ... ok. [2011- 4-30 22:17:41:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev39052.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/casd_sr10_boinc_nmr_control.1ff3B_20_abrelax_cs_frags_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 ====================================================== DONE :: 56 starting structures 14704.5 cpu seconds This process generated 56 decoys from 56 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]>
6) Message boards : Number crunching : Problems with Minirosetta Version 1.64/1.65 (Message 60988) Posted 4 May 2009 by Ian_D Post: 1PTQA_BOINC_MPZN_vanilla_abrelax_9106_12334_1 http://boinc.bakerlab.org/rosetta/result.php?resultid=248349357 <core_client_version>6.6.20</core_client_version> <![CDATA[ <message> Incorrect function. (0x1) - exit code 1 (0x1) </message> <stderr_txt> [2009- 5- 4 0:14:21:] :: BOINC:: Initializing ... ok. [2009- 5- 4 0:14:21:] :: 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 ERROR: Option matching -fragB_size not found in command line top-level context </stderr_txt> ]]>
7) Message boards : Number crunching : Is this a problem or is a bit of tuning requires on my part ? (Message 58680) Posted 8 Jan 2009 by Ian_D Post: http://boinc.bakerlab.org/rosetta/result.php?resultid=219125633 <core_client_version>6.2.15</core_client_version> <![CDATA[ <stderr_txt> semget failure! Cannot create semaphore! # cpu_run_time_pref: 21600 ====================================================== DONE :: 1 starting structures 21380.5 cpu seconds This process generated 10 decoys from 10 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down... called boinc_finish </stderr_txt> ]]>
8) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58565) Posted 6 Jan 2009 by Ian_D Post: <core_client_version>6.2.12</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> # cpu_run_time_pref: 28800 ERROR: phil how did we get here-2? ERROR:: Exit from: src/core/kinematics/AtomTree.cc line: 1378 called boinc_finish </stderr_txt> ]]> You're having a laugh, right ? http://boinc.bakerlab.org/rosetta/result.php?resultid=218842260
9) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58564) Posted 6 Jan 2009 by Ian_D Post: Duplicate post - wow it's slow.....
10) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58562) Posted 6 Jan 2009 by Ian_D Post: Duplicate post
11) Message boards : Number crunching : Predictor of the day (Message 58500) Posted 4 Jan 2009 by Ian_D Post: What gives chaps ? No updated "Predictor of the day" since 30th Nov 2008 ? Something not running ? Cheers
12) Message boards : Number crunching : Report long-running models here (Message 58280) Posted 31 Dec 2008 by Ian_D Post: http://boinc.bakerlab.org/rosetta/workunit.php?wuid=198560045 One whole decoy in 12.6 hrs - nice !! Ubuntu 8.10 on a P4 2.6GHz HT with 512 Mb memory with POEM@home running as well. CPU run time preference set to 8 hrs ("Home" in this case - have now changed to 6 hrs "Work" preference)
13) Message boards : Number crunching : Goodbye Rosetta@home (Message 58264) Posted 30 Dec 2008 by Ian_D Post: Not quite good-bye from me. Have deleted my BOINC "install" (manual download and unzip / chmod / .profile change etc.) and used Synaptic to install BOINC that comes with Intrepid Ibex (Ubuntu 8.10). Have also split my time between Rosetta and POEM in the ratio 2:1. Just want to see if the Computation Errors and SIGSEGVs go away using the Synaptic version of BOINC as it did appear to download a couple of packages that I'd not seen before. Maybe it was just me all along.......let's see shall we........ Cheers
14) Message boards : Number crunching : Report long-running models here (Message 58206) Posted 28 Dec 2008 by Ian_D Post: http://boinc.bakerlab.org/rosetta/result.php?resultid=217459230 <core_client_version>6.2.15</core_client_version> <![CDATA[ <stderr_txt> # cpu_run_time_pref: 14400 # cpu_run_time_pref: 7200 # cpu_run_time_pref: 7200 ******************************************************************** Rosetta is going too long. Watchdog is ending the run! CPU time: 26682.9 seconds. Greater than 3X preferred time: 7200 seconds ******************************************************************** called boinc_finish </stderr_txt> ]]>
15) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58205) Posted 28 Dec 2008 by Ian_D Post: * sigh * http://boinc.bakerlab.org/rosetta/result.php?resultid=217461782 <core_client_version>6.2.15</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63) </message> <stderr_txt> # cpu_run_time_pref: 14400 # cpu_run_time_pref: 7200 # cpu_run_time_pref: 7200 terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc SIGABRT: abort called Stack trace (27 frames): [0x8b979b7] [0x8bc20b0] [0xb7f22420] [0x8c24ca4] [0x8c12c5b] [0x8c10261] [0x8c10296] [0x8c0fe43] [0x8c0f86c] [0x8a88ba5] [0x8559c48] [0x83e8bc3] [0x87f80df] [0x87dc3c7] [0x80de412] [0x80d0686] [0x80d0b2e] [0x80c88b9] [0x80de971] [0x80d7d76] [0x8064271] [0x8117277] [0x8127c00] [0x8129a1a] [0x804b9c8] [0x8c1dbac] [0x8048111] Exiting... </stderr_txt> ]]> and http://boinc.bakerlab.org/rosetta/result.php?resultid=217459230 <core_client_version>6.2.15</core_client_version> <![CDATA[ <stderr_txt> # cpu_run_time_pref: 14400 # cpu_run_time_pref: 7200 # cpu_run_time_pref: 7200 ******************************************************************** Rosetta is going too long. Watchdog is ending the run! CPU time: 26682.9 seconds. Greater than 3X preferred time: 7200 seconds ******************************************************************** called boinc_finish </stderr_txt> ]]>
16) Message boards : Number crunching : Report long-running models here (Message 58196) Posted 28 Dec 2008 by Ian_D Post: http://boinc.bakerlab.org/rosetta/result.php?resultid=217325144 Nearly 16 hrs in when I spotted it and now it reports, after a manual abort, it has done 0 CPU time ?!?!
17) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58194) Posted 28 Dec 2008 by Ian_D Post: http://boinc.bakerlab.org/rosetta/result.php?resultid=217325144 Nearly 16 hrs in when I spotted it and now it reports, after a manual abort, it has done 0 CPU time ?!?!
18) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58183) Posted 27 Dec 2008 by Ian_D Post: After clean runs of memtest86+ 2.10 and prime95 for linux and I can no longer get decent results out of prime95 even though memtest86+ 2.10 will run fine. As you'd most likely expect I'm putting the errors below down to hardware !! Don't know if it's the CPU or more likely the mainboard northbridge. Have a newer CPU on order to rule that out. Have removed said machine from my "farm". Cheers and Happy Christmas and a computational bug free New Year CPU type GenuineIntel Intel(R) Pentium(R) 4 CPU 2.60GHz [Family 15 Model 2 Stepping 9] Number of CPUs 2 Operating System Linux 2.6.24-22-generic process exited with code 193 (0xc1, -63) Stack trace (22 frames): [0x8b979b7] [0x8bc20b0] [0xb7f03420] [0x83c53bc] [0x84356a0] [0x83c4fa3] [0x83ba6f8] [0x85c2f4e] [0x80cf524] [0x80de98f] [0x83376f7] [0x8337100] [0x8243364] [0x82a246c] [0x818e15a] [0x819bae3] [0x819b3aa] [0x8127771] [0x8129a1a] [0x804b9c8] [0x8c1dbac] [0x8048111] http://boinc.bakerlab.org/rosetta/result.php?resultid=215801702 process exited with code 193 (0xc1, -63) SIGSEGV: segmentation violation Stack trace (20 frames): [0x8b979b7] [0x8bc20b0] [0xb7fa5420] [0x83c4fa3] [0x83ba6f8] [0x85c2f4e] [0x80cf1ff] [0x80de98f] [0x83376f7] [0x8337100] [0x8243364] [0x82a246c] [0x818e15a] [0x819bae3] [0x819b3aa] [0x8127771] [0x8129a1a] [0x804b9c8] [0x8c1dbac] [0x8048111] http://boinc.bakerlab.org/rosetta/result.php?resultid=215414530 process exited with code 193 (0xc1, -63) SIGSEGV: segmentation violation Stack trace (23 frames): [0x8b979b7] [0x8bc20b0] [0xb7f48420] [0x8ace23a] [0x84348d3] [0x8ace5f6] [0x8acd739] [0x83b1c55] [0x862a631] [0x83f65af] [0x80cece6] [0x80de98f] [0x82c37e4] [0x82b897a] [0x82c16c1] [0x818d6ee] [0x819bae3] [0x819b3aa] [0x8127771] [0x8129a1a] [0x804b9c8] [0x8c1dbac] [0x8048111] http://boinc.bakerlab.org/rosetta/result.php?resultid=215035006 What's going on with the Rosetta Linux App ? Sometimes it works , sometimes it's duff ? Machine NOT overclocked in the slightest Cheers
19) Message boards : Number crunching : why do tasks check out ok on linux but crash on windows? (Message 58129) Posted 23 Dec 2008 by Ian_D Post: Huh ? Ubuntu - thought that was Linux ! Prime95 and Memtest86+ v2.10 clean several hours run so it's NOT the machine Stop whining about Windows, it's more than just you being affected !
20) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 58118) Posted 22 Dec 2008 by Ian_D Post: wuid=196939593 <core_client_version>6.2.15</core_client_version> <![CDATA[ <message> process got signal 8 </message> <stderr_txt> # cpu_run_time_pref: 7200 ******************************************************************** Rosetta is going too long. Watchdog is ending the run! CPU time: 26914 seconds. Greater than 3X preferred time: 7200 seconds ******************************************************************** called boinc_finish </stderr_txt> ]]>

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