Message boards : Number crunching : Minirosetta 2.00
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P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0 |
The large increase to the executable size could be due to the inclusion of a number of protocols that has been developed over the last 2 years. Those protocols were not able to compile with the boinc build until now. Hi. Does that mean that we Linux folk get to do more of the heavy lifting. ;) L.O.L. ![]() |
P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0 |
Hi. first error with mini 2.00. well sort of. This is an odd one only ran for 3 min's, i don't know what happened. No error in manager. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=269405320 mix_score12_B_rlbd_1ttz__IGNORE_THE_RESTlr13_DECOY_15619_826_0 Over__Validate error__Done__180.24 # cpu_run_time_pref: 14400 ====================================================== DONE :: 1 starting structures 1201 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ![]() |
![]() ![]() Send message Joined: 30 May 06 Posts: 5690 Credit: 5,859,226 RAC: 190 |
Also got my first 2.00 error https://boinc.bakerlab.org/rosetta/result.php?resultid=295408260 lr5_combine_smooth_torsion_it07_A_rlbd_1bm8_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15460_190_2 core_client_version>6.10.17</core_client_version> <![CDATA[ <message> Incorrect function. (0x1) - exit code 1 (0x1) </message> <stderr_txt> [2009-11-12 16:39:46:] :: BOINC:: Initializing ... ok. [2009-11-12 16:39:46:] :: 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 -new_icoor not found in command line top-level context </stderr_txt> ]]> |
![]() Send message Joined: 30 Nov 06 Posts: 6 Credit: 10,836,113 RAC: 0 |
Hi. I got a lot of errors too : lr5_dun08_it04_A_rlbd_4icb_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15799_439_0 <core_client_version>6.10.17</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63) </message> <stderr_txt> [2009-11-12 17:51:35:] :: BOINC:: Initializing ... ok. [2009-11-12 17:51:35:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/yfsong_lr5_dun08_it04_A.zip Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/lr5_4icb.out.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Fullatom mode .. # cpu_run_time_pref: 86400 Fullatom mode .. .. .. .. Fullatom mode .. SIGSEGV: segmentation violation Stack trace (27 frames): [0x9667f13] . . . [0x8048121] Exiting... </stderr_txt> ]]> And also : lr5_dun08_it04_A_rlbd_1ugh_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15799_445_0 <core_client_version>6.10.17</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63) </message> <stderr_txt> [2009-11-12 19:16:30:] :: BOINC:: Initializing ... ok. [2009-11-12 19:16:30:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/yfsong_lr5_dun08_it04_A.zip Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/lr5_1wdv.out.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. Fullatom mode .. # cpu_run_time_pref: 86400 Fullatom mode .. Fullatom mode .. Fullatom mode .. *** glibc detected *** free(): invalid next size (fast): 0xef219138 *** SIGABRT: abort called Stack trace (30 frames): [0x9667f13] . . . [0x8048121] Exiting... </stderr_txt> ]]> Any idea why ? And I got a lr5_dun08 blocked at 0.310% after 24h...I'm gonna cancel it I guess. MyUneo, the Cupid of Services |
Hefto99 Send message Joined: 11 Oct 05 Posts: 5 Credit: 4,182,240 RAC: 218 |
I have got several errors too (on 64-bit Linux): =========== <core_client_version>6.2.15</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63) </message> <stderr_txt> [2009-11-13 13: 7:12:] :: BOINC:: Initializing ... ok. [2009-11-13 13: 7:12:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 *** glibc detected *** corrupted double-linked list: 0x11b99940 *** SIGABRT: abort called Stack trace (23 frames): [0x9667f13] ============ <core_client_version>6.2.15</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63) </message> <stderr_txt> [2009-11-13 13:10: 5:] :: BOINC:: Initializing ... ok. [2009-11-13 13:10: 5:] :: 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/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 28800 *** glibc detected *** free(): invalid next size (normal): 0x11212198 *** SIGABRT: abort called Stack trace (21 frames): [0x9667f13] |
![]() Send message Joined: 30 Nov 06 Posts: 6 Credit: 10,836,113 RAC: 0 |
I got linux 64b too. I guess there is something wrong with our lib...? My second laptop with Linux 64b as well, does not have any error calculation... Do we have to install a particular lib ? Or what is wrong ? Thanks MyUneo, the Cupid of Services |
AMD_is_logical Send message Joined: 20 Dec 05 Posts: 299 Credit: 31,460,681 RAC: 0 |
Had some 3gbm WUs bomb out after 100 seconds or so. This was with 32bit Linux. In some cases the other cruncher returned a successful result (with Windows). https://boinc.bakerlab.org/rosetta/result.php?resultid=295903692 https://boinc.bakerlab.org/rosetta/result.php?resultid=295911236 https://boinc.bakerlab.org/rosetta/result.php?resultid=295912057 https://boinc.bakerlab.org/rosetta/result.php?resultid=295912773 |
Mod.Sense Volunteer moderator Send message Joined: 22 Aug 06 Posts: 4018 Credit: 0 RAC: 0 |
I got linux 64b too. Everything needed downloads with the work unit. It appears some specific tasks are having trouble and that is what this thread is for, to collect the descriptions of those so they can be corrected in future releases. Rosetta Moderator: Mod.Sense |
![]() Send message Joined: 30 Nov 06 Posts: 6 Credit: 10,836,113 RAC: 0 |
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svincent Send message Joined: 30 Dec 05 Posts: 219 Credit: 12,120,035 RAC: 8 |
sel_core_2.0_low50_beta_low200_start0_hb_t286__IGNORE_THE_REST_15751_714_1 Task 295582440 failed on Windows 7. ERROR: res1 != res2 ERROR:: Exit from: ....srccorekinematicsFoldTree.cc line: 2342 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]> |
svincent Send message Joined: 30 Dec 05 Posts: 219 Credit: 12,120,035 RAC: 8 |
mix_score13_C_rlbd_1ttz__IGNORE_THE_RESTlr13_DECOY_15917_345_1 task 296879164 gave a Validate Error on Mac OS X 10.6 after generating one decoy. "Too many error results" according to the Workunit log: it had been sent out once before with a similar result. |
![]() ![]() Send message Joined: 30 May 06 Posts: 5690 Credit: 5,859,226 RAC: 190 |
2 more errors - compute errors https://boinc.bakerlab.org/rosetta/result.php?resultid=297254753 https://boinc.bakerlab.org/rosetta/result.php?resultid=296995752 ERROR: res1 != res2 ERROR:: Exit from: ....srccorekinematicsFoldTree.cc line: 2342 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]> |
svincent Send message Joined: 30 Dec 05 Posts: 219 Credit: 12,120,035 RAC: 8 |
again_sel_core_2.0_low50_beta_low200_nostart_hb_t286__IGNORE_THE_REST_15859_550_1 (task 296161309) failed on Windows 7 ERROR: res1 != res2 ERROR:: Exit from: ....srccorekinematicsFoldTree.cc line: 2342 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]> |
Interboy Send message Joined: 28 Sep 05 Posts: 3 Credit: 730,102 RAC: 0 |
I aborted task "threading_bong_promals_3_hb_t305__IGNORE_THE_REST_16009_335_0" with unhandled exception on task 297355887. |
svincent Send message Joined: 30 Dec 05 Posts: 219 Credit: 12,120,035 RAC: 8 |
A couple more sel_core* tasks failing on Windows 7. Looking at the forum, it seems tasks with names containing t313 are quite prone to failure. sel_core_1.5_low200_beta_low200_nostart_hb_t313__IGNORE_THE_REST_15870_160_0 (task 296161514) sel_core_1.5_low200_beta_low200_nostart_hb_t328__IGNORE_THE_REST_15873_167_0(task 296161959) ERROR: res1 != res2 ERROR:: Exit from: ....srccorekinematicsFoldTree.cc line: 2342 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]> |
Telescope Adrian Send message Joined: 14 Nov 06 Posts: 9 Credit: 1,906,378 RAC: 0 |
Anybody noticed a new "facility" with 2.00 yet ? Run 2 jobs together ( AMD Athlon 64 X 2) and , after a while , one of the jobs goes idle meaning that the system idle process sits at 50% utilisation . Suspending Rosetta , then restarting it makes no difference to this behaviour. I used to see this feature a while ( many months) ago , but it went away I think at about Version 1.97 . Has anyone else this yet ? Best wishes |
![]() ![]() Send message Joined: 16 Oct 05 Posts: 711 Credit: 26,694,507 RAC: 0 |
Anybody noticed a new "facility" with 2.00 yet ? How much RAM do you have? Edit: I figured it myself (2GB). I don't know what the problem could be... you could've given Rosetta too little available RAM in your setting, maybe? ![]() |
Telescope Adrian Send message Joined: 14 Nov 06 Posts: 9 Credit: 1,906,378 RAC: 0 |
Anybody noticed a new "facility" with 2.00 yet ? Hello there . It's not a problem of store availability since I allow BOINC to use 75% of my available real store when I'm running projects . ( Virtual storage systems don't work like you seem to think ! ) . On this machine I usually have other jobs from Rosetta and Spinhenge queuing to run , but when the Rosetta job goes " idle " , no other job starts up to take its engine time up , so its nothing to do with OCP time utilisation either .As I said earlier , this facility used to show itself earlier this year , but went away at about Rosetta 1.97 . The workunit seems just to sit waiting for something , but I know not what ! Regards |
Mod.Sense Volunteer moderator Send message Joined: 22 Aug 06 Posts: 4018 Credit: 0 RAC: 0 |
Adrian, Rosetta does not decide what work runs at what time, BOINC decides this. It does this based on your preferences. Since BOINC does not have a configuration setting called "real store", you haven't really told us much about your settings. Even if you were indicating memory, you didn't tells us if this was the setting for when the machine is in use, or when it is idle. The main thing to check is... what does BOINC say the reason for not running it is? The task's status or the messages should indicate what's going on. Since you seem familiar with the Windows task manager, another idea would be to suspend the task that is active, and see if the other resumes running. And then look at how much memory it is using. Or easier yet, it should appear in the task list if you sort it alphabetically and show you how much memory it is using. If it is consuming too much memory then that would be something Rosetta might be able to address. Do you know which task name is causing you problems? Rosetta Moderator: Mod.Sense |
Mod.Sense Volunteer moderator Send message Joined: 22 Aug 06 Posts: 4018 Credit: 0 RAC: 0 |
Notes for Project Team: Looking at Adrian's task list, it looks like this one had a very long running model on the third decoy threading_bong_promals_4_hb_t328__IGNORE_THE_REST_16074_67_0 https://boinc.bakerlab.org/rosetta/result.php?resultid=297460595 Target runtime 14,400, 3 decoys ran in 23,000. The first two must have been done within 9,600 or it would have ended the task before starting the third. So that means the third ran for at least 13,400, which is nearly 4 hours. Rosetta Moderator: Mod.Sense |
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