Bug report for Rosetta version 5.97

Author	Message
dekim Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 20 Jan 06 Posts: 250 Credit: 543,579 RAC: 0	Message 4126 - Posted: 21 Jun 2008, 3:24:47 UTC Please post any 5.97 bugs here. This version is identical to 5.96 but includes a fix for a rare infinite loop in the boinc api. "The dreaded t405 issue". ID: 4126 · Reply Quote

Jipsu Send message Joined: 11 Mar 08 Posts: 26 Credit: 76,448 RAC: 0	Message 4128 - Posted: 21 Jun 2008, 12:18:55 UTC This stderr might be interesting, it still was a success though. https://ralph.bakerlab.org/result.php?resultid=1045195 ID: 4128 · Reply Quote

John Hunt Send message Joined: 16 Mar 07 Posts: 10 Credit: 28,654 RAC: 0	Message 4129 - Posted: 21 Jun 2008, 12:29:22 UTC Computation (client) error - https://ralph.bakerlab.org/result.php?resultid=1045289 ID: 4129 · Reply Quote

Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0	Message 4131 - Posted: 21 Jun 2008, 13:55:03 UTC Old "t405" is still raising it's ugly head, see this result <core_client_version>5.10.21</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63) </message> <stderr_txt> Graphics are disabled due to configuration... Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period # cpu_run_time_pref: 21600 # random seed: 1176122 Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period ====================================================== DONE :: 1 starting structures 20983.1 cpu seconds This process generated 11 decoys from 11 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down... called boinc_finish * glibc detected * free(): invalid next size (normal): 0x0959bb58 *** SIGABRT: abort called Stack trace (19 frames): [0x8e1b51f] [0x8e15eac] [0xb7f6b420] [0x8e87104] [0x8e9c06f] [0x8ea10d5] [0x8ea13b3] [0x8e71d61] [0x8e73789] [0x8070d59] [0x87cdb6a] [0x8e8764f] [0x8e17abc] [0x8e17bc7] [0x86290f2] [0x8768b46] [0x8768c66] [0x8e80044] [0x8048111] Exiting... </stderr_txt> ]]> Validate state Invalid ID: 4131 · Reply Quote

Pepo Send message Joined: 8 Sep 06 Posts: 104 Credit: 36,890 RAC: 0	Message 4132 - Posted: 21 Jun 2008, 14:58:27 UTC Last modified: 21 Jun 2008, 15:00:55 UTC Linux Boinc 6.2.4, t419N_autoalign_IGNORE_THE_REST_renumbered_4388_2_1: "Maximum disk usage exceeded". And a lot of Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period in the stderr_txt. Peter ID: 4132 · Reply Quote

dekim Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 20 Jan 06 Posts: 250 Credit: 543,579 RAC: 0	Message 4133 - Posted: 21 Jun 2008, 16:52:03 UTC You can ignore the unrecognized XML parse output in stderr.txt. There is still a possibility of getting access violations with the t405 jobs. We have to track down and fix the cause. What we are really concerned about is fixing the client stalling issue. This is a really bad problem since without any information sent back from the client, we can't determine the status of tasks and obviously a stalled client is a very bad situation. ID: 4133 · Reply Quote

David Emigh Send message Joined: 6 Jan 08 Posts: 27 Credit: 26,482 RAC: 0	Message 4137 - Posted: 22 Jun 2008, 13:56:07 UTC Last modified: 22 Jun 2008, 13:59:38 UTC This one threw a "Compute Error" at 0 seconds: t419N_autoalign_IGNORE_THE_REST_renumbered_4293_3_1 The error message was: Maximum disk usage exceeded RALPH and Rosie sittin' in a tree, F - O - L - D - I - N - G! ID: 4137 · Reply Quote

Pepo Send message Joined: 8 Sep 06 Posts: 104 Credit: 36,890 RAC: 0	Message 4139 - Posted: 23 Jun 2008, 21:01:28 UTC - in response to Message 4133. There is still a possibility of getting access violations with the t405 jobs. We have to track down and fix the cause. What we are really concerned about is fixing the client stalling issue. This is a really bad problem since without any information sent back from the client, we can't determine the status of tasks and obviously a stalled client is a very bad situation. If my tasks will stall again (as some already did in the past), what files from my slot/project folders would interest you? Peter ID: 4139 · Reply Quote

Odysseus Send message Joined: 4 May 07 Posts: 23 Credit: 16,331 RAC: 0	Message 4141 - Posted: 24 Jun 2008, 10:44:30 UTC My G5 got a computation error on t419N_autoalign_IGNORE_THE_REST_renumbered_4320_3: exit status 1 (0x1), “Unable to determine sequence length from pdb file”. ID: 4141 · Reply Quote

Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0	Message 4142 - Posted: 24 Jun 2008, 11:53:39 UTC > Another "t405" errored WU, see this WU. It has the same error as the one I reported previously. ID: 4142 · Reply Quote

Path7 Send message Joined: 11 Feb 08 Posts: 56 Credit: 4,974 RAC: 0	Message 4143 - Posted: 24 Jun 2008, 19:05:54 UTC Last modified: 24 Jun 2008, 19:20:33 UTC Hello all, Running Ubuntu 7.10 x86 the next WU errored with a -177 (0xffffffffffffff4f) error: t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2 While the stderr out gives a: ERROR:: Unable to determine sequence length from pdb file from Boinc messages I find: di 24 jun 2008 20:22:51 CEST\|ralph@home\|Aborting task t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2: exceeded disk limit: 569.28MB > 476.84MB di 24 jun 2008 20:22:52 CEST\|ralph@home\|Computation for task t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2 finished di 24 jun 2008 20:22:52 CEST\|ralph@home\|Output file t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2_0 for task t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2 absent note: di is short for Tuesday. Edit: Boinc disk usage is limited to 2.16 GB. Have a nice day, Path7. ID: 4143 · Reply Quote

Pepo Send message Joined: 8 Sep 06 Posts: 104 Credit: 36,890 RAC: 0	Message 4144 - Posted: 24 Jun 2008, 21:35:08 UTC - in response to Message 4143. t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2 di 24 jun 2008 20:22:51 CEST\|ralph@home\|Aborting task t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2: exceeded disk limit: 569.28MB > 476.84MB The t419N_autoalign_IGNORE_THE_REST_renumbered_4406_8_1: "Maximum disk usage exceeded". The same happened to all 3 wingmen (Mac, Linux, Vista). Peter ID: 4144 · Reply Quote