Bug report for Minirosetta version 1.29

Bug report for Minirosetta version 1.29

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Message boards : RALPH@home bug list : Bug report for Minirosetta version 1.29

Author	Message
dekim Forum moderator Project administrator Project developer Project scientist Joined: Jan 20 06 Posts: 146 ID: 1 Credit: 356,567 RAC: 1	Message 4127 - Posted 21 Jun 2008 3:27:17 UTC
	Please post any bugs/issues here regarding minirosetta version 1.29. This version includes a fix in the boinc api which prevents a rare infinite loop. It also includes a fix to the minirosetta database clean up code. ____________
	ID: 4127 \|

dekim Forum moderator Project administrator Project developer Project scientist Joined: Jan 20 06 Posts: 146 ID: 1 Credit: 356,567 RAC: 1	Message 4134 - Posted 21 Jun 2008 16:54:46 UTC
	can anyone confirm that this version is successfully deleting old minirosetta_database files? or report any issues. ____________
	ID: 4134 \|

David Emigh Joined: Jan 6 08 Posts: 27 ID: 3934 Credit: 26,482 RAC: 0	Message 4135 - Posted 21 Jun 2008 18:21:42 UTC
	None of my crunchers has yet been assigned a 1.29 workunit. I will be sure to report as soon as I see that I have finished one. ____________ RALPH and Rosie sittin' in a tree, F - O - L - D - I - N - G!
	ID: 4135 \|

Azurrio Joined: Jun 27 07 Posts: 12 ID: 3239 Credit: 8,020 RAC: 0	Message 4136 - Posted 22 Jun 2008 9:19:22 UTC
	It is a bit hard to report any possible issues with this app since there aren\'t any WUs to test it with...
	ID: 4136 \|

dekim Forum moderator Project administrator Project developer Project scientist Joined: Jan 20 06 Posts: 146 ID: 1 Credit: 356,567 RAC: 1	Message 4138 - Posted 23 Jun 2008 18:42:07 UTC
	We submitted a bunch of t405 tasks. We don\'t want to flood the queue with these tests since we need to keep it open for production CASP targets. ____________
	ID: 4138 \|

Jipsu Joined: Mar 11 08 Posts: 26 ID: 4117 Credit: 76,448 RAC: 0	Message 4140 - Posted 24 Jun 2008 10:43:47 UTC
	Yes it is deleting old minirosetta_database files. This is from stderr.txt windows xp sp3. Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev20412.zip Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev20940.zip Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev21566.zip Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev22619.zip # cpu_run_time_pref: 86400
	ID: 4140 \|

Jipsu Joined: Mar 11 08 Posts: 26 ID: 4117 Credit: 76,448 RAC: 0	Message 4146 - Posted 25 Jun 2008 5:02:58 UTC - in response to Message 4140. Last modified: 25 Jun 2008 5:04:55 UTC
	Yes it is deleting old minirosetta_database files. This is from stderr.txt windows xp sp3. Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev20412.zip Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev20940.zip Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev21566.zip Removed deprecated file: C:\\Program Files\\BOINC/projects/ralph.bakerlab.org\\minirosetta_database_rev22619.zip # cpu_run_time_pref: 86400 Ok now this is strange, rebooted my computer, which means rebooting boinc and it downloaded all the minirosetta_database files again. They will most likely get deleted again when I get a new 1.29 task, but is it supposed to do that? 6/25/2008 7:56:02 AM\|\|Starting BOINC client version 5.10.45 for windows_intelx86 6/25/2008 7:56:02 AM\|\|log flags: task, file_xfer, sched_ops 6/25/2008 7:56:02 AM\|\|Libraries: libcurl/7.18.0 OpenSSL/0.9.8e zlib/1.2.3 6/25/2008 7:56:02 AM\|\|Data directory: C:\\Program Files\\BOINC 6/25/2008 7:56:03 AM\|\|Processor: 2 GenuineIntel Intel(R) Core(TM)2 Duo CPU T7500 @ 2.20GHz [x86 Family 6 Model 15 Stepping 10] 6/25/2008 7:56:03 AM\|\|Processor features: fpu tsc sse sse2 mmx 6/25/2008 7:56:03 AM\|\|OS: Microsoft Windows XP: Professional Edition, Service Pack 3, (05.01.2600.00) 6/25/2008 7:56:03 AM\|\|Memory: 1.97 GB physical, 3.79 GB virtual 6/25/2008 7:56:03 AM\|\|Disk: 25.00 GB total, 13.65 GB free 6/25/2008 7:56:03 AM\|\|Local time is UTC +3 hours 6/25/2008 7:56:04 AM\|rosetta@home\|URL: http://boinc.bakerlab.org/rosetta/; Computer ID: 766606; location: (none); project prefs: default 6/25/2008 7:56:04 AM\|ralph@home\|URL: http://ralph.bakerlab.org/; Computer ID: 12866; location: (none); project prefs: default 6/25/2008 7:56:04 AM\|\|General prefs: from rosetta@home (last modified 13-May-2008 21:19:57) 6/25/2008 7:56:04 AM\|\|Host location: none 6/25/2008 7:56:04 AM\|\|General prefs: using your defaults 6/25/2008 7:56:04 AM\|\|Preferences limit memory usage when active to 1510.67MB 6/25/2008 7:56:04 AM\|\|Preferences limit memory usage when idle to 1510.67MB 6/25/2008 7:56:04 AM\|\|Preferences limit disk usage to 12.50GB 6/25/2008 7:56:05 AM\|\|file projects/ralph.bakerlab.org/minirosetta_database_rev20940.zip not found 6/25/2008 7:56:05 AM\|\|file projects/ralph.bakerlab.org/minirosetta_database_rev21566.zip not found 6/25/2008 7:56:05 AM\|\|file projects/ralph.bakerlab.org/minirosetta_database_rev20412.zip not found 6/25/2008 7:56:05 AM\|\|file projects/ralph.bakerlab.org/minirosetta_database_rev22619.zip not found 6/25/2008 7:56:05 AM\|rosetta@home\|Restarting task rb_06_23_11701_20993_T0467_IGNORE_THE_REST_09_16_4103_89_0 using minirosetta version 128 6/25/2008 7:56:05 AM\|ralph@home\|Restarting task h001b_BOINC_CASP8_ABRELAX_RANGE_t443_IGNORE_THE_REST-S25-10-S3-7--h001b-_4561_35_0 using minirosetta version 129 6/25/2008 7:56:06 AM\|ralph@home\|Started download of minirosetta_database_rev20940.zip 6/25/2008 7:56:06 AM\|ralph@home\|Started download of minirosetta_database_rev21566.zip 6/25/2008 7:56:49 AM\|ralph@home\|Finished download of minirosetta_database_rev20940.zip 6/25/2008 7:56:49 AM\|ralph@home\|Started download of minirosetta_database_rev20412.zip 6/25/2008 7:56:54 AM\|ralph@home\|Finished download of minirosetta_database_rev21566.zip 6/25/2008 7:56:54 AM\|ralph@home\|Started download of minirosetta_database_rev22619.zip 6/25/2008 7:56:56 AM\|rosetta@home\|Computation for task rb_06_23_11701_20993_T0467_IGNORE_THE_REST_09_16_4103_89_0 finished 6/25/2008 7:56:56 AM\|ralph@home\|Sending scheduler request: To fetch work. Requesting 1 seconds of work, reporting 0 completed tasks 6/25/2008 7:56:58 AM\|rosetta@home\|Started upload of rb_06_23_11701_20993_T0467_IGNORE_THE_REST_09_16_4103_89_0_0 6/25/2008 7:57:01 AM\|ralph@home\|Computation for task h001b_BOINC_CASP8_ABRELAX_RANGE_t443_IGNORE_THE_REST-S25-10-S3-7--h001b-_4561_35_0 finished 6/25/2008 7:57:02 AM\|ralph@home\|Scheduler request succeeded: got 0 new tasks 6/25/2008 7:57:03 AM\|ralph@home\|Started upload of h001b_BOINC_CASP8_ABRELAX_RANGE_t443_IGNORE_THE_REST-S25-10-S3-7--h001b-_4561_35_0_0 6/25/2008 7:57:07 AM\|rosetta@home\|Sending scheduler request: To fetch work. Requesting 2 seconds of work, reporting 1 completed tasks 6/25/2008 7:57:08 AM\|rosetta@home\|Finished upload of rb_06_23_11701_20993_T0467_IGNORE_THE_REST_09_16_4103_89_0_0 6/25/2008 7:57:10 AM\|ralph@home\|Finished upload of h001b_BOINC_CASP8_ABRELAX_RANGE_t443_IGNORE_THE_REST-S25-10-S3-7--h001b-_4561_35_0_0 6/25/2008 7:57:13 AM\|rosetta@home\|Scheduler request succeeded: got 1 new tasks 6/25/2008 7:57:15 AM\|rosetta@home\|Started download of rb_06_24_11702_20999_T0468_t000_.psipred_ss2 6/25/2008 7:57:15 AM\|rosetta@home\|Started download of rb_06_24_11702_20999_T0468_t000_.fasta 6/25/2008 7:57:16 AM\|rosetta@home\|Finished download of rb_06_24_11702_20999_T0468_t000_.psipred_ss2 6/25/2008 7:57:16 AM\|rosetta@home\|Finished download of rb_06_24_11702_20999_T0468_t000_.fasta 6/25/2008 7:57:16 AM\|rosetta@home\|Started download of rb_06_24_11702_20999_T0468_aat000_03_05.200_v1_3.gz 6/25/2008 7:57:16 AM\|rosetta@home\|Started download of rb_06_24_11702_20999_T0468_aat000_05_05.200_v1_3.gz 6/25/2008 7:57:20 AM\|rosetta@home\|Finished download of rb_06_24_11702_20999_T0468_aat000_03_05.200_v1_3.gz 6/25/2008 7:57:20 AM\|rosetta@home\|Started download of rb_06_24_11702_20999_T0468_aat000_10_05.200_v1_3.gz 6/25/2008 7:57:25 AM\|rosetta@home\|Finished download of rb_06_24_11702_20999_T0468_aat000_10_05.200_v1_3.gz 6/25/2008 7:57:27 AM\|rosetta@home\|Finished download of rb_06_24_11702_20999_T0468_aat000_05_05.200_v1_3.gz 6/25/2008 7:57:28 AM\|rosetta@home\|Starting rb_06_24_11702_20999_T0468_IGNORE_THE_REST_05_10_4109_130_0 6/25/2008 7:57:28 AM\|rosetta@home\|Starting task rb_06_24_11702_20999_T0468_IGNORE_THE_REST_05_10_4109_130_0 using minirosetta version 128 6/25/2008 7:57:40 AM\|ralph@home\|Finished download of minirosetta_database_rev20412.zip 6/25/2008 7:58:12 AM\|ralph@home\|Finished download of minirosetta_database_rev22619.zip
	ID: 4146 \|

Path7 Joined: Feb 11 08 Posts: 56 ID: 4036 Credit: 4,974 RAC: 0	Message 4147 - Posted 25 Jun 2008 20:05:23 UTC
	Mini 1.29 deletes old database files � old db files downloaded again after reboot. Hello all, Just as Jipsu mentioned above, the minirosetta 1.29 did remove the old database files on my Ubuntu 7.10 x86, Boinc 5.10.45 as it supposed to do. However, after rebooting my PC (and restarting Boinc) Boinc did download 3 old data base files: minirosetta_database_rev20940.zip minirosetta_database_rev21566.zip minirosetta_database_rev22619.zip After all the total effect: Disk usage Ralph@home went from (about) 123 MB to 92 MB right now. Last but not least: The WU: 5croA_JUMPRELAX_NAT_NEWFRAG_SAVE_ALL_OUT-5croA-_4568_4_0 with application Minirosetta 1.29 crunched fine. Have a nice day, Path7.
	ID: 4147 \|

Pepo Joined: Sep 8 06 Posts: 104 ID: 1812 Credit: 36,890 RAC: 0	Message 4148 - Posted 25 Jun 2008 21:20:11 UTC - in response to Message 4147.
	Mini 1.29 deletes old database files � old db files downloaded again after reboot. Obviously they\'re still being kept listed in client_state.xml... then it is not enough to just delete them. Peter
	ID: 4148 \|

Path7 Joined: Feb 11 08 Posts: 56 ID: 4036 Credit: 4,974 RAC: 0	Message 4149 - Posted 25 Jun 2008 21:32:34 UTC - in response to Message 4147. Last modified: 25 Jun 2008 21:40:18 UTC
	However, after rebooting my PC (and restarting Boinc) Boinc did download 3 old data base files: minirosetta_database_rev20940.zip minirosetta_database_rev21566.zip minirosetta_database_rev22619.zip Edit: Sorry I overlooked 1 database file, actually Boinc downloaded 4 old database files; including: minirosetta_database_rev20412.zip @ Pepo: Thanks for your thoughts, I guess you\'re right. Have a nice day, Path7.
	ID: 4149 \|

dekim Forum moderator Project administrator Project developer Project scientist Joined: Jan 20 06 Posts: 146 ID: 1 Credit: 356,567 RAC: 1	Message 4151 - Posted 26 Jun 2008 20:44:38 UTC
	okay, I was worried this might happen. I\'ll have to look into this. Thanks for the heads up. ____________
	ID: 4151 \|

ChertseyAl Joined: May 20 07 Posts: 3 ID: 3114 Credit: 51,055 RAC: 0	Message 4155 - Posted 3 Jul 2008 10:10:48 UTC - in response to Message 4127.
	Please post any bugs/issues here regarding minirosetta version 1.29. Don\'t know if you are interested in these, but I had a few of them over night. Here\'s a sample one: 03/07/2008 10:43:28\|ralph@home\|Starting 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1 03/07/2008 10:43:34\|ralph@home\|Starting task 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1 using minirosetta version 129 03/07/2008 10:43:36\|ralph@home\|Computation for task 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1 finished 03/07/2008 10:43:36\|ralph@home\|Output file 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1_0 for task 1pgx__ABRELAX_PREDFRAG_SAVE_ALL_OUT-1pgx_-_4605_4_1 absent http://ralph.bakerlab.org/workunit.php?wuid=928656 http://ralph.bakerlab.org/result.php?resultid=1050853 Al.
	ID: 4155 \|

JordanWeber Joined: May 9 08 Posts: 2 ID: 4290 Credit: 12,774 RAC: 0	Message 4157 - Posted 3 Jul 2008 13:55:16 UTC
	1050267 Task was aborted because it never started and never accumulated cpu time (this was on all night overnight). I\'ve been reporting this bug since at least mini 1.25. I was told from Rosetta@home boards to come here and help test mini. Since your guidelines say don\'t abort tasks, and since there\'s no way for the tasks to even start, I still had no choice but to abort.
	ID: 4157 \|

AdeB Joined: Dec 22 07 Posts: 61 ID: 3888 Credit: 51,577 RAC: 0	Message 4158 - Posted 3 Jul 2008 20:15:25 UTC Last modified: 3 Jul 2008 20:22:02 UTC
	Error in resultid=1050453 stderr out: <core_client_version>5.10.45</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> Unrecognized XML in parse_init_data_file: fraction_done_update_period Skipping: 1.000000 Skipping: /fraction_done_update_period ERROR: Option matching -fragdate not found in command line top-level context </stderr_txt> ]]>
	ID: 4158 \|

Azurrio Joined: Jun 27 07 Posts: 12 ID: 3239 Credit: 8,020 RAC: 0	Message 4159 - Posted 4 Jul 2008 7:32:29 UTC
	Three compute erros, each with 0 seconds of computing time. WU1 WU2 WU3
	ID: 4159 \|

Message boards : RALPH@home bug list : Bug report for Minirosetta version 1.29