Minirosetta 3.62-3.65

Author	Message
David E K Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 1 Jul 05 Posts: 1018 Credit: 4,334,829 RAC: 0	Message 78684 - Posted: 3 Sep 2015, 21:38:11 UTC The minirosetta application has been updated to the latest Rosetta source. This update includes a new optimized score function which improves all scientific benchmarks. Please post any bugs/issues related to this update here. ID: 78684 · Rating: 0 · rate: / Reply Quote

dcdc Send message Joined: 3 Nov 05 Posts: 1832 Credit: 119,664,803 RAC: 11,191	Message 78687 - Posted: 4 Sep 2015, 16:08:42 UTC Last modified: 4 Sep 2015, 16:08:57 UTC Is it possible to say/test what effect SSE is having? Presumably it varies by CPU and the same unit would have to be run with SSE off? ID: 78687 · Rating: 0 · rate: / Reply Quote

David E K Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 1 Jul 05 Posts: 1018 Credit: 4,334,829 RAC: 0	Message 78688 - Posted: 4 Sep 2015, 17:34:31 UTC - in response to Message 78687. Is it possible to say/test what effect SSE is having? Presumably it varies by CPU and the same unit would have to be run with SSE off? SSE is not being used in these updates. ID: 78688 · Rating: 0 · rate: / Reply Quote

Dr. Merkwürdigliebe Send message Joined: 5 Dec 10 Posts: 81 Credit: 2,657,273 RAC: 0	Message 78689 - Posted: 4 Sep 2015, 17:55:41 UTC minirosetta_3.62_x86_64-pc-linux-gnu: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), statically linked, for GNU/Linux 2.6.9, stripped A bit disappointed here... ID: 78689 · Rating: 0 · rate: / Reply Quote

Link Send message Joined: 4 May 07 Posts: 356 Credit: 382,349 RAC: 0	Message 78690 - Posted: 4 Sep 2015, 18:05:56 UTC I see the minirosetta_database got quite a lot larger, from 248MB to 411MB unpacked. Not so good considering this thing is extracted each time a new WU starts, lets see how my soon 10 years old laptop and it's hard drive will like it... . ID: 78690 · Rating: 0 · rate: / Reply Quote

Timo Send message Joined: 9 Jan 12 Posts: 185 Credit: 45,649,459 RAC: 0	Message 78691 - Posted: 4 Sep 2015, 20:12:55 UTC Last modified: 4 Sep 2015, 20:26:03 UTC I am showing so far that many 3.62 tasks are encountering 'Validate Errors', though not all of them. The following tasks are all variations of a project with the title like 'FFD__ xxxxx_abinitioDocking': Task 755931518 - Validate error Task 755927819 - Validate error What sucks is the tasks run for the full runtime (in my case, 8 hours) but end up failing validation .. However, it's not all bad news some other 3.62 tasks, one of which is 'FFD__xxxxx_insulin_fourH2_Thu_xxxx' are finishing successfully as well as most all of the 3.62 'rb_' type tasks which seem to be finishing successfully. This leads me to believe it may be an issue with some of the FFD abinitio docking jobs. ID: 78691 · Rating: 0 · rate: / Reply Quote

David E K Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 1 Jul 05 Posts: 1018 Credit: 4,334,829 RAC: 0	Message 78692 - Posted: 4 Sep 2015, 21:07:30 UTC - in response to Message 78691. I am showing so far that many 3.62 tasks are encountering 'Validate Errors', though not all of them. The following tasks are all variations of a project with the title like 'FFD__ xxxxx_abinitioDocking': Task 755931518 - Validate error Task 755927819 - Validate error What sucks is the tasks run for the full runtime (in my case, 8 hours) but end up failing validation .. However, it's not all bad news some other 3.62 tasks, one of which is 'FFD__xxxxx_insulin_fourH2_Thu_xxxx' are finishing successfully as well as most all of the 3.62 'rb_' type tasks which seem to be finishing successfully. This leads me to believe it may be an issue with some of the FFD abinitio docking jobs. Thanks for the heads up. We are currently looking into this. ID: 78692 · Rating: 0 · rate: / Reply Quote

wyxchari Send message Joined: 27 Nov 14 Posts: 11 Credit: 85,318 RAC: 0	Message 78693 - Posted: 4 Sep 2015, 21:52:53 UTC From September 3, not me work tasks. 756146726 685379842 4 Sep 2015 21:43:22 UTC 4 Sep 2015 21:47:31 UTC Over Client error Compute error 0.00 0.00 --- 756146379 685379499 4 Sep 2015 21:47:31 UTC 4 Sep 2015 21:51:38 UTC Over Client error Compute error 0.00 0.00 --- 756142269 685191678 4 Sep 2015 21:11:45 UTC 4 Sep 2015 21:43:22 UTC Over Client error Compute error 0.00 0.00 --- 756136139 685070740 4 Sep 2015 20:35:04 UTC 4 Sep 2015 21:11:45 UTC Over Client detached New 0.00 --- --- 756108060 685348417 4 Sep 2015 17:43:43 UTC 4 Sep 2015 20:35:04 UTC Over Client detached New 0.00 --- --- 756107378 685347883 4 Sep 2015 17:37:58 UTC 4 Sep 2015 20:35:04 UTC Over Client detached New 0.00 --- --- 756106387 685347020 4 Sep 2015 17:33:50 UTC 4 Sep 2015 17:37:58 UTC Over Client error Compute error 0.00 0.00 --- 756106282 685345669 4 Sep 2015 17:29:17 UTC 4 Sep 2015 17:33:50 UTC Over Client error Compute error 0.00 0.00 --- 756047933 685297734 4 Sep 2015 11:47:45 UTC 4 Sep 2015 17:29:17 UTC Over Client error Compute error 0.00 0.00 --- 756046735 685296655 4 Sep 2015 11:42:49 UTC 4 Sep 2015 11:43:37 UTC Over Client error Compute error 0.00 0.00 --- 756031213 685283552 4 Sep 2015 10:09:51 UTC 4 Sep 2015 10:13:57 UTC Over Client error Compute error 0.00 0.00 --- 756030152 685282685 4 Sep 2015 10:03:59 UTC 4 Sep 2015 10:05:43 UTC Over Client error Compute error 0.00 0.00 --- 755997565 685255620 4 Sep 2015 6:47:27 UTC 4 Sep 2015 10:03:59 UTC Over Client error Compute error 0.00 0.00 --- 755987746 685246348 4 Sep 2015 10:13:57 UTC 4 Sep 2015 11:42:49 UTC Over Client error Compute error 0.00 0.00 --- 755906084 685172826 3 Sep 2015 20:36:37 UTC 4 Sep 2015 6:51:35 UTC Over Success Done 5,786.07 12.84 8.77 ID: 78693 · Rating: 0 · rate: / Reply Quote

Timo Send message Joined: 9 Jan 12 Posts: 185 Credit: 45,649,459 RAC: 0	Message 78694 - Posted: 4 Sep 2015, 23:09:12 UTC Last modified: 4 Sep 2015, 23:09:38 UTC Just an update, I let a few more tasks finish and I still haven't had a single successful Abinitio docking job that has a title like FFD__xxxx. I've aborted all FFD__xxxx 'abinitioDocking' type jobs on all of my hosts. It definitely looks to be an issue with this particular job type. Thanks for your hard work David, wish there was more I could do on my end, don't hesitate to ping me if I can be of any help! Tim ID: 78694 · Rating: 0 · rate: / Reply Quote

Dr. Merkwürdigliebe Send message Joined: 5 Dec 10 Posts: 81 Credit: 2,657,273 RAC: 0	Message 78695 - Posted: 5 Sep 2015, 0:48:07 UTC Task ID 756094939 failed under Linux, too. ID: 78695 · Rating: 0 · rate: / Reply Quote

fseeger Volunteer moderator Project developer Project scientist Send message Joined: 3 Nov 14 Posts: 1 Credit: 75,725 RAC: 0	Message 78696 - Posted: 5 Sep 2015, 1:22:33 UTC - in response to Message 78695. Task ID 756094939 failed under Linux, too. Hi all, These seem to be mine but I am not sure what is going on. I submitted them a week ago and they seemed to have run fine until the update yesterday. Could you provide me with more information about the jobs that are failing? Thanks, Franziska ID: 78696 · Rating: 0 · rate: / Reply Quote

P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0	Message 78697 - Posted: 5 Sep 2015, 3:01:35 UTC You wanted more, enjoy. My rigs got validate error on these.( See below ) https://boinc.bakerlab.org/rosetta/workunit.php?wuid=682557581 1da894305e9a610bd5667cc03eeff6fd_hhhcommon_15_08_20_46_44_globalDocking_4_SAVE_ALL_OUT_292589_6_1 # cpu_run_time_pref: 14400 ====================================================== DONE :: 710 starting structures 14388.2 cpu seconds This process generated 710 decoys from 710 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> -------------------------------------------------- https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685290795 FFD__368f3629c8dc09f0ae4d4402193bd7e0_abinitioDocking_15_08_21_50_55_globalDocking_5_SAVE_ALL_OUT_301979_6_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 425 starting structures 14368.3 cpu seconds This process generated 425 decoys from 425 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> -------------------------------------------------------------- https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685229735 FFD__368f3629c8dc09f0ae4d4402193bd7e0_abinitioDocking_15_08_21_50_55_globalDocking_5_SAVE_ALL_OUT_301979_6_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 425 starting structures 14368.3 cpu seconds This process generated 425 decoys from 425 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ---------------------------------------------------------- https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685229735 FFD__61553d966fba4a94dcf25c2a24befc61_abinitioDocking_15_08_14_11_53_globalDocking_4_SAVE_ALL_OUT_299060_4_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 253 starting structures 14362.2 cpu seconds This process generated 253 decoys from 253 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ----------------------------------------- More validate errors. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685188207 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=682334661 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181282 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181270 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181239 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181197 ============================================================= These are Compute errors. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685185054 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181238 ID: 78697 · Rating: 0 · rate: / Reply Quote

Chilean Send message Joined: 16 Oct 05 Posts: 711 Credit: 26,694,507 RAC: 0	Message 78698 - Posted: 5 Sep 2015, 4:41:44 UTC - in response to Message 78689. minirosetta_3.62_x86_64-pc-linux-gnu: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), statically linked, for GNU/Linux 2.6.9, stripped A bit disappointed here... Same. At least we're now running a more advanced energy function, but still, I find it frustrating that we're not squeezing the best out of our CPUs. I mean, the extensions on the CPUs are there for a reason! Performance! Haha ID: 78698 · Rating: 0 · rate: / Reply Quote

wyxchari Send message Joined: 27 Nov 14 Posts: 11 Credit: 85,318 RAC: 0	Message 78699 - Posted: 5 Sep 2015, 17:01:59 UTC I gave a "do not ask for new tasks" in Rosetta. I add while other projects. ID: 78699 · Rating: 0 · rate: / Reply Quote

P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0	Message 78700 - Posted: 5 Sep 2015, 22:38:49 UTC More validate errors this morning. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685225333 FFD__1885c0418f264a32e397ffab4318bbf3_abinitioDocking_15_08_14_27_34_globalDocking_6_SAVE_ALL_OUT_298551_4_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 201 starting structures 14379.4 cpu seconds This process generated 201 decoys from 201 attempts ====================================================== BOINC :: WS_max 1.35666e-166 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ================================================= https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685381286 FFD__7a0bd05235f76b7c212c91d604e6b896_abinitioDocking_15_08_10_13_49_globalDocking_0_SAVE_ALL_OUT_300974_4_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 261 starting structures 14384 cpu seconds This process generated 261 decoys from 261 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ================================================= https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685381283 FFD__7a0bd05235f76b7c212c91d604e6b896_abinitioDocking_15_08_10_13_49_localDocking_8_SAVE_ALL_OUT_300974_4_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 273 starting structures 14369.2 cpu seconds This process generated 273 decoys from 273 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ========================================================= And more FFD validate errors. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685299006 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685330215 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685308187 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685291696 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685378382 ID: 78700 · Rating: 0 · rate: / Reply Quote

Chilean Send message Joined: 16 Oct 05 Posts: 711 Credit: 26,694,507 RAC: 0	Message 78701 - Posted: 6 Sep 2015, 3:57:47 UTC Validate errors here as well: https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685075655 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685375792 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685375707 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685307845 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685333968 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685333966 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685306097 ID: 78701 · Rating: 0 · rate: / Reply Quote

dkester788 Send message Joined: 22 Oct 14 Posts: 2 Credit: 1,285,173 RAC: 0	Message 78707 - Posted: 6 Sep 2015, 16:33:26 UTC I'm new to Rosetta@home in the last couple of days so the majority of the WUs that I've completed recently have ended up in a "Validation Failed" state. The bad part about it is the 5-6 hours of processing time for each job and we don't get any credit for the work. If I can provide additional error logs or information to fix the issue please let me know. I'd like to continue supporting this worthwhile project. Thanks! https://boinc.bakerlab.org/rosetta/result.php?resultid=756421006 https://boinc.bakerlab.org/rosetta/result.php?resultid=756420997 https://boinc.bakerlab.org/rosetta/result.php?resultid=756420978 https://boinc.bakerlab.org/rosetta/result.php?resultid=756420964 https://boinc.bakerlab.org/rosetta/result.php?resultid=756420963 https://boinc.bakerlab.org/rosetta/result.php?resultid=756420962 ID: 78707 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1995 Credit: 9,633,537 RAC: 7,232	Message 78708 - Posted: 6 Sep 2015, 17:05:15 UTC - in response to Message 78698. At least we're now running a more advanced energy function, but still, I find it frustrating that we're not squeezing the best out of our CPUs. I mean, the extensions on the CPUs are there for a reason! Performance! Haha +1 But it's better to have a stable version of app and after optimization. They have years of delay in optimizations, wait a little bit will not change much :-) ID: 78708 · Rating: 0 · rate: / Reply Quote

Sid Celery Send message Joined: 11 Feb 08 Posts: 2125 Credit: 41,249,734 RAC: 9,368	Message 78709 - Posted: 6 Sep 2015, 18:18:41 UTC Taking a look at mine, I have validate errors for FFD__3abb772f509ff20673e3db3ba6bd5b23_abinitioDocking_15_08_09_15_46_globalDocking_2_SAVE_ALL_OUT_298234_6_0 FFD__f39ecdd93693aa6c9f7041bfe2807e70_abinitioDocking_15_08_16_09_28_localDocking_9_SAVE_ALL_OUT_302177_6_0 FFD__14dbe8cafbf291760a429294a8d2b33a_abinitioDocking_15_08_07_29_16_globalDocking_2_SAVE_ALL_OUT_293179_6_0 FFD__ca38249e426d15dd7bcba74daffc6fec_abinitioDocking_15_08_10_30_33_globalDocking_4_SAVE_ALL_OUT_295421_4_0 FFD__ca38249e426d15dd7bcba74daffc6fec_abinitioDocking_15_08_10_30_33_globalDocking_4_SAVE_ALL_OUT_295421_4_0 FFD__4a08875fd86b75d6fb9e75758d3fd2c7_abinitioDocking_15_08_14_56_33_localDocking_8_SAVE_ALL_OUT_295567_4_1 FFD__cc71887ae41e282f8164f40af22faac6_abinitioDocking_15_08_13_27_21_globalDocking_1_SAVE_ALL_OUT_296571_6_0 FFD__cc758423a44ab5206e41382ff85987f2_abinitioDocking_15_08_07_17_34_globalDocking_2_SAVE_ALL_OUT_295398_4_1 FFD__9b9c8c57be964de37d8e6892fab9c249_abinitioDocking_15_08_08_17_54_globalDocking_2_SAVE_ALL_OUT_298082_5_1 FFD__516ef6a3ceed06822bf753aff1b909d2_abinitioDocking_15_08_22_17_49_localDocking_9_SAVE_ALL_OUT_300732_5_0 FFD__1c08f5de7feb7471e5d234979f67806a_abinitioDocking_15_08_04_28_25_globalDocking_0_SAVE_ALL_OUT_293896_6_0 FFD__025d259a867b146b4634e87d80278365_abinitioDocking_15_08_18_23_19_globalDocking_1_SAVE_ALL_OUT_294660_6_1 A pattern forms... ID: 78709 · Rating: 0 · rate: / Reply Quote

Trotador Send message Joined: 30 May 09 Posts: 108 Credit: 291,214,977 RAC: 0	Message 78710 - Posted: 6 Sep 2015, 19:44:03 UTC - in response to Message 78696. Task ID 756094939 failed under Linux, too. Hi all, These seem to be mine but I am not sure what is going on. I submitted them a week ago and they seemed to have run fine until the update yesterday. Could you provide me with more information about the jobs that are failing? Thanks, Franziska Any idea Franziska? I have suspended all FFD_ tasks. I do not want to abort them to avoid that a new copy is sent to another cruncher. Thanks for keeping us informed. ID: 78710 · Rating: 0 · rate: / Reply Quote