Message boards : Number crunching : Rosetta 4.1+ and 4.2+
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Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 12,116,986 RAC: 9,863 |
Looks like another bunch of dodgy Work Units. I assume they can easily see when tasks are returned as failures. No need for us to concern ourselves with it. |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Name: foldit0_2001734_0009_relax_dock_SAVE_ALL_OUT_1005379_3 Application: Rosetta v4.20 windows_x86_64 Device: 1759960 Task: 1234502102. WU: 1107127887 Status: Error while computing. Exit status: -1 (0xFFFFFFFF) Unknown error code Errors: Too many errors (may have bug) Too many total results. Stderr output: (unknown error) - exit code -1 (0xffffffff)Appears quite similar to Grant's reported error. Wingman also failed, but different error code (Signal 11). Note my system Windows and that system Apple. |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
First Android task I've processed in ages (also first Android error in ages). Also had a similar Validate Error for another Android "foldit" task. Name: foldit1_2001331_0001_00_asym_dock_SAVE_ALL_OUT_1005715_293_0 Application: Rosetta v4.20 arm-android-linux-gnu Device: 3396190 Task: https://boinc.bakerlab.org/rosetta/result.php?resultid=1235917770]1235917770[/url]. WU: 1108336404 Status: Validate error Exit status: 0 (0x00000000) Stderr output: WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x28ac |
Grant (SSSF) Send message Joined: 28 Mar 20 Posts: 1725 Credit: 18,382,444 RAC: 19,446 |
More foldit1 Validate errors after 30sec or less Runtime. foldit1_2000906_0004_00_asym_dock_SAVE_ALL_OUT_1005859_264_1 foldit1_2001860_0000_00_asym_dock_SAVE_ALL_OUT_1005893_296_0 foldit1_2008835_0000_00_asym_dock_SAVE_ALL_OUT_1005800_335_0 <core_client_version>7.6.22</core_client_version> <![CDATA[ <stderr_txt> command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe @foldit1_2008835_0000_global_dock_flags -in:file:boinc_wu_zip asym_dock_foldit1_2008835_0000_data.zip -patchdock foldit1_2008835_0000_patchdock.patchdock -patchdock_random_entry 1 5003 -in:file:s foldit1_2008835_0000_patchdock.pdb -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 1196927 Using database: database_357d5d93529_n_methylminirosetta_database [ ERROR ]: Caught exception: File: ......srcprotocolsrosetta_scriptsRosettaScriptsParser.cc:1313 Input rosetta scripts XML file "asym_dock_global.xml" failed to validate against the rosetta scripts schema. Use the option -parser::output_schema <output filename> to output the schema to a file to see all valid options. Your XML has failed validation. The error message below will tell you where in your XML file the error occurred. Here's how to fix it: 1) If the validation fails on something obvious, like an illegal attribute due to a spelling error (perhaps you used scorefnction instead of scorefunction), then you need to fix your XML file. 2) If you haven’t run the XML rewriter script and this might be pre-2017 Rosetta XML, run the rewriter script (tools/xsd_xrw/rewrite_rosetta_script.py) on your input XML first. The attribute values not being in quotes (scorefunction=talaris2014 instead of scorefunction="talaris2014") is a good indicator that this is your problem. 3) If you are a developer and neither 1 nor 2 worked - email the developer’s mailing list or try Slack. 4) If you are an academic or commercial user - try the Rosetta Forums https://www.rosettacommons.org/forum Error messages were: Error: AttValue: " or ' expected 1: <dock_design> 2: <SCOREFXNS> 3: <fullatom weights=talaris2013 symmetric=0> 4: </fullatom> 5: </SCOREFXNS> 6: 7: <FILTERS> 8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/> Error: attributes construct error 1: <dock_design> 2: <SCOREFXNS> 3: <fullatom weights=talaris2013 symmetric=0> 4: </fullatom> 5: </SCOREFXNS> 6: 7: <FILTERS> 8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/> Error: Couldn't find end of Start Tag fullatom line 3 1: <dock_design> 2: <SCOREFXNS> 3: <fullatom weights=talaris2013 symmetric=0> 4: </fullatom> 5: </SCOREFXNS> 6: 7: <FILTERS> 8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/> Error: Opening and ending tag mismatch: SCOREFXNS line 2 and fullatom 1: <dock_design> 2: <SCOREFXNS> 3: <fullatom weights=talaris2013 symmetric=0> 4: </fullatom> 5: </SCOREFXNS> 6: 7: <FILTERS> 8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/> 9: <Sasa name=sasa confidence=0/> Error: Opening and ending tag mismatch: dock_design line 1 and SCOREFXNS 1: <dock_design> 2: <SCOREFXNS> 3: <fullatom weights=talaris2013 symmetric=0> 4: </fullatom> 5: </SCOREFXNS> 6: 7: <FILTERS> 8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/> 9: <Sasa name=sasa confidence=0/> 10: <ShapeComplementarity name=shape verbose=1 confidence=0 jump=1/> Error: Extra content at the end of the document 2: <SCOREFXNS> 3: <fullatom weights=talaris2013 symmetric=0> 4: </fullatom> 5: </SCOREFXNS> 6: 7: <FILTERS> 8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/> 9: <Sasa name=sasa confidence=0/> 10: <ShapeComplementarity name=shape verbose=1 confidence=0 jump=1/> 11: </FILTERS> 12: ------------------------------------------------------------ Warning messages were: ------------------------------------------------------------ ------------------------ Begin developer's backtrace ------------------------- BACKTRACE: ------------------------- End developer's backtrace -------------------------- AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. DummyMover::apply() should never have been called! (JobDistributor/Parser should have replaced DummyMover.) ERROR: Function not implemented. ERROR:: Exit from: ......srcappspublicboincminirosetta.cc line: 101 23:43:47 (1468): called boinc_finish(0) </stderr_txt> ]]> Grant Darwin NT |
[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 2002 Credit: 9,780,807 RAC: 5,492 |
Some errors like this: <message> |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Another set of Foldit1 invalidation errors on my Android tablet (an Amazon Fire tablet): Name: foldit1_2008663_y688_00_asym_dock_SAVE_ALL_OUT_1005783_946_0 Application: Rosetta v4.20 arm-android-linux-gnu Device: 3396190 Task: 1238189780. WU: 1110337695 Status: Validate error Exit status: 0 (0x00000000) Stderr output: WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x28ac |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Other tasks which failed to validate for my Amazon tablet (3396190) included:
Task: 1238189780
Task: 1238189817
Task: 1238132060
Task: 1238131939
Task: 1238130586
Task: 1238130600
|
Grant (SSSF) Send message Joined: 28 Mar 20 Posts: 1725 Credit: 18,382,444 RAC: 19,446 |
Other tasks which failed to validate for my Amazon tablet (3396190) included:Yeah, seems to be an increasing number of errors with the foldit Work Units. Edit- foldit1 seem to be the problem Work Units, foldit0 Tasks are processing with out problems. Grant Darwin NT |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
More tasks which failed to validate for my Amazon tablet (3396190), as noted in message 98480, include:
Task: 1238599419 2. Name: foldit1_2008899_0006_00_asym_dock_SAVE_ALL_OUT_1005735_1039 Task: 1238585227 3. Name: foldit1_2008762_s009_00_asym_dock_SAVE_ALL_OUT_1005863_1039 Task: 1238585235 4. Name: foldit1_2001822_0008_00_asym_dock_SAVE_ALL_OUT_1005689_1031 Task: 1238545676 5. Name: foldit1_2001209_0006_00_asym_dock_SAVE_ALL_OUT_1005688_1031 Task: 1238545660 6. Name: foldit1_2008663_y239_00_asym_dock_SAVE_ALL_OUT_1005837_947 Task: 1238195355 7. Name: foldit1_2008663_s004_00_asym_dock_SAVE_ALL_OUT_1005838_947 Task: 1238195616 8. Name: foldit1_2008663_y688_00_asym_dock_SAVE_ALL_OUT_1005783_946 Task: 1238189780 Plus 5 more tasks. |
[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 2002 Credit: 9,780,807 RAC: 5,492 |
All "simsjn_out_Protein_A" wus failed after few seconds, like this 1238899458 <stderr_txt> Have you tested it on Ralph??? |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 12,116,986 RAC: 9,863 |
All "simsjn_out_Protein_A" wus failed after few seconds, like this They don't seem to make much use of Ralph. I signed up to it a few weeks ago with 6 computers (and put it on extremely high weighting so it always did it first), and all I've had is a few tasks on one machine. Maybe they didn't think this needed testing, or were in a hurry to get the work done? |
[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 2002 Credit: 9,780,807 RAC: 5,492 |
They don't seem to make much use of Ralph. I signed up to it a few weeks ago with 6 computers (and put it on extremely high weighting so it always did it first), and all I've had is a few tasks on one machine. Maybe they didn't think this needed testing, or were in a hurry to get the work done? It's not the first time of a batch completely wrong. My Ralph account is 2008, so it's a lot of time, and yes, it's under-used. And have no sense to be hurry and have a lot of errors... |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 12,116,986 RAC: 9,863 |
They don't seem to make much use of Ralph. I signed up to it a few weeks ago with 6 computers (and put it on extremely high weighting so it always did it first), and all I've had is a few tasks on one machine. Maybe they didn't think this needed testing, or were in a hurry to get the work done? Most of the tasks work, I've got 66 cores running Rosetta most of the time now. 10 million tasks in the server queue.... I just wish they had graphics card work. |
Grant (SSSF) Send message Joined: 28 Mar 20 Posts: 1725 Credit: 18,382,444 RAC: 19,446 |
All "simsjn_out_Protein_A" wus failed after few seconds, like thisSame here. 100% failure rate so far for simsjn Work Units. <core_client_version>7.6.33</core_client_version> <![CDATA[ <message> Incorrect function. (0x1) - exit code 1 (0x1) </message> <stderr_txt> command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -beta -frag3 00001.200.3mers -frag9 00001.200.9mers -abinitio::increase_cycles 10 -mute all -abinitio::fastrelax -relax::default_repeats 5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5 -abinitio::use_filters false -ex1 -ex2aro -in:file:boinc_wu_zip simsjn_out_Protein_A_v5_contacts_43_0_L20L2L1L2L2L2L2L3L20_fragments_fold_data.zip -abinitio::rg_reweight 0.5 -out:file:silent default.out -silent_gz -mute all -in:file:native 00001.pdb -out:file:silent_struct_type binary -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 2444184 Using database: database_357d5d93529_n_methylminirosetta_database ERROR: ERROR: FragmentIO: could not open file 00001.200.9mers ERROR:: Exit from: ......srccorefragmentFragmentIO.cc line: 233 BOINC:: Error reading and gzipping output datafile: default.out 15:16:31 (10040): called boinc_finish(1) </stderr_txt> ]]> Grant Darwin NT |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
I continue to receive validation errors (36 total today!) on my Android devices for the foldit1 tasks, today adding my Samsung phone (3182472). The only difference in the error descriptions of the 2 devices so far is that the Amazon tablet (3396190) includes the added remarks: WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x28acnot mentioned in the Samsung error. Of interest is the fact that Rosetta has not elected to rerun these particular validation errors with a wingperson. They have marked all these errors as "canonical." Also of interest is that all these errored tasks were created just this morning, despite the many reports of problems with this series of tasks!!! Doesn't appear anyone in "authority" bothers to read these posts, or just ignores them!! Examples of the validation errors previously quoted by myself in this thread, as well as by Grant. Today's errors include the following tasks: 1. Name: foldit1_2008492_0006_00_asym_dock_SAVE_ALL_OUT_1005840_1234 Task: 1239403625 on Amazon. 2. Name: foldit1_2001822_s003_00_asym_dock_SAVE_ALL_OUT_1005892_1233 Task: 1239397848 on Samsung. |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Name: simsjn_out_Protein_A_v5_contacts_36_7_L20L2L1L2L2L2L2L3L20_fragments_abinitio_SAVE_ALL_OUT_1006608_826_0 Application: Rosetta v4.20 windows_x86_64 Device: 1759960 Task: 1238685086. WU: 1110767160 Status: Error while computing Exit status: 1 (0x00000001) Unknown error code Stderr output: Incorrect function. |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Re: WU 1110767160 - simsjn_out_Protein_A_v5_contacts_36_7_L20L2L1L2L2L2L2L3L20_fragments_abinitio_SAVE_ALL_OUT_1006608_826_0 Just wanted to note that my wingman also got the same error as I, with notation "Too many errors (may have bug) Too many total results." |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
I continue to receive validation errors (8 total today) on my Android devices (3182472 and 3396190) for the foldit1 tasks. Again I question why these clearly erroneous tasks continue to be created! The batch in question today were created the morning of 8/14. What is to be gained by this waste of time, effort, and resources? The admins must know by now this particular set of tasks won't produce anything useful! Examples of the specific validation errors have previously been quoted by myself and others in this thread. Today's errors include the following tasks: 1. Name: foldit1_2008707_s008_00_asym_dock_SAVE_ALL_OUT_1005682_1795 Task: 1240650010 2. Name: foldit1_2008707_s007_00_asym_dock_SAVE_ALL_OUT_1005684_1795 Task: 1240650112 3. Name: foldit1_2008663_y239_00_asym_dock_SAVE_ALL_OUT_1005837_1622 Task: 1240466476 Etc. |
Grant (SSSF) Send message Joined: 28 Mar 20 Posts: 1725 Credit: 18,382,444 RAC: 19,446 |
The batch in question today were created the morning of 8/14. What is to be gained by this waste of time, effort, and resources? The admins must know by now this particular set of tasks won't produce anything useful!More importantly, the researcher submitting the jobs should have noticed that by now themselves. Grant Darwin NT |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 12,116,986 RAC: 9,863 |
The batch in question today were created the morning of 8/14. What is to be gained by this waste of time, effort, and resources? The admins must know by now this particular set of tasks won't produce anything useful!More importantly, the researcher submitting the jobs should have noticed that by now themselves. Not sure why everyone is all upset about this. The proportion of tasks going wrong is very small, and those that do go wrong only take 20 seconds to do so, so they don't waste your time, and probably help the programmers find out why they went wrong. |
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Number crunching :
Rosetta 4.1+ and 4.2+
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