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Profile [VENETO] boboviz

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Message 7033 - Posted: 24 Aug 2021, 10:36:01 UTC

On my Ryzen/Windows 10, all wus "degrader_site_4yc9_" failed after few seconds:
<stderr_txt>
command: projects/ralph.bakerlab.org/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10_tfirst--fuse--predictor_v13_degrader_plait_boinc--fuse--tslp_design_v2_degrader_plait_boinc.xml @degrader_site_4yc9_0_plait_-2.5_bcov_flags -in:file:silent degrader_site_4yc9_0_plait_-2.5_bcov_SAVE_ALL_OUT_IGNORE_THE_REST_8tb3kj5y.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip degrader_site_4yc9_0_plait_-2.5_bcov_SAVE_ALL_OUT_IGNORE_THE_REST_8tb3kj5y.zip @degrader_site_4yc9_0_plait_-2.5_bcov_SAVE_ALL_OUT_IGNORE_THE_REST_8tb3kj5y.flags -nstruct 10000 -cpu_run_time 3600 -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 3814192
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: Cannot find file 'mnthomebcovscdesigndegraderstructuresparams24yc9_0.params or minirosetta_databasechemical/residue_type_sets/fa_standard/residue_types/mnthomebcovscdesigndegraderstructuresparams24yc9_0.params'
ERROR:: Exit from: ......srccorechemicalresidue_io.cc line: 144
BOINC:: Error reading and gzipping output datafile: default.out
03:44:58 (5144): called boinc_finish(1)

</stderr_txt>
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Profile [VENETO] boboviz

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Message 7034 - Posted: 24 Aug 2021, 13:17:13 UTC - in response to Message 7033.  

On my Ryzen/Windows 10, all wus "degrader_site_4yc9_" failed after few seconds:


Also on my Intel mobile cpu....
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Message 7035 - Posted: 24 Aug 2021, 13:18:10 UTC

Same on my end on a Win10 host.
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Message 7036 - Posted: 24 Aug 2021, 18:31:59 UTC

Same on all my Linux systems
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Profile [VENETO] boboviz

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Message 7037 - Posted: 24 Aug 2021, 20:11:43 UTC
Last modified: 24 Aug 2021, 20:13:49 UTC

Also some validation errors after 3 minutes:
ERROR: index has exceeded selection range! Set=69 range_size=0
index has exceeded selection range! Set=70 range_size=0
set "-out:levels core.select.residue_selector.SliceResidueSelector:400" to debug!
ERROR:: Exit from: ......srccoreselectresidue_selectorSliceResidueSelector.cc line: 184
22:10:44 (1504): called boinc_finish(0)


Please, admin, stop this batch!!
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Profile [VENETO] boboviz

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Message 7038 - Posted: 24 Aug 2021, 20:15:05 UTC - in response to Message 7036.  

Same on all my Linux systems

I'm trying a linux machine.
All errors also here.
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Profile [VENETO] boboviz

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Message 7039 - Posted: 24 Aug 2021, 20:21:12 UTC - in response to Message 7037.  

Also some validation errors after 3 minutes:
ERROR: index has exceeded selection range! Set=69 range_size=0
index has exceeded selection range! Set=70 range_size=0
set "-out:levels core.select.residue_selector.SliceResidueSelector:400" to debug!
ERROR:: Exit from: ......srccoreselectresidue_selectorSliceResidueSelector.cc line: 184
22:10:44 (1504): called boinc_finish(0)


Please, admin, stop this batch!!


And other validation errors
ERROR: index has exceeded selection range! Set=10 range_size=0
index has exceeded selection range! Set=36 range_size=0
index has exceeded selection range! Set=37 range_size=0
index has exceeded selection range! Set=38 range_size=0
index has exceeded selection range! Set=51 range_size=0
set "-out:levels core.select.residue_selector.SliceResidueSelector:400" to debug!
ERROR:: Exit from: src/core/select/residue_selector/SliceResidueSelector.cc line: 184
22:17:11 (2774): called boinc_finish(0)
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Message 7040 - Posted: 24 Aug 2021, 22:10:00 UTC - in response to Message 7039.  

Virtually identical errors on arm64 ubuntu 20.04.2
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Message 7041 - Posted: 25 Aug 2021, 14:55:47 UTC

Still downloads and still errors
Please, stop it!
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Message 7042 - Posted: 25 Aug 2021, 19:12:22 UTC

New batch seems better....
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Message 7043 - Posted: 28 Aug 2021, 19:49:13 UTC

After a lot of good wus, new kinds of error:
5342641
ERROR: ERROR: Unable to open file %%id111%%.pssm!
ERROR:: Exit from: ......srccoresequenceSequenceProfile.cc line: 256
BOINC:: Error reading and gzipping output datafile: default.out
21:37:23 (7832): called boinc_finish(1)



5342574
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose.
ERROR:: Exit from: C:cygwin64homeboinc4.17Rosettamainsourcesrccore/conformation/Conformation.hh line: 508
BOINC:: Error reading and gzipping output datafile: default.out
21:37:43 (6184): called boinc_finish(1)
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Message 7044 - Posted: 31 Aug 2021, 4:02:36 UTC
Last modified: 31 Aug 2021, 4:04:54 UTC

55 WUs downloaded, 33 errored almost immediately with :-

ERROR: Cannot find file '/mnt/home/bcov/sc/design/degrader/structures/params2/NXXX.params or minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types//mnt/home/bcov/sc/design/degrader/structures/params2/NXXX.params'
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 144
BOINC:: Error reading and gzipping output datafile: default.out
03:07:07 (112938): called boinc_finish(1)

</stderr_txt>


The other 22 processed and valid.
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Profile [VENETO] boboviz

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Message 7045 - Posted: 1 Sep 2021, 9:48:19 UTC - in response to Message 7044.  

Another different error 5351337

ERROR: [ERROR] relaxscript argument fast_cart_no_ref_rosettacon2018_beta_nov16.txt should not have extensions. Additionally, fast_cart_no_ref_rosettacon2018_beta_nov16 does not appear to be a valid script name. Please look at main/database/sampling/relax_scripts/ or the wiki for valid names.
ERROR:: Exit from: ......srcprotocolsrelaxRelaxScriptManager.cc line: 168
BOINC:: Error reading and gzipping output datafile: default.out
11:44:01 (4100): called boinc_finish(1)
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Profile [VENETO] boboviz

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Message 7046 - Posted: 1 Sep 2021, 18:07:53 UTC
Last modified: 1 Sep 2021, 18:08:00 UTC

Other errors 5352485
ERROR: Called Constraint::remap_resid method from derived class UNKNOWN_TYPE,ended up in Constraint::remap_resid

ERROR:: Exit from: ......srccorescoringconstraintsConstraint.cc line: 188
BOINC:: Error reading and gzipping output datafile: default.out
19:44:57 (10712): called boinc_finish(1)
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Bryn Mawr

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Message 7047 - Posted: 1 Sep 2021, 18:11:37 UTC - in response to Message 7046.  
Last modified: 1 Sep 2021, 18:14:24 UTC

Other errors 5352485
ERROR: Called Constraint::remap_resid method from derived class UNKNOWN_TYPE,ended up in Constraint::remap_resid

ERROR:: Exit from: ......srccorescoringconstraintsConstraint.cc line: 188
BOINC:: Error reading and gzipping output datafile: default.out
19:44:57 (10712): called boinc_finish(1)


Just come in to report exactly the same error :-)

Task 5352904

ETA Plus 4 more, all 5nvx
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Message 7048 - Posted: 1 Sep 2021, 21:19:04 UTC
Last modified: 1 Sep 2021, 21:41:47 UTC

Mixed picture for me. About 50% of the tasks get validated. About 10% are deemed invalid and the remaining 40% have an error while computing listed.

In all tasks be it invalid or valid I do see the following errors listed in the stderr file.
ERROR: Called Constraint::remap_resid method from derived class UNKNOWN_TYPE,ended up in Constraint::remap_resid
ERROR:: Exit from: ......srccorescoringconstraintsConstraint.cc line: 188

For the error during computation ones I see the following quite often:
ERROR: ERROR: Unable to open file %%id040%%.pssm!
ERROR:: Exit from: ......srccoresequenceSequenceProfile.cc line: 256
BOINC:: Error reading and gzipping output datafile: default.out
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Message 7050 - Posted: 2 Sep 2021, 9:39:27 UTC - in response to Message 7048.  

In all tasks be it invalid or valid I do see the following errors listed in the stderr file.
ERROR: Called Constraint::remap_resid method from derived class UNKNOWN_TYPE,ended up in Constraint::remap_resid
ERROR:: Exit from: ......srccorescoringconstraintsConstraint.cc line: 188


Same here. This error is on valid and invalid wus.
My default runtime is 2h, but these wus finish after 15/20 minutes
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TH1813254617

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Message 7051 - Posted: 4 Sep 2021, 8:55:53 UTC - in response to Message 7050.  
Last modified: 4 Sep 2021, 8:56:05 UTC

Another task whose status is " Completed and validated" but actually errored out in 7 min 18 sec (I'm using the default run time).

degrader_site_4yc9_0_plait_-2.5_bcov_20.hbnet_4_SAVE_ALL_OUT_IGNORE_THE_REST_8qm1er0f_16181_1_1
<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/ralph.bakerlab.org/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10_tfirst--fuse--predictor_v13_degrader_plait_boinc--fuse--tslp_design_v2_degrader_plait_boinc.xml @degrader_site_4yc9_0_plait_-2.5_bcov_flags2 -in:file:silent degrader_site_4yc9_0_plait_-2.5_bcov_20.hbnet_4_SAVE_ALL_OUT_IGNORE_THE_REST_8qm1er0f.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip degrader_site_4yc9_0_plait_-2.5_bcov_20.hbnet_4_SAVE_ALL_OUT_IGNORE_THE_REST_8qm1er0f.zip @degrader_site_4yc9_0_plait_-2.5_bcov_20.hbnet_4_SAVE_ALL_OUT_IGNORE_THE_REST_8qm1er0f.flags -nstruct 10000 -cpu_run_time 3600 -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 3799928
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: Called Constraint::remap_resid method from derived class UNKNOWN_TYPE,ended up in Constraint::remap_resid

ERROR:: Exit from: ......srccorescoringconstraintsConstraint.cc line: 188
08:20:06 (8856): called boinc_finish(0)

</stderr_txt>
]]>


That'd be three errors out of three WUs.

The other two in late August resulted in:
ERROR: Cannot find file 'mnthomebcovscdesigndegraderstructuresparams23mup.params or minirosetta_databasechemical/residue_type_sets/fa_standard/residue_types/mnthomebcovscdesigndegraderstructuresparams23mup.params'
ERROR:: Exit from: ......srccorechemicalresidue_io.cc line: 144
BOINC:: Error reading and gzipping output datafile: default.out
22:52:06 (11012): called boinc_finish(1)
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Profile [VENETO] boboviz

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Message 7052 - Posted: 5 Sep 2021, 17:41:17 UTC - in response to Message 7050.  

In all tasks be it invalid or valid I do see the following errors listed in the stderr file.
ERROR: Called Constraint::remap_resid method from derived class UNKNOWN_TYPE,ended up in Constraint::remap_resid
ERROR:: Exit from: ......srccorescoringconstraintsConstraint.cc line: 188


Same here. This error is on valid and invalid wus.
My default runtime is 2h, but these wus finish after 15/20 minutes


Still a lot of these errors....
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Message 7053 - Posted: 6 Sep 2021, 13:55:36 UTC

Surprisingly, I did have two tasks in the current batch complete successfully, but the vast majority failed the same way as others have reported here.
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Message boards : RALPH@home bug list : All fail



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