Rosetta 4.1+ and 4.2+

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Profile [VENETO] boboviz

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Message 102512 - Posted: 31 Aug 2021, 16:39:02 UTC - in response to Message 102508.  
Last modified: 31 Aug 2021, 16:40:00 UTC

Those _5nvx_ degrader Tasks continue to produce nothing but errors.


This error was reported during test in Ralph.
I cannot understand why put in production these wus


I've just downloaded a batch of _5nvx_
Please, stop it (if there are admins who read the forum)
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Profile [VENETO] boboviz

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Message 102518 - Posted: 1 Sep 2021, 5:39:12 UTC - in response to Message 102512.  

I've just downloaded a batch of _5nvx_
Please, stop it (if there are admins who read the forum)


Still....
And no admins to stop the wus
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Profile [VENETO] boboviz

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Message 102523 - Posted: 1 Sep 2021, 10:08:12 UTC - in response to Message 102518.  

No, on Ralph, not only _5nvx_ error, but also other strange errors, like:

[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.

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Profile [VENETO] boboviz

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Message 102533 - Posted: 3 Sep 2021, 16:24:00 UTC

Still _5nvx_ on the road with the usual error....

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

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Message 102535 - Posted: 3 Sep 2021, 20:53:46 UTC - in response to Message 102533.  

Still _5nvx_ on the road with the usual error....

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
I have yet to see a single one of those Tasks run for longer than 2 minutes. 100% failure rate.
Barely an issue with any of the other degrader Tasks- it's just those _5nvx_ ones.
Grant
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Message 102892 - Posted: 6 Oct 2021, 11:01:55 UTC

Five errors all on the same computer.

CPU type Intel(R) Core(TM) i9-10850K CPU @ 3.60GHz [Family 6 Model 165 Stepping 5], 10 cores, 20 threads
Microsoft Windows 10 (Windows 11 Preview)
Professional x64 Edition, (10.00.22000.00)
Memory 32633.2 MB
Cache 256 KB
Swap space 52633.2 MB
Total disk space 231.73 GB
Free Disk Space 144.93 GB

Task 1433146193
Name 5nvx_graft_buwei_xaa_SAVE_ALL_OUT_IGNORE_THE_REST_6xp0ud7n_1731814_7_0
Workunit 1279020373
Created 5 Oct 2021, 7:58:38 UTC
Sent 5 Oct 2021, 9:00:03 UTC
Report deadline 8 Oct 2021, 9:00:03 UTC
Received 5 Oct 2021, 19:54:54 UTC
Server state Over
Outcome Validate error
Client state Done
Exit status 0 (0x00000000)
Computer ID 6145784
Run time 2 min 27 sec
CPU time 2 min 14 sec
Validate state Invalid
Credit 1.83
Device peak FLOPS 5.35 GFLOPS
Application version Rosetta v4.20
windows_x86_64
Peak working set size 1,171.66 MB
Peak swap size 1,157.65 MB
Peak disk usage 0.01 MB
Stderr output
<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10--fuse--predictor_v11_boinc_fix--fuse--tslp_design_v1_boinc_fix_plus6.xml @5nvx_graft_buwei_flags -in:file:silent 5nvx_graft_buwei_xaa_SAVE_ALL_OUT_IGNORE_THE_REST_6xp0ud7n.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 5nvx_graft_buwei_xaa_SAVE_ALL_OUT_IGNORE_THE_REST_6xp0ud7n.zip @5nvx_graft_buwei_xaa_SAVE_ALL_OUT_IGNORE_THE_REST_6xp0ud7n.flags -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 2879099
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: m_HHH_b1_05666_000000203_0001_1_18_H_._HHH_b2_04116_0001_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
15:27:46 (12172): called boinc_finish(0)

</stderr_txt>
]]>
Task 1433145641
Name 5nvx_graft_buwei_xab_SAVE_ALL_OUT_IGNORE_THE_REST_8or6ls4o_1731803_7_0
Workunit 1279019842
Created 5 Oct 2021, 7:58:32 UTC
Sent 5 Oct 2021, 8:58:25 UTC
Report deadline 8 Oct 2021, 8:58:25 UTC
Received 5 Oct 2021, 19:54:54 UTC
Server state Over
Outcome Validate error
Client state Done
Exit status 0 (0x00000000)
Computer ID 6145784
Run time 2 min 4 sec
CPU time 1 min 45 sec
Validate state Invalid
Credit 1.54
Device peak FLOPS 5.35 GFLOPS
Application version Rosetta v4.20
windows_x86_64
Peak working set size 1,163.05 MB
Peak swap size 1,149.98 MB
Peak disk usage 0.01 MB
Stderr output
<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10--fuse--predictor_v11_boinc_fix--fuse--tslp_design_v1_boinc_fix_plus6.xml @5nvx_graft_buwei_flags -in:file:silent 5nvx_graft_buwei_xab_SAVE_ALL_OUT_IGNORE_THE_REST_8or6ls4o.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 5nvx_graft_buwei_xab_SAVE_ALL_OUT_IGNORE_THE_REST_8or6ls4o.zip @5nvx_graft_buwei_xab_SAVE_ALL_OUT_IGNORE_THE_REST_8or6ls4o.flags -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 3991014
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: m_HHH_b2_05875_000000038_0001_18_34_H_._HHH_b1_07609_0002_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
15:23:08 (12720): called boinc_finish(0)

</stderr_txt>
]]>
Task 1433145664
ame 5nvx_graft_buwei_xac_SAVE_ALL_OUT_IGNORE_THE_REST_4xa0nd1n_1731806_7_0
Workunit 1279019845
Created 5 Oct 2021, 7:58:32 UTC
Sent 5 Oct 2021, 8:58:25 UTC
Report deadline 8 Oct 2021, 8:58:25 UTC
Received 5 Oct 2021, 19:54:54 UTC
Server state Over
Outcome Validate error
Client state Done
Exit status 0 (0x00000000)
Computer ID 6145784
Run time 2 min 9 sec
CPU time 1 min 49 sec
Validate state Invalid
Credit 1.60
Device peak FLOPS 5.35 GFLOPS
Application version Rosetta v4.20
windows_x86_64
Peak working set size 1,175.30 MB
Peak swap size 1,161.47 MB
Peak disk usage 0.79 MB
Stderr output
<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10--fuse--predictor_v11_boinc_fix--fuse--tslp_design_v1_boinc_fix_plus6.xml @5nvx_graft_buwei_flags -in:file:silent 5nvx_graft_buwei_xac_SAVE_ALL_OUT_IGNORE_THE_REST_4xa0nd1n.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 5nvx_graft_buwei_xac_SAVE_ALL_OUT_IGNORE_THE_REST_4xa0nd1n.zip @5nvx_graft_buwei_xac_SAVE_ALL_OUT_IGNORE_THE_REST_4xa0nd1n.flags -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 2680294
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: m_HHH_b1_00125_000000240_0001_19_36_H_._HHH_b1_05096_0001_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
15:25:17 (12492): called boinc_finish(0)

</stderr_txt>
]]>
Task 1433079377
Name 5nvx_graft_buwei_xac_SAVE_ALL_OUT_IGNORE_THE_REST_0dc3dy2e_1731806_7_0
Workunit 1278960465
Created 5 Oct 2021, 3:49:05 UTC
Sent 5 Oct 2021, 5:06:11 UTC
Report deadline 8 Oct 2021, 5:06:11 UTC
Received 5 Oct 2021, 12:55:19 UTC
Server state Over
Outcome Validate error
Client state Done
Exit status 0 (0x00000000)
Computer ID 6145784
Run time 2 min 48 sec
CPU time 2 min 21 sec
Validate state Invalid
Credit 2.08
Device peak FLOPS 5.35 GFLOPS
Application version Rosetta v4.20
windows_x86_64
Peak working set size 1,191.39 MB
Peak swap size 1,175.93 MB
Peak disk usage 0.87 MB
Stderr output
<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10--fuse--predictor_v11_boinc_fix--fuse--tslp_design_v1_boinc_fix_plus6.xml @5nvx_graft_buwei_flags -in:file:silent 5nvx_graft_buwei_xac_SAVE_ALL_OUT_IGNORE_THE_REST_0dc3dy2e.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 5nvx_graft_buwei_xac_SAVE_ALL_OUT_IGNORE_THE_REST_0dc3dy2e.zip @5nvx_graft_buwei_xac_SAVE_ALL_OUT_IGNORE_THE_REST_0dc3dy2e.flags -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 2777854
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: m_171548745b05b7c12176029d879d94b1_0001_000000162_0001_16_33_H_._HHH_b1_06566_0001_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
08:49:02 (6632): called boinc_finish(0)

</stderr_txt>
]]>
Task 1433060450
Name 5nvx_graft_buwei_xaa_SAVE_ALL_OUT_IGNORE_THE_REST_2nx3zn0r_1731815_7_0
Workunit 1278943653
Created 5 Oct 2021, 2:29:50 UTC
Sent 5 Oct 2021, 3:49:28 UTC
Report deadline 8 Oct 2021, 3:49:28 UTC
Received 5 Oct 2021, 12:40:44 UTC
Server state Over
Outcome Validate error
Client state Done
Exit status 0 (0x00000000)
Computer ID 6145784
Run time 2 min 41 sec
CPU time 2 min 26 sec
Validate state Invalid
Credit 2.00
Device peak FLOPS 5.35 GFLOPS
Application version Rosetta v4.20
windows_x86_64
Peak working set size 1,182.08 MB
Peak swap size 1,166.28 MB
Peak disk usage 0.80 MB
Stderr output
<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10--fuse--predictor_v11_boinc_fix--fuse--tslp_design_v1_boinc_fix_plus6.xml @5nvx_graft_buwei_flags -in:file:silent 5nvx_graft_buwei_xaa_SAVE_ALL_OUT_IGNORE_THE_REST_2nx3zn0r.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 5nvx_graft_buwei_xaa_SAVE_ALL_OUT_IGNORE_THE_REST_2nx3zn0r.zip @5nvx_graft_buwei_xaa_SAVE_ALL_OUT_IGNORE_THE_REST_2nx3zn0r.flags -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 1922019
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: m_HHH_b1_00589_000000109_0001_20_37_H_._HHH_b2_07773_0004_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
08:29:51 (14428): called boinc_finish(0)

</stderr_txt>
]]>
[/size]
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Profile Grant (SSSF)

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Message 102896 - Posted: 7 Oct 2021, 7:59:24 UTC - in response to Message 102892.  
Last modified: 7 Oct 2021, 7:59:40 UTC

Five errors all on the same computer.
ERROR: [ERROR] Unable to open constraints file: m_HHH_b1_05666_000000203_0001_1_18_H_._HHH_b2_04116_0001_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
15:27:46 (12172): called boinc_finish(0)
It's been an issue with some of those 5nvx_graft_buwei_ Tasks since they were first released.
Grant
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Profile [VENETO] boboviz

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Message 102982 - Posted: 19 Oct 2021, 9:13:43 UTC - in response to Message 102896.  

Five errors all on the same computer.
ERROR: [ERROR] Unable to open constraints file: m_HHH_b1_05666_000000203_0001_1_18_H_._HHH_b2_04116_0001_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
15:27:46 (12172): called boinc_finish(0)
It's been an issue with some of those 5nvx_graft_buwei_ Tasks since they were first released.


Issue still not solved...
1439065844
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Sid Celery

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Message 102992 - Posted: 20 Oct 2021, 16:16:34 UTC - in response to Message 102982.  

Five errors all on the same computer.
ERROR: [ERROR] Unable to open constraints file: m_HHH_b1_05666_000000203_0001_1_18_H_._HHH_b2_04116_0001_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
15:27:46 (12172): called boinc_finish(0)
It's been an issue with some of those 5nvx_graft_buwei_ Tasks since they were first released.

Issue still not solved...
1439065844

It's not going to be solved.
The runtime is so short it's a non-issue for users and the task of extracting them from tasks issued would take out too many perfectly good tasks, so they're going to be allowed to run, stop in minutes, credit anything over a minute or so runtime and weed them out that way.

And it'll be the same the next time someone points out the same thing over and over and over again
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Profile [VENETO] boboviz

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Message 103036 - Posted: 27 Oct 2021, 21:26:49 UTC

1442378790
1442378827
1442377552
etc

[ ERROR ]: Caught exception:


File: C:cygwin64homeboinc4.17Rosettamainsourcesrccore/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306
chi angle must be between -180 and 180: -nan(ind)
------------------------ Begin developer's backtrace -------------------------
BACKTRACE:
------------------------- End developer's backtrace --------------------------


AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

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Profile Grant (SSSF)

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Message 103916 - Posted: 26 Dec 2021, 23:27:52 UTC

Looks like a small batch of Rosetta 4.20 Tasks have been released, but unless they release a lot more they won't last long.
2 hours is the longest Runtime so far, only 22min for the shortest.
Grant
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Profile Grant (SSSF)

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Message 103919 - Posted: 27 Dec 2021, 9:24:07 UTC

And it looks like we've finished off that last batch of Rosetta 4.20 work.
Grant
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Greger

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Message 105445 - Posted: 15 Mar 2022, 18:49:36 UTC
Last modified: 15 Mar 2022, 19:06:27 UTC

Stderr output
<core_client_version>7.16.11</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu @preetham_gen_127_0001_0001_0.flags -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 1753783
Using database: database_357d5d93529_n_methyl/minirosetta_database

ERROR: Error in simple_cycpcp_predict app read_sequence() function!  The minimum number of residues for a cyclic peptide is 4.  (GenKIC requires three residues, plus a fourth to serve as an anchor).
ERROR:: Exit from: src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.cc line: 2264
BOINC:: Error reading and gzipping output datafile: default.out
11:21:46 (108818): called boinc_finish(1)

</stderr_txt>
]]>


Looks like it is a batch to "preetham_gen" units that affect host. all these error out after a few sec but not other units.
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MStenholm

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Message 105446 - Posted: 15 Mar 2022, 19:01:31 UTC - in response to Message 105445.  

Same thing on three Ubuntu systems.
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Jean-David Beyer

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Message 105447 - Posted: 15 Mar 2022, 19:35:04 UTC - in response to Message 105445.  

Me too. Running on Dell 5820 using Red Hat Enterprise Linux 8.5. Previous work units a few days ago worked just fine.
Here is one of them.

Task 1476864257
Name preetham_gen_25772_0001_0001_0_SAVE_ALL_OUT_2911448_79_1
Workunit 1315344093
Created 15 Mar 2022, 19:17:55 UTC
Sent 15 Mar 2022, 19:20:29 UTC
Report deadline 18 Mar 2022, 19:20:29 UTC
Received 15 Mar 2022, 19:25:39 UTC
Server state Over
Outcome Computation error
Client state Compute error
Exit status 1 (0x00000001) Unknown error code
Computer ID 5910575
Run time 30 sec
CPU time 18 sec
Validate state Invalid
Credit 0.00
Device peak FLOPS 6.58 GFLOPS
Application version Rosetta v4.20
x86_64-pc-linux-gnu
Peak working set size 291.81 MB
Peak swap size 361.26 MB
Peak disk usage 23.86 MB
Stderr output

<core_client_version>7.16.11</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu @preetham_gen_25772_0001_0001_0.flags -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 1573800
Using database: database_357d5d93529_n_methyl/minirosetta_database

ERROR: Error in simple_cycpcp_predict app read_sequence() function! The minimum number of residues for a cyclic peptide is 4. (GenKIC requires three residues, plus a fourth to serve as an anchor).
ERROR:: Exit from: src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.cc line: 2264
BOINC:: Error reading and gzipping output datafile: default.out
15:21:02 (182770): called boinc_finish(1)

</stderr_txt>
]]>
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Jean-David Beyer

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Message 105448 - Posted: 15 Mar 2022, 19:53:58 UTC - in response to Message 105447.  

I stopped getting new tasks. I seem to have failed over 130 (all of them) I got today.
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Profile [VENETO] boboviz

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Message 105449 - Posted: 15 Mar 2022, 20:36:10 UTC - in response to Message 105445.  

ERROR: Error in simple_cycpcp_predict app read_sequence() function!  The minimum number of residues for a cyclic peptide is 4.  (GenKIC requires three residues, plus a fourth to serve as an anchor).
ERROR:: Exit from: src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.cc line: 2264
BOINC:: Error reading and gzipping output datafile: default.out
11:21:46 (108818): called boinc_finish(1)

</stderr_txt>
]]>


Looks like it is a batch to "preetham_gen" units that affect host. all these error out after a few sec but not other units.


Same error on my win11 machines.
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XMARK
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Message 105450 - Posted: 15 Mar 2022, 21:07:39 UTC - in response to Message 105449.  

same problem here, ~50 attempts. switched off new downloads. has anyone had a response?
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.clair.

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Message 105451 - Posted: 15 Mar 2022, 21:20:53 UTC

Rosetta realy has gone downhill , backwards , badly .
Its like trying to run an `alpha` project where the admin haven't got their act together yet ,
Just more badly prepared non working units that crap out on both M$ and Linux this time.
and it looks like there is over a million of them to get through.
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Jean-David Beyer

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Message 105452 - Posted: 15 Mar 2022, 21:38:08 UTC - in response to Message 105451.  

Just more badly prepared non working units that crap out on both M$ and Linux this time.
and it looks like there is over a million of them to get through.


Should I resume accepting new work units so that Rosetta@home will get through those? Is there no-one there who can delete those at the server end?
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Message boards : Number crunching : Rosetta 4.1+ and 4.2+



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