Rosetta 4.1+ and 4.2+

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Profile Grant (SSSF)

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Message 100534 - Posted: 4 Feb 2021, 1:49:42 UTC

A whole bunch of ea00010f_nav1-7 Tasks crashed and burnt within seconds of starting. Have probably got only a 50% success rate for these Tasks at present.
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Sid Celery

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Message 100536 - Posted: 4 Feb 2021, 3:26:58 UTC - in response to Message 100534.  

A whole bunch of ea00010f_nav1-7 Tasks crashed and burnt within seconds of starting. Have probably got only a 50% success rate for these Tasks at present.

Ditto

Also the following crash in the same way, but after some hours running:
XW_JG_11222020_A_E5_BBEAA_H15_BAAB_E5_ABBB_E5_BAB_H14_BAAB_E5_1_20201115012036_combined_0001_0001_fold_SAVE_ALL_OUT_1039435_834_0
XW_JG_11222020_A_E5_BBEAA_H16_GB_E5_AEAB_E5_BAB_H14_BAAB_E5_1_20201115003503_combined_0001_0001_fold_SAVE_ALL_OUT_1036527_874_0
XW_JG_11222020_A_E5_BBEAA_H16_GB_E5_GAAA_E5_GBB_H14_BAAB_E5_1_20201115010844_combined_0001_0001_fold_SAVE_ALL_OUT_1039302_876_0
XW_JG_11222020_A_E5_BBEAA_H16_GB_E5_EAAA_E5_BAB_H14_BAAB_E5_1_20201115005359_combined_0001_0001_fold_SAVE_ALL_OUT_1041485_880_0
XW_JG_11222020_A_E5_BBEAA_H15_BAAB_E5_GGG_E5_BAB_H14_BAAB_E5_1_20201115010538_combined_0001_0001_fold_SAVE_ALL_OUT_1043178_888_0
XW_JG_11222020_A_E5_BBEAA_H15_BAAB_E5_BABE_E5_BAB_H14_BAAB_E5_1_20201115002019_combined_0001_0001_fold_SAVE_ALL_OUT_1038891_907_0
XW_JG_11222020_A_E5_BBEAA_H15_BAAB_E5_GEG_E5_BAB_H14_BAAB_E5_1_20201113180034_combined_0001_0001_fold_SAVE_ALL_OUT_1039676_912_0
XW_JG_11222020_A_E5_BBEAA_H16_GB_E5_GBAG_E5_BAB_H14_BAAB_E5_1_20201115005214_combined_0001_0001_fold_SAVE_ALL_OUT_1038560_915_0
XW_JG_11222020_A_E5_BBEAA_H16_GB_E5_GAA_E5_GBB_H14_BAAB_E5_1_20201115003127_combined_0001_0001_fold_SAVE_ALL_OUT_1036333_916_0
XW_JG_11222020_A_E5_BBEAA_H15_BAAB_E5_EEBG_E5_BAB_H14_BAAB_E5_1_20201115002608_combined_0001_0001_fold_SAVE_ALL_OUT_1041275_918_0
XW_JG_11222020_A_E5_BBEAA_H15_BAAB_E5_EBEG_E5_BAB_H14_BAAB_E5_1_20201115011731_combined_0001_0001_fold_SAVE_ALL_OUT_1040851_919_0
XW_JG_11222020_A_E5_BBEAA_H16_BAAB_E5_GBA_E5_BAB_H14_BAAB_E5_1_20201114234748_combined_0001_0001_fold_SAVE_ALL_OUT_1038996_921_0

rb_02_01_54553_53700_ab_t000__robetta_IGNORE_THE_REST_11_18_1060010_3_0

gmcsf.culled_gmcsf060_fragments_fold_SAVE_ALL_OUT_1059765_685_0


And the following come up with the following error after some hours running
[ ERROR ]: Caught exception:
File: ......srcprotocolsmotif_graftingmoversMotifGraftMover.cc:537
For this scaffold there are not suitable scaffold grafts within your constrains

tslp_site2_5j13_graft_bcov_design_v1_SAVE_ALL_OUT_IGNORE_THE_REST_3rf2hv7u_1059456_1_0
tnfa_site1_5m2j_graft_bcov_design_v1_SAVE_ALL_OUT_IGNORE_THE_REST_3on2fo6d_1059217_1_0
il4r_alpha_site1_6wgl_graft_bcov_design_v1_SAVE_ALL_OUT_IGNORE_THE_REST_6dz2xf8c_1059371_1_0
il4r_alpha_site2_3bpl_graft_bcov_design_v1_SAVE_ALL_OUT_IGNORE_THE_REST_8fq4il7y_1059469_1_1
il4r_alpha_site2_6wgl_graft_bcov_design_v1_SAVE_ALL_OUT_IGNORE_THE_REST_6ar7db9w_1059455_1_0
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Plomos

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Message 100564 - Posted: 7 Feb 2021, 16:12:17 UTC
Last modified: 7 Feb 2021, 16:12:52 UTC

I also had at least one of these error out because of no suitable grafts

https://boinc.bakerlab.org/rosetta/result.php?resultid=1332257408
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Profile [VENETO] boboviz

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Message 100576 - Posted: 8 Feb 2021, 13:12:31 UTC - in response to Message 100536.  

And the following come up with the following error after some hours running
[ ERROR ]: Caught exception:
File: ......srcprotocolsmotif_graftingmoversMotifGraftMover.cc:537
For this scaffold there are not suitable scaffold grafts within your constrains


Since August...
MotifGraftMover.cc:537
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Kissagogo27

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Message 100627 - Posted: 17 Feb 2021, 10:55:21 UTC

HHh00003_dummy_0001_281_abinitio_SAVE_ALL_OUT_1210531_234
Tâche
cliquer pour voir les détails	Ordinateur	Envoyé	Délai reporté
ou date limite 
explication	État	Temps de fonctionnement
(sec)	Temps de CPU
(sec)	Crédit	Application
1336791021	4183655	16 Feb 2021, 3:42:46 UTC	16 Feb 2021, 11:40:27 UTC	Erreur en cours de calculs	11.61	3.25	---	Rosetta v4.20 
windows_x86_64
1337008354	3984635	16 Feb 2021, 11:50:43 UTC	16 Feb 2021, 18:49:38 UTC	Erreur en cours de calculs	9.42	2.64	---	Rosetta v4.20 
windows_x86_64



HhH00003_dummy_0003_14_abinitio_SAVE_ALL_OUT_1210430_35
1336630206	6011180	15 Feb 2021, 19:48:50 UTC	16 Feb 2021, 18:54:11 UTC	Erreur en cours de calculs	14.71	3.29	---	Rosetta v4.20 
windows_x86_64
1337178671	5879499	16 Feb 2021, 19:00:53 UTC	17 Feb 2021, 3:02:30 UTC	Terminé et validé	28,751.59	28,705.30	277.88	Rosetta v4.20 
x86_64-pc-linux-gnu


Errored out with Windows but not with Linux ^^
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Jim1348

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Message 100629 - Posted: 17 Feb 2021, 15:51:58 UTC - in response to Message 100627.  

Errored out with Windows but not with Linux ^^

Yes, I see the same thing on Win10, but not on Ubuntu 18.04/20.04.
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Bryn Mawr

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Message 100718 - Posted: 12 Mar 2021, 19:09:06 UTC

For the first time in a long time I’ve had two WUs error out on me :-

https://boinc.bakerlab.org/rosetta/result.php?resultid=1350127477

https://boinc.bakerlab.org/rosetta/result.php?resultid=1350498193



The common part of the task name is _clean_0001_E110_Y29_S98d2bmob1_clean_0001_*.rd1.silent_nornMar01__

Although this might mean nothing as I have 7 valid WUs with the same naming.


The error message is :-

terminate called after throwing an instance of 'std::out_of_range'
what(): map::at

One wingman errored out with out of memory and the other completed and validated.
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mikey
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Message 100724 - Posted: 13 Mar 2021, 4:54:03 UTC - in response to Message 100718.  

For the first time in a long time I’ve had two WUs error out on me :-

https://boinc.bakerlab.org/rosetta/result.php?resultid=1350127477

https://boinc.bakerlab.org/rosetta/result.php?resultid=1350498193



The common part of the task name is _clean_0001_E110_Y29_S98d2bmob1_clean_0001_*.rd1.silent_nornMar01__

Although this might mean nothing as I have 7 valid WUs with the same naming.


The error message is :-

terminate called after throwing an instance of 'std::out_of_range'
what(): map::at

One wingman errored out with out of memory and the other completed and validated.


I wonder if it could be the lack of onboard gpu memory? You have 972mb of onboard gpu memory on one gpu and 978mb of memory on your gpu in other pc...I wonder if it's border line now? I know Einstein is sending out their GW tasks that require a gpu with at least 4gb or they regularly fail. As each project makes new tasks I wonder if they are pushing the envelope a bit?
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Bryn Mawr

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Message 100725 - Posted: 13 Mar 2021, 6:51:46 UTC - in response to Message 100724.  

For the first time in a long time I’ve had two WUs error out on me :-

https://boinc.bakerlab.org/rosetta/result.php?resultid=1350127477

https://boinc.bakerlab.org/rosetta/result.php?resultid=1350498193



The common part of the task name is _clean_0001_E110_Y29_S98d2bmob1_clean_0001_*.rd1.silent_nornMar01__

Although this might mean nothing as I have 7 valid WUs with the same naming.


The error message is :-

terminate called after throwing an instance of 'std::out_of_range'
what(): map::at

One wingman errored out with out of memory and the other completed and validated.


I wonder if it could be the lack of onboard gpu memory? You have 972mb of onboard gpu memory on one gpu and 978mb of memory on your gpu in other pc...I wonder if it's border line now? I know Einstein is sending out their GW tasks that require a gpu with at least 4gb or they regularly fail. As each project makes new tasks I wonder if they are pushing the envelope a bit?


But surely Rosetta is CPU only?
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Brian Nixon

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Message 100728 - Posted: 13 Mar 2021, 12:56:13 UTC - in response to Message 100718.  

The error message is :-

terminate called after throwing an instance of 'std::out_of_range'
  what():  map::at


One wingman errored out with out of memory

Those will be different manifestations of the same error. Linux is reporting the actual problem; Windows has a catch-all “(C++ Exception)” message. “Out Of Memory” is a red herring: any unhandled C++ exception will yield that message.

What will be happening is that the code is looking up a value in a data structure, expecting to find it – and because it doesn’t handle the case where the value is not present, it cannot continue. As Rosetta is massively data-driven it’s no surprise that this can happen on some workunits but not others (and not be caught in pre-release testing, which can only cover a small subset of the space explored after the batch of work is released to BOINC).
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Bryn Mawr

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Message 100730 - Posted: 13 Mar 2021, 14:37:28 UTC - in response to Message 100728.  

The error message is :-

terminate called after throwing an instance of 'std::out_of_range'
  what():  map::at


One wingman errored out with out of memory

Those will be different manifestations of the same error. Linux is reporting the actual problem; Windows has a catch-all “(C++ Exception)” message. “Out Of Memory” is a red herring: any unhandled C++ exception will yield that message.

What will be happening is that the code is looking up a value in a data structure, expecting to find it – and because it doesn’t handle the case where the value is not present, it cannot continue. As Rosetta is massively data-driven it’s no surprise that this can happen on some workunits but not others (and not be caught in pre-release testing, which can only cover a small subset of the space explored after the batch of work is released to BOINC).


Many thanks, nothing I can do about it so carry on as normal seems to be the message :-)
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Brian Nixon

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Message 100732 - Posted: 13 Mar 2021, 16:13:32 UTC - in response to Message 100730.  

Thank you for prompting me to investigate. I’ve had a handful of errors from those NornMar01 tasks myself, and had been mystified by the “Out of Memory” messages, as with 2 GB per core memory generally ought not to be a problem on my machines. I had just never happened upon a case where the other task had gone to a Linux host, so I didn’t see the message with the real cause until you pointed it out.
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Profile [VENETO] boboviz

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Message 102260 - Posted: 22 Jul 2021, 6:40:45 UTC

Some of these (pre_helical_bundles_round1_attempt1):
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pre_helix_boinc_v1.xml @helix_design.flags -in:file:silent pre_helical_bundles_round1_attempt1_SAVE_ALL_OUT_IGNORE_THE_REST_0vf8tj0z.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 pre_helical_bundles_round1_attempt1_SAVE_ALL_OUT_IGNORE_THE_REST_0vf8tj0z.zip @pre_helical_bundles_round1_attempt1_SAVE_ALL_OUT_IGNORE_THE_REST_0vf8tj0z.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 2089611
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: fb83ef25ead00d913a0ce3ba5abb4f94_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
08:32:46 (10468): called boinc_finish(0)

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Tomcat雄猫

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Message 102269 - Posted: 23 Jul 2021, 9:03:43 UTC - in response to Message 102260.  
Last modified: 23 Jul 2021, 9:05:15 UTC

Hmm, I wonder what this means:

Stderr output

<core_client_version>7.16.16</core_client_version>
<![CDATA[
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu -run:protocol jd2_scripting @flags_rb_07_21_95009_92489__t000__0_C3_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_07_21_95009_92489__t000__0_C3_robetta.zip -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 1258034
Extracting in project directory: database_357d5d93529_n_methyl.zip
Using database: database_357d5d93529_n_methyl/minirosetta_database

ERROR: Assertion `res2.is_bonded(res1)` failed.
ERROR:: Exit from: src/core/scoring/etable/count_pair/CountPairFactory.cc line: 222
 called boinc_finish(0)

</stderr_txt>
]]>


The task ran for 7 hours 31 min 15 sec on Android 11, was validated, and netted me 294.91credits (seems normal, if not a bit high. I guess the Snapdragon 888 is stupid fast if you give it enough cooling.).
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Profile [VENETO] boboviz

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Message 102329 - Posted: 2 Aug 2021, 4:59:40 UTC
Last modified: 2 Aug 2021, 5:00:42 UTC

All rb_ with errors
ERROR: FuncFactory: unknown constraint function type:
ERROR:: Exit from: ......srccorescoringfuncFuncFactory.cc line: 66
BOINC:: Error reading and gzipping output datafile: default.out
06:56:11 (6056): called boinc_finish(1)

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Sid Celery

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Message 102331 - Posted: 2 Aug 2021, 23:01:51 UTC - in response to Message 102329.  

All rb_ with errors
ERROR: FuncFactory: unknown constraint function type:
ERROR:: Exit from: ......srccorescoringfuncFuncFactory.cc line: 66
BOINC:: Error reading and gzipping output datafile: default.out
06:56:11 (6056): called boinc_finish(1)

I waited a little while because I had several coming up in my cache shortly.
Exactly the same outcome, all within 25 seconds of starting. Hmm...
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Sid Celery

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Message 102332 - Posted: 2 Aug 2021, 23:49:01 UTC - in response to Message 102331.  
Last modified: 3 Aug 2021, 0:02:01 UTC

All rb_ with errors
ERROR: FuncFactory: unknown constraint function type:
ERROR:: Exit from: ......srccorescoringfuncFuncFactory.cc line: 66
BOINC:: Error reading and gzipping output datafile: default.out
06:56:11 (6056): called boinc_finish(1)

I waited a little while because I had several coming up in my cache shortly.
Exactly the same outcome, all within 25 seconds of starting. Hmm...

Reported - and it hadn't been spotted on the server-side yet, so good catch.

All remaining tasks aborted by the server already, I assume for correction and re-issue. Thanks

Edit:
I also mentioned that it wasn't the best time, because the queue of tasks is now down to about 500k so hopefully that pre-empts us running out by the end of the week. Let's see on that one
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Profile Grant (SSSF)

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Message 102474 - Posted: 27 Aug 2021, 6:29:09 UTC

Getting the occasional error from the latest batch of work.
degrader_site_5nvx_jhr_bcov3_SAVE_ALL_OUT_IGNORE_THE_REST_1pl5px4m_1729329_1_0
degrader_site_5nvx_jhr_bcov3_SAVE_ALL_OUT_IGNORE_THE_REST_1xf6yz5e_1729329_1_0
degrader_site_5nvx_jhr_bcov3_SAVE_ALL_OUT_IGNORE_THE_REST_7ja6bs8e_1729329_1_1

All gave this error in just under 2 minutes.

<core_client_version>7.16.11</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 -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10_tfirst--fuse--predictor_v13_degrader_boinc--fuse--tslp_design_v2_degrader_boinc.xml @degrader_site_5nvx_jhr_bcov_flags2 -in:file:silent degrader_site_5nvx_jhr_bcov3_SAVE_ALL_OUT_IGNORE_THE_REST_1pl5px4m.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_5nvx_jhr_bcov3_SAVE_ALL_OUT_IGNORE_THE_REST_1pl5px4m.zip @degrader_site_5nvx_jhr_bcov3_SAVE_ALL_OUT_IGNORE_THE_REST_1pl5px4m.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 3758214
Using database: database_357d5d93529_n_methylminirosetta_database

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
12:00:41 (7756): called boinc_finish(1)

</stderr_txt>
]]>


And in just under 30min this one errored out (according to Stderr output), but Validated
degrader_site_3mup_plait_-2.5_bcov_30.hbnet_3_SAVE_ALL_OUT_IGNORE_THE_REST_8yc7vq7n_1729332_1_0

<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_tfirst--fuse--predictor_v13_degrader_plait_boinc--fuse--tslp_design_v2_degrader_plait_boinc.xml @degrader_site_3mup_plait_-2.5_bcov_flags2 -in:file:silent degrader_site_3mup_plait_-2.5_bcov_30.hbnet_3_SAVE_ALL_OUT_IGNORE_THE_REST_8yc7vq7n.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_3mup_plait_-2.5_bcov_30.hbnet_3_SAVE_ALL_OUT_IGNORE_THE_REST_8yc7vq7n.zip @degrader_site_3mup_plait_-2.5_bcov_30.hbnet_3_SAVE_ALL_OUT_IGNORE_THE_REST_8yc7vq7n.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 3745924
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
12:27:28 (7040): called boinc_finish(0)

</stderr_txt>
]]>



But most seem to be running to the Target CPU time & Validating OK.
Grant
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Profile Grant (SSSF)

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Message 102504 - Posted: 31 Aug 2021, 5:49:06 UTC

Those _5nvx_ degrader Tasks continue to produce nothing but errors.
At least they're quick to die.
Grant
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Profile [VENETO] boboviz

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Message 102508 - Posted: 31 Aug 2021, 11:46:16 UTC - in response to Message 102504.  

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
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Message boards : Number crunching : Rosetta 4.1+ and 4.2+



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