Rosetta Beta 6.00

Message boards : Number crunching : Rosetta Beta 6.00

To post messages, you must log in.

Previous · 1 . . . 3 · 4 · 5 · 6 · 7 · Next

AuthorMessage
Sid Celery

Send message
Joined: 11 Feb 08
Posts: 2122
Credit: 41,184,189
RAC: 10,001
Message 108782 - Posted: 26 Dec 2023, 22:08:48 UTC - in response to Message 108781.  

I don't know what your settings are but I'm getting nearly 100% valid tasks here on my both Windows and Linux pc;s.
Me too. Send more betas.

Some Robetta tasks - non-Beta - sneaking through atm.
Hardly any tbh, but not quite nothing
ID: 108782 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Sid Celery

Send message
Joined: 11 Feb 08
Posts: 2122
Credit: 41,184,189
RAC: 10,001
Message 108783 - Posted: 27 Dec 2023, 15:52:25 UTC - in response to Message 108782.  

I don't know what your settings are but I'm getting nearly 100% valid tasks here on my both Windows and Linux pc;s.
Me too. Send more betas.

Some Robetta tasks - non-Beta - sneaking through atm.
Hardly any tbh, but not quite nothing

Sneaking a few new8v Beta tasks now but similarly hard to come by
ID: 108783 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1994
Credit: 9,571,168
RAC: 7,168
Message 108840 - Posted: 12 Feb 2024, 15:58:36 UTC - in response to Message 108755.  

I think that the 6.xx branch of code makes the same things as the 4.xx plus other things.
But it's in beta since the beginning of April.
Why not abandon the 4.xx branch (that has over 3 years old code)?


Still
ID: 108840 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Grant (SSSF)

Send message
Joined: 28 Mar 20
Posts: 1678
Credit: 17,777,015
RAC: 22,716
Message 108957 - Posted: 9 Mar 2024, 11:13:06 UTC
Last modified: 9 Mar 2024, 11:15:03 UTC

Current batch of Beta tasks have the same naming convention as Rosetta 4.20, and use a similar amount of RAM.
Roughly 1.2GB of RAM required per Task.


Also running for around 8 hours, not the previous Task runtime of around 3hrs.
Grant
Darwin NT
ID: 108957 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1994
Credit: 9,571,168
RAC: 7,168
Message 108964 - Posted: 9 Mar 2024, 17:49:48 UTC - in response to Message 108957.  

Current batch of Beta tasks have the same naming convention as Rosetta 4.20, and use a similar amount of RAM.


And seems there are problems with the graphic...
ID: 108964 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1994
Credit: 9,571,168
RAC: 7,168
Message 108999 - Posted: 16 Mar 2024, 7:52:01 UTC

Some errors 1552811222, 1552784491, etc

ERROR: Error in protocols::cyclic_peptide_predict::SimpleCycpepPredictpplication::set_up_n_to_c_cyclization_mover() function: residue 1 does not have a LOWER_CONNECT.
ERROR:: Exit from: src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.cc line: 2442
BOINC:: Error reading and gzipping output datafile: default.out
08:36:42 (5544): called boinc_finish(1)

ID: 108999 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Grant (SSSF)

Send message
Joined: 28 Mar 20
Posts: 1678
Credit: 17,777,015
RAC: 22,716
Message 109002 - Posted: 16 Mar 2024, 10:49:43 UTC

Yep, another group of faulty Tasks in with the current batch.
Grant
Darwin NT
ID: 109002 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1994
Credit: 9,571,168
RAC: 7,168
Message 109020 - Posted: 21 Mar 2024, 6:17:29 UTC - in response to Message 109002.  
Last modified: 21 Mar 2024, 6:17:56 UTC

Yep, another group of faulty Tasks in with the current batch.


Today a lot of wus with this error:
residue 1 does not have a LOWER_CONNECT

ID: 109020 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Grant (SSSF)

Send message
Joined: 28 Mar 20
Posts: 1678
Credit: 17,777,015
RAC: 22,716
Message 109021 - Posted: 21 Mar 2024, 6:31:20 UTC - in response to Message 109020.  

New batch, same problem.
Grant
Darwin NT
ID: 109021 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1994
Credit: 9,571,168
RAC: 7,168
Message 109022 - Posted: 21 Mar 2024, 13:39:02 UTC - in response to Message 109021.  
Last modified: 21 Mar 2024, 13:40:40 UTC

New batch, same problem.


A little debug from admins is welcome.
ID: 109022 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1994
Credit: 9,571,168
RAC: 7,168
Message 109231 - Posted: 5 May 2024, 19:27:09 UTC - in response to Message 108999.  

ERROR: Error in protocols::cyclic_peptide_predict::SimpleCycpepPredictpplication::set_up_n_to_c_cyclization_mover() function: residue 1 does not have a LOWER_CONNECT.
ERROR:: Exit from: src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.cc line: 2442
BOINC:: Error reading and gzipping output datafile: default.out
08:36:42 (5544): called boinc_finish(1)


Still the same error.
After 2 months. Seems there is no debug of errors...
ID: 109231 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mad_Max

Send message
Joined: 31 Dec 09
Posts: 209
Credit: 25,910,924
RAC: 11,577
Message 109245 - Posted: 13 May 2024, 4:44:13 UTC
Last modified: 13 May 2024, 5:03:08 UTC

A bug report (in the unlikely event that one of the developers still read forum and decides to fix some of the bugs).

On one of my computers (this one: https://boinc.bakerlab.org/rosetta/results.php?hostid=1211592) ALL, without exception, tasks for the Rosetta Beta 6.xx application end with an error at the 1st minute of operation.
The error is always the same:
Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address ........... (address vary)

This is a fairly old, but still decent and stable computer running on an AMD Phenom II X6 processor (6 physical cores) and 16 GB of RAM

Tasks for Rosetta 4.x are performed on it without any problems (except for faulty tasks that cause errors on all computers like famous "CHI angle" or "residue LOWERCONNECT" errors) as well as many(thousands - literally) tasks for several other DC projects: Einstein@Home, World Community Grid, SiDock@Home.

This has been going on for several months by now (starting from Rosetta beta version 6.03, I think, because I've seen some valid WUs with early versions from the 6.x branch on this computer), killing many hundreds of WUs.
During this time, there were several computer reboots and I reset the project twice (this includes re-downloading of all executable files and data files).
Without changes.

I do not think that the problem is in the software configuration, because on other computers I have not just a similar, but almost identical setup (originally obtained by cloning the system disk from this one).
The main difference is that other computers have newer processors installed - also from AMD but from newer generations - Ryzen 7 2700 and Ryzen 5 5600X on which the Rosetta 6.xx application works without problems with same SW setup.

So one of the versions of the error causes is that the application is trying to use one of the new instruction sets (AVX maybe? or other never CPU features which old Phenom series lacking ) without proper verification of their availability causing errors on older CPUs.

It would be nice if someone from the owners of the old processors (like a Phenom or Core 2 DUO/QUAD) check this.
ID: 109245 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1994
Credit: 9,571,168
RAC: 7,168
Message 109407 - Posted: 22 Jun 2024, 6:58:46 UTC

Yesterday, a new kind of wus "test_asx_single_".
All errors after few seconds

ERROR: The residue ASX could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 116
BOINC:: Error reading and gzipping output datafile: default.out
06:55:44 (18124): called boinc_finish(1)

ID: 109407 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Dennis Walker

Send message
Joined: 8 Mar 20
Posts: 1
Credit: 1,245,926
RAC: 726
Message 109423 - Posted: 29 Jun 2024, 7:47:01 UTC - in response to Message 109245.  

I also have an old computer that cannot run the Beta 6.4 tasks but is fine for the 4.x tasks.

Name 8a_hal_k_hal_8aa_2jp2703_d31_1_0001_SAVE_ALL_OUT_2978406_105_0
Workunit 1403453387
Created 25 Jun 2024, 12:04:52 UTC
Sent 25 Jun 2024, 12:29:47 UTC
Report deadline 28 Jun 2024, 12:29:47 UTC
Received 25 Jun 2024, 13:31:34 UTC
Server state Over
Outcome Computation error
Client state Compute error
Exit status -1073741819 (0xC0000005) STATUS_ACCESS_VIOLATION
...
<core_client_version>7.16.20</core_client_version>
<![CDATA[
<message>
(unknown error) - exit code 3221225477 (0xc0000005)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_beta_6.04_windows_x86_64.exe @8a_hal_k_hal_8aa_2jp2703_d31_1_0001.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
Using database: database_0f7f01a1b07database


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x00007FF6296448CC read attempt to address 0xFFFFFFFF
...
(address may vary)
Reason: Access Violation (0xc0000005) at address 0x000000000000000F


CPU type AuthenticAMD
AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ [Family 15 Model 107 Stepping 1]
Number of processors 2
Coprocessors AMD ATI Radeon HD 5400/R5 210 series (Cedar) (2048MB) driver: 1.4.1848 OpenCL: 1.2


- Stopped using my computer from 1994 (free WIN95 upgrade) after 28 years. Outlived WIN98, XP, Vista computers.
ID: 109423 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Tern
Avatar

Send message
Joined: 25 Oct 05
Posts: 576
Credit: 4,695,359
RAC: 13
Message 109424 - Posted: 30 Jun 2024, 19:16:33 UTC - in response to Message 108305.  

Most projects let you choose whether you want to run beta applications or not.

I don't.

There's no way to shut these off other than stopping Rosetta work altogether.


That was 4/2023, now it's 6/2024, and this still hasn't been fixed? I came back wanting to run more Rosetta, but I'm getting 90% "beta" tasks that I don't want.

What happened to this being the best-run, best-communication, project on BOINC? Now it seems more like SZTAKI...
ID: 109424 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1994
Credit: 9,571,168
RAC: 7,168
Message 109427 - Posted: 3 Jul 2024, 8:30:24 UTC - in response to Message 109424.  

What happened to this being the best-run, best-communication, project on BOINC? Now it seems more like SZTAKI...


You're here, like me, for more than 15 years.
At the beginning there was a thread like "David Baker's Rosetta@home journal" (closed in 2017), the last news in the home page is June 2022, etc.
Maybe more "interaction" with volunteers can attract more people (and, listening us, to have a better app).

Maybe r@h became only a "divertissement" for IPD?
I don't think so, 'cause they would not be developing a new app as they are doing on Ralph.
But the lack of comunication is frustrating
ID: 109427 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1994
Credit: 9,571,168
RAC: 7,168
Message 109581 - Posted: 16 Aug 2024, 17:36:06 UTC

New app (6.06) errors also on linux
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_beta_6.06_x86_64-pc-linux-gnu @hal_8a_p_hal_8aa_3jp6791_d15_1_0001_1.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 1464901
Using database: database_f5ae1de8e1/database

ERROR: Unable to find desired residue 'DALA' with variant 'SIDECHAIN_CONJUGATION'. Attempted to add target variant(s) to ResidueType using both ResidueType base name 'DALA' and base ResidueType. Was attempting to add new variant type 'SIDECHAIN_CONJUGATION'
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 980
BOINC:: Error reading and gzipping output datafile: default.out
19:33:13 (3207): called boinc_finish(1)

ID: 109581 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Grant (SSSF)

Send message
Joined: 28 Mar 20
Posts: 1678
Credit: 17,777,015
RAC: 22,716
Message 109582 - Posted: 16 Aug 2024, 20:36:40 UTC
Last modified: 16 Aug 2024, 21:32:38 UTC

So far every 6.06 Task has errored out- none even making it to 1min 30 sec.

<core_client_version>8.0.2</core_client_version>
<![CDATA[
<message>
Incorrect function.
 (0x1) - exit code 1 (0x1)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_beta_6.06_windows_x86_64.exe @hal_8a_p_hal_8aa_3jp6519_d160_0001_1.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 1560302
Using database: database_f5ae1de8e1database

ERROR: Unable to find desired residue 'PHE' with variant 'SIDECHAIN_CONJUGATION'. Attempted to add target variant(s) to ResidueType using both ResidueType base name 'PHE' and base ResidueType. Was attempting to add new variant type 'SIDECHAIN_CONJUGATION'
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 980
BOINC:: Error reading and gzipping output datafile: default.out
03:15:20 (2416): called boinc_finish(1)

</stderr_txt>
]]>

Grant
Darwin NT
ID: 109582 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Jean-David Beyer

Send message
Joined: 2 Nov 05
Posts: 188
Credit: 6,410,516
RAC: 5,480
Message 109584 - Posted: 16 Aug 2024, 22:14:03 UTC - in response to Message 109582.  
Last modified: 16 Aug 2024, 22:38:42 UTC

Me too. It downloads me 17 tasks at a time, and they all error out almost immediately. This on my Linux machine.

I just set to get no more tasks.

While not identical, they all fail in a similar way. Here is one of them:

Task 1581485824
Name 	hal_8a_q_hal_8aa_3jp3179_d157_2_0001_1_SAVE_ALL_OUT_2979144_1_1
Workunit 	1407312834
Created 	16 Aug 2024, 15:02:43 UTC
Sent 	16 Aug 2024, 15:08:33 UTC
Report deadline 	19 Aug 2024, 15:08:33 UTC
Received 	16 Aug 2024, 21:53:02 UTC
Server state 	Over
Outcome 	Computation error
Client state 	Compute error
Exit status 	1 (0x00000001) Unknown error code
Computer ID 	5910575
Run time 	19 sec
CPU time 	1 sec
Validate state 	Invalid
Credit 	0.00
Device peak FLOPS 	6.06 GFLOPS
Application version 	Rosetta Beta v6.06
x86_64-pc-linux-gnu
Peak working set size 	120.74 MB
Peak swap size 	237.00 MB
Peak disk usage 	23.86 MB
Stderr output

<core_client_version>7.20.2</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_beta_6.06_x86_64-pc-linux-gnu @hal_8a_q_hal_8aa_3jp3179_d157_2_0001_1.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 1949704
Using database: database_f5ae1de8e1/database

ERROR: Unable to find desired residue 'LEU' with variant 'SIDECHAIN_CONJUGATION'. Attempted to add target variant(s) to ResidueType using both ResidueType base name 'LEU' and base ResidueType. Was attempting to add new variant type 'SIDECHAIN_CONJUGATION'
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 980
BOINC:: Error reading and gzipping output datafile: default.out
11:11:55 (1424400): called boinc_finish(1)

</stderr_txt>
]]>

ID: 109584 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Jean-David Beyer

Send message
Joined: 2 Nov 05
Posts: 188
Credit: 6,410,516
RAC: 5,480
Message 109586 - Posted: 17 Aug 2024, 0:24:56 UTC - in response to Message 109584.  

Same problem on my Windows 11 machine.
ID: 109586 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Previous · 1 . . . 3 · 4 · 5 · 6 · 7 · Next

Message boards : Number crunching : Rosetta Beta 6.00



©2024 University of Washington
https://www.bakerlab.org