Minirosetta 2.00

Message boards : Number crunching : Minirosetta 2.00

To post messages, you must log in.

Previous · 1 · 2 · 3 · 4 · 5 · Next

AuthorMessage
P . P . L .

Send message
Joined: 20 Aug 06
Posts: 581
Credit: 4,865,274
RAC: 0
Message 64023 - Posted: 11 Nov 2009, 21:35:10 UTC - in response to Message 64012.  

The large increase to the executable size could be due to the inclusion of a number of protocols that has been developed over the last 2 years. Those protocols were not able to compile with the boinc build until now.
There shouldn't be any difference in running the tasks though, the only difference is the time it takes to update.


Hi.

Does that mean that we Linux folk get to do more of the heavy lifting. ;) L.O.L.

ID: 64023 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
P . P . L .

Send message
Joined: 20 Aug 06
Posts: 581
Credit: 4,865,274
RAC: 0
Message 64028 - Posted: 12 Nov 2009, 2:00:27 UTC
Last modified: 12 Nov 2009, 2:02:11 UTC

Hi. first error with mini 2.00. well sort of.

This is an odd one only ran for 3 min's, i don't know what happened.

No error in manager.

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=269405320

mix_score12_B_rlbd_1ttz__IGNORE_THE_RESTlr13_DECOY_15619_826_0

Over__Validate error__Done__180.24

# cpu_run_time_pref: 14400
======================================================
DONE :: 1 starting structures 1201 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>
ID: 64028 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Greg_BE
Avatar

Send message
Joined: 30 May 06
Posts: 5652
Credit: 5,622,096
RAC: 0
Message 64030 - Posted: 12 Nov 2009, 20:43:51 UTC

Also got my first 2.00 error

https://boinc.bakerlab.org/rosetta/result.php?resultid=295408260
lr5_combine_smooth_torsion_it07_A_rlbd_1bm8_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15460_190_2

core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
[2009-11-12 16:39:46:] :: BOINC:: Initializing ... ok.
[2009-11-12 16:39:46:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
ERROR: Option matching -new_icoor not found in command line top-level context

</stderr_txt>
]]>
ID: 64030 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [AF>Libristes] Dudumomo

Send message
Joined: 30 Nov 06
Posts: 6
Credit: 10,826,140
RAC: 26
Message 64031 - Posted: 12 Nov 2009, 21:03:11 UTC - in response to Message 64030.  
Last modified: 12 Nov 2009, 21:04:03 UTC

Hi.
I got a lot of errors too :
lr5_dun08_it04_A_rlbd_4icb_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15799_439_0
<core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
[2009-11-12 17:51:35:] :: BOINC:: Initializing ... ok.
[2009-11-12 17:51:35:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
Loaded options.... ok
Processed options.... ok
Initializing random generators... ok
Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/yfsong_lr5_dun08_it04_A.zip
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/lr5_4icb.out.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Fullatom mode ..
# cpu_run_time_pref: 86400
Fullatom mode ..
..
..
..
Fullatom mode ..
SIGSEGV: segmentation violation
Stack trace (27 frames):
[0x9667f13]
.
.
.
[0x8048121]

Exiting...

</stderr_txt>
]]>

And also :

lr5_dun08_it04_A_rlbd_1ugh_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15799_445_0
<core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
[2009-11-12 19:16:30:] :: BOINC:: Initializing ... ok.
[2009-11-12 19:16:30:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
Loaded options.... ok
Processed options.... ok
Initializing random generators... ok
Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/yfsong_lr5_dun08_it04_A.zip
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/lr5_1wdv.out.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Fullatom mode ..
# cpu_run_time_pref: 86400
Fullatom mode ..
Fullatom mode ..
Fullatom mode ..
*** glibc detected *** free(): invalid next size (fast): 0xef219138 ***
SIGABRT: abort called
Stack trace (30 frames):
[0x9667f13]
.
.
.
[0x8048121]

Exiting...

</stderr_txt>
]]>

Any idea why ?

And I got a lr5_dun08 blocked at 0.310% after 24h...I'm gonna cancel it I guess.
MyUneo, the Cupid of Services
ID: 64031 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Hefto99

Send message
Joined: 11 Oct 05
Posts: 5
Credit: 3,542,183
RAC: 0
Message 64033 - Posted: 13 Nov 2009, 11:47:33 UTC

I have got several errors too (on 64-bit Linux):

===========
<core_client_version>6.2.15</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
[2009-11-13 13: 7:12:] :: BOINC:: Initializing ... ok.
[2009-11-13 13: 7:12:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
Loaded options.... ok
Processed options.... ok
Initializing random generators... ok
Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
# cpu_run_time_pref: 28800
*** glibc detected *** corrupted double-linked list: 0x11b99940 ***
SIGABRT: abort called
Stack trace (23 frames):
[0x9667f13]


============
<core_client_version>6.2.15</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
[2009-11-13 13:10: 5:] :: BOINC:: Initializing ... ok.
[2009-11-13 13:10: 5:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
Loaded options.... ok
Processed options.... ok
Initializing random generators... ok
Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev33769.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
# cpu_run_time_pref: 28800
*** glibc detected *** free(): invalid next size (normal): 0x11212198 ***
SIGABRT: abort called
Stack trace (21 frames):
[0x9667f13]

ID: 64033 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [AF>Libristes] Dudumomo

Send message
Joined: 30 Nov 06
Posts: 6
Credit: 10,826,140
RAC: 26
Message 64034 - Posted: 13 Nov 2009, 13:03:42 UTC - in response to Message 64033.  

I got linux 64b too.
I guess there is something wrong with our lib...?

My second laptop with Linux 64b as well, does not have any error calculation...

Do we have to install a particular lib ? Or what is wrong ?

Thanks
MyUneo, the Cupid of Services
ID: 64034 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
AMD_is_logical

Send message
Joined: 20 Dec 05
Posts: 299
Credit: 31,460,681
RAC: 0
Message 64035 - Posted: 13 Nov 2009, 17:34:04 UTC

ID: 64035 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator

Send message
Joined: 22 Aug 06
Posts: 4018
Credit: 0
RAC: 0
Message 64036 - Posted: 13 Nov 2009, 17:34:56 UTC - in response to Message 64034.  

I got linux 64b too.
I guess there is something wrong with our lib...?

My second laptop with Linux 64b as well, does not have any error calculation...

Do we have to install a particular lib ? Or what is wrong ?

Thanks


Everything needed downloads with the work unit. It appears some specific tasks are having trouble and that is what this thread is for, to collect the descriptions of those so they can be corrected in future releases.
Rosetta Moderator: Mod.Sense
ID: 64036 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [AF>Libristes] Dudumomo

Send message
Joined: 30 Nov 06
Posts: 6
Credit: 10,826,140
RAC: 26
Message 64037 - Posted: 13 Nov 2009, 22:09:33 UTC

Okay thanks !
I let my second computer running these WUs.
MyUneo, the Cupid of Services
ID: 64037 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
svincent

Send message
Joined: 30 Dec 05
Posts: 219
Credit: 11,805,838
RAC: 2
Message 64038 - Posted: 14 Nov 2009, 3:07:59 UTC

sel_core_2.0_low50_beta_low200_start0_hb_t286__IGNORE_THE_REST_15751_714_1

Task 295582440 failed on Windows 7.

ERROR: res1 != res2
ERROR:: Exit from: ....srccorekinematicsFoldTree.cc line: 2342
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

ID: 64038 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
svincent

Send message
Joined: 30 Dec 05
Posts: 219
Credit: 11,805,838
RAC: 2
Message 64065 - Posted: 17 Nov 2009, 16:27:30 UTC

mix_score13_C_rlbd_1ttz__IGNORE_THE_RESTlr13_DECOY_15917_345_1 task 296879164 gave a Validate Error on Mac OS X 10.6 after generating one decoy. "Too many error results" according to the Workunit log: it had been sent out once before with a similar result.

ID: 64065 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Greg_BE
Avatar

Send message
Joined: 30 May 06
Posts: 5652
Credit: 5,622,096
RAC: 0
Message 64076 - Posted: 18 Nov 2009, 18:08:15 UTC

2 more errors - compute errors

https://boinc.bakerlab.org/rosetta/result.php?resultid=297254753
https://boinc.bakerlab.org/rosetta/result.php?resultid=296995752

ERROR: res1 != res2
ERROR:: Exit from: ....srccorekinematicsFoldTree.cc line: 2342
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>


ID: 64076 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
svincent

Send message
Joined: 30 Dec 05
Posts: 219
Credit: 11,805,838
RAC: 2
Message 64084 - Posted: 19 Nov 2009, 5:29:59 UTC

again_sel_core_2.0_low50_beta_low200_nostart_hb_t286__IGNORE_THE_REST_15859_550_1 (task 296161309) failed on Windows 7

ERROR: res1 != res2
ERROR:: Exit from: ....srccorekinematicsFoldTree.cc line: 2342
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>
ID: 64084 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Interboy

Send message
Joined: 28 Sep 05
Posts: 3
Credit: 713,887
RAC: 93
Message 64085 - Posted: 19 Nov 2009, 8:34:10 UTC
Last modified: 19 Nov 2009, 8:35:07 UTC

I aborted task "threading_bong_promals_3_hb_t305__IGNORE_THE_REST_16009_335_0" with unhandled exception on task 297355887.
ID: 64085 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
svincent

Send message
Joined: 30 Dec 05
Posts: 219
Credit: 11,805,838
RAC: 2
Message 64089 - Posted: 19 Nov 2009, 17:08:26 UTC

A couple more sel_core* tasks failing on Windows 7. Looking at the forum, it seems tasks with names containing t313 are quite prone to failure.

sel_core_1.5_low200_beta_low200_nostart_hb_t313__IGNORE_THE_REST_15870_160_0 (task 296161514)
sel_core_1.5_low200_beta_low200_nostart_hb_t328__IGNORE_THE_REST_15873_167_0(task 296161959)

ERROR: res1 != res2
ERROR:: Exit from: ....srccorekinematicsFoldTree.cc line: 2342
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

ID: 64089 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Telescope Adrian

Send message
Joined: 14 Nov 06
Posts: 9
Credit: 1,906,378
RAC: 0
Message 64091 - Posted: 19 Nov 2009, 19:03:25 UTC

Anybody noticed a new "facility" with 2.00 yet ?
Run 2 jobs together ( AMD Athlon 64 X 2) and , after a while , one of the jobs goes idle meaning that the system idle process sits at 50% utilisation . Suspending Rosetta , then restarting it makes no difference to this behaviour.
I used to see this feature a while ( many months) ago , but it went away I think at about Version 1.97 .

Has anyone else this yet ?

Best wishes
ID: 64091 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Chilean
Avatar

Send message
Joined: 16 Oct 05
Posts: 711
Credit: 26,694,507
RAC: 0
Message 64092 - Posted: 19 Nov 2009, 19:40:18 UTC - in response to Message 64091.  
Last modified: 19 Nov 2009, 19:41:40 UTC

Anybody noticed a new "facility" with 2.00 yet ?
Run 2 jobs together ( AMD Athlon 64 X 2) and , after a while , one of the jobs goes idle meaning that the system idle process sits at 50% utilisation . Suspending Rosetta , then restarting it makes no difference to this behaviour.
I used to see this feature a while ( many months) ago , but it went away I think at about Version 1.97 .

Has anyone else this yet ?

Best wishes


How much RAM do you have?

Edit: I figured it myself (2GB). I don't know what the problem could be... you could've given Rosetta too little available RAM in your setting, maybe?
ID: 64092 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Telescope Adrian

Send message
Joined: 14 Nov 06
Posts: 9
Credit: 1,906,378
RAC: 0
Message 64093 - Posted: 19 Nov 2009, 20:19:54 UTC - in response to Message 64092.  

Anybody noticed a new "facility" with 2.00 yet ?
Run 2 jobs together ( AMD Athlon 64 X 2) and , after a while , one of the jobs goes idle meaning that the system idle process sits at 50% utilisation . Suspending Rosetta , then restarting it makes no difference to this behaviour.
I used to see this feature a while ( many months) ago , but it went away I think at about Version 1.97 .

Has anyone else this yet ?

Best wishes


How much RAM do you have?

Edit: I figured it myself (2GB). I don't know what the problem could be... you could've given Rosetta too little available RAM in your setting, maybe?


Hello there . It's not a problem of store availability since I allow BOINC to use 75% of my available real store when I'm running projects . ( Virtual storage systems don't work like you seem to think ! ) . On this machine I usually have other jobs from Rosetta and Spinhenge queuing to run , but when the Rosetta job goes " idle " , no other job starts up to take its engine time up , so its nothing to do with OCP time utilisation either .As I said earlier , this facility used to show itself earlier this year , but went away at about Rosetta 1.97 . The workunit seems just to sit waiting for something , but I know not what !
Regards
ID: 64093 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator

Send message
Joined: 22 Aug 06
Posts: 4018
Credit: 0
RAC: 0
Message 64096 - Posted: 20 Nov 2009, 4:54:39 UTC

Adrian, Rosetta does not decide what work runs at what time, BOINC decides this. It does this based on your preferences. Since BOINC does not have a configuration setting called "real store", you haven't really told us much about your settings. Even if you were indicating memory, you didn't tells us if this was the setting for when the machine is in use, or when it is idle.

The main thing to check is... what does BOINC say the reason for not running it is? The task's status or the messages should indicate what's going on. Since you seem familiar with the Windows task manager, another idea would be to suspend the task that is active, and see if the other resumes running. And then look at how much memory it is using. Or easier yet, it should appear in the task list if you sort it alphabetically and show you how much memory it is using.

If it is consuming too much memory then that would be something Rosetta might be able to address.

Do you know which task name is causing you problems?
Rosetta Moderator: Mod.Sense
ID: 64096 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator

Send message
Joined: 22 Aug 06
Posts: 4018
Credit: 0
RAC: 0
Message 64097 - Posted: 20 Nov 2009, 5:00:57 UTC

Notes for Project Team:

Looking at Adrian's task list, it looks like this one had a very long running model on the third decoy
threading_bong_promals_4_hb_t328__IGNORE_THE_REST_16074_67_0
https://boinc.bakerlab.org/rosetta/result.php?resultid=297460595

Target runtime 14,400, 3 decoys ran in 23,000. The first two must have been done within 9,600 or it would have ended the task before starting the third. So that means the third ran for at least 13,400, which is nearly 4 hours.
Rosetta Moderator: Mod.Sense
ID: 64097 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Previous · 1 · 2 · 3 · 4 · 5 · Next

Message boards : Number crunching : Minirosetta 2.00



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