minirosetta 1.80

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Yifan Song

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Message 4848 - Posted: 20 Jun 2009, 4:49:32 UTC

update on protein-protein docking protocols
new rotamer library for test
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Profile Bernd Vogler

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Message 4849 - Posted: 20 Jun 2009, 12:02:50 UTC

Crunched 4 WUs with Ubuntu 9.04 (32-bit). Everything is O.K.
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Message 4851 - Posted: 24 Jun 2009, 17:20:44 UTC

Most ran fine, but the last one errored out with this stderr:


<core_client_version>6.4.5</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
[2009- 6-24 12:37: 2:] :: BOINC:: Initializing ... ok.
[2009- 6-24 12:37: 2:] :: 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/ralph.bakerlab.org/minirosetta_database_rev30680.zip
Unpacking WU data ...
Unpacking data: ../../projects/ralph.bakerlab.org/real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.boinc_files.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.

ERROR: choice != 0
ERROR:: Exit from: src/protocols/jd2/ShuffleJobDistributor.cc line: 83
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>


This are the messages for the errored WU:
Mi 24 Jun 2009 12:36:21 CEST|ralph@home|Sending scheduler request: To fetch work. Requesting 4004 seconds of work, reporting 0 completed tasks
Mi 24 Jun 2009 12:36:27 CEST|ralph@home|Scheduler request completed: got 1 new tasks
Mi 24 Jun 2009 12:36:29 CEST|ralph@home|Started download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.flags.boinc
Mi 24 Jun 2009 12:36:29 CEST|ralph@home|Started download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.boinc_files.zip
Mi 24 Jun 2009 12:36:30 CEST|ralph@home|Finished download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.flags.boinc
Mi 24 Jun 2009 12:37:00 CEST|ralph@home|Finished download of real_core_1.5_low200_beta_low200.broker_corebuild.t303_.olange.boinc_files.zip
Mi 24 Jun 2009 12:37:01 CEST|ralph@home|Starting real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1
Mi 24 Jun 2009 12:37:01 CEST|ralph@home|Starting task real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 using minirosetta version 180
Mi 24 Jun 2009 12:37:16 CEST|ralph@home|Computation for task real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 finished
Mi 24 Jun 2009 12:37:16 CEST|ralph@home|Output file real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1_0 for task real_core_1.5_low200_beta_low200_hb_t303__IGNORE_THE_REST_10771_1_1 absent
Mi 24 Jun 2009 12:40:32 CEST|ralph@home|Sending scheduler request: To fetch work. Requesting 4004 seconds of work, reporting 1 completed tasks
Mi 24 Jun 2009 12:40:37 CEST|ralph@home|Scheduler request completed: got 0 new tasks


My computer ist this.
(ubuntu64 on C2Q)
Gruesse vom Saenger

For questions about Boinc look in the BOINC-Wiki
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Message 4852 - Posted: 1 Jul 2009, 2:06:17 UTC

Couple of quick errors:

BOINC_ABRELAX_1itf_CS_DISTEST_SAVE_ALL_OUT_11247_4_0

ERROR: in::file::boinc_wu_zip /work/rvernon/disulfides/TARGETS/zipfiles/zipfile.1itf.cs.set1.zip does not exist!
ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 114
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

BOINC_ABRELAX_1ry3_NN_DISCONTROL_SAVE_ALL_OUT_11248_9_1

ERROR: in::file::boinc_wu_zip /work/rvernon/disulfides/TARGETS/zipfiles/zipfile.1ry3.cs.set1.zip does not exist!
ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 114
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish



Snags
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Message 4853 - Posted: 1 Jul 2009, 15:30:47 UTC - in response to Message 4852.  

same here: task 1523280
ERROR: in::file::boinc_wu_zip /work/rvernon/disulfides/TARGETS/zipfiles/zipfile.1yl2.cs.set1.zip does not exist!
ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 114
BOINC:: Error reading and gzipping output datafile: default.out


AdeB
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Message 4854 - Posted: 4 Jul 2009, 19:38:35 UTC
Last modified: 4 Jul 2009, 20:02:04 UTC

Fri 03 Jul 2009 12:09:05 AM EDT|ralph@home|Starting 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0
Fri 03 Jul 2009 12:09:09 AM EDT|ralph@home|Starting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180
Fri 03 Jul 2009 12:12:17 AM EDT|ralph@home|Restarting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180
Fri 03 Jul 2009 12:18:33 AM EDT|ralph@home|Restarting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180
Fri 03 Jul 2009 12:21:39 AM EDT|ralph@home|Restarting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180

This wu kept restarting untill I caught it at Sat 04 Jul 2009 03:14:04 PM EDT|ralph@home|Restarting task 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0 using minirosetta version 180

39 hours+


Task ID 1524289
Name 1j8i_CS_DISTEST_BOINC_ABRELAX_SAVE_ALL_OUT_11249_3_0
Workunit 1350593
Created 30 Jun 2009 23:52:34 UTC
Sent 30 Jun 2009 23:59:02 UTC
Received 4 Jul 2009 19:20:18 UTC
Server state Over
Outcome Client error
Client state Aborted by user
Exit status -197 (0xffffffffffffff3b)
Computer ID 18184
Report deadline 4 Jul 2009 23:59:02 UTC
CPU time 0
stderr out

<core_client_version>6.2.18</core_client_version>
<![CDATA[
<message>
aborted by user
</message>
]]>

Validate state Invalid
Claimed credit 0
Granted credit 0
application version 1.80


(the next wu did the same thing. rebooted computer and it now wu's working fine)
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Tim

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Message 4855 - Posted: 8 Jul 2009, 10:16:01 UTC

Aborted picker-L1-sssim-1fkbA_11358_5 after it had run for 29 hours with 49.15% complete. All other similar tasks i ran lasted <4hrs. Needed to free up that core for a Rosetta task :)
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Message 4858 - Posted: 9 Jul 2009, 9:11:51 UTC

2 more quick errors about 12 minutes in:

frb_0_8__rnd2_aln_list_mike_chosen_bestaln.alns.combined.csts_hb_t362__IGNORE_THE_REST_1Z54A_2_11448_1_0

frb_0_8__rnd2_aln_list_mike_chosen_bestaln.alns.combined.csts_hb_t362__IGNORE_THE_REST_1NJKA_10_11448_1_0

Hbond tripped: [2009- 7- 9 2:41:29:]
interpolate rotamers bin out of range: MET_p:NtermProteinFull 0 nan -60.8264 -60.9057 -68.7799
27 27 10 11 2147483649 22 0 nan
ERROR:: Exit from: src/core/scoring/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh line: 590
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

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Message 4859 - Posted: 9 Jul 2009, 12:11:11 UTC

Just had two WUs run for over 10 hours for 1 decoy, my preferences are set for 6 hours.
They both wound down to 9 minutes 54 seconds left and sat there getting to 98.38% or thereabouts before failing and granting zero credit.
This problem has happened before but I can't find the version that had this problem.

See this result and this result

both had the following error

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<stderr_txt>
[2009- 7- 9 11:36:19:] :: BOINC:: Initializing ... ok.
[2009- 7- 9 11:36:19:] :: 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/ralph.bakerlab.org/minirosetta_database_rev30680.zip
Unpacking WU data ...
Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8__rnd2_mike_chosen.intersection_new.csts.foldcst_chunk_general_cf.t286_.mtyka.boinc_files.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
Setting up folding (abrelax) ...
Beginning folding (abrelax) ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Starting work on structure: _1BWPA_7_00001
# cpu_run_time_pref: 21600
Hbond tripped: [2009- 7- 9 12: 7:30:]
BOINC:: CPU time: 36557.3s, 14400s + 21600s[2009- 7- 9 21:47: 1:] :: BOINC
Output exists: default.out.gz
InternalDecoyCount: 0 (GZ)
======================================================
DONE :: 1 starting structures 36557.3 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish

</stderr_txt>
<message>
<file_xfer_error>
<file_name>frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t286__IGNORE_THE_REST_1BWPA_7_11514_1_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>
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Message 4861 - Posted: 10 Jul 2009, 9:38:19 UTC
Last modified: 10 Jul 2009, 9:47:44 UTC

That frb_0_8__rnd2_aln_list_within_4.alns.combined.csts_hb_t293__IGNORE_THE_REST_1WS6A_14_11496_1_0 erroed out.
<![CDATA[
<message>
Maximum disk usage exceeded
</message>
<stderr_txt>
.
.
.
I have no problem with disk space (aviable for Boinc 67 GB).

The same that frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t331__IGNORE_THE_REST_1DNLA_12_11526_1_0 task.
Both Win XP x86.
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Tim

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Message 4862 - Posted: 10 Jul 2009, 11:51:27 UTC

This task error'd
lr11_seq_score12_rlbd_1thx_IGNORE_THE_REST_DECOY_11409_1_1

ERROR: ct == final_atoms
ERROR:: Exit from: ..\..\src\core\scoring\rms_util.cc line: 368
BOINC:: Error reading and gzipping output datafile: default.out
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Message 4863 - Posted: 10 Jul 2009, 12:31:01 UTC - in response to Message 4859.  

Just had two WUs run for over 10 hours for 1 decoy, my preferences are set for 6 hours.
They both wound down to 9 minutes 54 seconds left and sat there getting to 98.38% or thereabouts before failing and granting zero credit.
This problem has happened before but I can't find the version that had this problem.

See this result and this result

both had the following error

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<stderr_txt>
[2009- 7- 9 11:36:19:] :: BOINC:: Initializing ... ok.
[2009- 7- 9 11:36:19:] :: 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/ralph.bakerlab.org/minirosetta_database_rev30680.zip
Unpacking WU data ...
Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8__rnd2_mike_chosen.intersection_new.csts.foldcst_chunk_general_cf.t286_.mtyka.boinc_files.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
Setting up folding (abrelax) ...
Beginning folding (abrelax) ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Starting work on structure: _1BWPA_7_00001
# cpu_run_time_pref: 21600
Hbond tripped: [2009- 7- 9 12: 7:30:]
BOINC:: CPU time: 36557.3s, 14400s + 21600s[2009- 7- 9 21:47: 1:] :: BOINC
Output exists: default.out.gz
InternalDecoyCount: 0 (GZ)
======================================================
DONE :: 1 starting structures 36557.3 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish

</stderr_txt>
<message>
<file_xfer_error>
<file_name>frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t286__IGNORE_THE_REST_1BWPA_7_11514_1_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>


Have had another with exactly the same problem on a different machine, same WU type, frb_0_8_rnd2,
also ran for 10 hours before failing (preference is 6 hours) after 1 decoy.
This Result
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Message 4864 - Posted: 11 Jul 2009, 8:16:18 UTC - in response to Message 4863.  

Just had two WUs run for over 10 hours for 1 decoy, my preferences are set for 6 hours.
They both wound down to 9 minutes 54 seconds left and sat there getting to 98.38% or thereabouts before failing and granting zero credit.
This problem has happened before but I can't find the version that had this problem.

See this result and this result

both had the following error

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<stderr_txt>
[2009- 7- 9 11:36:19:] :: BOINC:: Initializing ... ok.
[2009- 7- 9 11:36:19:] :: 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/ralph.bakerlab.org/minirosetta_database_rev30680.zip
Unpacking WU data ...
Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8__rnd2_mike_chosen.intersection_new.csts.foldcst_chunk_general_cf.t286_.mtyka.boinc_files.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
Setting up folding (abrelax) ...
Beginning folding (abrelax) ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Starting work on structure: _1BWPA_7_00001
# cpu_run_time_pref: 21600
Hbond tripped: [2009- 7- 9 12: 7:30:]
BOINC:: CPU time: 36557.3s, 14400s + 21600s[2009- 7- 9 21:47: 1:] :: BOINC
Output exists: default.out.gz
InternalDecoyCount: 0 (GZ)
======================================================
DONE :: 1 starting structures 36557.3 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish

</stderr_txt>
<message>
<file_xfer_error>
<file_name>frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t286__IGNORE_THE_REST_1BWPA_7_11514_1_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>


Have had another with exactly the same problem on a different machine, same WU type, frb_0_8_rnd2,
also ran for 10 hours before failing (preference is 6 hours) after 1 decoy.
This Result


Still another with the same Error,
ran for over 10 Hours then errored out, it was another frb_0_8_rnd2 WU
See This Result
also I aborted another Two work units after they had gone past 6 1/2 hours and only at 66%
See This Result and This Result

So that is over 62 Hours wasted on 6 WUs, as each only do 1 decoy and then error out with no credit given.
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Message 4867 - Posted: 12 Jul 2009, 8:17:50 UTC - in response to Message 4864.  
Last modified: 12 Jul 2009, 8:31:22 UTC

And here is another that ran to 10 hours and then failed after completing 1 decoy

See here

It's a pity these 10 hour WUs are getting zero credit.
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Message 4869 - Posted: 12 Jul 2009, 8:30:20 UTC - in response to Message 4864.  

Just had two WUs run for over 10 hours for 1 decoy, my preferences are set for 6 hours.
They both wound down to 9 minutes 54 seconds left and sat there getting to 98.38% or thereabouts before failing and granting zero credit.
This problem has happened before but I can't find the version that had this problem.

See this result and this result

both had the following error

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<stderr_txt>
[2009- 7- 9 11:36:19:] :: BOINC:: Initializing ... ok.
[2009- 7- 9 11:36:19:] :: 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/ralph.bakerlab.org/minirosetta_database_rev30680.zip
Unpacking WU data ...
Unpacking data: ../../projects/ralph.bakerlab.org/frb_0_8__rnd2_mike_chosen.intersection_new.csts.foldcst_chunk_general_cf.t286_.mtyka.boinc_files.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
Setting up folding (abrelax) ...
Beginning folding (abrelax) ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Starting work on structure: _1BWPA_7_00001
# cpu_run_time_pref: 21600
Hbond tripped: [2009- 7- 9 12: 7:30:]
BOINC:: CPU time: 36557.3s, 14400s + 21600s[2009- 7- 9 21:47: 1:] :: BOINC
Output exists: default.out.gz
InternalDecoyCount: 0 (GZ)
======================================================
DONE :: 1 starting structures 36557.3 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish

</stderr_txt>
<message>
<file_xfer_error>
<file_name>frb_0_8__rnd2_mike_chosen.intersection_new.csts_hb_t286__IGNORE_THE_REST_1BWPA_7_11514_1_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>


Have had another with exactly the same problem on a different machine, same WU type, frb_0_8_rnd2,
also ran for 10 hours before failing (preference is 6 hours) after 1 decoy.
This Result


Still another with the same Error,
ran for over 10 Hours then errored out, it was another frb_0_8_rnd2 WU
See This Result
also I aborted another Two work units after they had gone past 6 1/2 hours and only at 66%
See This Result and This Result

So that is over 62 Hours wasted on 6 WUs, as each only do 1 decoy and then error out with no credit given.


Hope I fixed up all the links as I forgot the //
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Tim

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Message 4871 - Posted: 13 Jul 2009, 10:26:53 UTC

This task ended with
ERROR: ct == final_atoms
ERROR:: Exit from: ..\..\src\core\scoring\rms_util.cc line: 368
BOINC:: Error reading and gzipping output datafile: default.out
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