Minirosetta 3.46

Message boards : Number crunching : Minirosetta 3.46

To post messages, you must log in.

Previous · 1 · 2 · 3 · 4 · Next

AuthorMessage
Brian Priebe

Send message
Joined: 27 Nov 09
Posts: 16
Credit: 33,020,247
RAC: 0
Message 75536 - Posted: 29 Apr 2013, 6:05:51 UTC - in response to Message 75493.  

minirosetta is updated to 3.46 to include recent developments in electron density and other scoring functions.
Are there any particular minimum requirements for this version? Despite resetting the project, I am still getting only 3.45 jobs on a 6.x version of BOINC.
ID: 75536 · 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 75537 - Posted: 29 Apr 2013, 7:51:51 UTC

Another that one erred after 28min.

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=525210001

rb_04_24_37778_72771__t000__2_C1_SAVE_ALL_OUT_IGNORE_THE_REST_79247_1030_0

# cpu_run_time_pref: 21600
dof_atom1 atomno= 3 rsd= 2
atom1 atomno= 1 rsd= 2
atom2 atomno= 2 rsd= 2
atom3 atomno= 5 rsd= 2
atom4 atomno= 6 rsd= 2
THETA1 nan
THETA3 nan
PHI2 0

ERROR: AtomTree::torsion_angle_dof_id: angle range error
ERROR:: Exit from: src/core/kinematics/AtomTree.cc line: 780
SIGSEGV: segmentation violation
Stack trace (17 frames):
[0xb2aef87]
[0xf7703400]
[0xa166837]
[0xa1f3edc]
[0xa1f4e3c]
[0x996c8d6]
[0x996df60]
[0x89561af]
[0x867d35e]
[0x992d14f]
[0x9931429]
[0x9aebcad]
[0x9b4f815]
[0x9b4d045]
[0x8054950]
[0xb33f328]
[0x8048131]

Exiting...

</stderr_txt>
]]>



ID: 75537 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1181
Credit: 5,048,108
RAC: 1,266
Message 75538 - Posted: 29 Apr 2013, 10:05:23 UTC - in response to Message 75536.  

Despite resetting the project, I am still getting only 3.45 jobs on a 6.x version of BOINC.


Still here, on 7.0.x version on boinc
Only 3.45....
ID: 75538 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 983
Credit: 10,698,494
RAC: 4,154
Message 75540 - Posted: 29 Apr 2013, 16:53:46 UTC - in response to Message 75536.  

minirosetta is updated to 3.46 to include recent developments in electron density and other scoring functions.
Are there any particular minimum requirements for this version? Despite resetting the project, I am still getting only 3.45 jobs on a 6.x version of BOINC.


The best I can tell, only the cryo workunits need the new features of 3.46.
ID: 75540 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Brian Priebe

Send message
Joined: 27 Nov 09
Posts: 16
Credit: 33,020,247
RAC: 0
Message 75541 - Posted: 29 Apr 2013, 17:47:54 UTC - in response to Message 75540.  

The best I can tell, only the cryo workunits need the new features of 3.46.

Yet on BOINC 7.0.28 under Windows 7 (64-bit), all work units are delivered to run under Mini Rosetta app 3.46. Such is not the case under BOINC 6.12.33 running under Windows 2003 Server (32-bit): they all still run app 3.45. And of course the "cryo" series are still bombing out under 3.45.
ID: 75541 · 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 75543 - Posted: 29 Apr 2013, 23:10:10 UTC - in response to Message 75541.  

The best I can tell, only the cryo workunits need the new features of 3.46.

Yet on BOINC 7.0.28 under Windows 7 (64-bit), all work units are delivered to run under Mini Rosetta app 3.46. Such is not the case under BOINC 6.12.33 running under Windows 2003 Server (32-bit): they all still run app 3.45. And of course the "cryo" series are still bombing out under 3.45.



Hi.

For whatever reason windows 32 hasn't been updated, see the app page.

Windows/x86 3.45 14 Nov 2012 19:40:42 UTC

ID: 75543 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Yifan Song
Volunteer moderator
Project developer
Project scientist

Send message
Joined: 26 May 09
Posts: 62
Credit: 7,322
RAC: 0
Message 75545 - Posted: 30 Apr 2013, 0:52:00 UTC
Last modified: 30 Apr 2013, 0:53:35 UTC

OK, I got it wrong earlier. The Windows/x86 version is for the actual application, not the graphics. For some reason that file didn't get updated the last time I ran the script. I just reran the update, and it looks ok now. I didn't even think that would be the problem. Sorry about the confusion.
ID: 75545 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Yuriy Naydenov

Send message
Joined: 17 Jun 12
Posts: 4
Credit: 4,333,316
RAC: 0
Message 75551 - Posted: 30 Apr 2013, 20:38:15 UTC
Last modified: 30 Apr 2013, 20:42:20 UTC

ID: 75551 · 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 75558 - Posted: 2 May 2013, 22:49:21 UTC
Last modified: 2 May 2013, 22:50:08 UTC

Hi.

I haven't had error like this for a long time, it ran for over 5hrs.

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=525740466

CASP9_bw_benchmark_hybridization_run49_T0534_2_C1_SAVE_ALL_OUT_IGNORE_THE_REST_46345_6031_0

# cpu_run_time_pref: 21600

Client error___Compute error___18,861.34

<core_client_version>7.0.27</core_client_version>
<![CDATA[
<message>
Maximum disk usage exceeded
</message>
<stderr_txt>
ID: 75558 · 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 75567 - Posted: 5 May 2013, 21:53:35 UTC
Last modified: 5 May 2013, 22:03:02 UTC

This thing had ran for over 9hrs, 40min without a check point, so when I restarted the rig this morning it went back to the 0/start again so I've aborted it.


endo_ab_Pan927.run.12_SAVE_ALL_OUT_IGNORE_THE_REST_79957_24_0


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=526157680

=============================

Also another one of these.

rb_04_24_37778_72771__t000__1_C1_SAVE_ALL_OUT_IGNORE_THE_REST_79247_1579_1

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=525205524

<core_client_version>7.0.27</core_client_version>
<![CDATA[
<message>
Maximum disk usage exceeded
</message>

<stderr_txt>
ID: 75567 · 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 75577 - Posted: 7 May 2013, 7:51:58 UTC
Last modified: 7 May 2013, 7:53:48 UTC

I'm getting sick of this, over 10hrs run time then this Not impressed at all.

If the watchdog killed it, why didn't it do so earlier?

cryo_bg__chain_d_l_subrun_003_SAVE_ALL_OUT_IGNORE_THE_REST_79148_309_1

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=524912436


# cpu_run_time_pref: 21600
BOINC:: CPU time: 36259.9s, 14400s + 21600s[2013- 5- 7 14:35:29:] :: BOINC
InternalDecoyCount: 45
======================================================
DONE :: 2 starting structures 36259.9 cpu seconds
This process generated 45 decoys from 45 attempts
======================================================
called boinc_finish
SIGSEGV: segmentation violation

</stderr_txt>
]]>

Validate state Invalid
Claimed credit 373.059569535114
Granted credit 0
application version 3.46
ID: 75577 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Yifan Song
Volunteer moderator
Project developer
Project scientist

Send message
Joined: 26 May 09
Posts: 62
Credit: 7,322
RAC: 0
Message 75581 - Posted: 7 May 2013, 22:25:07 UTC

I've been running debugging from my side for the last week on the same set of jobs, it's running a lot slower with the debug mode, so I haven't consistently reproduce the seg fault yet. My suspicion is that something is still not quite fixed in the gradient calculations.
ID: 75581 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 983
Credit: 10,698,494
RAC: 4,154
Message 75582 - Posted: 8 May 2013, 3:29:57 UTC - in response to Message 75577.  

I'm getting sick of this, over 10hrs run time then this Not impressed at all.

If the watchdog killed it, why didn't it do so earlier?

cryo_bg__chain_d_l_subrun_003_SAVE_ALL_OUT_IGNORE_THE_REST_79148_309_1

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=524912436


Looks like you might get more useful results if you decrease the allowed runtime for your workunits enough that they won't run over 10 hours.
ID: 75582 · 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 75586 - Posted: 9 May 2013, 6:00:52 UTC

I don't know what I've done to deserve these things, got'a love that credit for 8hrs work.

rb_05_07_37484_73467__t000__1_C1_SAVE_ALL_OUT_IGNORE_THE_REST_80583_498_0

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=526810531

Starting watchdog...
Watchdog active.
# cpu_run_time_pref: 14400
BOINC:: CPU time: 28814.8s, 14400s + 14400s[2013- 5- 9 15:34:10:] :: BOINC
InternalDecoyCount: 3
======================================================
DONE :: 2 starting structures 28814.8 cpu seconds
This process generated 3 decoys from 3 attempts
======================================================
called boinc_finish
SIGSEGV: segmentation violation
Stack trace (21 frames):
[0xb2aef87]
[0xf7745400]
[0xa6ce54c]
[0xa6e7659]
[0xa1648c7]
[0xa1f2dd2]
[0xa1f4df1]
[0x9d4d1a5]
[0x9f10187]
[0x9d56457]
[0x9d4265a]
[0x8925eca]
[0x8681018]
[0x992d14f]
[0x9931429]
[0x9aebcad]
[0x9b4f815]
[0x9b4d045]
[0x8054950]
[0xb33f328]
[0x8048131]

Exiting...

</stderr_txt>
]]>

Validate state__Valid
Claimed credit__222.194343136291
Granted credit__7.33239552472893
application version__3.46

ID: 75586 · 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 75591 - Posted: 9 May 2013, 22:44:54 UTC
Last modified: 9 May 2013, 23:13:08 UTC

Something odd with these new tasks, showing 0 for everything but are valid.

Both ran for longer then runtime shown, they went back when restarted & they both ran for over 7hrs.

idealdead2_test_abrelax_nohoms_1l9l_SAVE_ALL_OUT_80619_74_0

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=526963404

# cpu_run_time_pref: 14400
======================================================
DONE :: 0 starting structures 11822.6 cpu seconds
This process generated 0 decoys from 0 attempts
======================================================
BOINC :: WS_max 0

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

</stderr_txt>
]]>

Validate state Valid
Claimed credit 91.1614143589971
Granted credit 125.885524056059
application version 3.46

==============================================

idealdead2_test_abrelax_homs_1l9l_SAVE_ALL_OUT_80618_77_0

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=526964451

# cpu_run_time_pref: 14400
======================================================
DONE :: 0 starting structures 3917.32 cpu seconds
This process generated 0 decoys from 0 attempts
======================================================
BOINC :: WS_max 0

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

</stderr_txt>
]]>

Validate state Valid
Claimed credit 40.3030670421785
Granted credit 43.9948759779241
application version 3.46
ID: 75591 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Chilean
Avatar

Send message
Joined: 16 Oct 05
Posts: 710
Credit: 26,023,847
RAC: 856
Message 75592 - Posted: 10 May 2013, 5:27:52 UTC

ID: 75592 · 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 75593 - Posted: 10 May 2013, 5:58:20 UTC

Another one of these died, after 4sec's.

idealdead2_test_abrelax_nohoms_1jf8_SAVE_ALL_OUT_80619_456_0

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=527126051

Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
DKKTIYFISTGNSARSQMAEGWGKEILGEGWNVYSAGIETHGVNPKAIEAMKEVDIDISNHTSDLIDNDILKQSDLVVTLCSDADNNCPILPPNVKKEHWGFDDPAGKEWSEFQRVRDEIKLAIEKFKLRX
can not find a residue type that matches the residue Kat position 131

ERROR: core::util::switch_to_residue_type_set fails

ERROR:: Exit from: src/core/util/SwitchResidueTypeSet.cc line: 143
std::cerr: Exception was thrown:


[ERROR] EXCN_utility_exit has been thrown from: src/core/util/SwitchResidueTypeSet.cc line: 143
ERROR: core::util::switch_to_residue_type_set fails



</stderr_txt>
]]>

ID: 75593 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Yifan Song
Volunteer moderator
Project developer
Project scientist

Send message
Joined: 26 May 09
Posts: 62
Credit: 7,322
RAC: 0
Message 75596 - Posted: 10 May 2013, 20:15:42 UTC

Thanks! I'll let the person running the idealdead2 jobs know about this. -y
ID: 75596 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 983
Credit: 10,698,494
RAC: 4,154
Message 75599 - Posted: 11 May 2013, 2:27:52 UTC

A workunit that may have a problem:

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=527210644
another idealdead2 workunit

Now at 15:51:54 elapsed, even though I've set 12 hours as the workunit length for my computers.

Showing 98.956% progress, slowly increasing.

Remaining time shown as 00:10:03 and NOT decreasing.

No error messages visible.

I'll let it go to at least 16 hours before deciding if I should abort it.
ID: 75599 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 983
Credit: 10,698,494
RAC: 4,154
Message 75600 - Posted: 11 May 2013, 3:49:12 UTC - in response to Message 75599.  

A workunit that may have a problem:

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=527210644
another idealdead2 workunit

Now at 15:51:54 elapsed, even though I've set 12 hours as the workunit length for my computers.

Showing 98.956% progress, slowly increasing.

Remaining time shown as 00:10:03 and NOT decreasing.

No error messages visible.

I'll let it go to at least 16 hours before deciding if I should abort it.


It finished in a little more than 16 hours, and was declared a success.

However, several dozen of these errors in the output:

sin_cos_range ERROR: 1.#QNAN00 is outside of [-1,+1] sin and cos value legal range

Also around 20 NaN errors.
ID: 75600 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Previous · 1 · 2 · 3 · 4 · Next

Message boards : Number crunching : Minirosetta 3.46



©2020 University of Washington
https://www.bakerlab.org