Bug Reports for Minirosetta v1.38

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Chu
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Message 4286 - Posted: 22 Oct 2008, 18:25:35 UTC
Last modified: 22 Oct 2008, 19:56:17 UTC

Hi everyone,

Long time no see!

Please post issues/bugs relating to minirosetta version 1.38 here. In this version, we added two important applications to minirosetta, docking and protein folding with explicit zinc metal ion. Please pay extra attention to some new features of the graphics such as \"color by chain\" and \"spacefill display of metal ligand\" and let us know if you observe any problem or have suggestions or feedbacks. Thanks.

Here are two screen shots, one for protein folding with zinc metal (red ball) and one for docking of two protein structures (color by protein chain) to get their complex form.

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Message 4287 - Posted: 22 Oct 2008, 18:52:54 UTC
Last modified: 22 Oct 2008, 18:53:15 UTC

Chu! Long time no \"see\"! Welcome back.

What\'s with the little red ball?

Make this thread sticky. Maybe unsticky some others.
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Chu
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Message 4288 - Posted: 22 Oct 2008, 19:45:08 UTC - in response to Message 4287.  

That is the Zinc metal ion \"ZN2+\", modeled together with proteins which naturally bind them for structure stability and/or functional catalysis. I will post a more detailed description to explain the background of this prject and the goal we are hoping to achieve.
Chu! Long time no \"see\"! Welcome back.

What\'s with the little red ball?

Make this thread sticky. Maybe unsticky some others.

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Message 4291 - Posted: 23 Oct 2008, 21:02:55 UTC
Last modified: 23 Oct 2008, 21:05:46 UTC

Got a Segmentation Violation on result 1169994

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
SIGSEGV: segmentation violation
Stack trace (7 frames):
[0x8ab9c07]
[0x8ae4300]
[0xb7f7a420]
[0x819dc96]
[0x804c2ea]
[0x8b3fdfc]
[0x8048111]

Exiting...

Also got an error on result 1170096

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>

ERROR: Unable to open weights. Neither .//work/rvernon/frag_48kinds/boinc_submit/mini_oct22_08/fixed_bb_hb.wts nor minirosetta_database/scoring/weights//work/rvernon/frag_48kinds/boinc_submit/mini_oct22_08/fixed_bb_hb.wts exist
ERROR:: Exit from: src/core/scoring/ScoreFunctionFactory.cc line: 57
called boinc_finish

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Message 4292 - Posted: 23 Oct 2008, 21:08:52 UTC - in response to Message 4291.  
Last modified: 23 Oct 2008, 21:10:30 UTC

http://ralph.bakerlab.org/result.php?resultid=1170135

And several more.

10/23/2008 5:02:34 PM|ralph@home|Starting 1c8cA_BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--1c8cA-_5221_3_0
10/23/2008 5:02:34 PM|ralph@home|Starting task 1c8cA_BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--1c8cA-_5221_3_0 using minirosetta_split_terms version 101
10/23/2008 5:02:35 PM|ralph@home|Computation for task 1bkrA_BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--1bkrA-_5221_3_0 finished
10/23/2008 5:02:35 PM|ralph@home|Output file 1bkrA_BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--1bkrA-_5221_3_0_0 for task 1bkrA_BOINC_CASP8_ABRELAX_SPLIT_SPLIT_IGNORE_THE_REST-S25-9-S3-3--1bkrA-_5221_3_0 absent
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Message 4293 - Posted: 24 Oct 2008, 3:11:45 UTC

Nearly 38 hrs on a 24hr preferred runtime. Still on model one.

hombench_olange_foldcst_single_alignment_t374_
foldcst_single_alignment_t374__IGNORE_THE_REST_2FCKA_3_5191_5_0
Workunit 1006002

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Message 4294 - Posted: 24 Oct 2008, 12:01:32 UTC

Another two with the weight problem and also the wrong application number of 1.01
See this WU
and this WU

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>

ERROR: Unable to open weights. Neither .//work/rvernon/frag_48kinds/boinc_submit/mini_oct22_08/fixed_bb_hb.wts nor minirosetta_database/scoring/weights//work/rvernon/frag_48kinds/boinc_submit/mini_oct22_08/fixed_bb_hb.wts exist
ERROR:: Exit from: src/core/scoring/ScoreFunctionFactory.cc line: 57
called boinc_finish

</stderr_txt>
]]>

Validate state Invalid
Claimed credit 0.00944960901350064
Granted credit 0
application version 1.01
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Message 4295 - Posted: 24 Oct 2008, 17:23:55 UTC

FYI, v1.39 is still showing the issue where BOINC Manager is unable to suspend the task to run other projects. And so I\'m still seeing my HT processor running 3 tasks at the same time on Win XP Pro.

I was able to suspend the task, it continued to run. I then resumed it, and of course it continued to run. But then when I suspended it again, it did stop normally.
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Message 4296 - Posted: 24 Oct 2008, 18:59:21 UTC

Version 1.39 error:

<core_client_version>6.2.19</core_client_version>
<![CDATA[
<message>
- exit code -1073741819 (0xc0000005)
</message>
<stderr_txt>
recovering checkpoint of tag S_1D5WA_2_00000001 with id abrelax_rg_state

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x008106CA read attempt to address 0x00000000

Engaging BOINC Windows Runtime Debugger...
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Message 4298 - Posted: 25 Oct 2008, 17:07:58 UTC

Version 1.39:
Workunit http://ralph.bakerlab.org/result.php?resultid=1171026

Got this:
25/10/2008 16:30:48|ralph@home|Computation for task 1SPB_dockprotocol_BOUND_MRTM_PERT38_DOCK_5220_11_1 finished
25/10/2008 16:30:48|ralph@home|Output file 1SPB_dockprotocol_BOUND_MRTM_PERT38_DOCK_5220_11_1_0 for task 1SPB_dockprotocol_BOUND_MRTM_PERT38_DOCK_5220_11_1 exceeds size limit.
25/10/2008 16:30:48|ralph@home|File size: 60636800.000000 bytes. Limit: 25000000.000000 bytes
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