Minirosetta 1.82/1.88

Message boards : Number crunching : Minirosetta 1.82/1.88

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Mike Tyka

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Message 62226 - Posted: 14 Jul 2009, 17:13:54 UTC

Ok, 1.82 is out. This one has

- Support for Disulfides. New Science!
- Bug fixes for homology modelling with constraints
- SOme bugfixes in the watchdog


Mike

http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Billy

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Message 62233 - Posted: 15 Jul 2009, 2:01:50 UTC

Task 1554305

BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Starting work on structure: _1BG2A_2_00001
BOINC:: CPU time: 18235.1s, 14400s + 3600s[2009- 7-14 19:26:21:] :: BOINC
WARNING! cannot get file size for default.out.gz: could not open file.
Output exists: default.out.gz Size: -1
InternalDecoyCount: 0 (GZ)
-----
0
-----
Stream information inconsistent.
Writing W_0000001

Minirosetta 1.82
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googloo
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Message 62238 - Posted: 15 Jul 2009, 16:10:47 UTC

Please, please, please post notice of new versions to Rosetta Application Version Release Log. That\'s why we subscribe to it.
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P . P . L .

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Message 62244 - Posted: 16 Jul 2009, 6:33:28 UTC

Hi.

This one lasted around 7 sec.

lr10_seq_score12_rlbd_1ptq_IGNORE_THE_REST_DECOY_13841_3969_0

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=242762845


<core_client_version>6.2.14</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>

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Speedy
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Message 62245 - Posted: 16 Jul 2009, 6:53:14 UTC

G\'day
This one lasted around 5 minutes

lr8_seq_score12_ss5.0_rlbd_1ptq_IGNORE_THE_REST_DECOY_14281_655_0

http://boinc.bakerlab.org/rosetta/result.php?resultid=266057438

<core_client_version>6.6.28</core_client_version>
<![CDATA[
<message>
- exit code -1073741819 (0xc0000005)
</message>

Have a crunching good day!!
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AMD_is_logical

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Message 62252 - Posted: 16 Jul 2009, 17:56:00 UTC

This WU, lr8_seq_score12_ss5.0_rlbd_1ptq_IGNORE_THE_REST_DECOY_14281_1507_0, had a segmentation violation after 5 seconds on one of my Linux systems.
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Snags

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Message 62257 - Posted: 17 Jul 2009, 4:45:46 UTC

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Rob Lilley

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Message 62269 - Posted: 17 Jul 2009, 20:47:10 UTC

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x006C1C6D read attempt to address 0x00000000

Happened on this WU after 2 hrs 50 min. This machine worked fine with Rosetta Mini v1.80.
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Jimmy McNulty

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Message 62270 - Posted: 17 Jul 2009, 21:11:37 UTC

Sorry if this is the wrong thread or a problem with my computer instead of v1.82. Had another problem with a WU, 2.87% done after 6 hours, and no progress for the 45 minutes I watched it. Probably the 6th time it\'s happened since I rejoined the project a couple weeks ago. These WU won\'t abort by themselves, wasting CPU cycles until I check BOINC and abort them. Like I say this might be a problem with my computer, but it doesn\'t happen with any other project. The research you\'re doing is great, but i\'m suspending the project for now. I\'ll keep checking back with the new versions to see if the problem persists, but I had the same thing happen last Decemberish when I suspended it the first time, and it seems the updates since then haven\'t fixed it for me. Best of luck with the project, I hope I can contribute in the future.
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RC

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Message 62291 - Posted: 19 Jul 2009, 1:37:19 UTC

Not sure what happened to this one:

http://boinc.bakerlab.org/rosetta/result.php?resultid=266600560

<core_client_version>6.6.36</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
[2009- 7-18 8:29:15:] :: BOINC:: Initializing ... ok.
[2009- 7-18 8:29:15:] :: 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_rev30680.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: _00001
# cpu_run_time_pref: 28800
Starting work on structure: _00002
Starting work on structure: _00003
Starting work on structure: _00004
Starting work on structure: _00005
Starting work on structure: _00006
Starting work on structure: _00007
Starting work on structure: _00008
Starting work on structure: _00009
Starting work on structure: _00010
Starting work on structure: _00011
Starting work on structure: _00012
Starting work on structure: _00013
Starting work on structure: _00014
Starting work on structure: _00015
Starting work on structure: _00016
Starting work on structure: _00017
Starting work on structure: _00018
Starting work on structure: _00019
Starting work on structure: _00020
Starting work on structure: _00021
Starting work on structure: _00022
Starting work on structure: _00023
Starting work on structure: _00024
Starting work on structure: _00025
Starting work on structure: _00026
Starting work on structure: _00027
Starting work on structure: _00028
Starting work on structure: _00029
Starting work on structure: _00030
Starting work on structure: _00031
Starting work on structure: _00032
Starting work on structure: _00033
Starting work on structure: _00034
Starting work on structure: _00035
Starting work on structure: _00036
Starting work on structure: _00037
Starting work on structure: _00038
Starting work on structure: _00039
Starting work on structure: _00040
Starting work on structure: _00041
Starting work on structure: _00042
Starting work on structure: _00043
Starting work on structure: _00044
Starting work on structure: _00045
Starting work on structure: _00046
Starting work on structure: _00047
Starting work on structure: _00048
Starting work on structure: _00049
Starting work on structure: _00050
Starting work on structure: _00051
Starting work on structure: _00052
Starting work on structure: _00053
Starting work on structure: _00054
Starting work on structure: _00055
Starting work on structure: _00056
Starting work on structure: _00057
[2009- 7-18 20:37: 0:] :: BOINC:: Initializing ... ok.
[2009- 7-18 20:37: 0:] :: 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_rev30680.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.
# cpu_run_time_pref: 28800
Starting work on structure: _00057
Continuing computation from checkpoint: chk_S_00000057_ClassicAbinitio__stage_1 ... success!
Continuing computation from checkpoint: chk_S_00000057_ClassicAbinitio__stage_2 ... success!
SIGBUS: bus error

Crashed executable name: minirosetta_1.82_i686-apple-darwin
built using BOINC library version 6.5.0
Machine type Intel 80486 (32-bit executable)
System version: Macintosh OS 10.5.7 build 9J61
Sat Jul 18 20:37:10 2009

atos cannot load symbols for the file minirosetta_1.82_i686-apple-darwin.
0 0x00703b59 SIGPIPE: write on a pipe with no reader
1 0x004c2bd6 SIGPIPE: write on a pipe with no reader
2 0x909252bb SIGPIPE: write on a pipe with no reader
3 0xffffffff SIGPIPE: write on a pipe with no reader
4 0x00a7c005 SIGPIPE: write on a pipe with no reader
5 0x00158633 SIGPIPE: write on a pipe with no reader
6 0x0016e2e7 SIGPIPE: write on a pipe with no reader
7 0x005ea582 SIGPIPE: write on a pipe with no reader
8 0x00115072 SIGPIPE: write on a pipe with no reader
9 0x00128717 SIGPIPE: write on a pipe with no reader
10 0x000042a8 SIGPIPE: write on a pipe with no reader
11 0x0000204e SIGPIPE: write on a pipe with no reader
12 0x00001f75 SIGPIPE: write on a pipe with no reader
13 0x00000014
Thread 0 crashed with X86 Thread State (32-bit):
eax: 0xffffffe1 ebx: 0x908ed8c2 ecx: 0xbfff7c0c edx: 0x908b9286
edi: 0x00000000 esi: 0x00000000 ebp: 0xbfff7c48 esp: 0xbfff7c0c
ss: 0x0000001f efl: 0x00000206 eip: 0x908b9286 cs: 0x00000007
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037

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Exiting...

</stderr_txt>
]]>
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Profile bruce

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Message 62299 - Posted: 19 Jul 2009, 16:56:41 UTC

I\'ve been experiencing some issues with Minirosetta on 3 computers for quite some time. With no resolution, I had detached those computers from the project. Recently with release of 1.82 I decided to try the project again one computer and the problems continue.

Please reverence these links for background information:

http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4953&nowrap=true#62234
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4953&nowrap=true#62222
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4953&nowrap=true#62095

http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4876&nowrap=true#61739
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4876&nowrap=true#61424
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4876&nowrap=true#61359

For specifics on the WUs you can see the errored ones here:
http://boinc.bakerlab.org/rosetta/results.php?userid=205458&offset=100

is there anything else beyond what I\'ve supplied that can assist in resolving this issue?

Thanks.
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P . P . L .

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Message 62303 - Posted: 20 Jul 2009, 1:41:36 UTC

Hi.

Got this one this morning, it ran for 23min.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=243594843

Mon 20 Jul 2009 10:12:54 EST|rosetta@home|Output file lr8_score12_run02_rlbd_1wou_IGNORE_THE_REST_DECOY_12906_528_0_0 for task absent

<core_client_version>6.2.14</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>



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Profile Greg_BE
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Message 62305 - Posted: 20 Jul 2009, 8:00:30 UTC
Last modified: 20 Jul 2009, 8:01:26 UTC

Got a validate error out of this one frb_0_8_mike_chosen_intersection_new_hb_t367__IGNORE_THE_REST_1UFBA_4_13877_13_1.
Was granted only 4 credits for a fast run with 99 models. Only 1201 seconds run time! Something like 12 models a second?
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TimL

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Message 62309 - Posted: 20 Jul 2009, 10:12:04 UTC

This one lr8_seq_score12_ss5.0_rlbd_1aiu_IGNORE_THE_REST_DECOY_14281_320_0 caused

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x006C1C6D read attempt to address 0x00000000


Lots of windows debug info included in the error message for any who are willing and able.
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Message 62329 - Posted: 21 Jul 2009, 7:03:45 UTC - in response to Message 62299.  

I\'ve been experiencing some issues with Minirosetta on 3 computers for quite some time. With no resolution, I had detached those computers from the project. Recently with release of 1.82 I decided to try the project again one computer and the problems continue.

Please reverence these links for background information:

http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4953&nowrap=true#62234
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4953&nowrap=true#62222
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4953&nowrap=true#62095

http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4876&nowrap=true#61739
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4876&nowrap=true#61424
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4876&nowrap=true#61359

For specifics on the WUs you can see the errored ones here:
http://boinc.bakerlab.org/rosetta/results.php?userid=205458&offset=100

is there anything else beyond what I\'ve supplied that can assist in resolving this issue?

Thanks.


Sorry, should have made those proper links the first time...
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Message 62332 - Posted: 21 Jul 2009, 9:00:14 UTC

Compute error after 4,961 seconds:

http://boinc.bakerlab.org/rosetta/result.php?resultid=266802566

SIGSEGV: segmentation violation
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Message 62371 - Posted: 22 Jul 2009, 15:21:18 UTC

Compute error after 29,773 seconds:

http://boinc.bakerlab.org/rosetta/result.php?resultid=267060110

SIGSEGV: segmentation violation
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elninio

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Message 62383 - Posted: 23 Jul 2009, 5:01:16 UTC

1.82 is failing (but 5.98) works after i\'ve changed the number of days of workunits to fetch (7) - i\'ve tried detaching and resetting the project to no avail. What to do? ( 1.82 worked before)
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Message 62387 - Posted: 23 Jul 2009, 8:50:50 UTC - in response to Message 62383.  
Last modified: 23 Jul 2009, 8:53:33 UTC

1.82 is failing (but 5.98) works after i\'ve changed the number of days of workunits to fetch (7) - i\'ve tried detaching and resetting the project to no avail. What to do? ( 1.82 worked before)


occasionaly you get a bad batch of tasks such as lr8_seq_score12_ss5.0_rlbd_1h75_IGNORE_THE_REST_DECOY_14281_1247_0 which also errored out on another computer.

Exit status 193 (0xc1)
SIGABRT: abort called
Stack trace (14 frames):
[0x94fa937]
[0x9525044]
[0xb7f2c400]
[0x9589b04]
[0x959f853]
[0x95a48b9]
[0x95a4b97]
[0x9574871]
[0x94fe67a]
[0x94f9243]
[0x816a334]
[0x8048e92]
[0x9582a0c]
[0x8048111]


when you get failures like what is shown in that task..report it here.
this gives the team and other users an idea of what is going on with these tasks. if it is a common enough error the team notices from all the posts that something is wrong.

keep crunching...not everything fails.
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Message 62388 - Posted: 23 Jul 2009, 12:59:55 UTC - in response to Message 62383.  

1.82 is failing (but 5.98) works after i\'ve changed the number of days of workunits to fetch (7) - i\'ve tried detaching and resetting the project to no avail. What to do? ( 1.82 worked before)

While greg be might be correct and you\'ve just had a bit of bad luck with bad batches of tasks it\'s worth noting that quite a few of your failed tasks have been completed successfully by others. It may be possible that that some tasks only fail on a particular OS (Linux in your case)but it might be worth following Jorden\'s advice here and testing your memory.
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Message boards : Number crunching : Minirosetta 1.82/1.88



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