Minirosetta 1.81

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mtyka
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Message 4865 - Posted: 11 Jul 2009, 20:33:33 UTC
Last modified: 11 Jul 2009, 20:33:48 UTC

Supports this Disulfide bonds with encouraging initial results. We're eager to test this on a larger scale.

http://en.wikipedia.org/wiki/Disulfide_bond

Also includes bugfixes for some of the issues encountered over on BOINC.

As always, please post issues here!

M
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Message 4866 - Posted: 11 Jul 2009, 23:13:02 UTC - in response to Message 4865.  

Supports this Disulfide bonds with encouraging initial results. We're eager to test this on a larger scale.

http://en.wikipedia.org/wiki/Disulfide_bond

Also includes bugfixes for some of the issues encountered over on BOINC.

As always, please post issues here!

M


G'Day mtyka,
Does 1.81 include a fix for the work units that were running for over 4 hours past set preferences before failing due to taking too long to generate 1 decoy ? Like the ones I was reporting in the 1.80 thread.
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Message 4868 - Posted: 12 Jul 2009, 8:23:27 UTC

Errors with 1.81

<core_client_version>6.4.5</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
[2009- 7-12 7:33:46:] :: BOINC:: Initializing ... ok.
[2009- 7-12 7:33:46:] :: 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
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_cl1_8.foldcst_chunk_general_cf.t297_.mtyka.boinc_files.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
Setting up folding (abrelax) ...

ERROR: [ERROR] Unable to open constraints file: t297_.8.cst
ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 331
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

On this result

Also had a Validate Error when all appeared OK on This Result

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svincent

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Message 4870 - Posted: 12 Jul 2009, 15:41:52 UTC

This workunit 1541588 on Mac took 5 hours then failed with a Validate error

BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Starting work on structure: _1BG2A_2_00001
BOINC:: CPU time: 18467.3s, 14400s + 3600s[2009- 7-12 2:37:44:] :: BOINC
Output exists: default.out.gz
InternalDecoyCount: 0 (GZ)
0
Stream information inconsistent.
Writing W_0000001
======================================================
DONE :: 1 starting structures 18467.3 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish

</stderr_txt>
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Snagletooth

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Message 4872 - Posted: 13 Jul 2009, 10:46:16 UTC

frb_0_8_cl1_5_hb_t297__IGNORE_THE_REST_1FXWF_9_11640_1_1

ERROR: [ERROR] Unable to open constraints file: t297_.5.cst
ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 331
BOINC:: Error reading and gzipping output datafile: default.out
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Evan

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Message 4873 - Posted: 13 Jul 2009, 13:40:42 UTC

1544975
http://ralph.bakerlab.org/result.php?resultid=1544975

1544974
http://ralph.bakerlab.org/result.php?resultid=1544974

Errors with both the above. There is a 50% chance it was an operator induced error as they both occurred after I rebooted the computer.
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Billy

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Message 4874 - Posted: 14 Jul 2009, 2:41:06 UTC

Don't know if it is a bug or not. On my Intel iMac Core Duo, 1.81 is using 444 MB of real memory. This seems high compared to your recommended limit of 512 MB.
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svincent

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Message 4875 - Posted: 14 Jul 2009, 16:17:44 UTC

A couple of Validate errors on Mac: both generated 99 decoys in less than 15 minutes.

1548638
1548639
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Message 4876 - Posted: 14 Jul 2009, 16:56:18 UTC

Error in task 1543648.

Hbond tripped: [2009- 7-13  0:35: 0:]

ERROR: dis==0 in pairtermderiv!
ERROR:: Exit from: src/core/scoring/methods/PairEnergy.cc line: 334
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

AdeB
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Message 4877 - Posted: 15 Jul 2009, 1:30:28 UTC
Last modified: 15 Jul 2009, 1:54:26 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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Valter

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Message 4878 - Posted: 15 Jul 2009, 8:25:32 UTC

Hi, everyone.

I have a work unit running for 25 hours and at 45.230%. Rosetta Mini 1.81. Should I cancel it or go on running?

Thanks and regards,

Valter Aguiar
Brazil.
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Evan

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Message 4879 - Posted: 15 Jul 2009, 19:06:57 UTC

I am slowly working my way through the frb_0_8_cl_1... work units. No problems so far but I fear the lack of checkpoints will create a few complaints. So far on the long running models I am at aound 4 hours without a checkpoint.
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AdeB
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Message 4880 - Posted: 16 Jul 2009, 16:18:23 UTC

I never saw this error before:
In task 1548231 (frb_0_8_cl1_5_hb_t305__IGNORE_THE_REST_2G59A_7_11642_1_0):

<![CDATA[
<message>
Maximum memory exceeded
</message>


This is on a PC with 512MB memory, AMD Athlon XP running linux.

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Message 4881 - Posted: 23 Jul 2009, 10:03:49 UTC

This is a 1.83 WU error

<core_client_version>6.4.7</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
[2009- 7-23 9:34:44:] :: BOINC:: Initializing ... ok.
[2009- 7-23 9:34:44:] :: 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 -detect_disulphides not found in command line top-level context

See this WU

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AdeB
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Message 4882 - Posted: 23 Jul 2009, 18:09:01 UTC - in response to Message 4881.  

This is a 1.83 WU error

<core_client_version>6.4.7</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
[2009- 7-23 9:34:44:] :: BOINC:: Initializing ... ok.
[2009- 7-23 9:34:44:] :: 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 -detect_disulphides not found in command line top-level context

See this WU


The same error here

AdeB
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