Minirosetta 3.46

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TJ

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Message 75807 - Posted: 26 Jun 2013, 17:08:09 UTC - in response to Message 75803.  

Were these new jobs set up this way, or was this an oversight? I've already lost a number of hours/days of crunching because of this issue before I got an idea of what was happening. Is there a reasonable workaround for this problem? Thanks.


Target CPU run time: 1 hour..... :-)

I have seen this on preferences but have now idea what it does or where it is for.
Can someone please explain this?


Rosetta@Home workunits are set up in usually 100 sections, called decoys. They try to run however many of these decoys they expect to finish in the target CPU run time, but can go over if the last one takes longer than expected.

I'm not sure if the shutdown code runs properly if the last decoy that was finished reported an error instead of a good answer.

Does that mean that when I set the runtime at i.e. 2 hours, a Rosetta WU will be finished within 2 hours?
I have not set anything there at the moment and WU's take around 5 hours to finish.
Greetings,
TJ.
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Profile dcdc

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Message 75808 - Posted: 26 Jun 2013, 18:04:57 UTC - in response to Message 75807.  

Were these new jobs set up this way, or was this an oversight? I've already lost a number of hours/days of crunching because of this issue before I got an idea of what was happening. Is there a reasonable workaround for this problem? Thanks.


Target CPU run time: 1 hour..... :-)

I have seen this on preferences but have now idea what it does or where it is for.
Can someone please explain this?


Rosetta@Home workunits are set up in usually 100 sections, called decoys. They try to run however many of these decoys they expect to finish in the target CPU run time, but can go over if the last one takes longer than expected.

I'm not sure if the shutdown code runs properly if the last decoy that was finished reported an error instead of a good answer.

Does that mean that when I set the runtime at i.e. 2 hours, a Rosetta WU will be finished within 2 hours?
I have not set anything there at the moment and WU's take around 5 hours to finish.


It's a preference rather than a hard limit. If the decoys are small/quick to run in comparison to your preference time then there's a good chance that Rosetta will be able to complete the task near your target time, but it has to complete a minimum of one decoy so if one decoy takes longer than the run time then you'll be over the time limit. I guess if the decoys are very variable in run-time then that'll also reduce Rosetta's prediction accuracy on run-time.
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TJ

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Message 75812 - Posted: 27 Jun 2013, 20:24:06 UTC - in response to Message 75808.  

It's a preference rather than a hard limit. If the decoys are small/quick to run in comparison to your preference time then there's a good chance that Rosetta will be able to complete the task near your target time, but it has to complete a minimum of one decoy so if one decoy takes longer than the run time then you'll be over the time limit. I guess if the decoys are very variable in run-time then that'll also reduce Rosetta's prediction accuracy on run-time.

Thank you. In that case I leave it as it is.

Greetings,
TJ.
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Message 75834 - Posted: 11 Jul 2013, 9:59:49 UTC - in response to Message 75807.  

Does that mean that when I set the runtime at i.e. 2 hours, a Rosetta WU will be finished within 2 hours?
I have not set anything there at the moment and WU's take around 5 hours to finish.

Also note the wording "Target CPU run time". The task will try to run no more than the set CPU time, but if your CPU has a lot of other stuff to do, the actuall runtime might be a lot longer.
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Profile [VENETO] boboviz

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Message 75835 - Posted: 11 Jul 2013, 15:30:13 UTC

After 6 hours of crunch, error on 592222594:

# cpu_run_time_pref: 7200
BOINC:: CPU time: 21994.5s, 14400s + 7200s[2013- 7-11 16:58:11:] :: 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
======================================================
DONE :: 1 starting structures 21994.5 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>cryo_bb__t20s__SAVE_ALL_OUT_IGNORE_THE_REST_88799_4052_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

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Profile [VENETO] boboviz

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Message 75859 - Posted: 21 Jul 2013, 19:13:46 UTC

screensaver crashes with endo_ac_ wus....
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Nick Perry

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Message 75894 - Posted: 3 Aug 2013, 9:54:55 UTC - in response to Message 75859.  

screensaver crashes with endo_ac_ wus....

same issue here. Windows 7 system runs fine XP system ALL endo units error. NOT running the screensaver, just in BOINC manager.

Graphics fail after 2 to 5 minutes..
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Profile [VENETO] boboviz

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Message 75919 - Posted: 9 Aug 2013, 8:35:41 UTC

597301386

<core_client_version>7.0.27</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
[2013- 8- 9 10:33:41:] :: BOINC:: Initializing ... ok.
[2013- 8- 9 10:33:41:] :: 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: Illegal value specified for option -run:protocol : abinitio

</stderr_txt>
]]>
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Profile [VENETO] boboviz

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Message 76031 - Posted: 5 Sep 2013, 19:22:09 UTC - in response to Message 75859.  

screensaver crashes with endo_ac_ wus....


Again....no fix?
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Profile [VENETO] boboviz

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Message 76060 - Posted: 23 Sep 2013, 7:53:07 UTC

605202808

After 68 minutes

Continuing computation from checkpoint: chk_NoTag_FastRelax__chk1_fa ... success!
dof_atom1 atomno= 3 rsd= 8
atom1 atomno= 1 rsd= 8
atom2 atomno= 2 rsd= 8
atom3 atomno= 5 rsd= 8
atom4 atomno= 6 rsd= 8
THETA1 nan
THETA3 1.02049
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 (18 frames):
[0xb2aef87]
[0x85a400]
[0xa720abb]
[0xa166837]
[0xa1f3edc]
[0xa1f4e3c]
[0x996c8d6]
[0x996df60]
[0x89561af]
[0x867d35e]
[0x992d14f]
[0x9931429]
[0x9aebcad]
[0x9b4f815]
[0x9b4d045]
[0x8054950]
[0xb33f328]
[0x8048131]

Exiting...

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Profile [VENETO] boboviz

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Message 76090 - Posted: 2 Oct 2013, 15:51:33 UTC

607525909
607525911


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_rev54943.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/input_ac_t20s_reg_shift_6.0A_1pma_fit_INPUT_A0076-A0089_-3_yfsong.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
# cpu_run_time_pref: 7200
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
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P . P . L .

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Message 76091 - Posted: 3 Oct 2013, 1:06:47 UTC

I've had 7 of these fail 1 after the other all the same.


ab_t20s_reg_shift_4.1A_1pma_fit_INPUT_B0402-B0408_01_SAVE_ALL_OUT_IGNORE_THE_REST_99824_2_0

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=551792680

ERROR: Unable to open weights/patch file. None of (./)stage1 or (./)stage1.wts or minirosetta_database/scoring/weights/stage1 or minirosetta_database/scoring/weights/stage1.wts exist
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 2967
# cpu_run_time_pref: 14400
SIGSEGV: segmentation violation
Stack trace (9 frames):
[0xb2aef87]
[0xb7720400]
[0x99704f6]
[0x9aebb07]
[0x9b4f815]
[0x9b4d045]
[0x8054950]
[0xb33f328]
[0x8048131]

Exiting...

</stderr_txt>
]]>

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Profile Yuriy Naydenov

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Message 76694 - Posted: 6 May 2014, 22:33:39 UTC - in response to Message 75551.  

.
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Profile Yuriy Naydenov

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Message 76695 - Posted: 6 May 2014, 22:35:31 UTC - in response to Message 75551.  

.
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Message boards : Number crunching : Minirosetta 3.46



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