Minirosetta 3.62-3.65

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Profile David E K
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Message 78684 - Posted: 3 Sep 2015, 21:38:11 UTC

The minirosetta application has been updated to the latest Rosetta source. This update includes a new optimized score function which improves all scientific benchmarks. Please post any bugs/issues related to this update here.
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Message 78687 - Posted: 4 Sep 2015, 16:08:42 UTC
Last modified: 4 Sep 2015, 16:08:57 UTC

Is it possible to say/test what effect SSE is having? Presumably it varies by CPU and the same unit would have to be run with SSE off?
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Message 78688 - Posted: 4 Sep 2015, 17:34:31 UTC - in response to Message 78687.  

Is it possible to say/test what effect SSE is having? Presumably it varies by CPU and the same unit would have to be run with SSE off?


SSE is not being used in these updates.
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Profile Dr. Merkwürdigliebe
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Message 78689 - Posted: 4 Sep 2015, 17:55:41 UTC

minirosetta_3.62_x86_64-pc-linux-gnu: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), statically linked, for GNU/Linux 2.6.9, stripped

A bit disappointed here...
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Message 78690 - Posted: 4 Sep 2015, 18:05:56 UTC

I see the minirosetta_database got quite a lot larger, from 248MB to 411MB unpacked. Not so good considering this thing is extracted each time a new WU starts, lets see how my soon 10 years old laptop and it\'s hard drive will like it...
.
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Message 78691 - Posted: 4 Sep 2015, 20:12:55 UTC
Last modified: 4 Sep 2015, 20:26:03 UTC

I am showing so far that many 3.62 tasks are encountering \'Validate Errors\', though not all of them.

The following tasks are all variations of a project with the title like \'FFD__ xxxxx_abinitioDocking\':
Task 755931518 - Validate error
Task 755927819 - Validate error

What sucks is the tasks run for the full runtime (in my case, 8 hours) but end up failing validation

.. However, it\'s not all bad news some other 3.62 tasks, one of which is \'FFD__xxxxx_insulin_fourH2_Thu_xxxx\' are finishing successfully

as well as most all of the 3.62 \'rb_\' type tasks which seem to be finishing successfully. This leads me to believe it may be an issue with some of the FFD abinitio docking jobs.
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Profile David E K
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Message 78692 - Posted: 4 Sep 2015, 21:07:30 UTC - in response to Message 78691.  

I am showing so far that many 3.62 tasks are encountering \'Validate Errors\', though not all of them.

The following tasks are all variations of a project with the title like \'FFD__ xxxxx_abinitioDocking\':
Task 755931518 - Validate error
Task 755927819 - Validate error

What sucks is the tasks run for the full runtime (in my case, 8 hours) but end up failing validation

.. However, it\'s not all bad news some other 3.62 tasks, one of which is \'FFD__xxxxx_insulin_fourH2_Thu_xxxx\' are finishing successfully

as well as most all of the 3.62 \'rb_\' type tasks which seem to be finishing successfully. This leads me to believe it may be an issue with some of the FFD abinitio docking jobs.


Thanks for the heads up. We are currently looking into this.
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Message 78693 - Posted: 4 Sep 2015, 21:52:53 UTC

From September 3, not me work tasks.

756146726 685379842 4 Sep 2015 21:43:22 UTC 4 Sep 2015 21:47:31 UTC Over Client error Compute error 0.00 0.00 ---
756146379 685379499 4 Sep 2015 21:47:31 UTC 4 Sep 2015 21:51:38 UTC Over Client error Compute error 0.00 0.00 ---
756142269 685191678 4 Sep 2015 21:11:45 UTC 4 Sep 2015 21:43:22 UTC Over Client error Compute error 0.00 0.00 ---
756136139 685070740 4 Sep 2015 20:35:04 UTC 4 Sep 2015 21:11:45 UTC Over Client detached New 0.00 --- ---
756108060 685348417 4 Sep 2015 17:43:43 UTC 4 Sep 2015 20:35:04 UTC Over Client detached New 0.00 --- ---
756107378 685347883 4 Sep 2015 17:37:58 UTC 4 Sep 2015 20:35:04 UTC Over Client detached New 0.00 --- ---
756106387 685347020 4 Sep 2015 17:33:50 UTC 4 Sep 2015 17:37:58 UTC Over Client error Compute error 0.00 0.00 ---
756106282 685345669 4 Sep 2015 17:29:17 UTC 4 Sep 2015 17:33:50 UTC Over Client error Compute error 0.00 0.00 ---
756047933 685297734 4 Sep 2015 11:47:45 UTC 4 Sep 2015 17:29:17 UTC Over Client error Compute error 0.00 0.00 ---
756046735 685296655 4 Sep 2015 11:42:49 UTC 4 Sep 2015 11:43:37 UTC Over Client error Compute error 0.00 0.00 ---
756031213 685283552 4 Sep 2015 10:09:51 UTC 4 Sep 2015 10:13:57 UTC Over Client error Compute error 0.00 0.00 ---
756030152 685282685 4 Sep 2015 10:03:59 UTC 4 Sep 2015 10:05:43 UTC Over Client error Compute error 0.00 0.00 ---
755997565 685255620 4 Sep 2015 6:47:27 UTC 4 Sep 2015 10:03:59 UTC Over Client error Compute error 0.00 0.00 ---
755987746 685246348 4 Sep 2015 10:13:57 UTC 4 Sep 2015 11:42:49 UTC Over Client error Compute error 0.00 0.00 ---
755906084 685172826 3 Sep 2015 20:36:37 UTC 4 Sep 2015 6:51:35 UTC Over Success Done 5,786.07 12.84 8.77
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Message 78694 - Posted: 4 Sep 2015, 23:09:12 UTC
Last modified: 4 Sep 2015, 23:09:38 UTC

Just an update, I let a few more tasks finish and I still haven\'t had a single successful Abinitio docking job that has a title like FFD__xxxx.

I\'ve aborted all FFD__xxxx \'abinitioDocking\' type jobs on all of my hosts. It definitely looks to be an issue with this particular job type.

Thanks for your hard work David, wish there was more I could do on my end, don\'t hesitate to ping me if I can be of any help!

Tim
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Message 78695 - Posted: 5 Sep 2015, 0:48:07 UTC

Task ID 756094939 failed under Linux, too.
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Message 78696 - Posted: 5 Sep 2015, 1:22:33 UTC - in response to Message 78695.  

Task ID 756094939 failed under Linux, too.



Hi all,
These seem to be mine but I am not sure what is going on. I submitted them a week ago and they seemed to have run fine until the update yesterday. Could you provide me with more information about the jobs that are failing?

Thanks,
Franziska
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Message 78697 - Posted: 5 Sep 2015, 3:01:35 UTC

You wanted more, enjoy.

My rigs got validate error on these.( See below )

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=682557581

1da894305e9a610bd5667cc03eeff6fd_hhhcommon_15_08_20_46_44_globalDocking_4_SAVE_ALL_OUT_292589_6_1


# cpu_run_time_pref: 14400
======================================================
DONE :: 710 starting structures 14388.2 cpu seconds
This process generated 710 decoys from 710 attempts
======================================================
BOINC :: WS_max 0

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

</stderr_txt>
]]>

--------------------------------------------------

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685290795

FFD__368f3629c8dc09f0ae4d4402193bd7e0_abinitioDocking_15_08_21_50_55_globalDocking_5_SAVE_ALL_OUT_301979_6_0

# cpu_run_time_pref: 14400
======================================================
DONE :: 425 starting structures 14368.3 cpu seconds
This process generated 425 decoys from 425 attempts
======================================================
BOINC :: WS_max 0

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

</stderr_txt>
]]>

--------------------------------------------------------------


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685229735


FFD__368f3629c8dc09f0ae4d4402193bd7e0_abinitioDocking_15_08_21_50_55_globalDocking_5_SAVE_ALL_OUT_301979_6_0


# cpu_run_time_pref: 14400
======================================================
DONE :: 425 starting structures 14368.3 cpu seconds
This process generated 425 decoys from 425 attempts
======================================================
BOINC :: WS_max 0

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

</stderr_txt>
]]>

----------------------------------------------------------


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685229735


FFD__61553d966fba4a94dcf25c2a24befc61_abinitioDocking_15_08_14_11_53_globalDocking_4_SAVE_ALL_OUT_299060_4_0


# cpu_run_time_pref: 14400
======================================================
DONE :: 253 starting structures 14362.2 cpu seconds
This process generated 253 decoys from 253 attempts
======================================================
BOINC :: WS_max 0

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

</stderr_txt>
]]>

-----------------------------------------

More validate errors.

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685188207

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=682334661

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181282

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181270

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181239

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181197

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

These are Compute errors.

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685185054

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181238

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Message 78698 - Posted: 5 Sep 2015, 4:41:44 UTC - in response to Message 78689.  

minirosetta_3.62_x86_64-pc-linux-gnu: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), statically linked, for GNU/Linux 2.6.9, stripped

A bit disappointed here...


Same.
At least we\'re now running a more advanced energy function, but still, I find it frustrating that we\'re not squeezing the best out of our CPUs.
I mean, the extensions on the CPUs are there for a reason! Performance! Haha
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Message 78699 - Posted: 5 Sep 2015, 17:01:59 UTC

I gave a \"do not ask for new tasks\" in Rosetta.
I add while other projects.
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Message 78700 - Posted: 5 Sep 2015, 22:38:49 UTC

More validate errors this morning.


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685225333


FFD__1885c0418f264a32e397ffab4318bbf3_abinitioDocking_15_08_14_27_34_globalDocking_6_SAVE_ALL_OUT_298551_4_0

# cpu_run_time_pref: 14400
======================================================
DONE :: 201 starting structures 14379.4 cpu seconds
This process generated 201 decoys from 201 attempts
======================================================
BOINC :: WS_max 1.35666e-166

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

</stderr_txt>
]]>

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


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685381286


FFD__7a0bd05235f76b7c212c91d604e6b896_abinitioDocking_15_08_10_13_49_globalDocking_0_SAVE_ALL_OUT_300974_4_0


# cpu_run_time_pref: 14400
======================================================
DONE :: 261 starting structures 14384 cpu seconds
This process generated 261 decoys from 261 attempts
======================================================
BOINC :: WS_max 0

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

</stderr_txt>
]]>

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


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685381283


FFD__7a0bd05235f76b7c212c91d604e6b896_abinitioDocking_15_08_10_13_49_localDocking_8_SAVE_ALL_OUT_300974_4_0


# cpu_run_time_pref: 14400
======================================================
DONE :: 273 starting structures 14369.2 cpu seconds
This process generated 273 decoys from 273 attempts
======================================================
BOINC :: WS_max 0

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

</stderr_txt>
]]>

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

And more FFD validate errors.


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685299006


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685330215


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685308187


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685291696


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685378382
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Message 78701 - Posted: 6 Sep 2015, 3:57:47 UTC

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Message 78707 - Posted: 6 Sep 2015, 16:33:26 UTC

I\'m new to Rosetta@home in the last couple of days so the majority of the WUs that I\'ve completed recently have ended up in a \"Validation Failed\" state. The bad part about it is the 5-6 hours of processing time for each job and we don\'t get any credit for the work. If I can provide additional error logs or information to fix the issue please let me know. I\'d like to continue supporting this worthwhile project.

Thanks!

http://boinc.bakerlab.org/rosetta/result.php?resultid=756421006
http://boinc.bakerlab.org/rosetta/result.php?resultid=756420997
http://boinc.bakerlab.org/rosetta/result.php?resultid=756420978
http://boinc.bakerlab.org/rosetta/result.php?resultid=756420964
http://boinc.bakerlab.org/rosetta/result.php?resultid=756420963
http://boinc.bakerlab.org/rosetta/result.php?resultid=756420962
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Message 78708 - Posted: 6 Sep 2015, 17:05:15 UTC - in response to Message 78698.  

At least we\'re now running a more advanced energy function, but still, I find it frustrating that we\'re not squeezing the best out of our CPUs.
I mean, the extensions on the CPUs are there for a reason! Performance! Haha


+1
But it\'s better to have a stable version of app and after optimization.
They have years of delay in optimizations, wait a little bit will not change much :-)
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Message 78709 - Posted: 6 Sep 2015, 18:18:41 UTC

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Message 78710 - Posted: 6 Sep 2015, 19:44:03 UTC - in response to Message 78696.  

Task ID 756094939 failed under Linux, too.



Hi all,
These seem to be mine but I am not sure what is going on. I submitted them a week ago and they seemed to have run fine until the update yesterday. Could you provide me with more information about the jobs that are failing?

Thanks,
Franziska


Any idea Franziska? I have suspended all FFD_ tasks. I do not want to abort them to avoid that a new copy is sent to another cruncher.

Thanks for keeping us informed.

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Message boards : Number crunching : Minirosetta 3.62-3.65



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