minirosetta 2.15

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Yifan Song
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Message 67780 - Posted: 21 Sep 2010, 21:55:20 UTC

minirosetta is updated to add new protocols for symmetrical oligomers and membrane proteins.
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Murasaki
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Message 67782 - Posted: 21 Sep 2010, 22:09:51 UTC

Here is some more information about Oligomers and Membrane proteins from Wikipedia for those who are interested. If I hang around these forums for another 20 years I might learn enough Biochemistry to consider a pre-retirement career change.
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Message 67789 - Posted: 23 Sep 2010, 5:09:25 UTC
Last modified: 23 Sep 2010, 5:09:47 UTC

Even though the second attempt at this task ran fine, I\'m reporting this compute error.

http://boinc.bakerlab.org/rosetta/result.php?resultid=366882461

<core_client_version>6.10.58</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

|
|
|

ERROR: Option matching -docking:fake_native not found in command line top-level context
</stderr_txt>
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Message 67804 - Posted: 24 Sep 2010, 9:35:50 UTC

Does this version ignore the limit of 100 models per workunit?

I have a workunit which has reached 300 models and another has done 200. Both are only about 20% complete.
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Message 67810 - Posted: 24 Sep 2010, 13:36:37 UTC

The 100 model limit is only for certain protocols that are expected to complete models very rapidly. The main reason (to my knowledge anyway) for the imposition of that limit was due to large upload file sizes. Do you happen to know how large the uploads are getting? Size is shown in the transfers tab. But you\'d have to catch one before it is sent (suspend network activity for a short time until one completes would be a simple way to orchestrate keeping one around).
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Message 67811 - Posted: 24 Sep 2010, 13:50:19 UTC
Last modified: 24 Sep 2010, 13:50:43 UTC

Thanks for the response, Mod.Sense. My concern was that I had workunits which needed to be aborted.

I have some time yet before my first 2.15 task completes as I have selected a 10-hour run time option.

I\'ll try to catch the upload but may miss it.
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Message 67815 - Posted: 24 Sep 2010, 19:25:37 UTC

The upload is only 231KB, which is insignificant.
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Message 67817 - Posted: 24 Sep 2010, 22:23:38 UTC
Last modified: 24 Sep 2010, 22:26:26 UTC

Today i had me first WU http://boinc.bakerlab.org/rosetta/workunit.php?wuid=333863670 with V2.15, i see 1,1GB memmory beeing used, is this normal? And if so, why does is say 512MB minimal memmory requirment on the site?

I have 4 GB machine but with 2 other WU form other projects that exceed 1GB memory requirments, i have to start watching these mmemory requirments to stil do normal work with the machine.
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Message 67820 - Posted: 25 Sep 2010, 6:22:27 UTC

1+ GB is not normal. I seldom monitor the memory being used by a task, but I\'ve never seen this much memory being used before. I think it is particular to this type of task.
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Message 67825 - Posted: 25 Sep 2010, 20:41:44 UTC

I have this WU which uses about 900 MB of RAM, but cpu usage is down to 0%:
T0611_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22276_368_0

Yesterday I had a WU with the exact same behaviour, eating lots of RAM, but no cpu use, so it must have crashed or something... Pausing and resuming does not fix the problem by the way.
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Message 67834 - Posted: 26 Sep 2010, 9:32:04 UTC

This one crashed yesterday after 40 minutes:
T0528_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22246_78_0

When it crashed the memory consumption was 1.5 GB. The message says \'Directory not found\'.


<message>
Das System kann den angegebenen Pfad nicht finden. (0x3) - exit code 3 (0x3)
</message>


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Message 67839 - Posted: 27 Sep 2010, 3:21:17 UTC

Yeah, I have one Rosetta processing using 1.5 Gb of RAM at 2.3% completion and another using 1.15 Gb of RAM at 16% completion. All together Rosetta is using 70% of my 8 gigs of RAM. Granted I have a 6-core processor and therefore 6 threads running, but still, that\'s a lot of RAM.

The biggest RAM hogs currently, are named T0523_t4_rs_stg0_lrlxjcst_t000_casp9_SAVE_ALL_OUT_22242_375_0 and
T0520_t4_rs_stg0_lrlxjcst_t000_casp9_SAVE_ALL_OUT_22239_376_0


I was away for the weekend. Looking back at my results I show over 20 results that ended as \"Compute Error\" since 2.15, most of which came Friday or after. Never had one Compute Error in any work unit before that.
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Message 67846 - Posted: 27 Sep 2010, 20:49:25 UTC

I also appear to be having problems with WU\'s starting with T05**. They end up using almost 1.3GB of RAM.
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Ademers

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Message 67847 - Posted: 28 Sep 2010, 0:59:42 UTC - in response to Message 67846.  

I also appear to be having problems with WU\'s starting with T05**. They end up using almost 1.3GB of RAM.


I think i have a problem with the T0549_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22255_997
he run since 21 hours and reach 0.099% when i look at the properties, the calculating time is only 25 second !!!
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Message 67849 - Posted: 28 Sep 2010, 11:01:35 UTC

T0605_t2_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22177_296_1
ERROR: Error in traceback: pointer doesn\'t go anywhere!

ERROR:: Exit from: ..\\..\\src\\core\\sequence\\Aligner.cc line: 79
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

T0605_t2_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22177_1921_0
RROR: Error in traceback: pointer doesn\'t go anywhere!

ERROR:: Exit from: ..\\..\\src\\core\\sequence\\Aligner.cc line: 79
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

T0528_tj_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_21880_4843_2
<core_client_version>6.10.58</core_client_version>
<![CDATA[
<message>
The system cannot find the path specified. (0x3) - exit code 3 (0x3)
</message>



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Message 67850 - Posted: 28 Sep 2010, 16:01:11 UTC - in response to Message 67847.  


I think i have a problem with the T0549_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22255_997
he run since 21 hours and reach 0.099% when i look at the properties, the calculating time is only 25 second !!!


Ademers, double check the status shown in BOINC for that task. Does BOINC say it is \"running\"? And does the task manager show some other, higher priority task consuming your available CPU?

But otherwise that sounds like another issue that we see crop up once and a while. Best way to move it along seems to be to exit (not close) and restart BOINC.
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Message 67853 - Posted: 28 Sep 2010, 20:09:28 UTC - in response to Message 67850.  
Last modified: 28 Sep 2010, 20:10:43 UTC


I think i have a problem with the T0549_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22255_997
he run since 21 hours and reach 0.099% when i look at the properties, the calculating time is only 25 second !!!


Ademers, double check the status shown in BOINC for that task. Does BOINC say it is \"running\"? And does the task manager show some other, higher priority task consuming your available CPU?

But otherwise that sounds like another issue that we see crop up once and a while. Best way to move it along seems to be to exit (not close) and restart BOINC.


Good, I exit from BOINC and restart and the application is at 1.8% in 7 minutes and continue to go up !!!

Thank you Mod.Sense
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Message 67854 - Posted: 28 Sep 2010, 21:58:41 UTC

This one failed after 20sec.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=336639766

T0524_t3_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22207_1756_0

<core_client_version>6.2.14</core_client_version>
<![CDATA[
<message>
process got signal 11
</message>
<stderr_txt>



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Message 67858 - Posted: 29 Sep 2010, 5:24:03 UTC
Last modified: 29 Sep 2010, 5:26:47 UTC

I too am seeing an unusually high number of errors on 3 different machines (and 3 different operating systems) for Rosetta 2.15. 16 WU\'s in the last few days failed on various errors:

\"The system cannot find the path specified. (0x3) - exit code 3 (0x3)\"

\"Reason: Access Violation (0xc0000005) at address 0x00581B5C write attempt to address 0x00000024\"

\"Incorrect function. (0x1) - exit code 1 (0x1)\" (many different root causes per detailed error messages in the log. <ERROR: Error in traceback: pointer doesn\'t go anywhere!> occurred multiple times.)

\"Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x759AB727\"
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ingebrigtsen685

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Message 67865 - Posted: 29 Sep 2010, 11:13:06 UTC

I am repeatedly getting this message since the upgrade:

\"Microsoft Visual C++ Runtime Library

Runtime Error

....Bakerlab.org\\minirosetta_2.15_windows_intelx86.exe

This application has requested the Runtime to terminate it in an unusual way. Please contact the application\'s support team for more information.\"

It is difficult to remove the message which sometimes locks up the computer. What can be done to prevent this?
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Message boards : Number crunching : minirosetta 2.15



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