Problems with Rosetta version 5.85 (or 5.86 for linux)

Message boards : Number crunching : Problems with Rosetta version 5.85 (or 5.86 for linux)

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drghughes

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Message 49027 - Posted: 25 Nov 2007, 0:01:30 UTC

I also noticed high virtual memory usage on MolecularRep WUs

WU names were w005_1_MolecularRep_1_w005_1_bpdb90-1-2qpw_StructuralGenomics_a_2329_34465_0, w005_1_MolecularRep_1_w005_1_bpdb90-1-2qpw_StructuralGenomics_a_2329_58270_0 and w007_1_MolecularRep_1_w007_1_ffas03-1-2b0v_StructuralGenomics_a_2325_99663_0

WU numbers are in my post above asking about checkpointing.


drghughes
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P . P . L .

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Message 49028 - Posted: 25 Nov 2007, 1:59:54 UTC

I just got this one it's a resend, the user that had it first had lots

of problems with it. Do you want me to let it run or abort?

It's a BOINC_SYMM_FOLD_AND_DOCK_RELAX-1uis_-crystal_foldanddock.

boinc.bakerlab.org/rosetta/workunit.php?wuid=111015584

Pete.



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Rhiju
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Message 49034 - Posted: 25 Nov 2007, 6:24:46 UTC - in response to Message 49028.  

You should feel free to abort any of these BOINC_SYMM_FOLD_AND_DOCK_RELAX workunits.

And I'm contacting the person in charge of the MolecularRep workunits!

I just got this one it's a resend, the user that had it first had lots

of problems with it. Do you want me to let it run or abort?

It's a BOINC_SYMM_FOLD_AND_DOCK_RELAX-1uis_-crystal_foldanddock.

boinc.bakerlab.org/rosetta/workunit.php?wuid=111015584

Pete.




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Vatsan

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Message 49035 - Posted: 25 Nov 2007, 6:35:00 UTC

The MolecularRep WUs are mine.
I am investigating their high memory usage. Please feel to abort them. Sorry for the trouble !
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Prom

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Message 49042 - Posted: 25 Nov 2007, 14:08:17 UTC

I aborted the 5.85 workunits. There weren't hundreds, they were in the minority. Hopefully this will be sorted when I need more.
BBLounge - Broadband and Technology forum
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Profile Greg_BE
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Message 49047 - Posted: 25 Nov 2007, 16:47:47 UTC

The following all have this problem and error message

Server state Over
Outcome Client error
Client state Compute error
Exit status -185 (0xffffff47

stderr out

<core_client_version>5.10.28</core_client_version>
<![CDATA[
<message>
Can't link input file
</message>
]]>

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


Task ID 122454897
Name 1uis__BOINC_SYMM_FOLD_AND_DOCK_RELAX-1uis_-crystal_foldanddock__2318_61717_0
Workunit 111317628

Task ID 122402964
Name w007_1_MolecularRep_1_w007_1_ffas03-1-2b0v_StructuralGenomics_a_2325_7744_0
Workunit 111269680

Task ID 122381870
Name 1i8f__BOINC_SYMM_FOLD_AND_DOCK_RELAX-1i8f_-crystal_foldanddock__2318_54614_0
Workunit 111250295

Task ID 122350279
Name 1dcj__CONTROL_ABRELAX_FRAGPRED_FRAGS_SAVE_ALL_OUT-1dcj_-__2324_5508_0
Workunit 111221438

Task ID 122331077
Name 1uis__BOINC_SYMM_FOLD_AND_DOCK_RELAX-1uis_-crystal_foldanddock__2318_52078_0
Workunit 111204073

Task ID 122177508
Name 2a43__BOINC_RHO_OMEGA1_OMEGA2_HALFBACKBONEHB_RNA_ABINITIO-2a43_-_2322_27_0
Workunit 111064109

Task ID 122146596
Name 1uis__BOINC_SYMM_FOLD_AND_DOCK_RELAX-1uis_-crystal_foldanddock__2318_39440_0
Workunit 111036438

Task ID 122101299
Name 1uis__BOINC_SYMM_FOLD_AND_DOCK_RELAX-1uis_-crystal_foldanddock__2318_27602_0
Workunit 110996924

Task ID 122062255
Name 1uis__BOINC_SYMM_FOLD_AND_DOCK_RELAX-1uis_-crystal_foldanddock__2318_16018_0
Workunit 110962172

Task ID 122037923
Name 1i8f__BOINC_SYMM_FOLD_AND_DOCK_RELAX-1i8f_-crystal_foldanddock__2318_8647_0
Workunit 110940058

Task ID 122020436
Name 1uis__BOINC_SYMM_FOLD_AND_DOCK_RELAX-1uis_-crystal_foldanddock__2318_5384_0
Workunit 110924062

Task ID 121990705
Name w006_1_NMRREF_1_w006_1_id_model_01_0001IGNORE_THE_REST_idl_2320_2294_0
Workunit 110896941

Task ID 121969899
Name w006_1_NMRREF_1_w006_1_id_model_02_0001IGNORE_THE_REST_idl_2320_812_0
Workunit 110877677

Task ID 121905734
Name 157d__BOINC_RHO_OMEGA1_OMEGA2_RNA_ABINITIO-157d_-_2317_346_0
Workunit 110817491

Task ID 121895023
Name 1enh__ETABLE_ABRELAX-1enh_-frags83__2313_913_1
Workunit 110804518

Task ID 121865641
Name 256bA_ETABLE_ABRELAX-256bA-frags83__2313_813_0
Workunit 110779752


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Nidhogg

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Message 49064 - Posted: 26 Nov 2007, 11:32:31 UTC

Well, I don't know about any memory problems, but I certainly noticed a 65% increase in time it took to crunch a WU (1gidA_BOINC_WEAKVDW_RNA_ABINITIO_SAVE_...). My bucket usually needs about 3 hours to finish a unit, but now with this 5.85 Beta it took a whooping 4:57:15! The excess time was in fact the last 5-7% which are usually reported as being completed in about 10 minutes. This time, those 10 minutes took 2 hours...

Yes, I was sitting here and watching it almost constantly (as I was waiting for the WU to finish before I was going to shut off the client for a while), and no, I wasn't doing anything else that would have had any impact on CPU performance. This is a bit... ridiculous. Makes me wish for 5.86 already. :P
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MattDavis
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Message 49065 - Posted: 26 Nov 2007, 11:36:10 UTC - in response to Message 49064.  

Well, I don't know about any memory problems, but I certainly noticed a 65% increase in time it took to crunch a WU (1gidA_BOINC_WEAKVDW_RNA_ABINITIO_SAVE_...). My bucket usually needs about 3 hours to finish a unit, but now with this 5.85 Beta it took a whooping 4:57:15! The excess time was in fact the last 5-7% which are usually reported as being completed in about 10 minutes. This time, those 10 minutes took 2 hours...

Yes, I was sitting here and watching it almost constantly (as I was waiting for the WU to finish before I was going to shut off the client for a while), and no, I wasn't doing anything else that would have had any impact on CPU performance. This is a bit... ridiculous. Makes me wish for 5.86 already. :P


I can answer this one.

The 1gid work units have really big decoys that take a really long time to crunch, meaning Rosetta often has to go over your suggested time in order to crunch a decoy.

For example, I have a 4 hour run time, but with the 1gid units the decoys are so big that a couple of my computers take 8 hours just to crunch 1 decoy.

So, in sum: this is normal for the 1gids, and you're getting a proportionate amount of credit.
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hikerbiker

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Message 49069 - Posted: 26 Nov 2007, 18:05:10 UTC

Downloaded Boinc 5.10.29 fro the Mac and now i cant get any work units downloaded as BOINC complains about a lack of disk space ?


I've fiddled with the settings cant some up with anything that'll make it happy, anyone else ? And yes there's plenty of disk space.

Is it a problem with BOINC or Rosetta 5.85 ?
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Profile rochester new york
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Message 49070 - Posted: 26 Nov 2007, 18:13:30 UTC

i keep getting errors... after a year and a half of running ok
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MattDavis
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Message 49072 - Posted: 26 Nov 2007, 19:13:09 UTC - in response to Message 49069.  

Downloaded Boinc 5.10.29 fro the Mac and now i cant get any work units downloaded as BOINC complains about a lack of disk space ?


I've fiddled with the settings cant some up with anything that'll make it happy, anyone else ? And yes there's plenty of disk space.

Is it a problem with BOINC or Rosetta 5.85 ?


Check both local settings and your account settings (on the website) to make sure you have your settings high enough.
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MattDavis
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Message 49073 - Posted: 26 Nov 2007, 19:13:23 UTC - in response to Message 49070.  

i keep getting errors... after a year and a half of running ok


Can you be more specific?
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Profile dcdc

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Message 49077 - Posted: 26 Nov 2007, 20:26:45 UTC - in response to Message 49069.  
Last modified: 26 Nov 2007, 20:28:37 UTC

i just spent ages on a post and it got marked as spam and now i've lost it! Grrrr....

Basically, 5.85 is a VM hog over a range of tasks. I've got a dual CPU machine with 1GB RAM that's got 2GB of VM used for Rosetta. The 5.82 task is fine, but the 5.85 tasks are using 600-620MB VM each...

machine here: https://boinc.bakerlab.org/rosetta//show_host_detail.php?hostid=675526

P.S. can anyone at the project remove the spam filter until it's fixed? That's the second one i've lost!
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Profile rochester new york
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Message 49079 - Posted: 26 Nov 2007, 20:51:17 UTC - in response to Message 49073.  

i keep getting errors... after a year and a half of running ok


Can you be more specific?

you can see my computer.. its not hidden
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Message 49086 - Posted: 27 Nov 2007, 1:39:44 UTC
Last modified: 27 Nov 2007, 1:43:40 UTC

This one only lasted 1.125 seconds before crashing...
https://boinc.bakerlab.org/rosetta/result.php?resultid=122996820

CPU time 1.125
stderr out

<core_client_version>5.10.28</core_client_version>
<![CDATA[
<message>
The extended attributes are inconsistent. (0xff) - exit code 255 (0xff)
</message>
<stderr_txt>
# cpu_run_time_pref: 7200

</stderr_txt>
]]>

Validate state Invalid
application version 5.85

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Message 49087 - Posted: 27 Nov 2007, 1:48:41 UTC
Last modified: 27 Nov 2007, 1:53:33 UTC

Another compute error:

https://boinc.bakerlab.org/rosetta/result.php?resultid=122131601

CPU time 5.5
stderr out

<core_client_version>5.10.28</core_client_version>
<![CDATA[
<message>
- exit code -529697949 (0xe06d7363)
</message>
<stderr_txt>
# cpu_run_time_pref: 7200


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x7693B09E

Engaging BOINC Windows Runtime Debugger...
.
.
.
.
Exiting...

</stderr_txt>
]]>

Validate state Invalid
application version 5.85

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Profile Cureseekers~langzaam

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Message 49091 - Posted: 27 Nov 2007, 12:53:15 UTC
Last modified: 27 Nov 2007, 12:55:17 UTC

Rosetta Beta 5.85 WU's are using lot's of Memory and let my PC's crash. I cancel all 5.85 jobs. When not possible to cancel, Rosetta will be shut off until this problem is solved.

Kind regards.
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MattDavis
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Message 49092 - Posted: 27 Nov 2007, 14:44:01 UTC - in response to Message 49091.  

Rosetta Beta 5.85 WU's are using lot's of Memory and let my PC's crash. I cancel all 5.85 jobs. When not possible to cancel, Rosetta will be shut off until this problem is solved.

Kind regards.


Try increasing your virtual memory size. That stopped the errors for me.
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Message 49098 - Posted: 27 Nov 2007, 15:32:34 UTC
Last modified: 27 Nov 2007, 15:35:40 UTC

... another crash
https://boinc.bakerlab.org/rosetta/result.php?resultid=123272410

CPU time 0.84375
stderr out

<core_client_version>5.10.28</core_client_version>
<![CDATA[
<message>
The extended attributes are inconsistent. (0xff) - exit code 255 (0xff)
</message>
<stderr_txt>
# cpu_run_time_pref: 7200

</stderr_txt>
]]>
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Message 49100 - Posted: 27 Nov 2007, 15:38:28 UTC
Last modified: 27 Nov 2007, 15:42:46 UTC

... another crash

https://boinc.bakerlab.org/rosetta/result.php?resultid=123272420

CPU time 18.6875
stderr out

<core_client_version>5.10.28</core_client_version>
<![CDATA[
<message>
- exit code -1073741571 (0xc00000fd)
</message>
<stderr_txt>
# cpu_run_time_pref: 7200

</stderr_txt>
]]>

...
As echoed by several others ... please remove the spam filter until it's fixed!
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Message boards : Number crunching : Problems with Rosetta version 5.85 (or 5.86 for linux)



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