Minirosetta 3.54

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Profile David E K
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Message 78012 - Posted: 9 Mar 2015, 23:58:29 UTC

This update includes bug fixes to the symmetric modeling protocol and also an update to the windows graphics application to accommodate large models. Please post bugs/issues here.
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Profile Michael Hoffmann
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Message 78013 - Posted: 10 Mar 2015, 16:43:05 UTC
Last modified: 10 Mar 2015, 16:49:17 UTC

Not really a problem, but referring to the description that now large models are better supported by windows graphics application.
For me it\'s not working for
http://boinc.bakerlab.org/rosetta/result.php?resultid=722810814 and
http://boinc.bakerlab.org/rosetta/result.php?resultid=722775030

Application only goes to blank window. At least the application does not crash in full screen mode like the previous one.

Greetings, Michael

Update: From time to time the application window shows graphics. However, full screen mode still results in black screen.
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Profile David E K
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Message 78014 - Posted: 10 Mar 2015, 18:00:11 UTC - in response to Message 78013.  

Thanks for the heads up. I\'ll look into this. Anyone else seeing issues with the graphics?
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Message 78015 - Posted: 10 Mar 2015, 20:32:03 UTC

Still no graphics for Linux / Ubuntu after many years I think! :(

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Message 78016 - Posted: 11 Mar 2015, 16:16:14 UTC - in response to Message 78015.  

Still no graphics for Linux / Ubuntu after many years I think! :(


The reason is clear: There is no graphics for command-line interface ;)
Just kidding, hope there\'ll be a fix, soon.
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Message 78019 - Posted: 12 Mar 2015, 2:12:38 UTC

I\'m finding that these 3.54 Tasks are generating a MASSIVE number of Small Files in the Slot directory - 3853 files in each of two current Slots running MR 3.54 WUs.
Not only is this Much higher than I\'ve noticed for any older Tasks, but the Tasks when Checkpointing seem to work to Update most all of these Files. That means a HDD Queue Depth that THRASHES the HDD and KILLS the Win7 UI for any other App that happens to need a bit of Disk IO. (And my HDD is Cached to SSH using iRST...)

The vast majority of the Files in question are \".PDB\" and \".PATCHDOCK\" - the former each sized 170-188KB and the latter all 8-12KB.
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Message 78022 - Posted: 12 Mar 2015, 17:01:35 UTC - in response to Message 78019.  

I\'m finding that these 3.54 Tasks are generating a MASSIVE number of Small Files in the Slot directory - 3853 files in each of two current Slots running MR 3.54 WUs.
Not only is this Much higher than I\'ve noticed for any older Tasks, but the Tasks when Checkpointing seem to work to Update most all of these Files. That means a HDD Queue Depth that THRASHES the HDD and KILLS the Win7 UI for any other App that happens to need a bit of Disk IO. (And my HDD is Cached to SSH using iRST...)

The vast majority of the Files in question are \".PDB\" and \".PATCHDOCK\" - the former each sized 170-188KB and the latter all 8-12KB.



Thanks for the heads up, we are aware of this issue and the lab member is changer her job setup to fix it. We\'ll cancel the existing jobs.
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Message 78023 - Posted: 12 Mar 2015, 19:35:03 UTC - in response to Message 78019.  

I\'m finding that these 3.54 Tasks are generating a MASSIVE number of Small Files in the Slot directory - 3853 files in each of two current Slots running MR 3.54 WUs.
Not only is this Much higher than I\'ve noticed for any older Tasks, but the Tasks when Checkpointing seem to work to Update most all of these Files. That means a HDD Queue Depth that THRASHES the HDD and KILLS the Win7 UI for any other App that happens to need a bit of Disk IO. (And my HDD is Cached to SSH using iRST...)

The vast majority of the Files in question are \".PDB\" and \".PATCHDOCK\" - the former each sized 170-188KB and the latter all 8-12KB.


can you provide the name of this job?
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Message 78024 - Posted: 12 Mar 2015, 20:53:37 UTC - in response to Message 78023.  

can you provide the name of this job?


I had REAL DIFFICULTIES doing ANYTHING with my PC whilst the MiniRosetta Tasks were \"Having their Way\" with my PC, but I believe it was these two Tasks of which I finally was hit Bad Enough to Complain:
http://boinc.bakerlab.org/rosetta/result.php?resultid=722770395
http://boinc.bakerlab.org/rosetta/result.php?resultid=722770254

There were 2-3 other Active MR Tasks ongoing at the same time, but by watching which were reported Running at the Critical Times (couldn\'t really do Anything else), I believe that I identified the correct Suspects. (The Computer specifics are accurately listed...)

I\'ve since gone No New Tasks and Aborted all which were Loaded but not yet Started. I let the Offenders run to Completion - both to see if they would Complete, and to not have Wasted so much of my HDD/SSD\'s life and also waste the CPU and Science Work...

Please review and confirm whether these are the proper Culprits...
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Message 78025 - Posted: 12 Mar 2015, 22:07:35 UTC - in response to Message 78019.  

I\'m finding that these 3.54 Tasks are generating a MASSIVE number of Small Files in the Slot directory


Just curious, where is this slot directory you speak of? I checked all over the BOINC folders in \'ProgramData\' but couldn\'t find anything called \'Slot\' and I\'d like to check this out on my end.
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Message 78028 - Posted: 13 Mar 2015, 3:57:17 UTC

Well, there is total silence on the RALPH@Home site...

I got 4 WUs earlier today and all 4 are now stuck a various percentages, though running for more than 4 hours by now.
Are they still supposed to do something useful? Right now they just blocking everything else but I would hate to abort them just yet...

Ralf
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Message 78029 - Posted: 13 Mar 2015, 15:01:34 UTC - in response to Message 78028.  

Well, there is total silence on the RALPH@Home site...
I got 4 WUs earlier today and all 4 are now stuck a various percentages, though running for more than 4 hours by now.


They ask you the url of wus with problem, but you don\'t reply

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Message 78032 - Posted: 13 Mar 2015, 15:58:47 UTC - in response to Message 78025.  

I\'m finding that these 3.54 Tasks are generating a MASSIVE number of Small Files in the Slot directory


Just curious, where is this slot directory you speak of? I checked all over the BOINC folders in \'ProgramData\' but couldn\'t find anything called \'Slot\' and I\'d like to check this out on my end.


Yes:
C:\\ProgramData\\BOINC\\slots\\0 ... C:\\ProgramData\\BOINC\\slots\\1 ... thru C:\\ProgramData\\BOINC\\slots\\4
One Slot for each Processor Thread plus one Slot for each GPU (4 and 1 in my case)...
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Profile David E K
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Message 78034 - Posted: 13 Mar 2015, 17:04:02 UTC - in response to Message 78028.  

Well, there is total silence on the RALPH@Home site...

I got 4 WUs earlier today and all 4 are now stuck a various percentages, though running for more than 4 hours by now.
Are they still supposed to do something useful? Right now they just blocking everything else but I would hate to abort them just yet...

Ralf



Are these Ralph jobs? Can you provide the task names?
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Message 78035 - Posted: 13 Mar 2015, 17:05:25 UTC - in response to Message 78024.  

can you provide the name of this job?


I had REAL DIFFICULTIES doing ANYTHING with my PC whilst the MiniRosetta Tasks were \"Having their Way\" with my PC, but I believe it was these two Tasks of which I finally was hit Bad Enough to Complain:
http://boinc.bakerlab.org/rosetta/result.php?resultid=722770395
http://boinc.bakerlab.org/rosetta/result.php?resultid=722770254

There were 2-3 other Active MR Tasks ongoing at the same time, but by watching which were reported Running at the Critical Times (couldn\'t really do Anything else), I believe that I identified the correct Suspects. (The Computer specifics are accurately listed...)

I\'ve since gone No New Tasks and Aborted all which were Loaded but not yet Started. I let the Offenders run to Completion - both to see if they would Complete, and to not have Wasted so much of my HDD/SSD\'s life and also waste the CPU and Science Work...

Please review and confirm whether these are the proper Culprits...



I forwarded this post to the researcher who submitted the jobs. I\'m pretty sure these are the bad jobs and they have been canceled.
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Message 78036 - Posted: 13 Mar 2015, 17:47:00 UTC - in response to Message 78024.  

[/quote] I had REAL DIFFICULTIES doing ANYTHING with my PC whilst the MiniRosetta Tasks were \"Having their Way\" with my PC, but I believe it was these two Tasks of which I finally was hit Bad Enough to Complain:
http://boinc.bakerlab.org/rosetta/result.php?resultid=722770395
http://boinc.bakerlab.org/rosetta/result.php?resultid=722770254

There were 2-3 other Active MR Tasks ongoing at the same time, but by watching which were reported Running at the Critical Times (couldn\'t really do Anything else), I believe that I identified the correct Suspects. (The Computer specifics are accurately listed...)

I\'ve since gone No New Tasks and Aborted all which were Loaded but not yet Started. I let the Offenders run to Completion - both to see if they would Complete, and to not have Wasted so much of my HDD/SSD\'s life and also waste the CPU and Science Work...

Please review and confirm whether these are the proper Culprits...[/quote]

So sorry, these were both my jobs. We were aware of the issue (the protocol didn\'t like the naming convention of some of the input files and that was messing everything up) and thought we had deleted all of them. You must have gotten a couple stragglers that slipped through. I apologize. Thanks for letting me know. I have tracked all of the sub-batches down and made sure no more jobs were getting released for these. Thanks for donating computing time to our Rosetta@Home projects!
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Message 78038 - Posted: 14 Mar 2015, 2:40:01 UTC - in response to Message 78036.  

I had REAL DIFFICULTIES doing ANYTHING with my PC whilst the MiniRosetta Tasks were \"Having their Way\" with my PC, but I believe it was these two Tasks of which I finally was hit Bad Enough to Complain:
http://boinc.bakerlab.org/rosetta/result.php?resultid=722770395
http://boinc.bakerlab.org/rosetta/result.php?resultid=722770254

There were 2-3 other Active MR Tasks ongoing at the same time, but by watching which were reported Running at the Critical Times (couldn\'t really do Anything else), I believe that I identified the correct Suspects. (The Computer specifics are accurately listed...)

I\'ve since gone No New Tasks and Aborted all which were Loaded but not yet Started. I let the Offenders run to Completion - both to see if they would Complete, and to not have Wasted so much of my HDD/SSD\'s life and also waste the CPU and Science Work...

Please review and confirm whether these are the proper Culprits...[/quote]

So sorry, these were both my jobs. We were aware of the issue (the protocol didn\'t like the naming convention of some of the input files and that was messing everything up) and thought we had deleted all of them. You must have gotten a couple stragglers that slipped through. I apologize. Thanks for letting me know. I have tracked all of the sub-batches down and made sure no more jobs were getting released for these. Thanks for donating computing time to our Rosetta@Home projects![/quote]

No Problem...

Once I get the CPU/GPU done Chewing on the Hunk-O MilkyWay WUs that stepped up to fill the Void, I\'ll re-enable MiniRosetta...
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Message 78039 - Posted: 14 Mar 2015, 4:30:10 UTC - in response to Message 78034.  

Well, there is total silence on the RALPH@Home site...

I got 4 WUs earlier today and all 4 are now stuck a various percentages, though running for more than 4 hours by now.
Are they still supposed to do something useful? Right now they just blocking everything else but I would hate to abort them just yet...

Ralf



Are these Ralph jobs? Can you provide the task names?
Yes, they are RALPH jobs ;-)

I had suspended them for a while so some other project WUs could finish before their deadline and then resumed all 4 jobs. They seemed to have picked up on resume just fine and two of the already reported:

cb_mar11_dock_placestub_EEEH_1035_vegf_ProteinInterfaceDesign_20241_91_0_0
cb_mar11_dock_placestub_EEEH_1038_vegf_ProteinInterfaceDesign_20241_91_0_0

The other two are currently still crunching, named

cb_mar11_dock_placestub_EEEH_1037_vegf_ProteinInterfaceDesign_20241_91_0_0
cb_mar11_dock_placestub_EEEH_1036_vegf_ProteinInterfaceDesign_20241_91_0_0

and should finish within the next 15min or so...

Those got previously stuck for hours at 12% and 20% IIRC,

Ralf
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Message 78040 - Posted: 14 Mar 2015, 4:42:12 UTC - in response to Message 78029.  

Well, there is total silence on the RALPH@Home site...
I got 4 WUs earlier today and all 4 are now stuck a various percentages, though running for more than 4 hours by now.


They ask you the url of wus with problem, but you don\'t reply
Who asked me where?
I replied to the question of the WU names a bit earlier, after I got back to check in here. The main problem for me is that I don\'t necessarily have always the time to babysit. And there has been no post on the RALPH forum (if that is what you are referring to) for more than 30 days. And not that they ever have been very communicative in the first place...

Ralf
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Message 78041 - Posted: 14 Mar 2015, 7:13:40 UTC - in response to Message 78040.  
Last modified: 14 Mar 2015, 7:14:38 UTC

I replied to the question of the WU names a bit earlier, after I got back to check in here. The main problem for me is that I don\'t necessarily have always the time to babysit.

If you don\'t want to \"babysit\", don\'t partecipate to beta projects :-P

And there has been no post on the RALPH forum (if that is what you are referring to) for more than 30 days. And not that they ever have been very communicative in the first place...

Ok, they are not very comunicative (we know), but you post YOUR problem the 13 Mar 2015 3:47:36 UTC and Kripton reply you the 13 Mar 2015 4:33:20 UTC , 50 minutes later...
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Message boards : Number crunching : Minirosetta 3.54



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