Problems with minirosetta version 1.+

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Adam

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Message 51274 - Posted: 9 Feb 2008, 17:43:18 UTC

http://boinc.bakerlab.org/rosetta/result.php?resultid=139413056
<core_client_version>5.10.22</core_client_version>
<![CDATA[
<message>
Can\'t link input file
</message>
]]>

I\'m not sure what went wrong.
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Mike Gelvin
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Message 51275 - Posted: 9 Feb 2008, 18:14:40 UTC - in response to Message 51258.  

NOD 32 Antivirus is blocking the download. It says it is a virus?



I got the same problem on Ralph. 1.05 and 1.07 were identified as being a probable virus.
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googloo
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Message 51277 - Posted: 9 Feb 2008, 19:20:53 UTC

My first Mini seems to be running fine on this computer. Pentium D, Windows XP Home, 2M memory. Boinc 5.10.30
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Michael G.R.

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Message 51281 - Posted: 9 Feb 2008, 21:10:11 UTC

It\'s running well so far here too, but seems to be taking more RAM than the previous version. I\'d say about 160 megs for Mini vs. about 100 megs for 5.93.
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googloo
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Message 51282 - Posted: 9 Feb 2008, 21:19:02 UTC

Yes, it\'s taking more RAM. I\'m running one of each right now. Peak for 5.93 is 114,764K and for mini is 185,424. Current usage is 103M for 5.93 and 174M for mini.
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Profile David E K
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Message 51283 - Posted: 9 Feb 2008, 21:32:18 UTC - in response to Message 51265.  

We are running production minirosetta jobs on R@h. We have tested it on Ralph@home and it appears to be stable. No doubt there may be some issues on R@h because of the much larger diversity of computers but we\'ll do our best to take care of them as they appear. I\'ll asked the researcher who is currently running experiments to explain what he is doing with minirosetta. I\'ve suspended his jobs so more rosetta jobs will get issued soon. I checked the result summary and the minirosetta jobs have a 90% success rate on R@h which is lower than the old rosetta app but it\'s not bad. We have a little debugging to do to lessen the gap. I believe the rosetta app is at around 95-97% but I am not sure and will check.


Rosetta@Home should include a way to get around the mini application - at least until it is established that the new software works.

I joined because I want to cure people, not because I want to test software. I understand that with better software, the results might improve - however I would like to stick to the real rosetta for the time being.

So, please, include the option to work on mini rosetta or not to.

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googloo
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Message 51284 - Posted: 9 Feb 2008, 21:43:08 UTC

Are you going to add graphics to mini, and if so, when?
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Adam

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Message 51285 - Posted: 9 Feb 2008, 22:08:51 UTC

Additionally,
same error for tasks:

http://boinc.bakerlab.org/rosetta/result.php?resultid=139537971

and

http://boinc.bakerlab.org/rosetta/result.php?resultid=139605468

<core_client_version>5.10.22</core_client_version>
<![CDATA[
<message>
Can\'t link input file
</message>
]]>
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Path7

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Message 51286 - Posted: 9 Feb 2008, 22:30:28 UTC
Last modified: 9 Feb 2008, 22:35:53 UTC

Hello all,

Just finished 2 new minirosetta\'s. They run fine.
I noticed a lower use of virtual memory :) 200000 k instead of 350000 k
and a lower amount of granted credits :( 6.7 / hour instead of 9.1 / hour runtime.

I\'m not sure, but the amount of page files seems to have increased.

Edit: I\'m running window XP – home, 1 core AMD sempron 1.8 G Hz, 1400 MB RAM.

Have a nice day,
Path7.
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Message 51287 - Posted: 9 Feb 2008, 23:25:21 UTC

we are aware of the memory issue, and are working on it.

graphics will be available soon. I don\'t know exactly when but it is definitely under development.
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Message 51288 - Posted: 10 Feb 2008, 0:09:53 UTC

I got 9 mini 6 hour wu\'s today. I have had 5 of them \'freeze\' around 12-18 min and then go on to the next wu. I have not had this with Rosetta before today, but I have had some do this on MilkyWay. Is there any info I can leave to help? I am using Boinc 5.10.13.
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Narlanthrotep

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Message 51289 - Posted: 10 Feb 2008, 1:09:46 UTC

hope this helps

log from NOD32:
2/9/2008 5:58:05 PM
HTTP filter
file
http://srv4.bakerlab.org/rosetta/download/minirosetta_1.07_windows_intelx86.exe
probably a variant of Win32/Statik application
connection terminated - quarantined
<pc name>\\<user>
Threat was detected upon access to web by the application: C:\\Program Files\\BOINC\\boinc.exe.

Boinc ver. 5.10.30
NOD32 ver. 3.0.551.0
Virus sig. 2861 (20080209)
WinXP SP2

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Mike Tyka

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Message 51290 - Posted: 10 Feb 2008, 1:12:35 UTC

Hi, so we\'re excited to actually start running some serious jobs with mini! The first slightly larger scale test is batch 2833 (score13_hb_envtest62_A_*).

We\'ve been working on improving the objective energy function that Rosetta uses to evaluate each structure. In theory the native conformation should get the lowest energies but we had observed several cases in which this appeared not to be the case, i.e. we found \"wrong\" structures that were nevertheless lower in energy than the relaxed native state. Hence we tinkered with the energy components, re-weighting them and adding a new term which senses the environment of each amino acid. These innovations have been added to the new minirosetta and are looking promising. However, this is the first large scale test of our effords and we\'re excited to ee the results of this test. Its also the first large scale test of minirosetta on boinc. Hence, despite rigorous testing on ralph, we expect there to be occasional hickups which we\'ll try to catch and resolve. It is all still pretty fresh code.
Graphics are being worked on, as far as i know we\'re not far off.

Please do continue to post problems and give feedback, its all very valuable to us to iron out the remaining bugs.

Mike

http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Profile David E K
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Message 51291 - Posted: 10 Feb 2008, 2:47:58 UTC - in response to Message 51288.  

I got 9 mini 6 hour wu\'s today. I have had 5 of them \'freeze\' around 12-18 min and then go on to the next wu. I have not had this with Rosetta before today, but I have had some do this on MilkyWay. Is there any info I can leave to help? I am using Boinc 5.10.13.


You can help by joining the Ralph@home project for alpha testing if you haven\'t already.

http://ralph.bakerlab.org
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Message 51292 - Posted: 10 Feb 2008, 4:11:37 UTC - in response to Message 51291.  



You can help by joining the Ralph@home project for alpha testing if you haven\'t already.

http://ralph.bakerlab.org


That doesn\'t address my issue.
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Profile David E K
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Message 51293 - Posted: 10 Feb 2008, 5:07:08 UTC - in response to Message 51292.  
Last modified: 10 Feb 2008, 5:07:22 UTC



You can help by joining the Ralph@home project for alpha testing if you haven\'t already.

http://ralph.bakerlab.org


That doesn\'t address my issue.


I don\'t see any minirosetta jobs that have failed from your host yet. Did they error out or are they being suspended?
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Message 51294 - Posted: 10 Feb 2008, 5:45:57 UTC

Thumbs down.

I\'m running the 32-bit minirosetta 1.07 under the 32-bit BOINC client 5.10.28, on an AMD 64-bit dual-core system using 32-bit SuSE 10.2

So far I am only getting a 11% success rate on minirosetta -- various kinds of crashes, mostly segment violations. [My success rate on regular Rosetta is near 100%.]
.
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Message 51296 - Posted: 10 Feb 2008, 6:21:02 UTC - in response to Message 51263.  

Well, if it\'s like the last few Rosetta \"releases\" that have been inflicted on the users, the testing was measured in hours, and only a handful of WUs. Not exactly exhaustive testing.


While earlier versions, especially 1.03 - 1.06 were indeed tested on Ralph, with Mini Rosetta 1.07 there is a new record for \"test period\": 33 minutes and 14 seconds between the time it was released on Ralph and Rosetta. This means that there was not enough time to even get a single successful result!

I never received a single 1.07 workunit on Ralph, but have gotten several on Rosetta and they seem to be all successfull.
Team Helix
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Message 51297 - Posted: 10 Feb 2008, 6:51:30 UTC - in response to Message 51296.  

Well, if it\'s like the last few Rosetta \"releases\" that have been inflicted on the users, the testing was measured in hours, and only a handful of WUs. Not exactly exhaustive testing.


While earlier versions, especially 1.03 - 1.06 were indeed tested on Ralph, with Mini Rosetta 1.07 there is a new record for \"test period\": 33 minutes and 14 seconds between the time it was released on Ralph and Rosetta. This means that there was not enough time to even get a single successful result!

I never received a single 1.07 workunit on Ralph, but have gotten several on Rosetta and they seem to be all successfull.



1.06 was running stable except for a small bug accidentally introduced by a researcher not long ago. The bug was causing minirosetta to start with the beginning structure number after a restart. It was just the numbering that repeated and not the actual calculation and resulting coordinates but it was enough to cause our validator to invalidate the results that happened to restart after any structure was made. I added the fix quickly and decided that the 95+% success rate of 1.06 (even w/ the small bug) was good enough to start small tests on R@h after the quick fix. minirosetta is running with the same success rate as standard rosetta on R@h (90%). I\'ve seen rosetta@home w/ a better success rate and I\'ll talk to developers about trying to make both more stable.
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Message 51298 - Posted: 10 Feb 2008, 7:00:49 UTC - in response to Message 51294.  
Last modified: 10 Feb 2008, 7:11:13 UTC

Thumbs down.

I\'m running the 32-bit minirosetta 1.07 under the 32-bit BOINC client 5.10.28, on an AMD 64-bit dual-core system using 32-bit SuSE 10.2

So far I am only getting a 11% success rate on minirosetta -- various kinds of crashes, mostly segment violations. [My success rate on regular Rosetta is near 100%.]
.


EDIT: I just looked at your host and noticed that it\'s running linux so the following below does not apply. It would be interesting to run a debug version on your computer and get a trace. We can\'t reproduce these errors but it is obviously reproducible on your host. Sorry you\'re having these errors.

To help us debug, can you download our symbols file so that we can hopefully get more debugging information? we can\'t reproduce the access violations.

You can download it at:

http://ralph.bakerlab.org/download/minirosetta_1.07_windows_intelx86.pdb

It\'s unfortunately big, 25MB.

Can you place it in your BOINC installation in the BOINC/projects/boinc.bakerlab.org_rosetta directory?
and if you are running Ralph@home, can you place a copy in projects/ralph.bakerlab.org?
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Message boards : Number crunching : Problems with minirosetta version 1.+



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