Bug Reports for Rosetta Mini Versions 1.+

Message boards : RALPH@home bug list : Bug Reports for Rosetta Mini Versions 1.+

To post messages, you must log in.

Previous · 1 · 2 · 3 · 4 · 5 · Next

AuthorMessage
Andrew Leaver-Fay

Send message
Joined: 14 Apr 06
Posts: 2
Credit: 5,272
RAC: 0
Message 3812 - Posted: 8 Mar 2008, 18:13:30 UTC

Thanks for posting that message, AdeB. Our rotamer library has been producing NaN errors lately. The zero in that list of three values (3 0 3) is clearly the source of the bug. Thanks!

ID: 3812 · Report as offensive    Reply Quote
Thomas Leibold

Send message
Joined: 25 Feb 07
Posts: 27
Credit: 77,464
RAC: 0
Message 3813 - Posted: 8 Mar 2008, 22:08:50 UTC
Last modified: 8 Mar 2008, 22:42:08 UTC

Have there been enough workunits for Mini Rosetta 1.09 distributed ? I never got any of those. After the last Mini Rosetta 1.08 workunit there was about a day of the usual \'no work from project\' for Ralph and I\'m now getting Rosetta Beta 5.95 workunits (which makes sense since this too is a new client).

Just wondering if Mini Rosetta 1.09 gets the testing it deserves.


Edit: Looking again, it seems 1.09 was released after 5.95 so perhaps workunits are still coming. Now I wonder why I thought 1.09 had been out a day earlier ?
ID: 3813 · Report as offensive    Reply Quote
tallguy-13088
Avatar

Send message
Joined: 17 Feb 06
Posts: 10
Credit: 121,701
RAC: 0
Message 3814 - Posted: 9 Mar 2008, 12:35:37 UTC

Hello,

I just saw the announcement for MiniRosetta 1.09 and went to look for the Debug Symbols file and didn\'t see it. Are we \"fixed\" to the point where we don\'t need it anymore?
ID: 3814 · Report as offensive    Reply Quote
Profile dekim
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 20 Jan 06
Posts: 221
Credit: 534,200
RAC: 5
Message 3818 - Posted: 10 Mar 2008, 19:52:12 UTC

I just added the 1.09 symbols file to the symstore and also to the download directory.

The symbols file is 48MB!
ID: 3818 · Report as offensive    Reply Quote
tallguy-13088
Avatar

Send message
Joined: 17 Feb 06
Posts: 10
Credit: 121,701
RAC: 0
Message 3820 - Posted: 11 Mar 2008, 3:35:47 UTC

Dekim,

Got it! Thanks!
ID: 3820 · Report as offensive    Reply Quote
caesar1987

Send message
Joined: 10 Mar 08
Posts: 6
Credit: 190
RAC: 0
Message 3821 - Posted: 11 Mar 2008, 23:55:35 UTC
Last modified: 11 Mar 2008, 23:59:04 UTC

i cant stop rosetta mini. He ever calculate. When i give supsend project he calculate and calculate and calculate...

he do the same when boinc autochange to other project...

//edit

and he stoped on cca 74% and write in second 100%
ID: 3821 · Report as offensive    Reply Quote
Pepo
Avatar

Send message
Joined: 8 Sep 06
Posts: 104
Credit: 36,890
RAC: 0
Message 3822 - Posted: 12 Mar 2008, 0:07:29 UTC - in response to Message 3821.  

i cant stop rosetta mini. He ever calculate. When i give supsend project he calculate and calculate and calculate...

he do the same when boinc autochange to other project...

Happens sometimes, mostly to apps run under a wrapper (although this is not Rosetta Mini\'s case). Best to leave such task running, it will mostly finish correctly, just as a side-effect, (nCPUs + 1) tasks will be running in parallel.

Peter
ID: 3822 · Report as offensive    Reply Quote
caesar1987

Send message
Joined: 10 Mar 08
Posts: 6
Credit: 190
RAC: 0
Message 3823 - Posted: 12 Mar 2008, 0:13:10 UTC - in response to Message 3822.  

i cant stop rosetta mini. He ever calculate. When i give supsend project he calculate and calculate and calculate...

he do the same when boinc autochange to other project...

Happens sometimes, mostly to apps run under a wrapper (although this is not Rosetta Mini\'s case). Best to leave such task running, it will mostly finish correctly, just as a side-effect, (nCPUs + 1) tasks will be running in parallel.

Peter
he stoped but i thing, that this is not verry good bug.
ID: 3823 · Report as offensive    Reply Quote
Thomas Leibold

Send message
Joined: 25 Feb 07
Posts: 27
Credit: 77,464
RAC: 0
Message 3829 - Posted: 14 Mar 2008, 6:05:30 UTC

I had two 1.09 workunits fail with the message:
\"<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
ERROR: Unique best command line context option match not found for -weights

</stderr_txt>\"

Workunits 740191 and 740147.

This is on SuSE Linux (32bit) with Boinc 5.10.21.
ID: 3829 · Report as offensive    Reply Quote
Jipsu

Send message
Joined: 11 Mar 08
Posts: 26
Credit: 76,448
RAC: 0
Message 3830 - Posted: 18 Mar 2008, 10:07:11 UTC
Last modified: 18 Mar 2008, 10:08:13 UTC

One 1.09 WU failed

<core_client_version>5.10.28</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
ERROR: Unique best command line context option match not found for -weights

</stderr_txt>
]]>

Using gentoo linux 2.6.24-gentoo-r3

http://ralph.bakerlab.org/result.php?resultid=834298
ID: 3830 · Report as offensive    Reply Quote
Michael Tyka

Send message
Joined: 12 Jan 08
Posts: 1
Credit: 1,443
RAC: 0
Message 3831 - Posted: 18 Mar 2008, 18:29:40 UTC

Sorry - this last error concenrning -weights was my fault. Unfortunately the mini application is in constant flux, and someone had changed the name for that option such that my old command line was suddenly outof date without me realising it. I removed the workunits replacing them with the correct command lline as soon as i realised. sorry fir this glitch, it\'s fixed now!

Cheers, Mike
ID: 3831 · Report as offensive    Reply Quote
Path7

Send message
Joined: 11 Feb 08
Posts: 56
Credit: 4,974
RAC: 0
Message 3832 - Posted: 18 Mar 2008, 23:48:32 UTC
Last modified: 18 Mar 2008, 23:54:03 UTC

Hello to all readers,

My last 1.09: WU score13_hb_envtest62_A_1scjB_3394_2757_0
http://ralph.bakerlab.org/result.php?resultid=837840
ran fine & validated ok, however the message rapport from Boinc showed this:

19-3-2008 0:14:28|ralph@home|Resuming task score13_hb_envtest62_A_1scjB_3394_2757_0 using minirosetta version 109
19-3-2008 0:19:43|ralph@home|[error] minirosetta not responding to screensaver, requesting exit
19-3-2008 0:19:44|ralph@home|Task score13_hb_envtest62_A_1scjB_3394_2757_0 exited with zero status but no \'finished\' file
19-3-2008 0:19:44|ralph@home|If this happens repeatedly you may need to reset the project.
19-3-2008 0:19:44|ralph@home|Restarting task score13_hb_envtest62_A_1scjB_3394_2757_0 using minirosetta version 109
19-3-2008 0:20:13|ralph@home|Computation for task score13_hb_envtest62_A_1scjB_3394_2757_0 finished
19-3-2008 0:20:13|rosetta@home|Starting OL31__BOINC_SYMM_FOLD_AND_DOCK_RELAX-OL31_-foldanddock__2988_14505_0

Yes I did use the show graphic tab, and the text going with the graphics showed: not responding. The graphics seems to freeze for a second. I closed the graphics and the next moment the 1.09 was reported finished.

Good luck crunching Ralph,
Path7.
ID: 3832 · Report as offensive    Reply Quote
Profile KSMarksPsych
Avatar

Send message
Joined: 16 Feb 06
Posts: 40
Credit: 8,226
RAC: 0
Message 3834 - Posted: 19 Mar 2008, 11:08:29 UTC

BOINC 5.10.21, Fedora 7, RosettaMini 1.09, Intel Core Duo

I downloaded a bunch of Orbit work. It\'s currently running in EDF (high priority). I noticed that the CPU time wasn\'t ticking up once per second as I would have expected. A quick look at top shows that RosettaMini was getting a third of the processing power. Starting and stopping the daemon got the Rosetta app back under control.

Screenshot for your viewing pleasured...


Kathryn :o)
The BOINC FAQ Service
The Unofficial BOINC Wiki
The Trac System
More BOINC information than you can shake a stick of RAM at.
ID: 3834 · Report as offensive    Reply Quote
JChojnacki
Avatar

Send message
Joined: 16 Feb 06
Posts: 2
Credit: 24,627
RAC: 0
Message 3844 - Posted: 7 Apr 2008, 23:53:32 UTC

miniRosetta 1.10 Failure:
http://ralph.bakerlab.org/result.php?resultid=865199

stderr out

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
ERROR: Unique best command line context option match not found for -weights

</stderr_txt>
]]>

~Joel

ID: 3844 · Report as offensive    Reply Quote
Rolly

Send message
Joined: 7 May 06
Posts: 2
Credit: 24,104
RAC: 0
Message 3845 - Posted: 8 Apr 2008, 5:34:43 UTC

Following Dr. Bakers request I have connected to Ralph again. At this moment it seems that I won\'t be of any help as I am running Eset nod32 as a virus scanner. Every new version of rosettamini gives new false positives on the Win32/Statik virus.

I have also noticed Eset on this and I hope you two can work this out.

Good luck and I am looking forward to CASP

J
ID: 3845 · Report as offensive    Reply Quote
Jipsu

Send message
Joined: 11 Mar 08
Posts: 26
Credit: 76,448
RAC: 0
Message 3846 - Posted: 8 Apr 2008, 9:02:09 UTC

<core_client_version>5.10.28</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip: cannot find zipfile directory in one of minirosetta_database_rev20940.zip or
minirosetta_database_rev20940.zip.zip, and cannot find minirosetta_database_rev20940.zip.ZIP, period.

ERROR: Unable to open file: minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt

ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 85
called boinc_finish

</stderr_txt>
]]>


I\'m getting this for every Rosetta mini 1.10 WU on my Linux 2.6.24-gentoo-r4
ID: 3846 · Report as offensive    Reply Quote
Profile Conan
Avatar

Send message
Joined: 16 Feb 06
Posts: 362
Credit: 1,368,421
RAC: 0
Message 3847 - Posted: 8 Apr 2008, 10:26:09 UTC

Had 20 work units fail with same error



<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip: cannot find zipfile directory in one of minirosetta_database_rev20940.zip or
minirosetta_database_rev20940.zip.zip, and cannot find minirosetta_database_rev20940.zip.ZIP, period.

ERROR: Unable to open file: minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt

ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 85
called boinc_finish

First WU to fail
Last WU of 20 to fail

All failed on Host 13121, AMD Opteron 285, Linux Fedora Core 3.
ID: 3847 · Report as offensive    Reply Quote
Profile KSMarksPsych
Avatar

Send message
Joined: 16 Feb 06
Posts: 40
Credit: 8,226
RAC: 0
Message 3848 - Posted: 8 Apr 2008, 10:54:47 UTC - in response to Message 3847.  

Had 20 work units fail with same error



<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip: cannot find zipfile directory in one of minirosetta_database_rev20940.zip or
minirosetta_database_rev20940.zip.zip, and cannot find minirosetta_database_rev20940.zip.ZIP, period.

ERROR: Unable to open file: minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt

ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 85
called boinc_finish

First WU to fail
Last WU of 20 to fail

All failed on Host 13121, AMD Opteron 285, Linux Fedora Core 3.
\\

Same here. Host ID 11671, Intel Core Duo, Fedora 7, BOINC 5.10.21
Kathryn :o)
The BOINC FAQ Service
The Unofficial BOINC Wiki
The Trac System
More BOINC information than you can shake a stick of RAM at.
ID: 3848 · Report as offensive    Reply Quote
Path7

Send message
Joined: 11 Feb 08
Posts: 56
Credit: 4,974
RAC: 0
Message 3849 - Posted: 8 Apr 2008, 12:43:33 UTC
Last modified: 8 Apr 2008, 13:09:25 UTC

Hello, thanks for warning,

Also having the process exited with code 1 (0x1, -255).
Computer ID 13238, AMD Sempron 3000+, Ubuntu 7.10, Boinc 5.10.45.

I\'ve reset the project after 2 failed WU\'s, with no result at all.
After 4 failed WU\'s I\'ve decided to temporally stop downloading new Ralph work.

Edit: I\'ve rebooted my dual-boot machine and now running Windows XP-home, Boinc 5.10.45, (still Sempron 3000+).
The Rosetta Mini 1.10 has already crunched 10 minutes, much longer than on Linux.
I guess the lately reported errors are a Linux application issue.

Path7.
ID: 3849 · Report as offensive    Reply Quote
Jipsu

Send message
Joined: 11 Mar 08
Posts: 26
Credit: 76,448
RAC: 0
Message 3850 - Posted: 8 Apr 2008, 13:19:40 UTC

My windows machines are crunching just fine so it must be some error in linux application
ID: 3850 · Report as offensive    Reply Quote
Previous · 1 · 2 · 3 · 4 · 5 · Next

Message boards : RALPH@home bug list : Bug Reports for Rosetta Mini Versions 1.+



©2019 University of Washington
http://www.bakerlab.org