Bug Reports for Rosetta Mini Versions 1.+

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Pepo
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Message 3852 - Posted: 8 Apr 2008, 14:53:58 UTC
Last modified: 8 Apr 2008, 14:54:36 UTC

My Linux host has also got both types of task errors (\"Unique best command line context option match not found for -weights\" and \"End-of-central-directory signature not found...\")

Peter
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Message 3853 - Posted: 8 Apr 2008, 15:45:40 UTC
Last modified: 8 Apr 2008, 16:18:36 UTC

My first result for quite some time produced this error as well on my ubuntu 7.10_64 Computer running BOINC 5.10.45 on a C2D E6750@3,2GHz



stderr out	

<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

</stderr_txt>
]]>



Edith says:
I just looked in the projects directory and found the missing .zip, inly a second .ZIP was missing ;). In the described thread in there was the residue_types.txt, but if the stupid minirosetta looks for a double-zipped file, it can\'t find any of course.
Opening the .zip was no problem
Gruesse vom Saenger

For questions about Boinc look in the BOINC-Wiki
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Message 3855 - Posted: 8 Apr 2008, 16:56:06 UTC - in response to Message 3853.  

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.


Edith says:
I just looked in the projects directory and found the missing .zip, inly a second .ZIP was missing ;). In the described thread in there was the residue_types.txt, but if the stupid minirosetta looks for a double-zipped file, it can\'t find any of course.
Opening the .zip was no problem

Stay cool, Edith ;-) the stupid remarks about \"*.zip.zip\" and \"*.zip.ZIP\" belongs to the unzip library (its guesswork for possible typo errors). Example:
$ unzip -v archive
unzip:  cannot find or open archive, archive.zip or archive.ZIP.


Peter
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Message 3858 - Posted: 8 Apr 2008, 21:08:01 UTC

Probably not too serious but on the Mac version ( OSX 10.4.11 ) with Mini 1.10 there\'s a problem with the menu bar. It flashes briefly with some text when you do Show Graphics, then the menu bar goes blank apart from the blue Apple Icon at the left.

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Message 3859 - Posted: 8 Apr 2008, 21:47:07 UTC
Last modified: 8 Apr 2008, 21:49:22 UTC

Computer Project Date ID Message
.G33M02 ralph@home 4/8/2008 4:30:17 PM 580 Output file 1dhn__BOINC_ABINITIO_IGNORE_THE_REST-S25-7-S3-3--1dhn_-_3452_2_0_0 for task 1dhn__BOINC_ABINITIO_IGNORE_THE_REST-S25-7-S3-3--1dhn_-_3452_2_0 absent

Linux
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Message 3864 - Posted: 9 Apr 2008, 12:46:44 UTC

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<stderr_txt>
======================================================
DONE :: 1 starting structures 3075.03 cpu seconds
This process generated 3 decoys from 3 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...
called boinc_finish

</stderr_txt>
<message>
<file_xfer_error>
<file_name>bench80_mini_score13_abrelax_natfrag_1pohA_3475_8_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>
]]>

WU

MiniRosetta v1.1 Windows XP SP2
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Message 3866 - Posted: 9 Apr 2008, 13:47:11 UTC

My Linux host did get two of yesterday\'s failing 1.10 tasks. Today the scheduler suddenly incorrectly claimed the host lacks enough free disk space:
Message from server: No work sent (there was work but you don\'t have enough disk space allocated)
Message from server: Not enough disk space (only 393.9 MB free for BOINC). Review preferences for maximum disk space used.

The host\'s projects occupy 466 MB of the 1 GB reserved for Boinc (on the otherwise nearly empty disk), Ralph took its a bit less than 40 MB. (After writing this message: the complete BOINC/ tree disk usage is 599 MB).

I\'ve enlarged the limit to 1.6 GB - the host suddenly received one new 1.10 task consisting of three downloaded files - alltogether some 5 MBs. Ralph\'s disk usage rose to a bit more than 40 MB.

I\'ll keep the project\'s and task\'s slot disk usage in eye, but do not really believe that the intermediate files would grow to (much) more than 394 MB........ The requested limit must have changed during last few hours.

Peter
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Message 3867 - Posted: 9 Apr 2008, 13:51:09 UTC

HAD TWO 1.10 FAIL ON WINDOWS 2000 SP4 RUNNING AMD 5200+ 4GB RAM
<core_client_version>6.1.14</core_client_version>





http://ralph.bakerlab.org//result.php?resultid=873615
AND
http://ralph.bakerlab.org//result.php?resultid=873535

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Message 3869 - Posted: 9 Apr 2008, 14:28:12 UTC - in response to Message 3847.  
Last modified: 9 Apr 2008, 14:30:50 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.


Make that another 20 that have failed, all on Linux Fedora Core 3 and 6 as now happening on second Linux box, 3rd box has just gotten it\'s first 2 Wu\'s for awhile but I suspect they will fail as well.

ALL Work Units fail on my Linux machines.
Windows is working fine.

I am getting the SAME error as previously reported.
Linux problem not yet addressed.

Here are another two examples :-
WU 894731
WU 870168
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Message 3870 - Posted: 9 Apr 2008, 14:54:54 UTC

Rosetta Mini 1.10 error on Windows XP.

http://ralph.bakerlab.org/result.php?resultid=870821
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mirabilos

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Message 3872 - Posted: 10 Apr 2008, 1:12:02 UTC - in response to Message 3869.  
Last modified: 10 Apr 2008, 1:13:28 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



Make that another 20 that have failed


Add another two:
one on Debian GNU/Linux testing (i386),
the other one on MirBSD #10-current (i386) after temporarily
connecting with a hacked boinc executable to fool the server
into giving me a task, see http://ralph.bakerlab.org/forum_thread.php?id=376.

The ZIP archive extracts just fine in both cases by the way.
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Message 3876 - Posted: 10 Apr 2008, 13:21:22 UTC
Last modified: 10 Apr 2008, 13:26:42 UTC

Hello all,
For the third day I\'ve downloaded a Ralph WU and tried to let it crunch on my Linux (Ubuntu 7.10) computer.
The Rosetta mini 1.10 again error-ed out with process exited with code 1 (0x1, -255), zip.ZIP error, as mentioned above.

I can imagine the tench\'s are quiet busy these days, however it would nice to see a announcement to tell us Linux users when a reliable (Linux-)WU can be downloaded.

I\'m interested in what Wu\'s will come up the next days,
Path7.

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Message 3877 - Posted: 11 Apr 2008, 9:12:58 UTC

Windows Ralph WU\'s work fine, no errors.

Linux 5.96 WU\'s work fine and complete ok.

Linux mini 1.10 and 1.11 are a dismal failure, NONE of them work.

All error out after 0.28 to 0.33 seconds with the same error I reported over the last few days. Had close to a dozen fail on top of the 40 I reported before.

They are a waste of bandwidth at the moment.

What did you change as they were working before ??
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Message 3878 - Posted: 11 Apr 2008, 14:42:17 UTC

mini 1.11 3 more failed on 879993, 879985, 879983. all failed on windows 2000
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Message 3879 - Posted: 11 Apr 2008, 17:26:34 UTC


WinXP

Computer Project Date ID Message
.G33M01 ralph@home 4/11/2008 12:15:33 PM 9006 Output file 1utg__BOINC_ABINITIO_IGNORE_THE_REST-S25-10-S3-12--1utg_-_3452_1_0_0 for task 1utg__BOINC_ABINITIO_IGNORE_THE_REST-S25-10-S3-12--1utg_-_3452_1_0 absent
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Message 3880 - Posted: 11 Apr 2008, 17:40:19 UTC
Last modified: 11 Apr 2008, 17:42:19 UTC

Task ID 906094
Name bench80_mini_score13_abrelax_natfrag_1o7uA_3458_7_1
Workunit 778156
Created 10 Apr 2008 6:31:12 UTC
Sent 10 Apr 2008 7:02:21 UTC
Received 11 Apr 2008 17:33:54 UTC
Server state Over
Outcome Client error
Client state Compute error
Exit status 0 (0x0)
Computer ID 12421
Report deadline 14 Apr 2008 7:02:21 UTC
CPU time 4344.813
stderr out <core_client_version>5.10.45</core_client_version>
<![CDATA[
<stderr_txt>
======================================================
DONE :: 1 starting structures 4344.63 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...
called boinc_finish

</stderr_txt>
<message>
<file_xfer_error>
<file_name>bench80_mini_score13_abrelax_natfrag_1o7uA_3458_7_1_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>
]]>


Validate state Invalid
Claimed credit 18.0564036697952
Granted credit 0
application version 1.10


..2nd failure on this task
W. XP. AMD 4800 2 Cores..
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Message 3883 - Posted: 11 Apr 2008, 22:07:52 UTC

We\'ve tracked down the linux problem and think it has to do with the boinc libraries and not the mini executable.

Hopefully update v. 1.12 will fix this
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Message 3884 - Posted: 11 Apr 2008, 22:35:55 UTC - in response to Message 3883.  

We\'ve tracked down the linux problem and think it has to do with the boinc libraries and not the mini executable.

Hopefully update v. 1.12 will fix this

Hello Robert,

Many thanks for the update.
I\'m looking forward to the Linux MiniRosetta 1.12.

Have a nice day,
Path7.
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Message 3885 - Posted: 11 Apr 2008, 23:33:20 UTC
Last modified: 11 Apr 2008, 23:37:26 UTC

This workunit 790247 failed for both my wing man and I that attempted to run it.
I did notice alot of disk thrashing for the workunit also. My run/crash details below.

Task ID 901195
Name bench80_mini_score13_abrelax_natfrag_2ccvA_3475_8_1
Exit status 0 (0x0)
Computer ID 4103
CPU time 9485.52
stderr out

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<stderr_txt>
# cpu_run_time_pref: 7200
======================================================
DONE :: 1 starting structures 9485.48 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...
called boinc_finish

</stderr_txt>
<message>
<file_xfer_error>
<file_name>bench80_mini_score13_abrelax_natfrag_2ccvA_3475_8_1_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>
]]>

Validate state Invalid
Claimed credit 12.4958177801863
Granted credit 0
application version 1.10

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Message 3886 - Posted: 12 Apr 2008, 0:08:01 UTC

Computer Project Date ID Message
.G33M01 ralph@home 4/11/2008 6:38:15 PM 9770 Output file 1who__BOINC_ABINITIO_IGNORE_THE_REST-S25-10-S3-4--1who_-_3452_2_0_0 for task 1who__BOINC_ABINITIO_IGNORE_THE_REST-S25-10-S3-4--1who_-_3452_2_0 absent

WinXP
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