Problems with Minirosetta Version 1.64/1.65

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Robert

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Message 60902 - Posted: 29 Apr 2009, 21:52:18 UTC

We\'ve got a new minirosetta version, with some infrastructure changes and a new protocol for using experimental data from NMR.

Please report any issues here
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Sid Celery

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Message 60918 - Posted: 30 Apr 2009, 10:50:19 UTC
Last modified: 30 Apr 2009, 10:51:40 UTC

Some have come down, but I haven\'t started crunching them yet.

For those who run Norton Internet Security 2009 it would be wise to check the new executable hasn\'t been quarantined in the way previous versions have, as reported here. That message shows how to restore the file from quarantine and report it to Symantec as a false positive.

It isn\'t quarantined on my Norton 360 v3 system here, but neither did it when NIS2009 reported a problem. Don\'t know about the standalone Norton AV.
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Profile robertmiles

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Message 60938 - Posted: 1 May 2009, 12:14:34 UTC

1.64 appears not to be immune to the lockfile problem.

http://boinc.bakerlab.org/rosetta/result.php?resultid=247790244

It\'s not clear yet if it can start the lockfile problem, or only inherit it from a 1.54 workunit previously run in the same slot.

Have you thought of modifying the program so that, even after a lockfile error, it\'s capable of sending back all the completed decoys?

Also, something in the chain got confused about how long it should make the minirosetta workunits sent to my newer machine. First, it sent 1.54 workunits that actually took about 3 hours instead of the 12 hours I expected. Then, when I adjusted the requested length when logged in from that machine, the length that machine got was adjusted to 12 hours for 1.54 and I started getting 1.64 workunits with an expected length of 20 hours, now adjusted down to 19 hours. The work flow doesn\'t seem to have had time to adjust to the faster speed of the newer machine yet.
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Mel

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Message 60940 - Posted: 1 May 2009, 15:59:02 UTC - in response to Message 60902.  

We\'ve got a new minirosetta version, with some infrastructure changes and a new protocol for using experimental data from NMR.

Please report any issues here


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Mel

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Message 60941 - Posted: 1 May 2009, 16:02:11 UTC - in response to Message 60902.  

[quote]We\'ve got a new minirosetta version, with some infrastructure changes and a new protocol for using experimental data from NMR.

PlU please report any issues here [/quote}
How come each upload had been taking in excess of 25 minutes this week, it usually has only taken 20 seconds per work unit ? Have been on this upload now for 45 minutes and only upoading 80 work units.
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HW&JC

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Message 60942 - Posted: 1 May 2009, 18:45:33 UTC - in response to Message 60918.  

For those who run Norton Internet Security 2009 it would be wise to check the new executable hasn\'t been quarantined in the way previous versions have, as reported here. That message shows how to restore the file from quarantine and report it to Symantec as a false positive.

Yup, it does it again:

01/05/2009 19:33:03 rosetta@home Task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-17-S3-24--ARF1-_11731_60_0 exited with zero status but no \'finished\' file
01/05/2009 19:33:03 rosetta@home If this happens repeatedly you may need to reset the project.
01/05/2009 19:33:03 rosetta@home Task DvR115G_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-22-S3-21--DvR115G-_11729_82_0 exited with zero status but no \'finished\' file
01/05/2009 19:33:03 rosetta@home If this happens repeatedly you may need to reset the project.
01/05/2009 19:33:21 rosetta@home [error] Process creation failed: The system cannot find the file specified. (0x2)
01/05/2009 19:33:22 rosetta@home [error] Process creation failed: The system cannot find the file specified. (0x2)
01/05/2009 19:33:22 rosetta@home [error] Process creation failed: The system cannot find the file specified. (0x2)
01/05/2009 19:33:23 rosetta@home [error] Process creation failed: The system cannot find the file specified. (0x2)
01/05/2009 19:33:24 rosetta@home [error] Process creation failed: The system cannot find the file specified. (0x2)
01/05/2009 19:33:24 rosetta@home Computation for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-17-S3-24--ARF1-_11731_60_0 finished
01/05/2009 19:33:24 rosetta@home Output file ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-17-S3-24--ARF1-_11731_60_0_0 for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-17-S3-24--ARF1-_11731_60_0 absent
01/05/2009 19:33:24 rosetta@home Computation for task DvR115G_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-22-S3-21--DvR115G-_11729_82_0 finished
01/05/2009 19:33:24 rosetta@home Output file DvR115G_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-22-S3-21--DvR115G-_11729_82_0_0 for task DvR115G_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-22-S3-21--DvR115G-_11729_82_0 absent
01/05/2009 19:33:32 rosetta@home Starting DvR115G_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-23-S3-19--DvR115G-_11729_82_0
01/05/2009 19:33:32 rosetta@home Starting abinitio_norelax_homfrag__plus_native_1hoeA__SAVE_ALL_OUT_11263_2937_0
01/05/2009 19:33:32 rosetta@home Started download of minirosetta_1.64_windows_intelx86.exe
01/05/2009 19:33:32 rosetta@home Computation for task DvR115G_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-23-S3-19--DvR115G-_11729_82_0 finished
01/05/2009 19:33:32 rosetta@home Output file DvR115G_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-23-S3-19--DvR115G-_11729_82_0_0 for task DvR115G_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-23-S3-19--DvR115G-_11729_82_0 absent
01/05/2009 19:33:32 rosetta@home Computation for task abinitio_norelax_homfrag__plus_native_1hoeA__SAVE_ALL_OUT_11263_2937_0 finished
01/05/2009 19:33:32 rosetta@home Output file abinitio_norelax_homfrag__plus_native_1hoeA__SAVE_ALL_OUT_11263_2937_0_0 for task abinitio_norelax_homfrag__plus_native_1hoeA__SAVE_ALL_OUT_11263_2937_0 absent
01/05/2009 19:33:32 rosetta@home Starting ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-29-S3-20--ARF1-_11731_60_0
01/05/2009 19:33:32 rosetta@home Starting ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-29-S3-18--ARF1-_11731_60_0
01/05/2009 19:33:32 rosetta@home Starting ER553_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-6-S3-27--ER553-_11730_82_0
01/05/2009 19:33:32 rosetta@home Starting ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-21-S3-28--ARF1-_11731_62_0
01/05/2009 19:33:32 rosetta@home Starting ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-7-S3-12--ARF1-_11731_66_0
01/05/2009 19:33:32 rosetta@home Starting ER553_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-8-S3-12--ER553-_11730_69_0
01/05/2009 19:33:33 rosetta@home Computation for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-29-S3-20--ARF1-_11731_60_0 finished
01/05/2009 19:33:33 rosetta@home Output file ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-29-S3-20--ARF1-_11731_60_0_0 for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-29-S3-20--ARF1-_11731_60_0 absent
01/05/2009 19:33:33 rosetta@home Computation for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-29-S3-18--ARF1-_11731_60_0 finished
01/05/2009 19:33:33 rosetta@home Output file ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-29-S3-18--ARF1-_11731_60_0_0 for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-29-S3-18--ARF1-_11731_60_0 absent
01/05/2009 19:33:33 rosetta@home Computation for task ER553_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-6-S3-27--ER553-_11730_82_0 finished
01/05/2009 19:33:33 rosetta@home Output file ER553_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-6-S3-27--ER553-_11730_82_0_0 for task ER553_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-6-S3-27--ER553-_11730_82_0 absent
01/05/2009 19:33:33 rosetta@home Computation for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-21-S3-28--ARF1-_11731_62_0 finished
01/05/2009 19:33:33 rosetta@home Output file ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-21-S3-28--ARF1-_11731_62_0_0 for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-21-S3-28--ARF1-_11731_62_0 absent
01/05/2009 19:33:33 rosetta@home Computation for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-7-S3-12--ARF1-_11731_66_0 finished
01/05/2009 19:33:33 rosetta@home Output file ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-7-S3-12--ARF1-_11731_66_0_0 for task ARF1_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-7-S3-12--ARF1-_11731_66_0 absent
01/05/2009 19:33:33 rosetta@home Computation for task ER553_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-8-S3-12--ER553-_11730_69_0 finished
01/05/2009 19:33:33 rosetta@home Output file ER553_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-8-S3-12--ER553-_11730_69_0_0 for task ER553_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-8-S3-12--ER553-_11730_69_0 absent

Go to \"Security History\" and select the \"Resolved Security Risks\" option from the drop down. Click \"More Details\" and chose to \"Restore Risk\" and ensure that the MiniRosetta executable isn\'t rejected again. Not sure where the option went to report the false positive to Symantec, but it sorts you out.

Strange, because a lot of 1.64 tasks went through ok before it rejected all the tasks at once. Click my name on this message to see my reported results - but also note that I have a lot of computer problems anyway, so there are always a lot of errors. My fault rather than Rosetta\'s in those cases.
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jswolf19

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Message 60947 - Posted: 2 May 2009, 3:21:00 UTC

It seems that I\'m using Mini 1.65 instead of 1.64 for the current work unit, but I just wanted to say that I tried reapplying the day-of-week network-availability overrides in BOINC advanced preferences to see if the work unit would freeze as it did in 1.54, and it appears to be working fine. Thanks ^_^
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Mike Tyka

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Message 60954 - Posted: 2 May 2009, 18:08:12 UTC - in response to Message 60947.  

It seems that I\'m using Mini 1.65 instead of 1.64 for the current work unit, but I just wanted to say that I tried reapplying the day-of-week network-availability overrides in BOINC advanced preferences to see if the work unit would freeze as it did in 1.54, and it appears to be working fine. Thanks ^_^


Yes that\'s one of the fixes in this version :-D excellent !
http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Mike Tyka

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Message 60955 - Posted: 2 May 2009, 18:10:14 UTC

1.65 was released. This is a high-priority patch that should fix a problem with the uploads.
http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Profile Paul D. Buck

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Message 60956 - Posted: 2 May 2009, 19:29:20 UTC - in response to Message 60955.  

1.65 was released. This is a high-priority patch that should fix a problem with the uploads.

So are we going to see 1.65 in Ralph?
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googloo
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Message 60957 - Posted: 2 May 2009, 20:17:19 UTC

Please, please, please post version changes to Rosetta Application Version Release Log.
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HW&JC

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Message 60958 - Posted: 2 May 2009, 20:35:14 UTC - in response to Message 60942.  
Last modified: 2 May 2009, 20:36:20 UTC

Ditto for NIS2009 with MiniRosetta 1.65
Go to \"Security History\" and select the \"Resolved Security Risks\" option from the drop down. Click \"More Details\" and chose to \"Restore Risk\" and ensure that the MiniRosetta executable isn\'t rejected again. Not sure where the option went to report the false positive to Symantec, but it sorts you out.

I think the way to report the false positive is to chose the report option first, then restore risk. I did it wrong again but I\'ll remember next time.
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Message 60971 - Posted: 3 May 2009, 16:31:31 UTC

The lockfile problem again:

http://boinc.bakerlab.org/rosetta/result.php?resultid=248406598

Could you tell the BOINC developers that you need this feature, if you can\'t find it already?

Don\'t assign any workunit to run in a slot comtaining a boinc_lockfile file left over from a previous workunit run in that slot. If such a slot is not already in use, disable any use of it until the next reboot cleans things up. Instead, create a new slot and use that one.
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Profile Ian_D

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Message 60988 - Posted: 4 May 2009, 11:17:59 UTC
Last modified: 4 May 2009, 11:18:56 UTC

1PTQA_BOINC_MPZN_vanilla_abrelax_9106_12334_1

http://boinc.bakerlab.org/rosetta/result.php?resultid=248349357

<core_client_version>6.6.20</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
[2009- 5- 4 0:14:21:] :: BOINC:: Initializing ... ok.
[2009- 5- 4 0:14:21:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
ERROR: Option matching -fragB_size
not found in command line top-level context

</stderr_txt>
]]>


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Profile Paul D. Buck

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Message 61003 - Posted: 4 May 2009, 19:55:44 UTC

Reason: Access Violation (0xc0000005) at address 0x004F3D7B read attempt to address 0x00000004 on task Docking_benchmark_natives__1FBI.mppk.pdb.gzdock_score12_hi.xml_11809_243_0
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P . P . L .

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Message 61016 - Posted: 5 May 2009, 6:56:55 UTC

Hi.

This one had a problem, twice now.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=227016174

Tue 05 May 2009 16:46:02 EST|rosetta@home|Output file Docking_benchmark_natives__2KAI.mppk.pdb.gzdock_score12_hi.xml_11809_189_1_0 for task Docking_benchmark_natives__2KAI.mppk.pdb.gzdock_score12_hi.xml_11809_189_1 absent

Done with app 1.65.

pete.


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Profile Paul D. Buck

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Message 61018 - Posted: 5 May 2009, 11:11:51 UTC

Another Docking_benchmark_natives__2KAI.mppk.pdb.gzdock_score12_hi.xml_11809_378_0 crash.

Seems like a bad task definition to me ...
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Profile Sarel

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Message 61026 - Posted: 5 May 2009, 20:27:15 UTC - in response to Message 61018.  

Hello,

I\'ve tracked down the crashes in the docking runs to 4 runs within the batch. I\'ve now fixed the problem and should rerun those soon (first on ralph).

I\'m sorry for the trouble this has caused.

Thanks for your quick feedback!

Sarel.

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Profile Gavin Shaw
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Message 61027 - Posted: 5 May 2009, 22:58:44 UTC
Last modified: 5 May 2009, 22:59:42 UTC

Crashed unit using MiniRosetta 1.65.

Docking_benchmark_natives__1FBI.mppk.pdb.gzdock_score12_hi.xml_11809_52_1

Boinc error message: Unrecoverable error for result Docking_benchmark_natives__1FBI.mppk.pdb.gzdock_score12_hi.xml_11809_52_1 ( - exit code -1073741819 (0xc0000005))
Never surrender and never give up. In the darkest hour there is always hope.

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Speedy
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Message 61029 - Posted: 5 May 2009, 23:05:48 UTC - in response to Message 61027.  

Crashed unit using MiniRosetta 1.65.

Docking_benchmark_natives__1FBI.mppk.pdb.gzdock_score12_hi.xml_11809_52_1

Boinc error message: Unrecoverable error for result Docking_benchmark_natives__1FBI.mppk.pdb.gzdock_score12_hi.xml_11809_52_1 ( - exit code -1073741819 (0xc0000005))

The way I understand is that this issue has been fixed. There are some tasks still to be returned that have errors, your task was one of these by the looks of it.
Have a crunching good day!!
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