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Mike Tyka

Joined: Oct 20 05
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Message 65840 - Posted 26 Apr 2010 19:38:22 UTC

More bug fixes and CASP related preparrations !

Please continue to let us know about problems, its very useful to have your feedback !

Cheers, Mike

____________
http://beautifulproteins.blogspot.com/
http://www.miketyka.com/

Snagletooth

Joined: Feb 22 07
Posts: 193
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Credit: 1,425,415
RAC: 236
Message 65905 - Posted 30 Apr 2010 10:05:34 UTC

cs-only-2-T4lys_7-10_20161_4_0

process exited with code 1 (0x1, -255)

ERROR: rsd_type_list.size()
ERROR:: Exit from: src/core/fragment/Frame.cc line: 62
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

Greg_BE Profile
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Joined: May 30 06
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Message 65920 - Posted 1 May 2010 18:18:20 UTC
Last modified: 1 May 2010 18:21:04 UTC

prior to the below task, this task rs_stg0_lrlx_t388__boincid_SAVE_ALL_OUT_19633_731_0 also suffered the same problem shown below.
rs_stg0_lrlx_t370__fullseq_run4_SAVE_ALL_OUT_20137_295_0
Outcome Client error
Client state Compute error
Exit status -177 (0xffffff4f)
CPU time 10239
stderr out

<core_client_version>6.10.43</core_client_version>
<![CDATA[
<message>
Maximum elapsed time exceeded
Reason: Breakpoint Encountered (0x80000003) at address 0x7C90120E

Jochen

Joined: Jun 6 06
Posts: 133
ID: 91626
Credit: 3,847,433
RAC: 0
Message 65922 - Posted 1 May 2010 19:27:23 UTC

I have got two client errors as well:

334732044
Server state Over
Outcome Client error
Client state Aborted by user
Exit status -197 (0xffffff3b)
CPU time 0

334733457
Server state Over
Outcome Client error
Client state Aborted by user
Exit status -197 (0xffffff3b)
CPU time 7707.375

Jochen
____________

Mod.Sense
Forum moderator
Project administrator

Joined: Aug 22 06
Posts: 3389
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Message 65925 - Posted 2 May 2010 1:16:31 UTC - in response to Message ID 65922.

I have got two client errors as well:

334732044
Server state Over
Outcome Client error
Client state Aborted by user
Exit status -197 (0xffffff3b)
CPU time 0

334733457
Server state Over
Outcome Client error
Client state Aborted by user
Exit status -197 (0xffffff3b)
CPU time 7707.375

Jochen


...are you saying you did NOT abort them?

____________
Rosetta Moderator: Mod.Sense

Jochen

Joined: Jun 6 06
Posts: 133
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Credit: 3,847,433
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Message 65927 - Posted 2 May 2010 8:15:13 UTC - in response to Message ID 65925.

...are you saying you did NOT abort them?

No, I did abort them.
The first one wasn't creating any CPU load (not even after restarting BOINC). The second one was a 'long running model', I aborted because it would have been running for a couple of more hours.

Sorry, should have written this in the first place...

Jochen
____________

Darren LaKous Profile

Joined: Mar 13 10
Posts: 2
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Credit: 174,999
RAC: 10
Message 65945 - Posted 3 May 2010 18:54:37 UTC

rs_stg0_lrlx_t000__casp8_test_SAVE_ALL_OUT.IGNORE_THE_REST_A_20212_6434_0

exit code 1073807364 (0x40010004)

Not sure what's up with this one.
____________

Tackleway

Joined: May 3 10
Posts: 3
ID: 379274
Credit: 11,886
RAC: 0
Message 65946 - Posted 3 May 2010 22:31:13 UTC

Very new to this project so please bear with me.
I've had three failures this evening with W.Units
no's 306695360 task id 335895445,
306692344 task id 335892188 &
305866751 task id 335003355
All finish with
Outcome Client error
Client state Compute error and
stderr out <core_client_version>6.10.43</core_client_version>
<![CDATA[
<message>
The system cannot find the path specified.
(0x3) - exit code 3(0x3)
</message>
<stderr_txt>
on Computer ID 1278225 running Window XP (SP 3)
If it's the machine that's not up for the gig, Please let me know

Kind regards, Tackleway

____________

Sid Celery

Joined: Feb 11 08
Posts: 806
ID: 241409
Credit: 10,030,156
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Message 65948 - Posted 4 May 2010 2:38:36 UTC - in response to Message ID 65946.

If it's the machine that's not up for the gig, Please let me know.

How much RAM do you have? Rosetta WUs require 512Mb per WU minimum.

____________

Tackleway

Joined: May 3 10
Posts: 3
ID: 379274
Credit: 11,886
RAC: 0
Message 65953 - Posted 4 May 2010 9:22:36 UTC - in response to Message ID 65948.

If it's the machine that's not up for the gig, Please let me know.

How much RAM do you have? Rosetta WUs require 512Mb per WU minimum.


Hole in one! thanks, I'll carry on with another machine whilst some additional
RAM is installed in the other. Cheers, Tackleway

lugal

Joined: Jul 16 08
Posts: 2
ID: 269388
Credit: 175,028
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Message 65957 - Posted 4 May 2010 17:13:12 UTC

Hi, minirosetta 2.11 was just killed off by my Symantec protection system with the remark "danger level high"

regards lugal

transient
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Posts: 376
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RAC: 4,046
Message 65961 - Posted 4 May 2010 20:43:51 UTC - in response to Message ID 65957.

Hi, minirosetta 2.11 was just killed off by my Symantec protection system with the remark "danger level high"

regards lugal


I'm guessing that's a false positive. Anyway, I've not encountered similar problems on my computer. I'm using Eset.
____________

Ohelig

Joined: May 2 10
Posts: 2
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Message 65974 - Posted 5 May 2010 12:23:06 UTC

I got an error with rb_05_04_129_340_rs_stg0_lrlx_t000__casp9_SAVE_ALL_OUT.IGNORE_THE_REST_B_20284_2938_1

ERROR: ERROR: no template_pdb provided for alignment 1DEGA_1
ERROR:: Exit from: ..\..\src\protocols\jd2\ThreadingJobInputter.cc line: 258
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

svincent

Joined: Dec 30 05
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Credit: 4,404,794
RAC: 6,286
Message 65979 - Posted 5 May 2010 15:54:23 UTC

Same error as ohelig above (on Mac OS X)

Task 336126568 rb_05_04_129_340_rs_stg0_lrlx_t000__casp9_SAVE_ALL_OUT.IGNORE_THE_REST_B_20284_1401_0

ERROR: ERROR: no template_pdb provided for alignment 1DEGA_1
ERROR:: Exit from: src/protocols/jd2/ThreadingJobInputter.cc line: 258
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>

smpaulsen

Joined: Dec 4 05
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Message 66002 - Posted 6 May 2010 14:05:00 UTC - in response to Message ID 65957.

Hi, minirosetta 2.11 was just killed off by my Symantec protection system with the remark "danger level high"

regards lugal


5/6/2010 9:50 AM,
High,
minirosetta_2.11_windows_intelx86.exe detected by SONAR,
Quarantined,Resolved - No Action,
SONAR,
2010.05.05.048,109.2.3.12,
minirosetta_2.11_windows_intelx86.exe,
File Based,
Fully removed

I had a similar experience with minirosetta_2.10

Why does Symantec think this is a threat?
____________

transient
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Joined: Sep 30 06
Posts: 376
ID: 115553
Credit: 7,834,811
RAC: 4,046
Message 66004 - Posted 6 May 2010 16:20:03 UTC - in response to Message ID 66002.

Hi, minirosetta 2.11 was just killed off by my Symantec protection system with the remark "danger level high"

regards lugal


5/6/2010 9:50 AM,
High,
minirosetta_2.11_windows_intelx86.exe detected by SONAR,
Quarantined,Resolved - No Action,
SONAR,
2010.05.05.048,109.2.3.12,
minirosetta_2.11_windows_intelx86.exe,
File Based,
Fully removed

I had a similar experience with minirosetta_2.10

Why does Symantec think this is a threat?


Have you tried asking Symantec? I imagine they can give you the best answer. Likely the answer will be something like: "the heuristic analysis engine sees some code that is similar to code of known malware/virii. Please submit the suspect file for further analysis."

____________

sep

Joined: Aug 16 09
Posts: 1
ID: 338254
Credit: 312,778
RAC: 0
Message 66012 - Posted 7 May 2010 0:39:30 UTC

Rosetta 2.11 works well on a Pentium Quad core, but still "hangs" on a PIII 1.4 GHz, like earlier versions did on both of my machines. The program is still running and graphics can be viewed, but the RMSD flatlines and there is no progress. I also run SETI@home without issues on both machines.
____________

Mod.Sense
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Joined: Aug 22 06
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Message 66022 - Posted 7 May 2010 16:39:39 UTC

A flat RMSD is not indicative of a problem. It just means that the program is having trouble finding a better configuration for the protein. Are there any other symptoms of "hangs"?
____________
Rosetta Moderator: Mod.Sense

Mike Tyka

Joined: Oct 20 05
Posts: 96
ID: 5612
Credit: 2,190
RAC: 0
Message 66024 - Posted 7 May 2010 17:28:01 UTC

Wrt to RMS "flatlines":

We are now running real live true blind targets, which means we do not know the answer (unlike during testing where we do) and so we cannot compute the RMSD since there is nothing to compare to (RMSD is the root mean square deviation from the experimentally determined fold found in nature).
Hence the RMSD flatlines!

Mike
____________
http://beautifulproteins.blogspot.com/
http://www.miketyka.com/

Sid Celery

Joined: Feb 11 08
Posts: 806
ID: 241409
Credit: 10,030,156
RAC: 9,347
Message 66026 - Posted 8 May 2010 0:23:33 UTC - in response to Message ID 66002.
Last modified: 8 May 2010 0:24:55 UTC

Hi, minirosetta 2.11 was just killed off by my Symantec protection system with the remark "danger level high"

regards lugal

5/6/2010 9:50 AM,
High,
minirosetta_2.11_windows_intelx86.exe detected by SONAR,
Quarantined,Resolved - No Action,
SONAR,
2010.05.05.048,109.2.3.12,
minirosetta_2.11_windows_intelx86.exe,
File Based,
Fully removed

I had a similar experience with minirosetta_2.10

Why does Symantec think this is a threat?

In the past this has come up with Norton Internet Security, even though Norton Antivirus (standalone) and Norton 360 find no problems.

If that's the case for you (running NIS) try and exclude the rosetta executable, or set up NIS not to scan the folder in which it's found. The first is a temporary solution that needs to be re-done each time a new rosetta version comes out, while the latter is a permanent fix which risks a real problem getting in there (none I've ever noticed though).
____________

nenym Profile

Joined: Jun 27 09
Posts: 1
ID: 323839
Credit: 1,035,613
RAC: 0
Message 66043 - Posted 10 May 2010 9:03:19 UTC
Last modified: 10 May 2010 9:03:53 UTC

All tasks erroed out when downloading.

<core_client_version>6.10.43</core_client_version>
<![CDATA[
<message>
WU download error: couldn't get input files:
<file_xfer_error>
<file_name>relax_options_lrm_ghoo_sc12_run01_A_yfsong</file_name>
<error_code>-224</error_code>
<error_message>file not found</error_message>
</file_xfer_error>
<file_xfer_error>
<file_name>S_rb1_1unr_native_0000.pdb</file_name>
<error_code>-224</error_code>
<error_message>file not found</error_message>
</file_xfer_error>
<file_xfer_error>
<file_name>yfsong_lrm_ghoo_sc12_run01_A.zip</file_name>
<error_code>-224</error_code>
<error_message>file not found</error_message>
</file_xfer_error>
<file_xfer_error>
<file_name>boinc_rb1_1unr.pdb</file_name>
<error_code>-224</error_code>
<error_message>file not found</error_message>
</file_xfer_error>

</message>
]]>
I have reset and reattached the project with no result, stll the same error. Any idea what to do more? 7 different machines (Intel C2D, Xeon, WinXP x86, WinXP x64).

deesy58

Joined: Apr 20 10
Posts: 75
ID: 377880
Credit: 193,831
RAC: 0
Message 66051 - Posted 10 May 2010 19:49:20 UTC

One of my two running Rosetta tasks completed, and no new task was downloaded. In fact, no new Rosetta tasks have downloaded for a couple of days. Windows Task Manager shows two instances of minirosetta_2.11 running, but only a single Rosetta task is indicated by the BOINC Manager, and it is running at high priority.

I began running the Colatz Conjecture tasks on my GPU a couple of days ago, and I don't believe that Rosetta has downloaded any new WUs since that time (although I could be mistaken). Do these projects interfere with each other?

I also wondered why two instances of minirosetta are running on my two CPUs if only a single task is being processed. The processing certainly does not appear to be any faster. In fact, it appears to have slowed down.

Is there anything I need to do to correct this situation?

deesy

Yifan Song
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Project developer
Project scientist

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Message 66052 - Posted 10 May 2010 20:08:13 UTC - in response to Message ID 66043.

It could be an error with server timed out. It's been busy with the app/database update as well as casp prep.

All tasks erroed out when downloading.
<core_client_version>6.10.43</core_client_version>
<![CDATA[
<message>
WU download error: couldn't get input files:
<file_xfer_error>
<file_name>relax_options_lrm_ghoo_sc12_run01_A_yfsong</file_name>
<error_code>-224</error_code>
<error_message>file not found</error_message>
</file_xfer_error>
<file_xfer_error>
<file_name>S_rb1_1unr_native_0000.pdb</file_name>
<error_code>-224</error_code>
<error_message>file not found</error_message>
</file_xfer_error>
<file_xfer_error>
<file_name>yfsong_lrm_ghoo_sc12_run01_A.zip</file_name>
<error_code>-224</error_code>
<error_message>file not found</error_message>
</file_xfer_error>
<file_xfer_error>
<file_name>boinc_rb1_1unr.pdb</file_name>
<error_code>-224</error_code>
<error_message>file not found</error_message>
</file_xfer_error>

</message>
]]>
I have reset and reattached the project with no result, stll the same error. Any idea what to do more? 7 different machines (Intel C2D, Xeon, WinXP x86, WinXP x64).

Greg_BE Profile
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Message 66055 - Posted 10 May 2010 21:06:39 UTC

5/10/2010 11:01:35 PM rosetta@home Sending scheduler request: Requested by user.
5/10/2010 11:01:35 PM rosetta@home Not reporting or requesting tasks
5/10/2010 11:01:43 PM Project communication failed: attempting access to reference site
5/10/2010 11:01:44 PM Internet access OK - project servers may be temporarily down.
5/10/2010 11:01:45 PM rosetta@home Scheduler request failed: Couldn't connect to server


server page shows everything in green
what's going on?

deesy58

Joined: Apr 20 10
Posts: 75
ID: 377880
Credit: 193,831
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Message 66059 - Posted 10 May 2010 22:42:19 UTC - in response to Message ID 66051.

One of my two running Rosetta tasks completed, and no new task was downloaded. In fact, no new Rosetta tasks have downloaded for a couple of days. Windows Task Manager shows two instances of minirosetta_2.11 running, but only a single Rosetta task is indicated by the BOINC Manager, and it is running at high priority.

I began running the Colatz Conjecture tasks on my GPU a couple of days ago, and I don't believe that Rosetta has downloaded any new WUs since that time (although I could be mistaken). Do these projects interfere with each other?

I also wondered why two instances of minirosetta are running on my two CPUs if only a single task is being processed. The processing certainly does not appear to be any faster. In fact, it appears to have slowed down.

Is there anything I need to do to correct this situation?

deesy


I have now received a new WU, and Rosetta is processing normally again.

deesy

Snagletooth

Joined: Feb 22 07
Posts: 193
ID: 149031
Credit: 1,425,415
RAC: 236
Message 66060 - Posted 10 May 2010 22:43:15 UTC - in response to Message ID 66051.

One of my two running Rosetta tasks completed, and no new task was downloaded. In fact, no new Rosetta tasks have downloaded for a couple of days. Windows Task Manager shows two instances of minirosetta_2.11 running, but only a single Rosetta task is indicated by the BOINC Manager, and it is running at high priority.

What's the deadline on that task? In this message Mike Tyka mentions that some of the casp9 WUs have 3 day instead of the usual 10 day deadlines. BOINC won't download another rosetta task as long as it is running one at high priority.

I began running the Colatz Conjecture tasks on my GPU a couple of days ago, and I don't believe that Rosetta has downloaded any new WUs since that time (although I could be mistaken). Do these projects interfere with each other?


Someone else will have to chime in here as I haven't a clue.

I also wondered why two instances of minirosetta are running on my two CPUs if only a single task is being processed. The processing certainly does not appear to be any faster. In fact, it appears to have slowed down.

Do you have the graphics window open? Since BOINC 6 graphics have run as a separate application. Using Activity Manager on my Mac I had to widen the window in order to see the whole name, and thus distinguish between the graphics app and the app doing the actual crunching. And, if memory serves, not all graphics apps have been clearly named as such (though maybe that was just for rosetta beta apps/graphics?) If by slowing down you mean it's taking more elapsed time then well,yea, running with the graphics window open uses up CPU time that's then not available for crunching. (There is a setting in your rosetta@home preferences for "percentage of CPU time used for graphics" but I don't know how this works or it's effects. I mentioned it in your other thread hoping someone would pipe up with an explanation or volunteer to try some tests but so far no takers :(

Is there anything I need to do to correct this situation?

Check the deadline, close the graphics window, and report back.


Best,
Snags

Raziel-CZ

Joined: Aug 7 09
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RAC: 4
Message 67376 - Posted 26 Aug 2010 21:51:11 UTC

Rosetta@home has been stopped on all my computers. Not sending new tasks. What happend? I'am always online and wainting. It's ok or not? Oh, sorry for my english, I'am from Czech Republic ;)

transient
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Message 67383 - Posted 27 Aug 2010 4:45:16 UTC

Nobody is getting work. Not in significant amounts anyway. There's nothing wrong with the application or your computers. We will have to wait for someone from Rosetta to fix this.
____________

Message boards : Number crunching : minirosetta 2.11


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