minirosetta 2.11

Message boards : Number crunching : minirosetta 2.11

To post messages, you must log in.

1 · 2 · Next

AuthorMessage
Mike Tyka

Send message
Joined: 20 Oct 05
Posts: 96
Credit: 2,190
RAC: 0
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/
ID: 65840 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Snags

Send message
Joined: 22 Feb 07
Posts: 194
Credit: 1,509,393
RAC: 435
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
ID: 65905 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Greg_BE
Avatar

Send message
Joined: 30 May 06
Posts: 4835
Credit: 3,079,068
RAC: 567
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
ID: 65920 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Jochen

Send message
Joined: 6 Jun 06
Posts: 133
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
ID: 65922 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator
Project administrator

Send message
Joined: 22 Aug 06
Posts: 3434
Credit: 0
RAC: 0
Message 65925 - Posted: 2 May 2010, 1:16:31 UTC - in response to Message 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
ID: 65925 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Jochen

Send message
Joined: 6 Jun 06
Posts: 133
Credit: 3,847,433
RAC: 0
Message 65927 - Posted: 2 May 2010, 8:15:13 UTC - in response to Message 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
ID: 65927 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Darren LaKous

Send message
Joined: 13 Mar 10
Posts: 2
Credit: 176,150
RAC: 0
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.
ID: 65945 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Tackleway

Send message
Joined: 3 May 10
Posts: 3
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

ID: 65946 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Sid Celery

Send message
Joined: 11 Feb 08
Posts: 857
Credit: 11,830,805
RAC: 9,199
Message 65948 - Posted: 4 May 2010, 2:38:36 UTC - in response to Message 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.

ID: 65948 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Tackleway

Send message
Joined: 3 May 10
Posts: 3
Credit: 11,886
RAC: 0
Message 65953 - Posted: 4 May 2010, 9:22:36 UTC - in response to Message 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
ID: 65953 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
lugal

Send message
Joined: 16 Jul 08
Posts: 2
Credit: 175,028
RAC: 0
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
ID: 65957 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
transient
Avatar

Send message
Joined: 30 Sep 06
Posts: 376
Credit: 8,276,181
RAC: 10,426
Message 65961 - Posted: 4 May 2010, 20:43:51 UTC - in response to Message 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.
ID: 65961 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Ohelig

Send message
Joined: 2 May 10
Posts: 2
Credit: 84,515
RAC: 0
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
ID: 65974 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
svincent

Send message
Joined: 30 Dec 05
Posts: 205
Credit: 5,149,841
RAC: 1,719
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>
ID: 65979 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
smpaulsen

Send message
Joined: 4 Dec 05
Posts: 1
Credit: 3,136,000
RAC: 1,367
Message 66002 - Posted: 6 May 2010, 14:05:00 UTC - in response to Message 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?
ID: 66002 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
transient
Avatar

Send message
Joined: 30 Sep 06
Posts: 376
Credit: 8,276,181
RAC: 10,426
Message 66004 - Posted: 6 May 2010, 16:20:03 UTC - in response to Message 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.\"

ID: 66004 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
sep

Send message
Joined: 16 Aug 09
Posts: 1
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.
ID: 66012 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator
Project administrator

Send message
Joined: 22 Aug 06
Posts: 3434
Credit: 0
RAC: 0
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
ID: 66022 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mike Tyka

Send message
Joined: 20 Oct 05
Posts: 96
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/
ID: 66024 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Sid Celery

Send message
Joined: 11 Feb 08
Posts: 857
Credit: 11,830,805
RAC: 9,199
Message 66026 - Posted: 8 May 2010, 0:23:33 UTC - in response to Message 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).
ID: 66026 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
1 · 2 · Next

Message boards : Number crunching : minirosetta 2.11



©2017 University of Washington
http://www.bakerlab.org