Problems with Minirosetta Version 1.67

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Mod.Sense
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Message 61074 - Posted: 9 May 2009, 15:43:07 UTC
Last modified: 9 May 2009, 15:44:50 UTC

Version 1.67 has a nifty new threading mode built in. And corrects some of the validator problems people have reported in prior releases.

Please report any problems with this version in this thread.
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svincent

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Message 61075 - Posted: 9 May 2009, 17:07:46 UTC

I've lost 5 tasks out of 10 with this problem in task termination on Mac. Until it's fixed I'm not crunching any more 1.67 workunits.

Sample task 249815019

and error message fragment

Thread 0 Crashed:
0 ...etta_1.67_i686-apple-darwin 0x00efc966 __ZN7utility7signals9SignalHubIvN4core12conformation7signals16DestructionEventEE11send_signalES5_ + 1870
1 ...etta_1.67_i686-apple-darwin 0x0002a4a7 __ZN4core12conformation12ConformationD1Ev + 7373
2 ...etta_1.67_i686-apple-darwin 0x000910d0 __ZN4core4pose4PoseD1Ev + 4652



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Murasaki
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Message 61078 - Posted: 9 May 2009, 21:55:50 UTC
Last modified: 9 May 2009, 22:03:14 UTC

My second 1.67 work unit appears to have validated correctly, but the log includes the following error message:

ERROR: pose.fold_tree().is_cutpoint( *it )
ERROR:: Exit from: ....srcprotocolstopology_brokerTopologyBroker.cc line: 560
called boinc_finish



Here is the link to the task details: threading_broker_hb_t303__IGNORE_THE_REST_11860_719_0
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Message 61080 - Posted: 10 May 2009, 0:02:51 UTC
Last modified: 10 May 2009, 0:03:14 UTC

lr8_seq_score12_rlbd_1fkb_IGNORE_THE_REST_DECOY_11810_1955_0

graphics box shows no activity with 2hrs and 52 mins to go.
also says stage unknown.
it is on model 55 but stop = 0

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Message 61081 - Posted: 10 May 2009, 0:06:19 UTC

threading_broker_hb_t342__IGNORE_THE_REST_11876_188_0 ran into the famous 0xc error. But my firewall triggered on it. Funny thing is the other tasks before this one did not trigger the firewall.
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Snags

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Message 61095 - Posted: 10 May 2009, 19:43:42 UTC
Last modified: 10 May 2009, 19:47:47 UTC

And another on my Mac as well:

threading_broker_hb_t370__IGNORE_THE_REST_11885_966_0

# cpu_run_time_pref: 36000
SIGBUS: bus error

Crashed executable name: minirosetta_1.67_i686-apple-darwin
built using BOINC library version 6.5.0
Machine type Intel 80486 (32-bit executable)
System version: Macintosh OS 10.5.6 build 9G55
Sun May 10 14:11:14 2009

sh: /usr/bin/atos: No such file or directory
0 0x006c0345 SIGPIPE: write on a pipe with no reader
1 0x004a3d8e SIGPIPE: write on a pipe with no reader
2 0x90a9e2bb SIGPIPE: write on a pipe with no reader
3 0xffffffff SIGPIPE: write on a pipe with no reader
4 0x0002a4a7 SIGPIPE: write on a pipe with no reader
5 0x000910d0 SIGPIPE: write on a pipe with no reader
6 0x00518bdc SIGPIPE: write on a pipe with no reader
7 0x00b59c20 SIGPIPE: write on a pipe with no reader
8 0x0013b70a SIGPIPE: write on a pipe with no reader
9 0x00005a5b SIGPIPE: write on a pipe with no reader
10 0x0000292e SIGPIPE: write on a pipe with no reader
11 0x00002855 SIGPIPE: write on a pipe with no reader
12 0x00000019
Thread 0 crashed with X86 Thread State (32-bit):
eax: 0xffffffe1 ebx: 0x90a66802 ecx: 0xbfffc23c edx: 0x90a321c6
edi: 0x00000000 esi: 0x00000000 ebp: 0xbfffc278 esp: 0xbfffc23c
ss: 0x0000001f efl: 0x00000206 eip: 0x90a321c6 cs: 0x00000007
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037

etc.

From the BOINC message log:
Sun May 10 14:11:16 2009|rosetta@home|Computation for task threading_broker_hb_t370__IGNORE_THE_REST_11885_966_0 finished
Sun May 10 14:11:16 2009|rosetta@home|Output file threading_broker_hb_t370__IGNORE_THE_REST_11885_966_0_0 for task threading_broker_hb_t370__IGNORE_THE_REST_11885_966_0 absent
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Message 61096 - Posted: 10 May 2009, 20:36:32 UTC

This was weird, I had one work task that finished and have a claimed credit of 137.07 but a granted credit of 0.00.
Anybody else have this weird problem?
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Message 61098 - Posted: 10 May 2009, 21:14:39 UTC
Last modified: 10 May 2009, 21:15:53 UTC

Gen X has a 2POIA_BOINC_MPZN_with_zinc_abrelax task showing a Validate state of Workunit error - check skipped from BOINC 6.6.20 in Win XP. But no other errors are shown, and no credit issued.
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Message 61099 - Posted: 10 May 2009, 21:39:26 UTC - in response to Message 61098.  
Last modified: 10 May 2009, 22:09:16 UTC

Gen X has a 2POIA_BOINC_MPZN_with_zinc_abrelax task showing a Validate state of Workunit error - check skipped from BOINC 6.6.20 in Win XP. But no other errors are shown, and no credit issued.


Looking at the workunit details I see "too many total results"
Cruncher #1 missed his deadline, cruncher #2 had a validate error, Gen X becomes cruncher #3, cruncher #1 returns successfully completed wu late but before cruncher #3, cruncher #3(Gen X) misses out.

Cruncher #2 has been given credit presumably because the validate error has been deemed not his fault.

Forgive my hazy memory but hasn't this been discussed before?

Snags

edit: Here's one discussion from 2007

edit#2: Following links from that thread; David E K explains the max results #'s and mentions trying to find a fix and the BOINC trac ticket remains open
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Message 61110 - Posted: 11 May 2009, 16:29:20 UTC

Should the home page be updated to include a link to this thread?
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Message 61115 - Posted: 11 May 2009, 21:19:51 UTC

compute errors

threading_broker_hb_t342__IGNORE_THE_REST_11876_188_0

Log:

-1073741819 (0xc0000005)
Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x0088A3C2 write attempt to address 0x00000000

Engaging BOINC Windows Runtime Debugger...

CPU time 2805.672

and

abinitio_norelax_homfrag__plus_native_1fkb_0001A__SAVE_ALL_OUT_11817_3500_0

Log:

Client state Compute error
Exit status -177 (0xffffff4f)
Computer ID 871217
Report deadline 19 May 2009 6:13:24 UTC
CPU time 0
stderr out

<core_client_version>6.6.20</core_client_version>
<![CDATA[
<message>
Maximum elapsed time exceeded - note: CPU time 0
</message>

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Message 61117 - Posted: 11 May 2009, 22:08:51 UTC

Compute error on this WU:

https://boinc.bakerlab.org/rosetta/result.php?resultid=249863167

Outcome Client error
Client state Compute error
Exit status -1073741819 (0xc0000005)
Computer ID 1043369
Report deadline 18 May 2009 23:41:27 UTC
CPU time 21000.18


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Message 61122 - Posted: 12 May 2009, 6:38:49 UTC
Last modified: 12 May 2009, 6:44:17 UTC

Here's a bizarre one I'd like to throw out there. I installed Windows 7 on an old 40gb 54oo rpm hard drive I have, just to check it out, and of coarse I had to run Rosetta on it. You can see the result under Larry-PC. But I had a problem with it that I cannot explain...after finishing one task, it wouldn't download anymore, saying I needed 14000 kb/mb more room or something like that. Even though I liked the windows 7, since it wouldn't run anymore tasks, and I have 14gb free on the hard drive and at least 1 gb of memory free, I just put my windows XP hard drive back on. But I have been a bit surprised by the granted credit on the one completed task on that OS, as well as the last few on the one I am using now. Same set up as you can see, just different hard drives with different OS on them.

Oh yeah, I forgot to mention that it would only run one work unit one one core instead of 2. that was my first clue that something was funky.
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Message 61125 - Posted: 12 May 2009, 10:05:07 UTC

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Profile [AF>Slappyto] popolito

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Message 61126 - Posted: 12 May 2009, 10:43:10 UTC

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=228717046
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Message 61127 - Posted: 12 May 2009, 11:09:05 UTC

Why am I getting validate errors?

https://boinc.bakerlab.org/rosetta/result.php?resultid=250683203

https://boinc.bakerlab.org/rosetta/result.php?resultid=250621029
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Message 61132 - Posted: 12 May 2009, 13:28:57 UTC - in response to Message 61127.  

i've got 2 validate errors today

https://boinc.bakerlab.org/rosetta/result.php?resultid=250671695
https://boinc.bakerlab.org/rosetta/result.php?resultid=250671693
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Message 61133 - Posted: 12 May 2009, 16:09:51 UTC

woow, in half a day i got a 12 Validate error units vs. 3 correct units. What a mess!
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svincent

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Message 61135 - Posted: 12 May 2009, 17:27:35 UTC

After updating from BOINC 6.2.18 to 6.6.20 I've yet to see the termination error I reported earlier (and shown again below) , although its a pretty small sample size of tasks.

Thread 0 Crashed:
0 ...etta_1.67_i686-apple-darwin 0x00efc966 __ZN7utility7signals9SignalHubIvN4core12conformation7signals16DestructionEventEE11send_signalES5_ + 1870

------

I'm seeing several validation errors though as others are doing: all have exited after quickly doing 99 decoys.


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Mike Tyka

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Message 61137 - Posted: 12 May 2009, 18:04:11 UTC

The validator error has been found: Our data format was changed and the validator was not updated. We're doing that now.


http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Message boards : Number crunching : Problems with Minirosetta Version 1.67



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