minirosetta 2.05

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Profile Conan
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Message 5073 - Posted: 16 Feb 2010, 6:31:04 UTC

Got this Error on five Work Units so far

ERROR: did not find topology_file: beta_lowE.top
ERROR:: Exit from: ..\..\src\protocols\topology_broker\TemplateJumpClaimer.cc line: 93
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

Work Units are 1745497
1745711
1745710
1745699
1745697

Also had

"Error Code 161"
"/file_xfer_error/"

on This WU

They all ran for only a short time before failing.
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Profile Krzychu P.

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Message 5074 - Posted: 16 Feb 2010, 8:06:48 UTC

Task 1746139

At the "stderr out":

<message>
Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
</message>
(...)
ERROR: did not find topology_file: beta_lowE.top
ERROR:: Exit from: ..\..\src\protocols\topology_broker\TemplateJumpClaimer.cc line: 93
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


In the manager message window:
2010-02-16 08:28:03	ralph@home	Starting t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0
2010-02-16 08:28:06	ralph@home	[task_debug] task_state=EXECUTING for t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0 from start
2010-02-16 08:28:06	ralph@home	Starting task t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0 using minirosetta version 205
2010-02-16 08:28:13	ralph@home	update requested by user
2010-02-16 08:28:24	ralph@home	[task_debug] Process for t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0 exited
2010-02-16 08:28:24	ralph@home	[task_debug] task_state=EXITED for t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0 from handle_exited_app
2010-02-16 08:28:24	ralph@home	[task_debug] result state=COMPUTE_ERROR for t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0 from CS::report_result_error
2010-02-16 08:28:24	ralph@home	[task_debug] Process for t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0 exited
2010-02-16 08:28:24	ralph@home	[task_debug] exit code 1 (0x1): Niepoprawna funkcja. (0x1)
2010-02-16 08:28:24	ralph@home	Computation for task t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0 finished
2010-02-16 08:28:24	ralph@home	Output file t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0_0 for task t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0 absent
2010-02-16 08:28:24	ralph@home	[task_debug] result state=COMPUTE_ERROR for t290__boinc__sel_core_1.5.broker_corebuild_tex_IGNORE_THE_REST_14338_8_0 from CS::app_finished

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Tonno

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Message 5075 - Posted: 16 Feb 2010, 8:34:12 UTC - in response to Message 5074.  

ERROR: Option file open failed for: relax_options_lr5_rama09_mix01_it03_run01_A_yfsong

1744059
1744057
1743941
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Profile [VENETO] boboviz

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Message 5076 - Posted: 16 Feb 2010, 14:36:52 UTC

1742734
1742963

<message>
<file_xfer_error> <file_name>igfhum_brub1_2dsrI_3FLG_ProteinInterfaceDesign_12Feb2010_14326_1_1_0
</file_name>
<error_code>-161</error_code>
</file_xfer_error>
</message>
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Tonno

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Message 5077 - Posted: 16 Feb 2010, 23:34:05 UTC - in response to Message 5076.  

1746875
<core_client_version>6.10.32</core_client_version>
<![CDATA[
<message>
Input file t286__boinc_corebuild_round2_rerun_sel_core_1.5.broker_corebuild_tex.boinc.flags missing or invalid: -119
</message>
]]>
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svincent

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Message 5078 - Posted: 19 Feb 2010, 1:05:34 UTC

Some recent failures on Mac OS X

1749862
1749890
1749891

all failed as follows:

ERROR: start_res != middle_res
ERROR:: Exit from: src/protocols/moves/KinematicMover.cc line: 132
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>

1749898

failed differently

SIGPIPE: write on a pipe with no reader
0 0x006e2839 SIGPIPE: write on a pipe with no reader
1 0x00338ace SIGPIPE: write on a pipe with no reader

etc.

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Message 5079 - Posted: 19 Feb 2010, 8:19:06 UTC

1749893


- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x007E4651 read attempt to address 0x00000008

Engaging BOINC Windows Runtime Debugger...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x007E4651 read attempt to address 0x00000008

- Registers -
eax=00000000 ebx=00000000 ecx=017fe47c edx=07886300 esi=017f9d38 edi=00c08198
eip=007e4651 esp=017f8ffc ebp=017f9730
cs=001b ss=0023 ds=0023 es=0023 fs=003b gs=0000 efl=00010246

- Callstack -
ChildEBP RetAddr Args to Child
017f9730 0074785d 017fe47c 40d35fcd 017fe944 017fe47c minirosetta_2.05_windows_intelx!protocols::moves::KinematicMover::apply+0xf (d:\boinc_build\minirosetta_2.04\mini\src\protocols\moves\kinematicmover.cc:343)
017f9f70 006c9d40 017fe47c 40d3570d 078f28f0 00000010 minirosetta_2.05_windows_intelx!protocols::loops::LoopMover_Refine_KIC::apply+0x0 (d:\boinc_build\minirosetta_2.04\mini\src\protocols\loops\loopmover_kic.cc:780)
017fe33c 0068b980 017fe47c 40d32bc1 00000000 00000009 minirosetta_2.05_windows_intelx!protocols::loops::LoopRelaxMover::apply+0x0 (d:\boinc_build\minirosetta_2.04\mini\src\protocols\loops\looprelaxmover.cc:740)
017fed44 00405754 00000001 40d32551 00001db0 00000002 minirosetta_2.05_windows_intelx!protocols::loops::LoopRelax_main+0x0 (d:\boinc_build\minirosetta_2.04\mini\src\protocols\loops\loopbuild.cc:283)
017feedc 00405bb5 00000021 017feef4 000b2300 017feef4 minirosetta_2.05_windows_intelx!main+0x7 (d:\boinc_build\minirosetta_2.04\mini\src\apps\public\boinc\minirosetta.cc:197)
017ffef0 00418647 00400000 00000000 000b2342 0000000a minirosetta_2.05_windows_intelx!WinMain+0x0 (d:\boinc_build\minirosetta_2.04\mini\src\apps\public\boinc\minirosetta.cc:264)
017fff88 768b1174 7ffdf000 017fffd4 7716b3f5 7ffdf000 minirosetta_2.05_windows_intelx!__tmainCRTStartup+0x1c (f:\sp\vctools\crt_bld\self_x86\crt\src\crt0.c:324)
017fff94 7716b3f5 7ffdf000 47b5e9f0 00000000 00000000 kernel32!@BaseThreadInitThunk@12+0x0 (f:\sp\vctools\crt_bld\self_x86\crt\src\crt0.c:324)
017fffd4 7716b3c8 004186b0 7ffdf000 00000000 00000000 ntdll!___RtlUserThreadStart@8+0x0 (f:\sp\vctools\crt_bld\self_x86\crt\src\crt0.c:324)
017fffec 00000000 004186b0 7ffdf000 00000000 00000000 ntdll!__RtlUserThreadStart@8+0x0 (f:\sp\vctools\crt_bld\self_x86\crt\src\crt0.c:324)

*** Dump of thread ID 2892 (state: Initialized): ***

- Information -
Status: Base Priority: Normal, Priority: Normal, , Kernel Time: 0.000000, User Time: 0.000000, Wait Time: 0.000000

- Registers -
eax=03c2f880 ebx=00000000 ecx=00000005 edx=0000007c esi=03c2ff48 edi=00000000
eip=771564f4 esp=03c2ff04 ebp=03c2ff6c
cs=001b ss=0023 ds=0023 es=0023 fs=003b gs=0000 efl=00000206

- Callstack -
ChildEBP RetAddr Args to Child
03c2ff00 77154c1c 753a1876 00000000 03c2ff48 4267f096 ntdll!_KiFastSystemCallRet@0+0x0 FPO: [0,0,0]
03c2ff04 753a1876 00000000 03c2ff48 4267f096 00000000 ntdll!_ZwDelayExecution@8+0x0 FPO: [2,0,0]
03c2ff6c 753a1818 00000064 00000000 03c2ff94 004088ab KERNELBASE!_SleepEx@8+0x0
03c2ff7c 004088ab 00000064 00000000 768b1174 00000000 KERNELBASE!_Sleep@4+0x0
03c2ff88 768b1174 00000000 03c2ffd4 7716b3f5 00000000 minirosetta_2.05_windows_intelx!timer_thread+0x0 (d:\boinc_build\minirosetta_2.04\mini\external\boinc\api\boinc_api.cpp:922)
03c2ff94 7716b3f5 00000000 4508e9f0 00000000 00000000 kernel32!@BaseThreadInitThunk@12+0x0 (d:\boinc_build\minirosetta_2.04\mini\external\boinc\api\boinc_api.cpp:922)
03c2ffd4 7716b3c8 004088a0 00000000 00000000 00000000 ntdll!___RtlUserThreadStart@8+0x0 (d:\boinc_build\minirosetta_2.04\mini\external\boinc\api\boinc_api.cpp:922)
03c2ffec 00000000 004088a0 00000000 00000000 fb8de5f8 ntdll!__RtlUserThreadStart@8+0x0 (d:\boinc_build\minirosetta_2.04\mini\external\boinc\api\boinc_api.cpp:922)

*** Dump of thread ID 3452 (state: Initialized): ***

- Information -
Status: Base Priority: Normal, Priority: Normal, , Kernel Time: 0.000000, User Time: 0.000000, Wait Time: 0.000000

- Registers -
eax=094dfe28 ebx=075d7900 ecx=094de734 edx=000000b9 esi=094dfdfc edi=00000000
eip=771564f4 esp=094dfdb8 ebp=094dfe20
cs=001b ss=0023 ds=0023 es=0023 fs=003b gs=0000 efl=00000206

- Callstack -
ChildEBP RetAddr Args to Child
094dfdb4 77154c1c 753a1876 00000000 094dfdfc 48e8f1da ntdll!_KiFastSystemCallRet@0+0x0 FPO: [0,0,0]
094dfdb8 753a1876 00000000 094dfdfc 48e8f1da 000000bb ntdll!_ZwDelayExecution@8+0x0 FPO: [2,0,0]
094dfe20 753a1818 000007d0 00000000 768aef66 006a42d1 KERNELBASE!_SleepEx@8+0x0
094dfe30 006a42d1 000007d0 48e136cd 00000000 075d7908 KERNELBASE!_Sleep@4+0x0
094dff40 006a44e7 00000000 00414e2c 00000000 48e1370d minirosetta_2.05_windows_intelx!protocols::boinc::watchdog::main_watchdog+0x0 (d:\boinc_build\minirosetta_2.04\mini\src\protocols\boinc\watchdog.cc:316)
094dff48 00414e2c 00000000 48e1370d 00000000 075d7908 minirosetta_2.05_windows_intelx!protocols::boinc::watchdog::main_watchdog_windows+0x7 (d:\boinc_build\minirosetta_2.04\mini\src\protocols\boinc\watchdog.cc:94)
094dff80 00414ed1 00000000 768b1174 075d7908 094dffd4 minirosetta_2.05_windows_intelx!_callthreadstartex+0x6 (f:\sp\vctools\crt_bld\self_x86\crt\src\threadex.c:348)
094dff88 768b1174 075d7908 094dffd4 7716b3f5 075d7908 minirosetta_2.05_windows_intelx!_threadstartex+0x5 (f:\sp\vctools\crt_bld\self_x86\crt\src\threadex.c:326)
094dff94 7716b3f5 075d7908 4f87e9f0 00000000 00000000 kernel32!@BaseThreadInitThunk@12+0x0 (f:\sp\vctools\crt_bld\self_x86\crt\src\threadex.c:326)
094dffd4 7716b3c8 00414e52 075d7908 00000000 00000000 ntdll!___RtlUserThreadStart@8+0x0 (f:\sp\vctools\crt_bld\self_x86\crt\src\threadex.c:326)
094dffec 00000000 00414e52 075d7908 00000000 09690000 ntdll!__RtlUserThreadStart@8+0x0 (f:\sp\vctools\crt_bld\self_x86\crt\src\threadex.c:326)


*** Debug Message Dump ****
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Profile Conan
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Message 5080 - Posted: 19 Feb 2010, 8:52:31 UTC

Had the following Error message

ERROR: start_res != middle_res
ERROR:: Exit from: ..\..\src\protocols\moves\KinematicMover.cc line: 132
BOINC:: Error reading and gzipping output datafile: default.out

It was on 1749596
1749597
1749598
1749871

Happened after only a couple of hundred seconds.
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Profile [VENETO] boboviz

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Message 5081 - Posted: 26 Feb 2010, 8:05:31 UTC
Last modified: 26 Feb 2010, 8:10:59 UTC

1544269
1544268
1544270
1544271

After different calculation times, all the same error:

ERROR: [ERROR] Unable to open constraints file: aqp9_.dist_csts
ERROR:: Exit from: ..\..\src\core\scoring\constraints\ConstraintIO.cc line: 332
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish
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AdeB
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Message 5082 - Posted: 26 Feb 2010, 23:06:22 UTC - in response to Message 5081.  

1544269
1544268
1544270
1544271

After different calculation times, all the same error:

ERROR: [ERROR] Unable to open constraints file: aqp9_.dist_csts
ERROR:: Exit from: ..\..\src\core\scoring\constraints\ConstraintIO.cc line: 332
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


Same error in task 1750870.

AdeB
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Profile [VENETO] boboviz

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Message 5083 - Posted: 3 Mar 2010, 6:45:02 UTC

A lot of validate error

1755041
1755043
1755051
etc, etc, etc
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Cyph3r
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Message 5087 - Posted: 11 Mar 2010, 14:46:36 UTC
Last modified: 11 Mar 2010, 15:10:25 UTC

I had the following error message:
1757476

SIGSEGV: segmentation violation
Stack trace (17 frames):
[0x96c49b3]
[0x96ee888]
[0xf7f90400]
[0x8d2a923]
[0x8d2aaf2]
[0x8d6efb3]
[0x8c49cb5]
[0x8f95cf0]
[0x88b5050]
[0x88b97a6]
[0x873763f]
[0x812a54a]
[0x812b82d]
[0x86aa16b]
[0x8049a26]
[0x974c15c]
[0x8048121]

Exiting...
------------//------------
and:
1757331

*** glibc detected *** free(): invalid pointer: 0xec562de1 ***
SIGABRT: abort called
Stack trace (20 frames):
[0x96c49b3]
[0x96ee888]
[0xf7fef400]
[0x97532d4]
[0x9768fc2]
[0x976def3]
[0x976e3bb]
[0x973e0c1]
[0x81bdfb1]
[0x902371b]
[0x8486f0d]
[0x900bc5c]
[0x8f9b5d9]
[0x8627747]
[0x812a167]
[0x812b82d]
[0x86aa16b]
[0x8049a26]
[0x974c15c]
[0x8048121]

Exiting...


Other WUs in the same machine (Linux have similar errors:

1758427
1757675
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Evan

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Message 5088 - Posted: 11 Mar 2010, 18:02:44 UTC

100% validate errors (11 out of 11) using win xp and the hard drive is going continuously as it processes 4 units at a time. The work units are fcDE-W3.....
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Message 5089 - Posted: 11 Mar 2010, 20:32:27 UTC

I wouldn't be surprised if there is going to be a chorus of complaints from the Rosetta users about the way these fcDE-W3.. units are hogging the hard drive. I have found that if you want to open files, access the internet etc you have to put boinc on snooze because the hard drive is otherwise occupied. The task manager shows the processors changing from 0 to 100% at very frequent intervals. In the past the indicator show a steady 100%. To top it all, the validation error is still staying at a constant 100%.
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Message 5090 - Posted: 12 Mar 2010, 0:04:01 UTC

While the validate errors seem to have been corrected (at least the ones I am processing now), they all have quite short run times and ALL of them process 10,000 Decoys then finish.

This is a new record, it is the most decoys I have seen since I started this project (I certain I think).

Looks like this is an inbuilt maximum number of decoys that can be processed for a work unit.
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Message 5091 - Posted: 12 Mar 2010, 9:27:07 UTC - in response to Message 5090.  

While the validate errors seem to have been corrected (at least the ones I am processing now)


I hope.....
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Tonno

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Message 5092 - Posted: 12 Mar 2010, 11:51:21 UTC - in response to Message 5091.  

The "fcDE-W3" WUs have something wrong.
The graphics show only one structure of three and the stage and energy are always at "zero".

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Message 5093 - Posted: 13 Mar 2010, 6:40:13 UTC

A gunn-fragments error:

1759776

ERROR: ct == final_atoms
ERROR:: Exit from: ..\..\src\core\scoring\rms_util.cc line: 397
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


and,usualy, a tons of validate error in fcDE-W3 wu.....
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Message 5094 - Posted: 15 Mar 2010, 19:07:06 UTC - in response to Message 5092.  

thanks for pointing this one out. We are working on a fix for those jobs.
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Profile [VENETO] boboviz

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Message 5096 - Posted: 16 Mar 2010, 20:58:35 UTC

As usual, validate errors
1765734
1765727
1765728

Most of errors are on my Phaenom II X4 (and windows 7)....problems with L3 cache? SSE extension?
No problems with Turion X2 (windows 7) or Amd Mobile single core (windows xp).

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