Rosetta 4.0+

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Profile [VENETO] boboviz

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Message 91105 - Posted: 11 Sep 2019, 11:57:49 UTC

Again, out of memory on some wus (1092708763, 1092708790, etc) in a 8gb machine (4 wus running)
<core_client_version>7.14.2</core_client_version>
<![CDATA[
<message>
(unknown error) - exit code -529697949 (0xe06d7363)</message>
<stderr_txt>

Unhandled Exception Detected...
- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x75653442

Engaging BOINC Windows Runtime Debugger...

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James W

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Message 91108 - Posted: 12 Sep 2019, 7:00:46 UTC

Application version: Rosetta v4.07 windows_intelx86
Device: 3710630, Task: 1091771140, and WU 983399738.
Name: rb_09_05_8094_8054__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_866427_129_0
Status: Error while computing
Exit status: 1 (0x00000001) Unknown error code
<core_client_version>7.14.2</core_client_version>
Incorrect function. (0x1) - exit code 1 (0x1)
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_intelx86.exe -run:protocol jd2_scripting @flags_rb_09_05_8094_8054__t000__0_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_09_05_8094_8054__t000__0_C1_robetta.zip -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3783518
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James W

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Message 91109 - Posted: 12 Sep 2019, 7:17:07 UTC

These WUs/tasks on same host with same errors:

Application version: Rosetta v4.07 windows_intelx86
Device: 3710630, Task: 1091771191, and WU 983399763.
Names:
rb_09_05_8094_8054__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_866427_129_0
rb_09_05_8094_8054__t000__3_C1_SAVE_ALL_OUT_IGNORE_THE_REST_866427_131_0
Status: Error while computing
Exit status: 1 (0x00000001) Unknown error code
<core_client_version>7.14.2</core_client_version>
Incorrect function. (0x1) - exit code 1 (0x1)
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_intelx86.exe -run:protocol jd2_scripting @flags_rb_09_05_8094_8054__t000__3_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_09_05_8094_8054__t000__3_C1_robetta.zip -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3781716
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Message 91110 - Posted: 12 Sep 2019, 7:32:19 UTC
Last modified: 12 Sep 2019, 7:40:40 UTC

Application version: Rosetta v4.07 windows_intelx86
Device: 3710630, Task: 1091771058, and WU 983399675.
Name: rb_09_05_8094_8054__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_866427_110_0
Status: Error while computing
Exit status: -529697949 (0xE06D7363) Unknown error code
[CDATA[<message>
(unknown error) - exit code -529697949 (0xe06d7363)</message><stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_intelx86.exe -run:protocol jd2_scripting @flags_rb_09_05_8094_8054__t000__0_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_09_05_8094_8054__t000__0_C1_robetta.zip -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3783537

Unhandled Exception Detected...
Unhandled Exception Record -
Reason: Out Of Memory(C++ Exception) (0xe06d7363) at address 0x761BC5AF

Engaging BOINC Windows Runtime Debugger...

Same error with task 1091771102 and WU 983399704
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Jim1348

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Message 91112 - Posted: 12 Sep 2019, 12:04:32 UTC - in response to Message 91110.  

Reason: Out Of Memory(C++ Exception) (0xe06d7363) at address 0x761BC5AF

You have 4 GB of memory. Windows will need 1 GB, and each work unit can take 1 GB (sometimes more).
So don't run more than three at a time.
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Message 91139 - Posted: 21 Sep 2019, 20:18:03 UTC - in response to Message 91112.  

Reason: Out Of Memory(C++ Exception) (0xe06d7363) at address 0x761BC5AF

You have 4 GB of memory. Windows will need 1 GB, and each work unit can take 1 GB (sometimes more).


No. It's a 8gb machine (Intel(R) Core(TM) i7-6700 CPU, memory 8088.59 MB)
So, i have to crunch 3 wus with 8 gb of ram?
I think it's better if they work on memory optimization/pointers/etc
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Message 91140 - Posted: 21 Sep 2019, 20:21:29 UTC - in response to Message 91109.  
Last modified: 21 Sep 2019, 20:23:38 UTC

Exit status: 1 (0x00000001) Unknown error code
<core_client_version>7.14.2</core_client_version>
Incorrect function. (0x1) - exit code 1 (0x1)
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_intelx86.exe -run:protocol jd2_scripting @flags_rb_09_05_8094_8054__t000__3_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_09_05_8094_8054__t000__3_C1_robetta.zip -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3781716


A lot of this error today
(my run time prefernce is 2hs, this error arrive after 5/6hs)
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Message 91141 - Posted: 21 Sep 2019, 21:07:24 UTC - in response to Message 91139.  

Reason: Out Of Memory(C++ Exception) (0xe06d7363) at address 0x761BC5AF

You have 4 GB of memory. Windows will need 1 GB, and each work unit can take 1 GB (sometimes more).


No. It's a 8gb machine (Intel(R) Core(TM) i7-6700 CPU, memory 8088.59 MB)
So, i have to crunch 3 wus with 8 gb of ram?
I think it's better if they work on memory optimization/pointers/etc

I was referring to the post by James W. His machine is 4 GB.
https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=3710630
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Profile [VENETO] boboviz

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Message 91142 - Posted: 21 Sep 2019, 21:47:26 UTC - in response to Message 91141.  

I was referring to the post by James W. His machine is 4 GB.
https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=3710630


Ah, ok.
I notice that, despite "out of memory" error, i have over 6gb of free ram during crunch, so it seems that is not a problem of lack of memory.
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Message 91143 - Posted: 21 Sep 2019, 22:15:50 UTC - in response to Message 91142.  
Last modified: 21 Sep 2019, 22:18:19 UTC

I was referring to the post by James W. His machine is 4 GB.
https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=3710630


Ah, ok.
I notice that, despite "out of memory" error, i have over 6gb of free ram during crunch, so it seems that is not a problem of lack of memory.

Check if you've limited how much memory BOINC is allowed to use.

Also check is the operating system (probably Windows) is running in 32-bit mode, where it can't reach more than 4 GB of memory even if more if present.

Also, is the application program is running in 32-bit mode?
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Message 91146 - Posted: 22 Sep 2019, 7:16:18 UTC - in response to Message 91143.  

Check if you've limited how much memory BOINC is allowed to use.

No, this is not the problem. I've set 95% of use of ram.

Also check is the operating system (probably Windows) is running in 32-bit mode, where it can't reach more than 4 GB of memory even if more if present.

No. I'm using Win10 64 bit and system see correctly all ram.

Also, is the application program is running in 32-bit mode?

No, application is 64 bit, but we know that window's app version is not 64 bit native.

I think it's only a problem of ram pointers in c++
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Message 91166 - Posted: 27 Sep 2019, 17:14:48 UTC
Last modified: 27 Sep 2019, 17:25:21 UTC

I am aborting any and all 4.07 tasks. They don't work on my pc.
Instead of counting down, they reach around 40% and count up.
Useless for me to waste my cpu time on these.

Can someone explain the name of the application version name: Rosetta v4.07
windows_intelx86?

Is this an version oriented towards INTEL chips or what?
I have a 50% or there about rate of success with these applications.

BTW...someone should tell the webmaster who writes the code for the user section, to give us the option to select which versions we want to run. How can I opt out of 4.07 Intel?
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Message 91168 - Posted: 28 Sep 2019, 8:51:29 UTC - in response to Message 91166.  

Can someone explain the name of the application version name: Rosetta v4.07
windows_intelx86?
Is this an version oriented towards INTEL chips or what?


No. Intel X86 is a generic name of x86 architecture of cpu, it's not strictly referred to hw producer.
Also AMD have the x86 architecture.
X86
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Message 91178 - Posted: 30 Sep 2019, 6:33:29 UTC

Well no wonder 4.07 takes so long. There is lots of wasted time.
I had a look at one task running on my system, the searching box ran blank for 4 cycles before I closed it.
That's a lot of wasted time.
It's no wonder it takes 15 hrs to run on my system!

Is this a bug or is it just not finding anything to chart?
Seems weird because I thought ALL TASKS ALWAYS had something in the searching box.
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Message 91263 - Posted: 14 Oct 2019, 7:00:48 UTC

1099036469

ERROR: Assertion `std::abs( coordsys_rot.det() - 1.0 ) < 1e-6` failed.
ERROR:: Exit from: ..\..\..\src\core\pose\symmetry\util.cc line: 898
BOINC:: Error reading and gzipping output datafile: default.out
08:56:33 (7860): called boinc_finish(1)

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Message 91307 - Posted: 27 Oct 2019, 14:25:31 UTC

A lot of errors, of two kind.
- First, 1101585441, 11015854472, etc
<message>
finish file present too long</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_x86_64.exe -run:protocol jd2_scripting @flags_rb_10_25_9050_10061__t000__1_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_10_25_9050_10061__t000__1_C1_robetta.zip -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1411942
Starting watchdog...
Watchdog active.
13:30:14 (11536): Can't acquire lockfile (32) - waiting 35s
13:30:49 (11536): Can't acquire lockfile (32) - exiting
3:30:49 (11536): Error: Cannot acces to file. File &#232; is used by another process.


- Second, 11015854410, 1101585496, etc
<message>
(unknown error) - exit code -1073741819 (0xc0000005)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_x86_64.exe -run:protocol jd2_scripting @flags_rb_10_25_9050_10061__t000__1_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_10_25_9050_10061__t000__1_C1_robetta.zip -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1411949
Starting watchdog...
Watchdog active.

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x000000000000000F

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Message 91329 - Posted: 3 Nov 2019, 9:37:30 UTC

Again, a lot of memory errors
Es.
- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x00007FFAC4FFA839

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Message 91371 - Posted: 16 Nov 2019, 21:30:28 UTC

Some access violation
1105155391
1105155820
etc

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address...............

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Message 91374 - Posted: 17 Nov 2019, 8:38:41 UTC

And, today a lot of these:
1105146565

Watchdog active.
00:59:19 (1876): Can't acquire lockfile (32) - waiting 35s
00:59:54 (1876): Can't acquire lockfile (32) - exiting
00:59:54 (1876): Error: Cannot access to file. File &#232; is used by another process.

(0x20)
01:19:49 (2452): Can't acquire lockfile (32) - waiting 35s
======================================================
DONE :: 1 starting structures 7209.45 cpu seconds
This process generated 218 decoys from 218 attempts
======================================================
BOINC :: WS_max 2.79945e+08

BOINC :: Watchdog shutting down...
01:20:04 (8408): called boinc_finish(0)

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Breakpoint Encountered (0x80000003) at address 0x00007FFB903A0192

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Message 91375 - Posted: 17 Nov 2019, 10:53:58 UTC
Last modified: 17 Nov 2019, 10:55:35 UTC

many WU like these in the last few days: 11051374411

<core_client_version>7.12.1</core_client_version>
<![CDATA[
<message>
(unknown error) - exit code -529697949 (0xe06d7363)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_intelx86.exe -run:protocol jd2_scripting @flags_rb_11_15_11159_11207__t000__0_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_11_15_11159_11207__t000__0_C1_robetta.zip -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1246077
Starting watchdog...
Watchdog active.


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x7680C5AF


RAM requirements more then 3 GB / WU ... isn't fun anymore
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