Minirosetta 3.54

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sgaboinc

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Message 78043 - Posted: 16 Mar 2015, 12:43:31 UTC
Last modified: 16 Mar 2015, 12:45:36 UTC

minirosetta_3.54_x86_64-pc-linux-gnu
Linux 3.11.6 x86_64 GNU/Linux
Suse Linux 13.1
Intel(R) Core(TM) i7-4771 CPU @ 3.50GHz ASUS H87-Pro

so far so good, no errors after about 20-30 jobs
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sgaboinc

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Message 78047 - Posted: 19 Mar 2015, 2:01:52 UTC
Last modified: 19 Mar 2015, 2:03:47 UTC

foldit_2000402_0000_fold_and_dock_SAVE_ALL_OUT_245631_6672_1
https://boinc.bakerlab.org/rosetta/workunit.php?wuid=655680893

https://boinc.bakerlab.org/rosetta/result.php?resultid=724631548
SIGSEGV: segmentation violation

https://boinc.bakerlab.org/rosetta/result.php?resultid=723811914
Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x00E83207 read attempt to address 0x3F2D1720
--------
errors for this particular task
other tasks completed without errors
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Killersocke@rosetta

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Message 78050 - Posted: 21 Mar 2015, 14:11:28 UTC

Client state: Compute error

Workunits:

656971493
Task ID 725226351

656976823
Task ID 725232167

656977330
Task ID 725232713

656985825
Task ID 725241846

656990110
Task ID 725246508

656991178
Task ID 725247675

656992427
Task ID 725249048

656993656
Task ID 725250457

stderr out
<core_client_version>7.4.36</core_client_version>
<![CDATA[
<message>
app_version download error: couldn\'t get input files:
<file_xfer_error>
<file_name>minirosetta_3.54_windows_x86_64.exe</file_name>
<error_code>-120 (RSA key check failed for file)</error_code>
<error_message>signature verification failed</error_message>
</file_xfer_error>

</message>
]]>


Think i\'ll stop my work :-(
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jesse1919

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Message 78051 - Posted: 21 Mar 2015, 20:51:56 UTC

It will not use full CPU time- only ~15%. Have it set at 99% and it usually does that. 8 tasks are \"running\" however only 1 actually has progress % increasing. So obviously it\'s only really running one core. I also just upgraded BIONIC to 7.4.36. The tasks no longer show up in the task manager> Processes. No process is > 1% CPU. RAM is OK, 4/6 GB. WIN7-64, I7-940.
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jesse1919

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Message 78054 - Posted: 23 Mar 2015, 0:45:29 UTC - in response to Message 78051.  

It will not use full CPU time- only ~15%. Have it set at 99% and it usually does that. 8 tasks are \"running\" however only 1 actually has progress % increasing. So obviously it\'s only really running one core. I also just upgraded BIONIC to 7.4.36. The tasks no longer show up in the task manager> Processes. No process is > 1% CPU. RAM is OK, 4/6 GB. WIN7-64, I7-940.


update. I tried World Community Grid tasks and they run to about 1.1% complete and then they reset to 0% complete and 0 time elapsed. This time it is actually using 100% CPU on 8 WCG tasks. Apparently it\'s not useful work if they keep restarting. So it\'s definitely a Bionic issue.

Been running 24/7 for years...shutting it down.

I posted this on the Bionic forum too.
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Arnaud

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Message 78055 - Posted: 23 Mar 2015, 9:02:53 UTC

Hello everyone,

I wanted to report a problem that I had with the previous version too (3.52).
My machine is configured to calculate during the night. But in the morning when I arrive at work, calculations are stopped but minirosetta programs are still in memory (and after a weekend, they take 12GB).
Every morning I have to kill them in the task manager.

Other projects programs close properly.

I am running Windows 8 Pro X64, admin of my machine.

Thank you for reading,

Arnaud P.
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Message 78058 - Posted: 23 Mar 2015, 21:32:54 UTC - in response to Message 78055.  

Hello everyone,

I wanted to report a problem that I had with the previous version too (3.52).
My machine is configured to calculate during the night. But in the morning when I arrive at work, calculations are stopped but minirosetta programs are still in memory (and after a weekend, they take 12GB).
Every morning I have to kill them in the task manager.

Other projects programs close properly.

I am running Windows 8 Pro X64, admin of my machine.

Thank you for reading,

Arnaud P.



Arnaud, if you run multiple projects, and the BOINC Manager has cycled to the others, then the suspended R@h tasks show on the task list (when you have selected the option for tasks to remain \"in memory\"). But if BOINC is not actively running the tasks, they are quickly swapped out until they resume. In your case, you may be achieving the same thing by your time of day settings on when to use CPU. But by cancelling the tasks each morning, you are losing everything that has been done since the last checkpoint was reached.

Does the existence of these tasks seem to interfere in some way with other work on the machine?
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Arnaud

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Message 78065 - Posted: 26 Mar 2015, 12:40:52 UTC - in response to Message 78058.  



Arnaud, if you run multiple projects, and the BOINC Manager has cycled to the others, then the suspended R@h tasks show on the task list (when you have selected the option for tasks to remain \"in memory\"). But if BOINC is not actively running the tasks, they are quickly swapped out until they resume. In your case, you may be achieving the same thing by your time of day settings on when to use CPU. But by cancelling the tasks each morning, you are losing everything that has been done since the last checkpoint was reached.

Does the existence of these tasks seem to interfere in some way with other work on the machine?



Hi David,

I unchecked the box to keep them in memory applications (already done).
And yes, these tasks bother me when they are in memory as they take (cumulative) many gygabytes of RAM memory (like 12).
During the night it does not bother me; During the day, I need all my RAM :)

When the BOINC Manager cycles, the other projects (other than Rosetta) close well.

I am running Windows 8.1 Pro x64.

I have the same problem if I tell the BOINC Manager calculated without taking into account the préférences (during the day for example), and then I told him to follow the preferences. Only Rosetta tasks remain in memory. Other close.

Greetings,
Arnaud
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Message 78067 - Posted: 27 Mar 2015, 0:49:44 UTC

That sounds like BOINC Manager is not properly removing the application from memory then. But it should not impact the performance of your machine, because when the tasks are not running, the memory gets swapped out to disk.

Has anyone heard of such memory allocation issues in BOINC 7.4.36 on Windows 8.1?
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Arnaud

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Message 78100 - Posted: 8 Apr 2015, 8:47:42 UTC - in response to Message 78067.  

That sounds like BOINC Manager is not properly removing the application from memory then. But it should not impact the performance of your machine, because when the tasks are not running, the memory gets swapped out to disk.

Has anyone heard of such memory allocation issues in BOINC 7.4.36 on Windows 8.1?


Am I the only one?? :)

In the task manager, the memory used by the Rosetta applications is not marked as swapped out to disk.

In any case, I found how to solve the problem.
It occurs when the application processes a \"out of time\" request. By removing this requests (I do not know why I have them), the problem no longer occurs.

Thanks you for your answers

Arnaud
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svincent

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Message 78145 - Posted: 21 Apr 2015, 16:27:49 UTC

Task 731275755
( R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0005_fold_and_dock_SAVE_ALL_OUT_263848_834_0 )
got stuck getting no CPU time and I aborted it.

Properties were:

CPU time at last checkpoint : 8:06
CPU time : 8.39
Elapsed time : 11:55:19
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Profile [VENETO] boboviz

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Message 78146 - Posted: 21 Apr 2015, 17:51:15 UTC

A lot of invalid wus like this
731222459


ERROR: std::abs( coordsys_rot.det() - 1.0 ) < 1e-6
ERROR:: Exit from: ..\\..\\..\\src\\core\\pose\\symmetry\\util.cc line: 889
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TeligentEMS

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Message 78149 - Posted: 23 Apr 2015, 1:15:27 UTC

I have a machine running WU 731205450 and I\'m starting to get concerned about it. It\'s been running this task for about 50 hours and BOINC reports that there are still 665 hours to go. If that\'s even remotely correct, the deadline (5/4) is in doubt. Do I abort?
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Message 78150 - Posted: 23 Apr 2015, 1:44:58 UTC
Last modified: 23 Apr 2015, 1:46:58 UTC

I installed BOINC 7.4.42 yesterday. This evening when I got on my computer, I found 5 crash tabs for Minirosetta on the task bar. While I was checking the event log, another one popped up. This time, the WU (662459755) errored out completely.

Event log contents for Rosetta (sorry for the screen kludge; spoiler tags didn\'t work):

4/21/2015 2:45:04 PM | | Starting BOINC client version 7.4.42 for windows_x86_64
4/21/2015 2:45:04 PM | | log flags: file_xfer, sched_ops, task
4/21/2015 2:45:04 PM | | Libraries: libcurl/7.39.0 OpenSSL/1.0.1j zlib/1.2.8
4/21/2015 2:45:04 PM | | Data directory: C:\\ProgramData\\BOINC
4/21/2015 2:45:04 PM | | Running under account Dee
4/21/2015 2:45:04 PM | | CUDA: NVIDIA GPU 0: GeForce GT 610 (driver version 344.75, CUDA version 6.5, compute capability 2.1, 1024MB, 933MB available, 156 GFLOPS peak)
4/21/2015 2:45:04 PM | | OpenCL: NVIDIA GPU 0: GeForce GT 610 (driver version 344.75, device version OpenCL 1.1 CUDA, 1024MB, 933MB available, 156 GFLOPS peak)
4/21/2015 2:45:04 PM | | OpenCL CPU: Intel(R) Pentium(R) CPU G645 @ 2.90GHz (OpenCL driver vendor: Intel(R) Corporation, driver version 1.1, device version OpenCL 1.1 (Build 31360.31441))
4/21/2015 2:45:04 PM | | Host name: Dee-PC
4/21/2015 2:45:04 PM | | Processor: 2 GenuineIntel Intel(R) Pentium(R) CPU G645 @ 2.90GHz [Family 6 Model 42 Stepping 7]
4/21/2015 2:45:04 PM | | Processor features: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss htt tm pni ssse3 cx16 sse4_1 sse4_2 popcnt syscall nx lm vmx tm2 pbe
4/21/2015 2:45:04 PM | | OS: Microsoft Windows 7: Home Premium x64 Edition, Service Pack 1, (06.01.7601.00)
4/21/2015 2:45:04 PM | | Memory: 3.97 GB physical, 7.94 GB virtual
4/21/2015 2:45:04 PM | | Disk: 465.66 GB total, 113.33 GB free
4/21/2015 2:45:04 PM | | Local time is UTC -6 hours
4/21/2015 2:45:04 PM | | VirtualBox version: 4.3.12
4/21/2015 2:45:04 PM | | Config: don\'t use GPUs while Frozen Throne.exe is running
4/21/2015 2:45:04 PM | | Config: don\'t use GPUs while StarCraft.exe is running
4/21/2015 2:45:04 PM | | Config: don\'t use GPUs while war3.exe is running
4/21/2015 2:45:04 PM | | Config: don\'t use GPUs while Wing Commander Saga.exe is running
4/21/2015 2:45:04 PM | | Config: don\'t use GPUs while Wow.exe is running
4/21/2015 2:45:04 PM | | Config: don\'t use GPUs while Bethesda.net_Launcher.exe is running
4/21/2015 2:45:04 PM | | Config: don\'t use GPUs while launcher.exe is running
4/21/2015 2:45:04 PM | | Config: don\'t use GPUs while Oblivion.exe is running
4/21/2015 2:45:04 PM | rosetta@home | URL http://boinc.bakerlab.org/rosetta/; Computer ID 1624591; resource share 100
4/21/2015 2:45:04 PM | | Reading preferences override file
4/21/2015 2:45:04 PM | | Preferences:
4/21/2015 2:45:04 PM | | max memory usage when active: 2032.67MB
4/21/2015 2:45:04 PM | | max memory usage when idle: 4065.34MB
4/21/2015 2:45:04 PM | | max disk usage: 7.00GB
4/21/2015 2:45:04 PM | | suspend work if non-BOINC CPU load exceeds 65%
4/21/2015 2:45:04 PM | | (to change preferences, visit a project web site or select Preferences in the Manager)
4/21/2015 2:45:04 PM | | Not using a proxy
4/21/2015 2:45:41 PM | rosetta@home | Sending scheduler request: To report completed tasks.
4/21/2015 2:45:41 PM | rosetta@home | Reporting 1 completed tasks
4/21/2015 2:45:41 PM | rosetta@home | Requesting new tasks for NVIDIA GPU
4/21/2015 2:45:43 PM | rosetta@home | Scheduler request completed: got 0 new tasks
4/21/2015 3:01:38 PM | rosetta@home | Task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_209_0 exited with zero status but no \'finished\' file
4/21/2015 3:01:38 PM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/21/2015 5:51:39 PM | rosetta@home | Task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_209_0 exited with zero status but no \'finished\' file
4/21/2015 5:51:39 PM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/21/2015 6:38:01 PM | rosetta@home | Task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_209_0 exited with zero status but no \'finished\' file
4/21/2015 6:38:01 PM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/21/2015 7:10:42 PM | rosetta@home | Computation for task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_209_0 finished
4/21/2015 7:10:42 PM | rosetta@home | Starting task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_213_0
4/21/2015 7:10:46 PM | rosetta@home | Started upload of rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_209_0_0
4/21/2015 7:10:54 PM | rosetta@home | Finished upload of rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_209_0_0
4/21/2015 8:11:23 PM | rosetta@home | Sending scheduler request: To report completed tasks.
4/21/2015 8:11:23 PM | rosetta@home | Reporting 1 completed tasks
4/21/2015 8:11:23 PM | rosetta@home | Requesting new tasks for NVIDIA GPU
4/21/2015 8:11:29 PM | rosetta@home | Scheduler request completed: got 0 new tasks
4/21/2015 10:21:39 PM | rosetta@home | Task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_213_0 exited with zero status but no \'finished\' file
4/21/2015 10:21:39 PM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/21/2015 10:51:47 PM | rosetta@home | Sending scheduler request: To fetch work.
4/21/2015 10:51:47 PM | rosetta@home | Requesting new tasks for CPU and NVIDIA GPU
4/21/2015 10:51:49 PM | rosetta@home | Scheduler request completed: got 4 new tasks
4/21/2015 10:51:51 PM | rosetta@home | Started download of rb_04_16_55057_100418_ab_stage0_h001___robetta_FLAGS
4/21/2015 10:51:51 PM | rosetta@home | Started download of rb_04_16_55057_100418_ab_stage0_h001___robetta.zip
4/21/2015 10:51:54 PM | rosetta@home | Finished download of rb_04_16_55057_100418_ab_stage0_h001___robetta_FLAGS
4/21/2015 10:51:54 PM | rosetta@home | Started download of rb_04_16_55057_100418_ab_stage0_h001___robetta_h001_.200.3mers.gz
4/21/2015 10:52:00 PM | rosetta@home | Finished download of rb_04_16_55057_100418_ab_stage0_h001___robetta.zip
4/21/2015 10:52:00 PM | rosetta@home | Started download of rb_04_16_55057_100418_ab_stage0_h001___robetta_h001_.200.11mers.gz
4/21/2015 10:52:01 PM | rosetta@home | Finished download of rb_04_16_55057_100418_ab_stage0_h001___robetta_h001_.200.3mers.gz
4/21/2015 10:52:01 PM | rosetta@home | Started download of rb_04_16_55057_100418_ab_stage0_h001___robetta_h001_.200.8mers.gz
4/21/2015 10:52:38 PM | rosetta@home | Finished download of rb_04_16_55057_100418_ab_stage0_h001___robetta_h001_.200.8mers.gz
4/21/2015 10:52:38 PM | rosetta@home | Started download of rb_04_16_55057_100418_ab_stage0_h001___robetta_h001_.200.5mers.gz
4/21/2015 10:52:41 PM | rosetta@home | Finished download of rb_04_16_55057_100418_ab_stage0_h001___robetta_h001_.200.11mers.gz
4/21/2015 10:52:41 PM | rosetta@home | Started download of TL_05370175_0684_2099_0312_0530_0229_0035_0022_0031_0001_0086_1081_0003_0161_0005_2606_0001_031_data.zip
4/21/2015 10:53:00 PM | rosetta@home | Finished download of rb_04_16_55057_100418_ab_stage0_h001___robetta_h001_.200.5mers.gz
4/21/2015 10:53:00 PM | rosetta@home | Started download of fold_and_dock_foldit_2000569_1028_data.zip
4/21/2015 10:53:08 PM | rosetta@home | Finished download of TL_05370175_0684_2099_0312_0530_0229_0035_0022_0031_0001_0086_1081_0003_0161_0005_2606_0001_031_data.zip
4/21/2015 10:53:08 PM | rosetta@home | Started download of foldit_2000569_1028_fold_and_dock_flags
4/21/2015 10:53:09 PM | rosetta@home | Finished download of foldit_2000569_1028_fold_and_dock_flags
4/21/2015 10:53:29 PM | rosetta@home | Finished download of fold_and_dock_foldit_2000569_1028_data.zip
4/21/2015 11:03:48 PM | rosetta@home | Sending scheduler request: To fetch work.
4/21/2015 11:03:48 PM | rosetta@home | Requesting new tasks for NVIDIA GPU
4/21/2015 11:03:49 PM | rosetta@home | Scheduler request completed: got 0 new tasks
4/21/2015 11:11:15 PM | rosetta@home | Computation for task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_213_0 finished
4/21/2015 11:11:15 PM | rosetta@home | Starting task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_08_10_263917_188_0
4/21/2015 11:11:25 PM | rosetta@home | Started upload of rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_213_0_0
4/21/2015 11:11:32 PM | rosetta@home | Finished upload of rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_04_11_263917_213_0_0
4/22/2015 12:12:08 AM | rosetta@home | Sending scheduler request: To report completed tasks.
4/22/2015 12:12:08 AM | rosetta@home | Reporting 1 completed tasks
4/22/2015 12:12:08 AM | rosetta@home | Not requesting tasks: don\'t need (CPU: not highest priority project; NVIDIA GPU: job cache full)
4/22/2015 12:12:11 AM | rosetta@home | Scheduler request completed
4/22/2015 1:18:04 AM | rosetta@home | Task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_08_10_263917_188_0 exited with zero status but no \'finished\' file
4/22/2015 1:18:04 AM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/22/2015 3:02:13 AM | rosetta@home | Computation for task rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_08_10_263917_188_0 finished
4/22/2015 3:02:13 AM | rosetta@home | Starting task zibochen.helix.control22_fold_and_dock_SAVE_ALL_OUT_251159_1686_1
4/22/2015 3:02:21 AM | rosetta@home | Started upload of rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_08_10_263917_188_0_0
4/22/2015 3:02:33 AM | rosetta@home | Finished upload of rb_04_19_55184_100483_ab_stage0_h002___robetta_IGNORE_THE_REST_08_10_263917_188_0_0
4/22/2015 4:03:03 AM | rosetta@home | Sending scheduler request: To report completed tasks.
4/22/2015 4:03:03 AM | rosetta@home | Reporting 1 completed tasks
4/22/2015 4:03:03 AM | rosetta@home | Not requesting tasks: don\'t need (CPU: not highest priority project; NVIDIA GPU: job cache full)
4/22/2015 4:03:07 AM | rosetta@home | Scheduler request completed
4/22/2015 11:11:17 AM | rosetta@home | Computation for task zibochen.helix.control22_fold_and_dock_SAVE_ALL_OUT_251159_1686_1 finished
4/22/2015 11:11:17 AM | rosetta@home | Starting task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0
4/22/2015 11:11:30 AM | rosetta@home | Started upload of zibochen.helix.control22_fold_and_dock_SAVE_ALL_OUT_251159_1686_1_0
4/22/2015 11:11:53 AM | rosetta@home | Finished upload of zibochen.helix.control22_fold_and_dock_SAVE_ALL_OUT_251159_1686_1_0
4/22/2015 11:34:11 AM | rosetta@home | Task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0 exited with zero status but no \'finished\' file
4/22/2015 11:34:11 AM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/22/2015 11:55:56 AM | rosetta@home | Task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0 exited with zero status but no \'finished\' file
4/22/2015 11:55:56 AM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/22/2015 12:12:25 PM | rosetta@home | Sending scheduler request: To report completed tasks.
4/22/2015 12:12:25 PM | rosetta@home | Reporting 1 completed tasks
4/22/2015 12:12:25 PM | rosetta@home | Not requesting tasks: don\'t need (CPU: not highest priority project; NVIDIA GPU: job cache full)
4/22/2015 12:12:27 PM | rosetta@home | Scheduler request completed
4/22/2015 12:17:09 PM | rosetta@home | Task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0 exited with zero status but no \'finished\' file
4/22/2015 12:17:09 PM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/22/2015 12:53:26 PM | rosetta@home | Task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0 exited with zero status but no \'finished\' file
4/22/2015 12:53:26 PM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/22/2015 1:27:22 PM | | Suspending computation - CPU is busy
4/22/2015 1:27:32 PM | | Resuming computation
4/22/2015 1:50:21 PM | rosetta@home | Task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0 exited with zero status but no \'finished\' file
4/22/2015 1:50:21 PM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/22/2015 4:14:28 PM | rosetta@home | Task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0 exited with zero status but no \'finished\' file
4/22/2015 4:14:28 PM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/22/2015 5:07:30 PM | rosetta@home | Task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0 exited with zero status but no \'finished\' file
4/22/2015 5:07:30 PM | rosetta@home | If this happens repeatedly you may need to reset the project.
4/22/2015 5:46:17 PM | | Suspending computation - CPU is busy
4/22/2015 5:46:27 PM | | Resuming computation
4/22/2015 6:20:18 PM | | Suspending computation - CPU is busy
4/22/2015 6:20:28 PM | | Resuming computation
4/22/2015 7:15:29 PM | rosetta@home | Computation for task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0 finished
4/22/2015 7:15:29 PM | rosetta@home | Output file R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0_0 for task R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003_fold_and_dock_SAVE_ALL_OUT_263856_287_0 absent
4/22/2015 7:15:29 PM | rosetta@home | Starting task zibochen.helix.control25_fold_and_dock_SAVE_ALL_OUT_251162_2317_0
4/22/2015 7:29:31 PM | rosetta@home | update requested by user
4/22/2015 7:29:33 PM | rosetta@home | Sending scheduler request: Requested by user.
4/22/2015 7:29:33 PM | rosetta@home | Reporting 1 completed tasks
4/22/2015 7:29:33 PM | rosetta@home | Requesting new tasks for NVIDIA GPU
4/22/2015 7:29:37 PM | rosetta@home | Scheduler request completed: got 0 new tasks


While I have frequently had Rosetta WUs cycle through multiple \"exited with zero status but no \'finished\' file\" before completing, I have never had one pop up a program crash tab, much less multiple ones.
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Message 78153 - Posted: 23 Apr 2015, 19:22:48 UTC - in response to Message 78145.  

Task 731275755
( R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0005_fold_and_dock_SAVE_ALL_OUT_263848_834_0 )
got stuck getting no CPU time and I aborted it.

Properties were:

CPU time at last checkpoint : 8:06
CPU time : 8.39
Elapsed time : 11:55:19


Yes same here, those ones do not seem running correctly.
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Message 78154 - Posted: 24 Apr 2015, 6:27:34 UTC
Last modified: 24 Apr 2015, 6:28:57 UTC

Issues here too, with a heap of crash notification dialogs after the night:

24.04.2015 02:39:04 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 02:39:04 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 03:01:56 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 03:01:56 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 03:24:48 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 03:24:48 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 03:47:41 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 03:47:41 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 04:10:32 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 04:10:32 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 04:33:25 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 04:33:25 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 04:56:06 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 04:56:06 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 05:18:48 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 05:18:48 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 05:20:38 | rosetta@home | Task TL_03590726_0415_2119_0169_0549_0114_0058_0025_0050_0001_0275_0167_0005_2204_0001_1960_0001__fold_SAVE_ALL_OUT_259977_515_0 exited with zero status but no \'finished\' file
24.04.2015 05:20:38 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 05:41:31 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 05:41:31 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:04:32 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 06:04:32 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:24:54 | rosetta@home | Task zibochen.helix.1start3_fold_and_dock_SAVE_ALL_OUT_246434_2553_0 exited with zero status but no \'finished\' file
24.04.2015 06:24:54 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:26:33 | rosetta@home | Task TL_03590726_0415_2119_0169_0549_0114_0058_0025_0050_0001_0275_0167_0005_2204_0001_1960_0001__fold_SAVE_ALL_OUT_259977_515_0 exited with zero status but no \'finished\' file
24.04.2015 06:26:33 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:27:15 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 06:27:15 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:49:57 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 06:49:57 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 07:12:39 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 07:12:39 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 07:35:22 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 07:35:22 | rosetta@home | If this happens repeatedly you may need to reset the project.


Well ... do I have to reset?

CPU: AMD Phenom-II X4 (in case that may be interesting).
Fun and success!

Jobs: holzon + 12angebote
Hobbies: doom9/Gleitz + PlaneShift
ID: 78154 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Betting Slip

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Message 78156 - Posted: 24 Apr 2015, 12:02:51 UTC - in response to Message 78154.  

Issues here too, with a heap of crash notification dialogs after the night:

24.04.2015 02:39:04 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 02:39:04 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 03:01:56 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 03:01:56 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 03:24:48 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 03:24:48 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 03:47:41 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 03:47:41 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 04:10:32 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 04:10:32 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 04:33:25 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 04:33:25 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 04:56:06 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 04:56:06 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 05:18:48 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 05:18:48 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 05:20:38 | rosetta@home | Task TL_03590726_0415_2119_0169_0549_0114_0058_0025_0050_0001_0275_0167_0005_2204_0001_1960_0001__fold_SAVE_ALL_OUT_259977_515_0 exited with zero status but no \'finished\' file
24.04.2015 05:20:38 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 05:41:31 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 05:41:31 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:04:32 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 06:04:32 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:24:54 | rosetta@home | Task zibochen.helix.1start3_fold_and_dock_SAVE_ALL_OUT_246434_2553_0 exited with zero status but no \'finished\' file
24.04.2015 06:24:54 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:26:33 | rosetta@home | Task TL_03590726_0415_2119_0169_0549_0114_0058_0025_0050_0001_0275_0167_0005_2204_0001_1960_0001__fold_SAVE_ALL_OUT_259977_515_0 exited with zero status but no \'finished\' file
24.04.2015 06:26:33 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:27:15 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 06:27:15 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 06:49:57 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 06:49:57 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 07:12:39 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 07:12:39 | rosetta@home | If this happens repeatedly you may need to reset the project.
24.04.2015 07:35:22 | rosetta@home | Task R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004_fold_and_dock_SAVE_ALL_OUT_263849_196_0 exited with zero status but no \'finished\' file
24.04.2015 07:35:22 | rosetta@home | If this happens repeatedly you may need to reset the project.


Well ... do I have to reset?

CPU: AMD Phenom-II X4 (in case that may be interesting).


Reset project, it can\'t do any harm.
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natteruw

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Message 78159 - Posted: 24 Apr 2015, 19:21:27 UTC

Hi all,

I apologize for those of you who have experienced job crashes related to any of the follow jobs:

R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0002
R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003
R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0005
R01463_dSASA1439.3_5H2LD1_Ttj05_NMdock_0019_0001_C_asu_1_0001
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0001
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0002
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0003
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0005

They have all been taken off of Rosetta@home. These jobs may have been different enough from ones that had been tested on a local computer that they should have been tested themselves beforehand. I will try my best such that this does not happen again.

In case you are wondering what I am trying to computationally validate...I am designing symmetric oligomers, which are proteins that self-assemble into a symmetric complex (for example, a clover leaf has 3-fold symmetry). What is special about these oligomers is that they consist of two building blocks that we have already experimentally characterized that are now undergoing a designed fusion meaning that the two pieces will become one, and should self-assemble. I am trying to test their docking on Rosetta@home. These could be extremely useful as building blocks for making protein biomaterials.

Let me know if you have any questions about the job crashes or the project :)

Best, natteruw
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Message 78160 - Posted: 25 Apr 2015, 13:32:41 UTC - in response to Message 78159.  

Hi all,

I apologize for those of you who have experienced job crashes related to any of the follow jobs:

R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0002
R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003
R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0005
R01463_dSASA1439.3_5H2LD1_Ttj05_NMdock_0019_0001_C_asu_1_0001
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0001
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0002
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0003
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004
R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0005

They have all been taken off of Rosetta@home. These jobs may have been different enough from ones that had been tested on a local computer that they should have been tested themselves beforehand. I will try my best such that this does not happen again.

In case you are wondering what I am trying to computationally validate...I am designing symmetric oligomers, which are proteins that self-assemble into a symmetric complex (for example, a clover leaf has 3-fold symmetry). What is special about these oligomers is that they consist of two building blocks that we have already experimentally characterized that are now undergoing a designed fusion meaning that the two pieces will become one, and should self-assemble. I am trying to test their docking on Rosetta@home. These could be extremely useful as building blocks for making protein biomaterials.

Let me know if you have any questions about the job crashes or the project :)

Best, natteruw


Thanks for informing us on the issue. This project is about investigation and it is understandable that things some times won\'t go like it was intented. What we appreciatte is communication from the investigators and that our errors reports are attended.

What would be the application of those protein biomaterials?


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natteruw

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Message 78170 - Posted: 28 Apr 2015, 23:35:30 UTC - in response to Message 78160.  

Protein biomaterials have a lot of potential applications in health, energy, environment, and maybe even electronics. Recently, for example, a paper was published on protein \"nanocages\" designed by members of the Rosetta group. These could be used for drug delivery or localizing enzymes for things like biofuel production.

(http://www.bakerlab.org/Accurate-design-of-co-assembling-multi-component-protein-nanomaterials/)



[quote]

Thanks for informing us on the issue. This project is about investigation and it is understandable that things some times won\'t go like it was intented. What we appreciatte is communication from the investigators and that our errors reports are attended.

What would be the application of those protein biomaterials?



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