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David E K Profile
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Message 76668 - Posted 29 Apr 2014 9:17:57 UTC
Last modified: 29 Apr 2014 9:35:22 UTC

The minirosetta application has been updated to 3.50. This version includes improvements to the score function and protocols amended for distributed computing which include docking and optimized forward folding.

With this update, we may no longer support 32-bit Mac OSX platforms due to compiler issues with Rosetta. However, we will try our best to resolve these issues, if possible.

Please post problems related to this update here.

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Message 76673 - Posted 1 May 2014 2:40:21 UTC

Hi.

Lucky me, I got this error after 3+ hrs.


PD1_1hz6A_denovo_1L7E2L7E2L9H4L7E5L7E1L_1-2.A.0_1-4.P.0_3-4.A.0_SAVE_ALL_OUT__162682_23_0

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=596368735


# cpu_run_time_pref: 14400
======================================================
DONE :: 1 starting structures 11650.4 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 5.92856e+79

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc

</stderr_txt>

____________


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Message 76674 - Posted 1 May 2014 4:40:02 UTC
Last modified: 1 May 2014 5:34:38 UTC

And yet another one erred, after over 6+ hrs.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=596368733


PD1_1hz6A_denovo_1L8E2L8E2L14H3L8E5L8E1L_1-2.A.0_1-4.P.0_3-4.A.0_SAVE_ALL_OUT__162682_6_0


# cpu_run_time_pref: 14400
======================================================
DONE :: 1 starting structures 24370.7 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 5.92856e+79

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc

</stderr_txt>

-------------------------------------------------------------------------

And another! Over 4hrs.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=596368784


PD1_1hz6A_denovo_1L5E3L5E2L12H3L5E5L5E1L_1-2.A.0_1-4.P.0_3-4.A.0_SAVE_ALL_OUT__162684_3_0


# cpu_run_time_pref: 14400
======================================================
DONE :: 21 starting structures 14160.1 cpu seconds
This process generated 21 decoys from 21 attempts
======================================================
BOINC :: WS_max 5.92856e+79

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc

</stderr_txt>
------------------------------------------------------------------------

And another, over 7hrs lost this time!

I will be aborting these from now on.!!!!!!!!!!!!!


http://boinc.bakerlab.org/rosetta/workunit.php?wuid=596368786


PD1_1hz6A_denovo_1L8E2L8E2L15H4L8E5L8E1L_1-2.A.0_1-4.P.0_3-4.A.0_SAVE_ALL_OUT__162683_23_0


# cpu_run_time_pref: 14400
======================================================
DONE :: 1 starting structures 25992.6 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 5.92856e+79

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc

</stderr_txt>
____________


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Message 76676 - Posted 1 May 2014 9:27:52 UTC

Guys, I signed up for 47 WU's. Two of them aborted as comp errors, 0 file or whatever. The others gummed up my machine so it darn near wouldn't run. This sort of thing has happened before to me, and I can't suffer it. I'll have to detach for now until you can send me something you can guarantee will run as well as the average WU from somewhere else... sorry...
____________
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Message 76678 - Posted 1 May 2014 15:43:34 UTC

657407219
657407221

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x018380DB write attempt to address 0x00000000

- Registers -
eax=00000000 ebx=00000000 ecx=00000000 edx=00000001 esi=00000000 edi=00000001
eip=018380db esp=00d5d604 ebp=00d5d894
cs=0023 ss=002b ds=002b es=002b fs=0053 gs=002b efl=00010246
____________

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Message 76680 - Posted 1 May 2014 21:42:43 UTC

Compute error after a few seconds.

657311120

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x014980DB write attempt to address 0x00000000

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Message 76687 - Posted 3 May 2014 14:36:47 UTC

Hello,
Sorry those are my boinc jobs that caused the computational errors on the clients. These are protein design calculations that aim to generate ideal protein topology to bind cancer target PD1. To generate a good structure, it requires searching a large space in both protein topology (composition and arrangement of protein secondary structures) and protein conformation. The generated structure undergoes strict filtering to ensure good quality control. This most of time results in few or no structures even after a couple of hours of computing. We used boinc to survey a large number of protein topologies on the order of 100,000 (each topology is sampled on the order of 10-100 times). The initial results can be used to guide further focused sampling on promising topologies.
I am not sure what caused the malloc errors and quick terminating of the computations. Some of my jobs which are set up in the same way return good structures. I will work together with the boinc team to resolve this problem and prevent those from happening in the future.
At last, I really appreciate your generosity to donating your computational resources. This speeds up a lot with our efforts to find binders that can potentially cure diseases. I have benefit a lot from boinc to design binders for Ebola virus very recently.
Thanks for the feedback.
Best regards,
Lei

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Message 76693 - Posted 6 May 2014 16:36:13 UTC - in response to Message ID 76687.

Hello,
Sorry those are my boinc jobs that caused the computational errors on the clients. These are protein design calculations that aim to generate ideal protein topology to bind cancer target PD1. To generate a good structure, it requires searching a large space in both protein topology (composition and arrangement of protein secondary structures) and protein conformation. The generated structure undergoes strict filtering to ensure good quality control. This most of time results in few or no structures even after a couple of hours of computing. We used boinc to survey a large number of protein topologies on the order of 100,000 (each topology is sampled on the order of 10-100 times). The initial results can be used to guide further focused sampling on promising topologies.
I am not sure what caused the malloc errors and quick terminating of the computations. Some of my jobs which are set up in the same way return good structures. I will work together with the boinc team to resolve this problem and prevent those from happening in the future.
At last, I really appreciate your generosity to donating your computational resources. This speeds up a lot with our efforts to find binders that can potentially cure diseases. I have benefit a lot from boinc to design binders for Ebola virus very recently.
Thanks for the feedback.
Best regards,
Lei


Thank you very much for the background information! I personally have no problems with computing errors - after all, this process belongs to such a project. After all, it's science, which inherently means try & error, right?

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Message 76702 - Posted 8 May 2014 12:01:39 UTC - in response to Message ID 76687.
Last modified: 8 May 2014 12:02:20 UTC

Dear Lei, few recognize possible errors, this honors to him like person and
Investigator.
I have few errors, goes the normal thing as always.
What if I have observed it is that the number of credits has been diminishing until reaching
a total reduction of 500 credits to the day.
The server is had to accustom to the new system or is something that has varied in the system of concession of credits?
I congratulate to them by its work for the humanity.
Best regards
Salvador Cutchet

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Message 76703 - Posted 9 May 2014 10:23:07 UTC

659224447
659224446

Both WU's finished fine and were ready to upload. Upload transfer went fine but when I check my tasks it says "Client Error" but not as a Compute Error... gives claimed credit but 0.0 granted credit... What gives?

Nikita_Kovalyov

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Message 76704 - Posted 9 May 2014 10:38:56 UTC

659148088
659148090
659224444

All 3 have "Client Error" But not as a Compute Error...

Example:
DONE :: 11 starting structures 10575.4 cpu seconds
This process generated 11 decoys from 11 attempts
======================================================
BOINC :: WS_max 4.65121e+008

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>
<message>
app_version download error: couldn't get input files:
<file_xfer_error>
<file_name>minirosetta_database_3d2618f.zip</file_name>
<error_code>-120 (RSA key check failed for file)</error_code>
<error_message>signature verification failed</error_message>
</file_xfer_error>

</message>
]]>

Validate state Invalid
Claimed credit 37.7243021595233

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Message 76705 - Posted 9 May 2014 15:50:14 UTC - in response to Message ID 76703.

gives claimed credit but 0.0 granted credit... What gives?


I can't answer on the cause of the error, but failed tasks are granted credit within 24 hours (after an overnight script is run). This type of credit will only show up in one of the screens though (I can't remember which one).

Matthias Lehmkuhl

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Message 76706 - Posted 10 May 2014 16:48:35 UTC

I got also on Ubuntu 14.04 an error after finishing the result
# cpu_run_time_pref: 36000
======================================================
DONE :: 3 starting structures 31590.2 cpu seconds
This process generated 3 decoys from 3 attempts
======================================================
BOINC :: WS_max 3.13151e-294

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc

</stderr_txt>

Ebola_strand_repeat_41limit_1L13H3L8E7L8E1L_25_33_c_312_1-2.P.0_SAVE_ALL_OUT__162400_11
http://boinc.bakerlab.org/rosetta/result.php?resultid=659471415
____________
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Message 76709 - Posted 10 May 2014 19:43:52 UTC

I guess it is ME TOO for this issue. I do not crunch for this project very often anymore as I had reached my goal of 1 million credits a while ago, but when other projects are not busy I pull a few WU's to keep my PC's busy.

But now I see I am getting "client error" notifications on the last few I tried.

My work
____________
Hi all you enthusiastic crunchers.....

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Message 76715 - Posted 12 May 2014 19:12:39 UTC

I am having a serious issue with this update. Cores aren't being utilized at 100%, cores are stagnating on throttling up, and just general instability of operations. I had thought the issue was with Windows 8.1 Update, but this change in the minirosetta application seems to be more in line with the drop in productivity from my systems.

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Message 76719 - Posted 14 May 2014 0:33:58 UTC

i just started crunching a few days ago. completed one wu successfully with rosetta
, but got the following errors since:
/13/2014 3:20:27 AM | rosetta@home | Task aftimidv2_7_fold_SAVE_ALL_OUT_165014_1039_0 exited with zero status but no 'finished' file
5/13/2014 3:20:27 AM | rosetta@home | If this happens repeatedly you may need to reset the project.


5/13/2014 3:49:23 AM | rosetta@home | Task tj_5_11_2helixspiral_X24_GBB_27_BAB_o2_5_5_c_fragments_abinitio_SAVE_ALL_OUT_165084_54_0 exited with zero status but no 'finished' file
5/13/2014 3:49:23 AM | rosetta@home | If this happens repeatedly you may need to reset the project.

5/13/2014 4:40:20 AM | rosetta@home | Task tj_5_11_2helixspiral_X24_GBB_27_BAB_o2_5_5_c_fragments_abinitio_SAVE_ALL_OUT_165084_54_0 exited with zero status but no 'finished' file
5/13/2014 4:40:20 AM | rosetta@home | If this happens repeatedly you may need to reset the project.

5/13/2014 5:36:15 AM | rosetta@home | Task aftimidv2_7_fold_SAVE_ALL_OUT_165014_1039_0 exited with zero status but no 'finished' file
5/13/2014 5:36:15 AM | rosetta@home | If this happens repeatedly you may need to reset the project.

5/13/2014 11:47:52 AM | rosetta@home | Task rb_05_12_47255_92655__t000__2_C1_SAVE_ALL_OUT_IGNORE_THE_REST_165044_630_0 exited with zero status but no 'finished' file
5/13/2014 11:47:52 AM | rosetta@home | If this happens repeatedly you may need to reset the project.

5/13/2014 1:03:45 PM | rosetta@home | Task aftimidv2_7_fold_SAVE_ALL_OUT_165014_1039_0 exited with zero status but no 'finished' file
5/13/2014 1:03:45 PM | rosetta@home | If this happens repeatedly you may need to reset the project.

5/13/2014 7:34:08 PM | rosetta@home | Task rms_cutoff_5_2_enrique_contact_opt_iteration_5_44a8b832b2f44aebb203c9d152a3c002_fold_SAVE_ALL_OUT_164706_1446_1 exited with zero status but no 'finished' file
5/13/2014 7:34:08 PM | rosetta@home | If this happens repeatedly you may need to reset the project.


All other projects are finishing ok.
Will try here again in a few weeks, and in the meantime look for answers in these message boards.

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Message 76747 - Posted 18 May 2014 11:18:37 UTC - in response to Message ID 76719.

i just started crunching a few days ago. completed one wu successfully with rosetta
, but got the following errors since:
/13/2014 3:20:27 AM | rosetta@home | Task aftimidv2_7_fold_SAVE_ALL_OUT_165014_1039_0 exited with zero status but no 'finished' file
5/13/2014 3:20:27 AM | rosetta@home | If this happens repeatedly you may need to reset the project.





All other projects are finishing ok.
Will try here again in a few weeks, and in the meantime look for answers in these message boards.


BOINC FAQ Service

earlier post

Hope this helps.
Snags

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Message 76752 - Posted 21 May 2014 10:34:13 UTC

I am not sure these new 3.50's are working I have been doing them since last night and they are less than 50% finished in over 11 hours. Others are less than done also, 20% in over 6 hours. What is going on here?
____________

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Message 76753 - Posted 21 May 2014 21:10:50 UTC - in response to Message ID 76668.

The minirosetta application has been updated to 3.50. This version includes improvements to the score function and protocols amended for distributed computing which include docking and optimized forward folding.

With this update, we may no longer support 32-bit Mac OSX platforms due to compiler issues with Rosetta. However, we will try our best to resolve these issues, if possible.

Please post problems related to this update here.


A unit now takes much longer for not a proportionate credit. May take over 20 hours each as opposed to 3 hours or even less time. I liked the previous units better.

Miklos,M

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Message 76755 - Posted 22 May 2014 13:17:23 UTC - in response to Message ID 76753.

The minirosetta application has been updated to 3.50. This version includes improvements to the score function and protocols amended for distributed computing which include docking and optimized forward folding.

With this update, we may no longer support 32-bit Mac OSX platforms due to compiler issues with Rosetta. However, we will try our best to resolve these issues, if possible.

Please post problems related to this update here.


A unit now takes much longer for not a proportionate credit. May take over 20 hours each as opposed to 3 hours or even less time. I liked the previous units better.

Looks like the credit given for these longer 24 hour+ units is given in proportion. However, a heads up before sending them out would have been helpful. Just to alert us that these are expected to take much longer to complete.

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Message 76759 - Posted 24 May 2014 12:54:17 UTC - in response to Message ID 76755.

The minirosetta application has been updated to 3.50. This version includes improvements to the score function and protocols amended for distributed computing which include docking and optimized forward folding.

With this update, we may no longer support 32-bit Mac OSX platforms due to compiler issues with Rosetta. However, we will try our best to resolve these issues, if possible.

Please post problems related to this update here.


A unit now takes much longer for not a proportionate credit. May take over 20 hours each as opposed to 3 hours or even less time. I liked the previous units better.

Looks like the credit given for these longer 24 hour+ units is given in proportion. However, a heads up before sending them out would have been helpful. Just to alert us that these are expected to take much longer to complete.


Hi Miklos,M,

I believe the normal way of working is for Rosetta to keep calculating new decoys until you have reached your preferred run time and then stop at the next completed decoy. In cases where the final decoy is taking an extremely long time to complete, the watchdog should step in and terminate the task.

A 20 hour task based on a 3 hour preferred run time sounds very strange.

Can you post a link to the results page for the affected task(s) (or just the task ID)? That will help the project scientists to investigate the problem.

Miklos,M

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Message 76761 - Posted 24 May 2014 23:47:18 UTC - in response to Message ID 76759.

The minirosetta application has been updated to 3.50. This version includes improvements to the score function and protocols amended for distributed computing which include docking and optimized forward folding.

With this update, we may no longer support 32-bit Mac OSX platforms due to compiler issues with Rosetta. However, we will try our best to resolve these issues, if possible.

Please post problems related to this update here.


A unit now takes much longer for not a proportionate credit. May take over 20 hours each as opposed to 3 hours or even less time. I liked the previous units better.

Looks like the credit given for these longer 24 hour+ units is given in proportion. However, a heads up before sending them out would have been helpful. Just to alert us that these are expected to take much longer to complete.


Hi Miklos,M,

I believe the normal way of working is for Rosetta to keep calculating new decoys until you have reached your preferred run time and then stop at the next completed decoy. In cases where the final decoy is taking an extremely long time to complete, the watchdog should step in and terminate the task.

A 20 hour task based on a 3 hour preferred run time sounds very strange.

Can you post a link to the results page for the affected task(s) (or just the task ID)? That will help the project scientists to investigate the problem.

662522208 601098858 21 May 2014 2:16:13 UTC 23 May 2014 19:45:50 UTC Over Success Done 84,811.41 511.02 617.13

P . P . L .
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Message 76762 - Posted 25 May 2014 0:33:53 UTC
Last modified: 25 May 2014 0:45:40 UTC

Hi Miklos,M

I just had a look at 2 of your rigs the i7-4960X and FX-8150 they both have

# cpu_run_time_pref: 86400 seconds you selected which is about 24hrs run time, so what's the problem?

If the W.U. can finish faster then your selected run time for some reason like hitting (99)decoys they will but otherwise they will run the full length of time.
____________


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Message 76763 - Posted 25 May 2014 0:43:25 UTC - in response to Message ID 76762.

Hi Miklos,M

I just had a look at 2 of your rigs the i7-4960X and FX-8150 they both have

# cpu_run_time_pref: 86400 seconds you selected which is about 24hrs run time, so what's the problem?

If the W.U. can finish faster then your selected run time for some reason like hitting (99) they will but otherwise they will run the full length of time.


5/24/2014 8:30:46 PM | rosetta@home | Computation for task syil2dnd2v4_2_fold_SAVE_ALL_OUT_166165_580_0 finished
5/24/2014 8:30:46 PM | rosetta@home | Starting task rb_05_22_48582_94175_ab_stage0_t000___robetta_cstwt_3.0_IGNORE_THE_REST_03_09_166190_90_0
5/24/2014 8:30:50 PM | rosetta@home | Started upload of syil2dnd2v4_2_fold_SAVE_ALL_OUT_166165_580_0_0
5/24/2014 8:30:55 PM | rosetta@home | Finished upload of syil2dnd2v4_2_fold_SAVE_ALL_OUT_166165_580_0_0

Miklos,M

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Message 76764 - Posted 25 May 2014 19:09:23 UTC - in response to Message ID 76762.

Hi Miklos,M

I just had a look at 2 of your rigs the i7-4960X and FX-8150 they both have

# cpu_run_time_pref: 86400 seconds you selected which is about 24hrs run time, so what's the problem?

If the W.U. can finish faster then your selected run time for some reason like hitting (99)decoys they will but otherwise they will run the full length of time.


Would that explain why my computers suddenly take over a day to work one unit, when in the past it used to be about 3 hours and I see many others are still taking about 3 hours with their work units? How do I change I back, if I chose to do so?

Thanks.

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Message 76765 - Posted 25 May 2014 20:10:34 UTC
Last modified: 25 May 2014 20:11:18 UTC

When you have several host computers, you can organize them by "venue". There is a setting on R@h for Target CPU run time. The default value is 3hrs, the maximum is 24hrs. This value can be set for each venue. This is done here on the website. Click the "Participants" link at the top, then click on the Rosetta@home preferences.
____________
Rosetta Moderator: Mod.Sense

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Message 76767 - Posted 25 May 2014 20:54:47 UTC - in response to Message ID 76765.

When you have several host computers, you can organize them by "venue". There is a setting on R@h for Target CPU run time. The default value is 3hrs, the maximum is 24hrs. This value can be set for each venue. This is done here on the website. Click the "Participants" link at the top, then click on the Rosetta@home preferences.


Thank you. gave it a try at 4 hours.

Miklos,M

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Message 76768 - Posted 25 May 2014 22:30:00 UTC - in response to Message ID 76668.

The minirosetta application has been updated to 3.50. This version includes improvements to the score function and protocols amended for distributed computing which include docking and optimized forward folding.

With this update, we may no longer support 32-bit Mac OSX platforms due to compiler issues with Rosetta. However, we will try our best to resolve these issues, if possible.

Please post problems related to this update here.


My huge apologies. The mistake was on my end as I just found out. Somehow I set it on "one day", as opposed to the default of 3 hours where it was for a long time.

Message boards : Number crunching : Minirosetta 3.50


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