Minirosetta 3.50

Message boards : Number crunching : Minirosetta 3.50

To post messages, you must log in.

1 · 2 · Next

AuthorMessage
Profile David E K
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 1 Jul 05
Posts: 985
Credit: 2,630,856
RAC: 1,168
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.
ID: 76668 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
P . P . L .

Send message
Joined: 20 Aug 06
Posts: 581
Credit: 4,865,274
RAC: 0
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>

ID: 76673 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
P . P . L .

Send message
Joined: 20 Aug 06
Posts: 581
Credit: 4,865,274
RAC: 0
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>
ID: 76674 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Cesium_133*
Avatar

Send message
Joined: 1 Dec 08
Posts: 28
Credit: 116,452
RAC: 127
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...
The lovely lady you see isn't I, but Hayley Westenra, a classical crossover singer from Christchurch, NZ. There is no known voice as hers. Check her out- she's seraphic.

ID: 76676 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 588
Credit: 1,674,163
RAC: 703
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
ID: 76678 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Murasaki
Avatar

Send message
Joined: 20 Apr 06
Posts: 303
Credit: 399,319
RAC: 128
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
ID: 76680 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
shilei
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 25 Aug 11
Posts: 5
Credit: 1,014,314
RAC: 0
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
ID: 76687 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Michael Hoffmann
Avatar

Send message
Joined: 5 Jun 08
Posts: 9
Credit: 987,706
RAC: 763
Message 76693 - Posted: 6 May 2014, 16:36:13 UTC - in response to Message 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?
ID: 76693 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Cutchet Salvador

Send message
Joined: 1 Feb 10
Posts: 17
Credit: 10,687,724
RAC: 6
Message 76702 - Posted: 8 May 2014, 12:01:39 UTC - in response to Message 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
ID: 76702 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Nikita_Kovalyov

Send message
Joined: 25 Apr 13
Posts: 2
Credit: 134,306
RAC: 369
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?
ID: 76703 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Nikita_Kovalyov

Send message
Joined: 25 Apr 13
Posts: 2
Credit: 134,306
RAC: 369
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
ID: 76704 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Murasaki
Avatar

Send message
Joined: 20 Apr 06
Posts: 303
Credit: 399,319
RAC: 128
Message 76705 - Posted: 9 May 2014, 15:50:14 UTC - in response to Message 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).
ID: 76705 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Matthias Lehmkuhl

Send message
Joined: 20 Nov 05
Posts: 10
Credit: 798,043
RAC: 1,122
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
Matthias

ID: 76706 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Viking69
Avatar

Send message
Joined: 3 Oct 05
Posts: 18
Credit: 1,512,619
RAC: 28
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.....
ID: 76709 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile CDRF

Send message
Joined: 27 Aug 13
Posts: 1
Credit: 29,328,343
RAC: 0
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.

ID: 76715 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
bgw

Send message
Joined: 7 May 14
Posts: 1
Credit: 132,578
RAC: 151
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.
ID: 76719 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Snags

Send message
Joined: 22 Feb 07
Posts: 193
Credit: 1,455,116
RAC: 212
Message 76747 - Posted: 18 May 2014, 11:18:37 UTC - in response to Message 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
ID: 76747 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Miklos,M

Send message
Joined: 8 Dec 13
Posts: 23
Credit: 4,942,189
RAC: 0
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?
ID: 76752 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Miklos,M

Send message
Joined: 8 Dec 13
Posts: 23
Credit: 4,942,189
RAC: 0
Message 76753 - Posted: 21 May 2014, 21:10:50 UTC - in response to Message 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.
ID: 76753 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Miklos,M

Send message
Joined: 8 Dec 13
Posts: 23
Credit: 4,942,189
RAC: 0
Message 76755 - Posted: 22 May 2014, 13:17:23 UTC - in response to Message 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.
ID: 76755 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
1 · 2 · Next

Message boards : Number crunching : Minirosetta 3.50



©2017 University of Washington
http://www.bakerlab.org