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.

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

https://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>

---

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

https://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.

https://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.!!!!!!!!!!!!!


https://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>

---

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.

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

---

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

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

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?

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

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?

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

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).

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
https://boinc.bakerlab.org/rosetta/result.php?resultid=659471415

---

Matthias

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.....

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.

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.

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

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?

---

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.

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.