Rosetta 4.1+ and 4.2+

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Profile Grant (SSSF)

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Message 94216 - Posted: 12 Apr 2020, 6:28:52 UTC - in response to Message 94206.  
Last modified: 12 Apr 2020, 6:33:01 UTC

It looks like there's going to be some problems with v 4.15- Estimated completion times are 39min 18sec; that's going to lead to a lot of overfilled caches & Tasks timing out....
The first v4.15 tasks I got were also noted to be in the 39 min. range. However, my BOINC manager revised their completion times to 01:14:54, almost twice as long. Will see if I get same results as you did.
The problem is that revised Estimated time doesn't get sent back to the Servers until the Task is finished, by which time more work has already been sent based on the lower Estimated completion time. And with the Runtimes of these Tasks, it takes a week (or more or less depending on how many cores & threads your system has) for the Estimates to match the actual Runtime.

I'd suggest you check your cache size & settings for when Rosetta can run as you have more Tasks that have timed out & missed the deadlines than ones that you have in your Valid list (and your i3 may run in to memory issues when larger RAM requirement Tasks make their return).
A very small cache & giving BOINC more memory if it needs it should stop the missed deadlines, & help avoid RAM issues with the i3 in the future.

Your Account page, Computing Settings,
Computing
   Usage limits	
                                   Use at most 100% of the CPUs
                                   Use at most 100% of CPU time

   When to suspend	
           Suspend when computer is on battery (not selected)
               Suspend when computer is in use (not selected)
 Suspend GPU computing when computer is in use (not selected)
   'In use' means mouse/keyboard input in last 3 minutes
  Suspend when no mouse/keyboard input in last --- minutes
     Suspend when non-BOINC CPU usage is above --- %
                          Compute only between ---

   Other	
                                Store at least 1 days of work
                     Store up to an additional 0.02 days of work
                    Switch between tasks every 60 minutes
     Request tasks to checkpoint at most every 60 seconds

   Disk
                              Use no more than 20 GB
                                Leave at least 2 GB free
                              Use no more than 60 % of total

   Memory
          When computer is in use, use at most 95 %
      When computer is not in use, use at most 95 %
 Leave non-GPU tasks in memory while suspended (not selected)
                   Page/swap file: use at most 75 %

Grant
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James W

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Message 94220 - Posted: 12 Apr 2020, 9:40:42 UTC - in response to Message 94216.  
Last modified: 12 Apr 2020, 9:44:49 UTC

Thanks for the setup suggestions. I hadn't changed configuration since I set up BOINC and began working on Seti. Started with a Pentium II, then III, and up to Pentium IV with XP before getting my Optiplex over 6 yrs ago. How "state-of-the-art" does change! I mainly used my Optiplex (i5) for working as a medical transcriptionist, so didn't want BOINC getting in the way. Rosetta was just a backup project at the time. I boosted RAM from 4 to 8G, which made a major difference. Motherboard only has 2 RAM slots, however. (I remember how RAM used to cost a mint.)

With Rosetta's current short deadlines as a regular thing of late, and its being a memory glutton, can be a challenge keeping a moderate desktop unit able to keep pace.

Thanks again! :-)

PS: for v4.15 apps, my estimated completion time is now up to 4 hrs.
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Profile Grant (SSSF)

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Message 94222 - Posted: 12 Apr 2020, 9:53:23 UTC - in response to Message 94220.  

PS: for v4.15 apps, my estimated completion time is now up to 4 hrs.
It'll take a while for it to match reality (being the default Target CPU runtime of 8hrs, or whatever you select in the Rosetta preferences.).
Grant
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Greger

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Message 94239 - Posted: 12 Apr 2020, 13:18:46 UTC

<core_client_version>7.16.1</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.12_x86_64-pc-linux-gnu -silent_gz -mute all -s chainA_chainB_20_04_15_28_13.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol local_docking_20_04_15_28_13.xml -out:nstruct 10000 -jd2:ntrials 100 -ex1 -ex2aro -beta -use_input_sc -in:file:native chainA_chainB_20_04_15_28_13.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1004427

ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF
ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 380
BOINC:: Error reading and gzipping output datafile: default.out
15:03:18 (67461): called boinc_finish(1)

</stderr_txt>
]]>


Task: https://boinc.bakerlab.org/rosetta/result.php?resultid=1147139880

Unsupported file? any solution for this?
Worked well but recently got this issue and host got 4 valid with application Rosetta v4.12 x86_64-pc-linux-gnu.
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Tomcat雄猫

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Message 94254 - Posted: 12 Apr 2020, 16:42:19 UTC - in response to Message 94239.  
Last modified: 12 Apr 2020, 16:43:28 UTC

I got two of the same errors on my Android devices running Rosetta v4.15 arm-android-linux-gnu. Rosetta for Portable Devices v4.12 arm-android-linux-gnu tasks run fine.


<core_client_version>7.4.39</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu -silent_gz -mute all -s chainA_chainB_20_04_15_28_11.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol local_docking_20_04_15_28_11.xml -out:nstruct 10000 -jd2:ntrials 100 -ex1 -ex2aro -beta -use_input_sc -in:file:native chainA_chainB_20_04_15_28_11.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3981396

ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF
ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 380
BOINC:: Error reading and gzipping output datafile: default.out
 called boinc_finish(1)

</stderr_txt>
]]>
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Millenium

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Message 94263 - Posted: 12 Apr 2020, 18:50:28 UTC
Last modified: 12 Apr 2020, 18:50:49 UTC

Just had this with a 4.15 WU

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<message>
Funzione non corretta.
 (0x1) - exit code 1 (0x1)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.15_windows_x86_64.exe -silent_gz -mute all -s chainA_chainB_20_04_15_28_12.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol local_docking_20_04_15_28_12.xml -out:nstruct 10000 -jd2:ntrials 100 -ex1 -ex2aro -beta -use_input_sc -in:file:native chainA_chainB_20_04_15_28_12.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3986571

ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF
ERROR:: Exit from: ......srccoreimport_poseimport_pose.cc line: 380
BOINC:: Error reading and gzipping output datafile: default.out
20:41:28 (3556): called boinc_finish(1)

</stderr_txt>
]]>

Task: https://boinc.bakerlab.org/rosetta/result.php?resultid=1147880898

All the others are running fine, just reporting this particular one, another user too received it and had the same error so it is a bugged WU.
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James W

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Message 94316 - Posted: 13 Apr 2020, 4:51:31 UTC

Name: 2d1014c00c014fc0ae96dda2d79baef5_dock_ens3_20_04_15_58_03_localDocking_8_SAVE_ALL_OUT_912589_8_0
Application: Rosetta v4.15 arm-android-linux-gnu
Device: 3396190--an Amazon Fire tablet running Android
3.18.19-g4bb6ac47eed (Android 5.1.1)
.
Task: 1148219229, and WU: 1033312411.
Status: Completed and validated.
Exit status: 0 (0x00000000)
Stderr output:
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x28ac
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu: unused DT entry: type 0x6fffffff arg 0x2
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu -silent_gz -mute all -s chainA_chainB_20_04_15_58_03.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol local_docking_20_04_15_58_03.xml -out:nstruct 10000 -jd2:ntrials 100 -ex1 -ex2aro -beta -use_input_sc -in:file:native chainA_chainB_20_04_15_58_03.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 1000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3406453
======================================================
DONE :: 1000 starting structures 1544.29 cpu seconds
This process generated 1000 decoys from 1000 attempts
======================================================

My first task on my Amazon Fire. Small credit number (5+) with 1000 decoys, but doing something. Hopefully result would be of use. Worth keeping this device available to crunch?
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James W

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Message 94322 - Posted: 13 Apr 2020, 8:57:06 UTC

27bc1069693f209043a6da29aa50df68_dock_ens3_20_04_15_58_39_globalDocking_1_SAVE_ALL_OUT_912570_8_0
Application: Rosetta v4.15 arm-android-linux-gnu
Device: 3396190--an Amazon Fire tablet running Android
3.18.19-g4bb6ac47eed (Android 5.1.1).
Task: 1148219018, and WU: 1033312234.
Status: Completed and validated.
Exit status: 0 (0x00000000)
Stderr output:
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x28ac
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu: unused DT entry: type 0x6fffffff arg 0x2
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu -silent_gz -mute all -s chainA_chainB_patchdock_split_01_20_04_15_58_39.pdb -patchdock chainA_chainB_patchdock_split_01_20_04_15_58_39.patchdock -patchdock_random_entry 1 6 -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol global_docking_20_04_15_58_39.xml -out:nstruct 10000 -ex1 -ex2aro -beta -jd2:ntrials 100 -use_input_sc -in:file:native chainA_chainB_20_04_15_58_39.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 1000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3414333
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 126 starting structures 12126.5 cpu seconds
This process generated 126 decoys from 126 attempts
======================================================
Note that the above WARNINGs repeat multiple times.
Previous task on this Amazon Fire was "....localDocking...." This task was for "....globalDocking...." with 26+ credit versus 5+. Just a bit better.
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James W

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Message 94347 - Posted: 13 Apr 2020, 14:26:44 UTC

Name: 1b539b9096d09aa7756c5d884dd3ad0d_dock_ens_20_04_15_28_11_localDocking_0_SAVE_ALL_OUT_910393_35_0
Application: Rosetta v4.15 windows_x86_64
Device: 1759960, Task: 1147167016, and WU: 1032418450.
Status: Error while computing.
Exit status: 1 (0x00000001) Unknown error code
Stderr output:
Incorrect function. (0x1) - exit code 1 (0x1)
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.15_windows_x86_64.exe -silent_gz -mute all -s chainA_chainB_20_04_15_28_11.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol local_docking_20_04_15_28_11.xml -out:nstruct 10000 -jd2:ntrials 100 -ex1 -ex2aro -beta -use_input_sc -in:file:native chainA_chainB_20_04_15_28_11.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3979246
ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF
ERROR:: Exit from: ......srccoreimport_poseimport_pose.cc line: 380
BOINC:: Error reading and gzipping output datafile: default.out
This is an error seen in a number of reports from different users involving the "localDocking" tasks (and Windows in my case). Able to crunch using my Amazon tablet however.
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juan BFP

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Message 94362 - Posted: 13 Apr 2020, 17:51:01 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=1147882702

Credit	20.00


Run this Wu for >12 Hrs, exit normally and receive only 20 credits.
If that right or i miss something?
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Message 94364 - Posted: 13 Apr 2020, 18:35:30 UTC - in response to Message 94362.  

The task was ended by the watchdog. There is currently an issue with the i686 Linux version of the application. See discussion here.
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Keith Myers
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Message 94368 - Posted: 13 Apr 2020, 19:43:07 UTC - in response to Message 94362.  

https://boinc.bakerlab.org/rosetta/result.php?resultid=1147882702

Credit	20.00


Run this Wu for >12 Hrs, exit normally and receive only 20 credits.
If that right or i miss something?

Don't run any of the i686 applications. Only the x86_64 applications work. Use the <no_alt_platform>1</no_alt_platform> in the cc_config.xml file to only run native x86_64 applications.
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Message 94392 - Posted: 13 Apr 2020, 22:15:36 UTC - in response to Message 94206.  

It looks like there's going to be some problems with v 4.15- Estimated completion times are 39min 18sec; that's going to lead to a lot of overfilled caches & Tasks timing out....
The first v4.15 tasks I got were also noted to be in the 39 min. range. However, my BOINC manager revised their completion times to 01:14:54, almost twice as long. Will see if I get same results as you did.

It is typical for any new versions of BOINC apps running on your computer to have initial estimated completion fairly far off their actual completion times. It typically takes about ten successful tasks with the new version for BOINC to work out how to correct those initial completion time estimates for your computer.
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Message 94396 - Posted: 13 Apr 2020, 22:28:18 UTC - in response to Message 94220.  

Thanks for the setup suggestions. I hadn't changed configuration since I set up BOINC and began working on Seti. Started with a Pentium II, then III, and up to Pentium IV with XP before getting my Optiplex over 6 yrs ago. How "state-of-the-art" does change! I mainly used my Optiplex (i5) for working as a medical transcriptionist, so didn't want BOINC getting in the way. Rosetta was just a backup project at the time. I boosted RAM from 4 to 8G, which made a major difference. Motherboard only has 2 RAM slots, however. (I remember how RAM used to cost a mint.)

With Rosetta's current short deadlines as a regular thing of late, and its being a memory glutton, can be a challenge keeping a moderate desktop unit able to keep pace.

Thanks again! :-)

PS: for v4.15 apps, my estimated completion time is now up to 4 hrs.

These days, many memory boards have more memory per board. If you know enough information about what motherboard you are using, this site offers help determining whether you can get boards that are compatible but have more and faster memory per board:

https://www.crucial.com/
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James W

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Message 94424 - Posted: 14 Apr 2020, 8:49:21 UTC

Name: xxxxx_dock_ens_20_04_15_28_XX_localDocking_0_SAVE_ALL_OUT_xxxxx
Application: Rosetta v4.15 windows_x86_64
Device: 3710630
Status: Error while computing.
Exit status: 1 (0x00000001) Unknown error code
Stderr output:
Incorrect function. (0x1) - exit code 1 (0x1)
ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF
ERROR:: Exit from: ......srccoreimport_poseimport_pose.cc line: 380
BOINC:: Error reading and gzipping output datafile: default.out
I rec'd the following batch of 5 tasks for above device which all errored as noted. They errored between 1 and 2 minutes into their run. They were all "localDocking" tasks as I've noted earlier for both of my PCs. "GlobalDocking" tasks work okay. Also, I got the "luck of the draw" to receive them all after they'd failed for other hosts!
I'm going to just abort these "localDocking" tasks until I hear of a fix.

https://boinc.bakerlab.org/rosetta/result.php?resultid=1148949326
https://boinc.bakerlab.org/rosetta/result.php?resultid=1148949325
https://boinc.bakerlab.org/rosetta/result.php?resultid=1148949291
https://boinc.bakerlab.org/rosetta/result.php?resultid=1148950274
https://boinc.bakerlab.org/rosetta/result.php?resultid=1148950273
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Message 94435 - Posted: 14 Apr 2020, 11:58:23 UTC

Hi,

Linux Mint 19.3 on a i3 8300 with 8GB Ram.

Rosetta v4.15 i686-pc-linux-gnu runs 16h for 20 Points.

stdrr out:
======================================================
DONE :: 1 starting structures 57613 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================

The WUs should run 12h (Rosetta mini do it so and get good Point with a lot more than 1 decoys from 1 attempts).
Another member of Seti Germany use Ryzen with Linux an the same Problem. His preference is 6h for a WU. Rosetta mini do it well, but the Rosetta v4.15 i686-pc-linux-gnu go up to 10h. Yes, the same 4h more like at mine 12h to 16h.
Is it normal, that Rosetta stoppt crunching at 4h over the given time at Rosetta preferences?

I believe we wastet CPU-time here? Under Windows noch Problem with that...i think.

Tschau Norman
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Message 94440 - Posted: 14 Apr 2020, 12:58:26 UTC - in response to Message 94435.  
Last modified: 14 Apr 2020, 12:58:57 UTC

To any that have found this thread because they are having Linux i686 issues, please join Ralph (project url is: http://ralph.bakerlab.org/) with your machine. This will help with testing when changes are made to address this, and confirm they are working.

No promises on when a new version will be available there. It may take some time.

If you would like to try creating a simple cc_config.xml file, you can get BOINC to use the x86_64 version instead of the i686 version that is having trouble. There is an example here.
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Message 94445 - Posted: 14 Apr 2020, 13:52:37 UTC
Last modified: 14 Apr 2020, 13:59:03 UTC

Will creating the cc_config.xml file input that is recommended also limit Rosetta Mini WUs that are also i686? They seem to be working fine (actually working quite well based on RAC) on my Linux rigs. It is only the 4.12 and now 4.15 i686 WUs that are having problems.

(...and I got signed up on Ralph, awaiting test WUs when they are available for one of my Linux rigs.)
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James W

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Message 94509 - Posted: 15 Apr 2020, 6:49:40 UTC

Name: xxxxx_dock_ens_20_04_15_28_XX_localDocking_0_SAVE_ALL_OUT_xxxxx
Application: Rosetta v4.15 windows_x86_64
Device: 1759960
Task: 1150250651. WU: 1032321020
Status: Error while computing.
Exit status: 1 (0x00000001) Unknown error code
Errors: Too many errors (may have bug) Too many total results.
Stderr output:
Incorrect function. (0x1) - exit code 1 (0x1)
ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF
ERROR:: Exit from: ......srccoreimport_poseimport_pose.cc line: 380
BOINC:: Error reading and gzipping output datafile: default.out
Errored with run time 1 minute & 5 seconds. Again was a "localDocking" task as I've noted earlier for both of my PCs. See my previous message 94424 "GlobalDocking" tasks work okay. This type of task should not be distributed for Rosetta v4.15 windows_x86_64 as they will fail and are a waste of time and energy.
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Message 94657 - Posted: 17 Apr 2020, 6:50:47 UTC

Some problems with "12v1n_" wus.
I have 4hs wus (in my profile), but these are crunching over 10hs and with NO checkpoint
This is and example 1152133806:
Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Breakpoint Encountered (0x80000003) at address 0x75C1E062

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