Rosetta 4.1+ and 4.2+

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Raistmer

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Message 95707 - Posted: 1 May 2020, 23:55:13 UTC - in response to Message 95678.  

I updated the rosetta app version to 4.20 for the arm, android, and mac platforms. I will update the remaining platforms in the next day or so.

Please post issues regarding this updated app version here.

This update includes:

1. extraction of the Rosetta database into the project directory with all following jobs reading from the same database rather than extracting into the slot directory for every job. This significantly reduces the disk usage per job.
2. checkpointing in the Rosetta comparative modeling protocol. This should significantly reduce wasted cpu time if jobs are preempted often, particularly for jobs that take a long time to produce models.


Observed first run of 4 v4.20 tasks simultaneously for my quad host.
First instance extracted archive (big I/O counts) then 3 others just use it (low I/O counts).
No issues and no fallbacks on this host.
Excelent!
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Profile Grant (SSSF)

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Message 95708 - Posted: 2 May 2020, 0:04:34 UTC - in response to Message 95706.  

but this is a brand new system so it is trying to sort itself
And with new applications just released, it's going to have to start from scratch all over again.
Grant
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sgaboinc

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Message 95761 - Posted: 2 May 2020, 4:21:13 UTC
Last modified: 2 May 2020, 4:21:34 UTC

4.20 is very space efficient i've got 3 threads on rosetta@home running on Pi4 it used a mere 1.54 GB of disk space.
previously 3 threads would have used some 4 GB of disk space
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OBI

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Message 95805 - Posted: 2 May 2020, 14:18:40 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=1165528117

Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_7qc4vs2m_924647_9_0

<core_client_version>7.16.5</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.15_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol jhr_boinc_v4.xml @flags -in:file:silent Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_7qc4vs2m.silent -in:file:silent_struct_type binary -silent_gz -mute all -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_7qc4vs2m.zip @Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_7qc4vs2m.flags -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 1027299
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.

ERROR: Assertion `copy_pose.size() == native.size()` failed. MSG:the reference pose must be the same size as the working pose
ERROR:: Exit from: ......srcprotocolsprotein_interface_designfiltersRmsdFilter.cc line: 323
10:34:17 (3376): called boinc_finish(0)

</stderr_txt>
]]>
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Tomcat雄猫

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Message 95807 - Posted: 2 May 2020, 14:24:04 UTC - in response to Message 95805.  
Last modified: 2 May 2020, 14:24:28 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=1165528117

Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_7qc4vs2m_924647_9_0

<core_client_version>7.16.5</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.15_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol jhr_boinc_v4.xml @flags -in:file:silent Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_7qc4vs2m.silent -in:file:silent_struct_type binary -silent_gz -mute all -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_7qc4vs2m.zip @Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_7qc4vs2m.flags -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 1027299
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.

ERROR: Assertion `copy_pose.size() == native.size()` failed. MSG:the reference pose must be the same size as the working pose
ERROR:: Exit from: ......srcprotocolsprotein_interface_designfiltersRmsdFilter.cc line: 323
10:34:17 (3376): called boinc_finish(0)

</stderr_txt>
]]>


Hmm, did you somehow stopped the task by any chance? I have a chance of getting that error whenever I stop a HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_ and it needs to continue from a checkpoint. That's the only repeatable way of getting this error that I've observed.
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OBI

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Message 95808 - Posted: 2 May 2020, 14:28:32 UTC - in response to Message 95807.  
Last modified: 2 May 2020, 14:29:21 UTC

My tasks indeed get started and stopped quite often since i'm using the machine for other things too.
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Tomcat雄猫

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Message 95811 - Posted: 2 May 2020, 14:40:31 UTC - in response to Message 95808.  
Last modified: 2 May 2020, 14:40:45 UTC

My tasks indeed get started and stopped quite often since i'm using the machine for other things too.

BTW, this thread is an interesting read, regarding that specific error with those tasks. It claims that the BOINC screensaver causes issues.
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13825
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Message 95878 - Posted: 2 May 2020, 22:13:31 UTC

I now seem to have several slots with the 960MB folder called "minirosetta_database", I also have in the projects directory a 960MB folder called "database_357d5d93529_n_methyl". I have only Rosetta and Ralph v4.20 work onboard at this point. I was expecting to no longer see the large folder in the slots directory. But they seem to have different names?
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Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
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Admin
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Message 95882 - Posted: 2 May 2020, 22:54:53 UTC - in response to Message 95878.  

A researcher recently submitted some "minirosetta" app jobs and these still extract the database into the slot directory as "minirosetta_database". Might you have some "minirosetta" jobs running?
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Profile Feet1st
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Message 95894 - Posted: 3 May 2020, 3:33:15 UTC - in response to Message 95882.  
Last modified: 3 May 2020, 3:37:18 UTC

The task list shows the application for all is Rosetta 4.20 on my host.

Is there a symbolic link in each slots directory back to the project expanded DB?

Each slot seems to have a file called "minirosetta_database.zip.is_extracted"
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Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/
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Billy

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Message 95896 - Posted: 3 May 2020, 3:57:28 UTC

I am getting a few Tasks with this type of error, but they validate and Outcome is Success. Running on Mac. Task 1168032844

<core_client_version>7.16.6</core_client_version>
<![CDATA[
<stderr_txt>
ing freed was not allocated
*** set a breakpoint in malloc_error_break to debug
rosetta_4.20_x86_64-apple-darwin(71802,0x7fffa915f3c0) malloc: *** error for object 0x112ed70c0: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
rosetta_4.20_x86_64-apple-darwin(71802,0x7fffa915f3c0) malloc: *** error for object 0x112ed70c0: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
rosetta_4.20_x86_64-apple-darwin(71802,0x7fffa915f3c0) malloc: *** error for object 0x112ed70c0: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
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MarkJ

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Message 95899 - Posted: 3 May 2020, 5:45:01 UTC

The methyl database, zip file and the fft file, which I assume is a TrueType font, seem to be flagged as executable under Linux.

# ls -lh
<snipped>
drwxr-xr-x 3 boinc boinc 4.0K May  3 11:51 database_357d5d93529_n_methyl
-rwxr-xr-x 1 boinc boinc 485M May  3 11:50 database_357d5d93529_n_methyl.zip
<more snipping>
-rwxr-xr-x 1 boinc boinc 345K May  3 11:42 LiberationSans-Regular.ttf

BOINC blog
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brendi000

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Message 95923 - Posted: 3 May 2020, 12:57:19 UTC

Almost instant error access violation with
WU 3cl_9aa_6lu7_modified_AVLstub_relaxed_renumbered_0200_101_extract_B_SAVE_ALL_OUT_926298_299

Log:
https://boinc.bakerlab.org/rosetta/result.php?resultid=1168708291[/url]
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Ivailo Bonev

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Message 95932 - Posted: 3 May 2020, 14:49:35 UTC - in response to Message 95923.  
Last modified: 3 May 2020, 14:49:51 UTC

Same error
3cl_9aa_6lu7_modified_AVLstub_relaxed_renumbered_0004_76_extract_B_SAVE_ALL_OUT_926264_295_1

https://boinc.bakerlab.org/rosetta/result.php?resultid=1168836107

Probably these are "bad" units.
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Profile Feet1st
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Message 96077 - Posted: 4 May 2020, 23:04:38 UTC - in response to Message 95894.  

BOINC hung up and, when I rebooted my computer, it seems to have cancelled all of the WUs it had, and downloaded a new batch of v4.20 junior halfroids.

I now have a 1GB minirosetta_database directory in each of my 4 slot directories, along with a file called minirosetta_database.zip.is_extracted

The project directory has a 1GB database_357d5d93529_n_methyl directory. along with the .zip, a .zip.is_bad and a .zip.is_extracted.

The application shown is Rosetta 4.20 (not mini).

The creation dates in the slots are from when I rebooted. The creation dates on the project directory are from the 2nd when I got v4.20.

I was expecting all v4.20 tasks to use the directory under the project rather than within the slot.
Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/
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Message 96078 - Posted: 4 May 2020, 23:12:58 UTC - in response to Message 96077.  

For some reason your computer is not able to extract the database in the project directory. Can you email me, this is David K, and maybe we can work together to try to debug this. I was not able to reproduce this issue.
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ZhiweiLiang

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Message 96086 - Posted: 5 May 2020, 7:29:19 UTC - in response to Message 88767.  

Can you reduce the size of task for Android phones? I have Samsung S20 equiped with Qualcomm flagship processor Snapdragon 865, and it could take more than half day to finish one task. And the deadline was set to about 3 days after task downloaded. I have to keep my phone charged most time of a day to finish the tasks received. This is not reasonable and gave me a lot of pressure. So, could you please reduce the size of each task? Thanks
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michelv

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Message 96087 - Posted: 5 May 2020, 7:40:17 UTC

WinXP:

"Why should I not shake hands with a Corona infected person?"
https://www.bbc.com/news/uk-52192604

"Why use an operating system that has been EOL for years..."
https://null-byte.wonderhowto.com/how-to/hack-like-pro-exploit-and-gain-remote-access-pcs-running-windows-xp-0134709/

People, please stop supporting people that still use XP. That is the only way to finally get rid of it.
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sgaboinc

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Message 96091 - Posted: 5 May 2020, 8:07:35 UTC

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PorkyPies

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Message 96097 - Posted: 5 May 2020, 10:00:14 UTC - in response to Message 96091.  
Last modified: 5 May 2020, 10:01:23 UTC

3 finish file present too long errors on Pi4 Rosetta v4.20 aarch64-unknown-linux-gnu

That’s a BOINC issue. If you can get a 7.16.5 or later one might help. They extended the time limit before BOINC complains about the files still being in the slot directory.
MarksRpiCluster
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Message boards : Number crunching : Rosetta 4.1+ and 4.2+



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