Problems and Technical Issues with Rosetta@home

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Profile Grant (SSSF)

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Message 102582 - Posted: 11 Sep 2021, 0:03:56 UTC

I don't want to jinx things, but so far no errors on any of the new Tasks.
Grant
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Message 102583 - Posted: 11 Sep 2021, 0:30:16 UTC - in response to Message 102581.  


The only thing that will stop (or should stop) you from getting work is if the Task won't be returned before the deadline. Having zero cache means just that- no cache. You will still get work- but only have the work you are presently processing, When it's done another Task will be downloaded.

That is so only if he is not running any other projects. But it appeared to me that he is.


Indeed, I have WCG running. My issue is that WCG appears to have a higher priority than Rosetta despite my resource settings. Rosetta has 200 resource share vs 100 for WCG.

When my devices complete a task, they seem to prefer downloading WCG tasks over Rosetta ones. I do NOT have a bunch of tasks piled up. With my current settings BOINC only downloads new tasks if the current ones are almost complete.

BTW, is there currently a shortage of Android tasks? It's been a really long time since my phone received a Rosetta task.
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Tomcat雄猫

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Message 102584 - Posted: 11 Sep 2021, 0:30:18 UTC - in response to Message 102581.  
Last modified: 11 Sep 2021, 0:31:46 UTC

Double post please delete.
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Tomcat雄猫

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Message 102585 - Posted: 11 Sep 2021, 0:30:20 UTC - in response to Message 102581.  
Last modified: 11 Sep 2021, 0:32:44 UTC

Please delete, dunno why there were this many duplicate posts.
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Tomcat雄猫

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Message 102586 - Posted: 11 Sep 2021, 0:30:21 UTC - in response to Message 102581.  
Last modified: 11 Sep 2021, 0:31:14 UTC

Triple post please delete
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Message 102587 - Posted: 11 Sep 2021, 1:09:20 UTC - in response to Message 102583.  

[snip]

When my devices complete a task, they seem to prefer downloading WCG tasks over Rosetta ones. I do NOT have a bunch of tasks piled up. With my current settings BOINC only downloads new tasks if the current ones are almost complete.

WCG usually has more tasks available. Lately, Rosetta usually doesn't.
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Profile Grant (SSSF)

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Message 102588 - Posted: 11 Sep 2021, 1:51:33 UTC - in response to Message 102583.  

BTW, is there currently a shortage of Android tasks? It's been a really long time since my phone received a Rosetta task.
There are no Android or Linux or Windows Tasks, they can all be processed by the appropriate application.
However many of the current Tasks need over 1GB of RAM. Depending on your BOINC memory settings & the amount of available RAM on the Android device it may not be possible for it to process them, so it won't get any even if Rosetta is owed processing time on the device.
Grant
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Message 102589 - Posted: 11 Sep 2021, 7:09:55 UTC - in response to Message 102576.  
Last modified: 11 Sep 2021, 7:12:52 UTC

Thank you, I modified the cache settings and resource share on the i5-machine. For the last months Rosetta was the only project on this PC, yesterday I started yoyo@home because of the idle process.
It is 100-100 the resource share between Rosetta and yoyo, but no new tasks in Rosetta again.

I want to run Rosetta on i5 and Ryzen5 only.

Most of recent Rosetta tasks use a huge amount of memory, the 32 bit system can handle less than 4 GB. I wait for a while and reinstall the system with 64 bit and I will increase the RAM to 8 GB.

I hope it will help.
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Tomcat雄猫

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Message 102590 - Posted: 11 Sep 2021, 9:21:12 UTC - in response to Message 102588.  
Last modified: 11 Sep 2021, 9:24:15 UTC

There are no Android or Linux or Windows Tasks, they can all be processed by the appropriate application.
However many of the current Tasks need over 1GB of RAM. Depending on your BOINC memory settings & the amount of available RAM on the Android device it may not be possible for it to process them, so it won't get any even if Rosetta is owed processing time on the device.



Understood, thanks!

I should in theory have over 6 GB of RAM available, my RAM limit is at 100% (12GB). Let's see if I get any Rosetta tasks. I've gotten 2 Ralph tasks a few weeks back but so far it's been WCG for weeks.

It has to be noted that the resource share of Rosetta@home on my phone has been set to 100, just like WCG. I guess if a resource share of 200 for Rosetta and 100 for WCG results in BOINC seemingly favouring WCG tasks, equal resource share will just make it worse.
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Profile Grant (SSSF)

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Message 102591 - Posted: 12 Sep 2021, 4:30:44 UTC
Last modified: 12 Sep 2021, 4:36:42 UTC

Just had 2 5nvx_graft_buwei_ Tasks, one ran for 10min the other 26min. They both Validated although they produced errors

<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10--fuse--predictor_v11_boinc_fix--fuse--tslp_design_v1_boinc_fix_plus6.xml @5nvx_graft_buwei_flags -in:file:silent 5nvx_graft_buwei_xaf_SAVE_ALL_OUT_IGNORE_THE_REST_5ht6pv3o.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 5nvx_graft_buwei_xaf_SAVE_ALL_OUT_IGNORE_THE_REST_5ht6pv3o.zip @5nvx_graft_buwei_xaf_SAVE_ALL_OUT_IGNORE_THE_REST_5ht6pv3o.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 2084657
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: m_ems_3hM_2942_000000222_0001_44_63_H_._HHH_b2_01435_0001_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
13:57:22 (7176): called boinc_finish(0)

</stderr_txt>
]]>



<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10--fuse--predictor_v11_boinc_fix--fuse--tslp_design_v1_boinc_fix_plus6.xml @5nvx_graft_buwei_flags -in:file:silent 5nvx_graft_buwei_xaf_SAVE_ALL_OUT_IGNORE_THE_REST_4do0cs3f.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 5nvx_graft_buwei_xaf_SAVE_ALL_OUT_IGNORE_THE_REST_4do0cs3f.zip @5nvx_graft_buwei_xaf_SAVE_ALL_OUT_IGNORE_THE_REST_4do0cs3f.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 1332669
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: m_036bed11a46af16b1bcff1c055f4941a_0001_000000269_0001_15_31_H_._HHH_b1_04870_0001_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
13:25:06 (6244): called boinc_finish(0)

</stderr_txt>
]]>



Edit- just got a 3rd one that lasted for 15min.

<core_client_version>7.16.11</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10--fuse--predictor_v11_boinc_fix--fuse--tslp_design_v1_boinc_fix_plus6.xml @5nvx_graft_buwei_flags -in:file:silent 5nvx_graft_buwei_xaf_SAVE_ALL_OUT_IGNORE_THE_REST_8oi6gv3g.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 5nvx_graft_buwei_xaf_SAVE_ALL_OUT_IGNORE_THE_REST_8oi6gv3g.zip @5nvx_graft_buwei_xaf_SAVE_ALL_OUT_IGNORE_THE_REST_8oi6gv3g.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 1500897
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: m_HHH_b2_00235_000000121_0001_23_40_H_._HHH_b2_05032_0002_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
14:01:48 (1528): called boinc_finish(0)

</stderr_txt>
]]>

Grant
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Message 102592 - Posted: 12 Sep 2021, 6:44:53 UTC - in response to Message 102591.  

Just had 2 5nvx_graft_buwei_ Tasks, one ran for 10min the other 26min. They both Validated although they produced errors


Same errors on Ralph
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Profile Grant (SSSF)

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Message 102594 - Posted: 12 Sep 2021, 9:19:21 UTC

I've now got 4 of those 5nvx_graft_buwei_ Tasks that died after 2min or less, which are Invalid due to a Validate error, even though they are giving the same Stderr output error as the ones that run for (slightly) longer & Validate.
And 2 more of those short runs (but longer than 2min) producing errors that Validate.

I've got 2 5nvx_graft_buwei_ Tasks that are still running- 3hrs and 4hr 45min and counting. Will be interesting to see if they make it to 8 hours, and if there is an error in the Stderr output when they are done or not.
Grant
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Message 102595 - Posted: 12 Sep 2021, 19:55:04 UTC - in response to Message 102594.  
Last modified: 12 Sep 2021, 19:58:23 UTC

I've now got 4 of those 5nvx_graft_buwei_ Tasks that died after 2min or less, which are Invalid due to a Validate error, even though they are giving the same Stderr output error as the ones that run for (slightly) longer & Validate.
And 2 more of those short runs (but longer than 2min) producing errors that Validate.

I've got 2 5nvx_graft_buwei_ Tasks that are still running- 3hrs and 4hr 45min and counting. Will be interesting to see if they make it to 8 hours, and if there is an error in the Stderr output when they are done or not.
So far i have 3 _5nvx_graft_buwei_ Tasks that produced Decoys & Validated.
All the others (Valids & Invalids) just resulted in error messages.

Roughly a 82% failure rate.

No signs of issues with any of the other Tasks yet.
Grant
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Message 102596 - Posted: 12 Sep 2021, 19:57:26 UTC - in response to Message 102594.  

I've got 2 5nvx_graft_buwei_ Tasks that are still running- 3hrs and 4hr 45min and counting. Will be interesting to see if they make it to 8 hours, and if there is an error in the Stderr output when they are done or not.


I cannot understand.
Correct wus have the same error, but it's validated

ERROR: [ERROR] Unable to open constraints file: m_HHH_b1_05679_000000205_0001_20_37_H_._HHH_b1_02798_0002_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
21:42:17 (7880): called boinc_finish(0)

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Profile Grant (SSSF)

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Message 102597 - Posted: 12 Sep 2021, 20:01:48 UTC - in response to Message 102596.  

I cannot understand.
Correct wus have the same error, but it's validated

[quote]ERROR: [ERROR] Unable to open constraints file: m_HHH_b1_05679_000000205_0001_20_37_H_._HHH_b1_02798_0002_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
21:42:17 (7880): called boinc_finish(0)
Yep.
If it dies early, you get a Validation error. If it runs for more than a few minutes, but less than the full time, it Validates- even though it doesn't produce any decoys & it gives the same error as the ones that die in 2 min or less.
Grant
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Message 102604 - Posted: 14 Sep 2021, 16:57:33 UTC

Name 5nvx_graft_buwei_xab_SAVE_ALL_OUT_IGNORE_THE_REST_0oe9kw2f_1731803_2_0

Server state Over
Outcome Computation error
Client state Compute error
Exit status 1 (0x00000001) Unknown error code

Stderr output:
<core_client_version>7.16.11</core_client_version>
<![CDATA[
<message>
Funktio ei kelpaa.
(0x1) - exit code 1 (0x1)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol pdblite_boinc_120_10--fuse--predictor_v11_boinc_fix--fuse--tslp_design_v1_boinc_fix_plus6.xml @5nvx_graft_buwei_flags -in:file:silent 5nvx_graft_buwei_xab_SAVE_ALL_OUT_IGNORE_THE_REST_0oe9kw2f.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 5nvx_graft_buwei_xab_SAVE_ALL_OUT_IGNORE_THE_REST_0oe9kw2f.zip @5nvx_graft_buwei_xab_SAVE_ALL_OUT_IGNORE_THE_REST_0oe9kw2f.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 3752359
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: m_ems_3hC_506_000000211_0001_43_58_H_._HHH_b2_02864_0001_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
BOINC:: Error reading and gzipping output datafile: default.out
18:28:53 (10104): called boinc_finish(1)

</stderr_txt>
]]>

What to do?
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YAG

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Message 102605 - Posted: 14 Sep 2021, 18:31:00 UTC

Good afternoon,

I have received four tasks of the application "rosetta python projects v1.03 (vbox64) x86_64-pc-linux-gnu". All of the tasks failed with the same error: "-186 (0xFFFFFF46) ERR_RESULT_DOWNLOAD". In the logs appears the following:
WU download error: couldn't get input files:
<file_xfer_error>
<file_name>AIMNet_vm_v2.vdi</file_name>
<error_code>-119 (md5 checksum failed for file)</error_code>
<error_message>MD5 check failed</error_message>


This is the computer who obtained the errors: https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=5909874

Here are the tasks:
https://boinc.bakerlab.org/rosetta/result.php?resultid=1425336189
https://boinc.bakerlab.org/rosetta/result.php?resultid=1425334597
https://boinc.bakerlab.org/rosetta/result.php?resultid=1425332824
https://boinc.bakerlab.org/rosetta/result.php?resultid=1425333029


Regards,
YAG
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Message 102606 - Posted: 14 Sep 2021, 18:56:00 UTC - in response to Message 102604.  

[snip]

ERROR: [ERROR] Unable to open constraints file: m_ems_3hC_506_000000211_0001_43_58_H_._HHH_b2_02864_0001_1_0001.MSAcst

What to do?

That's the important line of the error messages.

That usually means that one of the input files for the task was not downloaded correctly.

Lately, that has often been because the file was not in the correct place on the server. If so, you can't do much other than wait for a better task.

If anyone else who gets a task from the same workunit and has it fail the same way, you'll get a little bit of credit for trying to run the task.
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Message 102608 - Posted: 14 Sep 2021, 19:29:02 UTC - in response to Message 102605.  
Last modified: 14 Sep 2021, 19:30:13 UTC

Good afternoon,

I have received four tasks of the application "rosetta python projects v1.03 (vbox64) x86_64-pc-linux-gnu". All of the tasks failed with the same error: "-186 (0xFFFFFF46) ERR_RESULT_DOWNLOAD". In the logs appears the following:
WU download error: couldn't get input files:
<file_xfer_error>
<file_name>AIMNet_vm_v2.vdi</file_name>
<error_code>-119 (md5 checksum failed for file)</error_code>
<error_message>MD5 check failed</error_message>



Same error on Win 10
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Message 102625 - Posted: 15 Sep 2021, 17:13:22 UTC

My Boinc is set up as follows (from 32Gb total RAM):

15/09/2021 14:43:09 | | max memory usage when active: 21241.68 MB
15/09/2021 14:43:09 | | max memory usage when idle: 27777.58 MB


I've got one task "Waiting for Memory" so I stopped processing all new tasks to find out at what point it will run.
I'm currently down to just one other task running (from 16 cores) and it's still not able to continue yet, so I looked further and in Properties the task is showing

Virtual memory size 98.98 GB
Working set size 27.05 GB


"Houston, we have a problem..."
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Message boards : Number crunching : Problems and Technical Issues with Rosetta@home



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