Rosetta 4.1+ and 4.2+

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Profile Grant (SSSF)

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Joined: 28 Mar 20
Posts: 1364
Credit: 13,624,788
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Message 96550 - Posted: 16 May 2020, 4:23:22 UTC
Last modified: 16 May 2020, 4:27:06 UTC

Looks like we might have a batch of dodgy Work Units- 4 Tasks, 4 failures.
I'm thinking there is an issue with the length of the file name (or maybe some characters in it?) which results in the upload of the finished result failing- because there is no result file to upload.
WARNING! attempt to create gzipped file ../../projects/boinc.bakerlab.org_rosetta/split_pass_bp_agba... ... failed.


split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509201412_0001_0001_fragments_fold_SAVE_ALL_OUT_929542_251_0

<core_client_version>7.6.33</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -abinitio::fastrelax 1 -ex2aro 1 -frag3 00001.200.3mers.index -in:file:native 00001.pdb -silent_gz 1 -frag9 00001.200.9mers.index -out:file:silent default.out -ex1 1 -abinitio::rsd_wt_loop 0.5 -relax::default_repeats 5 -abinitio::use_filters false -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.5 -beta 1 -abinitio::rg_reweight 0.5 -in:file:boinc_wu_zip split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509201412_0001_0001_fragments_data.zip -out:file:silent default.out -silent_gz -mute all -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 1681922
Using database: database_357d5d93529_n_methylminirosetta_database
WARNING! attempt to create gzipped file ../../projects/boinc.bakerlab.org_rosetta/split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509201412_0001_0001_fragments_fold_SAVE_ALL_OUT_929542_251_0_r676684231_0 failed.
======================================================
DONE ::     1 starting structures  28322.4 cpu seconds
This process generated     28 decoys from      28 attempts
======================================================
BOINC :: WS_max 5.5067e+08
06:36:27 (1128): called boinc_finish(0)

</stderr_txt>
<message>
upload failure: <file_xfer_error>
  <file_name>split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509201412_0001_0001_fragments_fold_SAVE_ALL_OUT_929542_251_0_r676684231_0</file_name>
  <error_code>-161 (not found)</error_code>
</file_xfer_error>

</message>
]]>




split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509201412_0001_0001_fragments_fold_SAVE_ALL_OUT_929542_255_0

<core_client_version>7.6.22</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -abinitio::fastrelax 1 -ex2aro 1 -frag3 00001.200.3mers.index -in:file:native 00001.pdb -silent_gz 1 -frag9 00001.200.9mers.index -out:file:silent default.out -ex1 1 -abinitio::rsd_wt_loop 0.5 -relax::default_repeats 5 -abinitio::use_filters false -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.5 -beta 1 -abinitio::rg_reweight 0.5 -in:file:boinc_wu_zip split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509201412_0001_0001_fragments_data.zip -out:file:silent default.out -silent_gz -mute all -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 1681918
Using database: database_357d5d93529_n_methylminirosetta_database
WARNING! attempt to create gzipped file ../../projects/boinc.bakerlab.org_rosetta/split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509201412_0001_0001_fragments_fold_SAVE_ALL_OUT_929542_255_0_r2090853116_0 failed.
======================================================
DONE ::     1 starting structures  28935.4 cpu seconds
This process generated     29 decoys from      29 attempts
======================================================
BOINC :: WS_max 5.4961e+08
06:45:40 (4072): called boinc_finish(0)

</stderr_txt>
<message>
upload failure: <file_xfer_error>
  <file_name>split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509201412_0001_0001_fragments_fold_SAVE_ALL_OUT_929542_255_0_r2090853116_0</file_name>
  <error_code>-161 (not found)</error_code>
</file_xfer_error>

</message>
]]>




split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509203824_0001_0001_fragments_fold_SAVE_ALL_OUT_929543_307_0

<core_client_version>7.6.22</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -abinitio::fastrelax 1 -ex2aro 1 -frag3 00001.200.3mers.index -in:file:native 00001.pdb -silent_gz 1 -frag9 00001.200.9mers.index -out:file:silent default.out -ex1 1 -abinitio::rsd_wt_loop 0.5 -relax::default_repeats 5 -abinitio::use_filters false -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.5 -beta 1 -abinitio::rg_reweight 0.5 -in:file:boinc_wu_zip split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509203824_0001_0001_fragments_data.zip -out:file:silent default.out -silent_gz -mute all -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 1680316
Using database: database_357d5d93529_n_methylminirosetta_database
WARNING! attempt to create gzipped file ../../projects/boinc.bakerlab.org_rosetta/split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509203824_0001_0001_fragments_fold_SAVE_ALL_OUT_929543_307_0_r622229529_0 failed.
======================================================
DONE ::     1 starting structures  28909.8 cpu seconds
This process generated     27 decoys from      27 attempts
======================================================
BOINC :: WS_max 5.53181e+08
07:17:09 (3412): called boinc_finish(0)

</stderr_txt>
<message>
upload failure: <file_xfer_error>
  <file_name>split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509203824_0001_0001_fragments_fold_SAVE_ALL_OUT_929543_307_0_r622229529_0</file_name>
  <error_code>-161 (not found)</error_code>
</file_xfer_error>

</message>
]]>




split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509235721_0001_0001_fragments_relax_SAVE_ALL_OUT_929550_34_0

<core_client_version>7.6.33</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -out:file:silent default.out -in:file:s 00001.pdb -frag3 00001.200.3mers.index -in:file:native 00001.pdb -frag9 00001.200.9mers.index -silent_gz 1 -ex2aro 1 -relax::default_repeats 5 -in:file:fullatom 1 -beta 1 -run:protocol relax -ex1 1 -in:file:boinc_wu_zip split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509235721_0001_0001_fragments_data.zip -out:file:silent default.out -silent_gz -mute all -in:file:native 00001.pdb -in:file:fullatom -in:file:s 00001.pdb -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 1668239
Using database: database_357d5d93529_n_methylminirosetta_database
WARNING! attempt to create gzipped file ../../projects/boinc.bakerlab.org_rosetta/split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509235721_0001_0001_fragments_relax_SAVE_ALL_OUT_929550_34_0_r2007884068_0 failed.
======================================================
DONE ::    84 starting structures  28778.6 cpu seconds
This process generated     84 decoys from      84 attempts
======================================================
BOINC :: WS_max 5.2145e+08
02:14:31 (7808): called boinc_finish(0)

</stderr_txt>
<message>
upload failure: <file_xfer_error>
  <file_name>split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509235721_0001_0001_fragments_relax_SAVE_ALL_OUT_929550_34_0_r2007884068_0</file_name>
  <error_code>-161 (not found)</error_code>
</file_xfer_error>

</message>
]]>

Grant
Darwin NT
ID: 96550 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Ivailo Bonev

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Message 96555 - Posted: 16 May 2020, 9:41:48 UTC - in response to Message 96550.  
Last modified: 16 May 2020, 9:42:13 UTC

ID: 96555 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
James W

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Message 96557 - Posted: 16 May 2020, 9:55:08 UTC - in response to Message 96383.  

Name: rb_05_14_24901_24822_ab_t000__robetta_cstwt_5.0_FT_IGNORE_THE_REST_05_05_929579_20_0
Application: Rosetta v4.20 windows_x86_64
Device: 3710630
Task: 1180432738. WU: 1060460046
Status: Error while computing.
Exit status: 1 (0x00000001) Unknown error code
Stderr output:
Incorrect function. (0x1) - exit code 1 (0x1)
[ ERROR ]: Caught exception:
File: C:cygwin64homeboinc4.17Rosettamainsourcesrccore/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306
chi angle must be between -180 and 180: -nan(ind)
------------------------ Begin developer's backtrace -------------------------
BACKTRACE:
------------------------- End developer's backtrace --------------------------

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
My task was the first one of this WU. As Grant experienced with this same type of WU, will see if the replacement task also fails for above reason. Note that the library file in question quoted above was apparently originally included in version 4.17 of the app, or am I wrong?
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James W

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Message 96583 - Posted: 17 May 2020, 8:19:18 UTC - in response to Message 96555.  

Name: split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200510015953_0001_0001_fragments_fold_SAVE_ALL_OUT_929551_60_0
Application: Rosetta v4.20 windows_x86_64
Device: 1759960
Task: 1180381374. WU: 1060415032
Status: Error while computing.
Exit status: 0 (0x00000000)
Stderr output:
WARNING! attempt to create gzipped file ../../projects/boinc.bakerlab.org_rosetta/split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200510015953_0001_0001_fragments_fold_SAVE_ALL_OUT_929551_60_0_r1690932850_0 failed.
upload failure: <file_xfer_error>
<file_name>split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200510015953_0001_0001_fragments_fold_SAVE_ALL_OUT_929551_60_0_r1690932850_0</file_name>
<error_code>-240 (stat() failed)</error_code>
</file_xfer_error>
Thankful I still rec'd credit with the 12+ hours run time spent and creation of 20 decoys!
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James W

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Message 96598 - Posted: 18 May 2020, 7:31:48 UTC - in response to Message 96583.  
Last modified: 18 May 2020, 7:33:20 UTC

As a followup, the 2nd task for this "failed" WU also failed because of same reasons as for mine. Again grateful for credit being given for time spent creating models/decoys.
Name: split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200510015953_0001_0001_fragments_fold_SAVE_ALL_OUT_929551_60_0
Application: Rosetta v4.20 windows_x86_64
Device: 1759960
Task: 1180381374. WU: 1060415032
Errors: Too many errors (may have bug) Too many total results.
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Sid Celery

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Message 96604 - Posted: 18 May 2020, 12:48:13 UTC

Some errors on my Samsung Galaxy S8 running Android 9.
Note, I've reduced running tasks from 4 at a time to 3 at a time due to repeated restarts.
Do people think I should reduce again to 2 at a time, because I note some use 1.3Mb - and the most recent one over 1.4Mb - I think I've answered my own question

Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_4nl6pw4e_929381_1_1
<core_client_version>7.4.53</core_client_version>
<![CDATA[
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu -run:protocol jd2_scripting -parser:protocol jhr_boinc_v4_cart.xml @flags -in:file:silent Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_4nl6pw4e.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 Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_4nl6pw4e.zip @Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_4nl6pw4e.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 3604480
Using database: database_357d5d93529_n_methyl/minirosetta_database
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
Can't acquire lockfile (-154) - waiting 35s
BOINC client no longer exists - exiting
timer handler: client dead, exiting
Can't acquire lockfile (-154) - waiting 35s
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 1 starting structures 80432.9 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 0
called boinc_finish(0)

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_4nl6pw4e_929381_1_1_r1455539898_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>

Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_0dd8md7w_929576_1_0
<core_client_version>7.4.53</core_client_version>
<![CDATA[
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu -run:protocol jd2_scripting -parser:protocol jhr_boinc_v4_cart.xml @flags -in:file:silent Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_0dd8md7w.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 Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_0dd8md7w.zip @Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_0dd8md7w.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 3507240
Using database: database_357d5d93529_n_methyl/minirosetta_database
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 1 starting structures 78982.3 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 0
called boinc_finish(0)

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_0dd8md7w_929576_1_0_r374516517_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>



yournamehere_out_file_0513_d1a75a_v6_4AS_pb_ASW0_TERM20_length55_0060_fragments_abinitio_SAVE_ALL_OUT_929709_154_0
<core_client_version>7.4.53</core_client_version>
<![CDATA[
<message>
finish file present too long
</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu -beta -frag3 00001.200.3mers -frag9 00001.200.9mers -abinitio::increase_cycles 10 -mute all -abinitio::fastrelax -relax::default_repeats 5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5 -abinitio::use_filters false -ex1 -ex2aro -in:file:boinc_wu_zip yournamehere_out_file_0513_d1a75a_v6_4AS_pb_ASW0_TERM20_length55_0060_fragments_fold_data.zip -abinitio::rg_reweight 0.5 -out:file:silent default.out -silent_gz -mute all -in:file:native 00001.pdb -out:file:silent_struct_type binary -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 1610432
Using database: database_357d5d93529_n_methyl/minirosetta_database
======================================================
DONE :: 1 starting structures 28526 cpu seconds
This process generated 37 decoys from 37 attempts
======================================================
BOINC :: WS_max 0
called boinc_finish(0)

Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_8fu6gq7z_929581_12_0
<core_client_version>7.4.53</core_client_version>
<![CDATA[
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu -run:protocol jd2_scripting -parser:protocol jhr_boinc_v4_cart.xml @flags -in:file:silent Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_8fu6gq7z.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 Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_8fu6gq7z.zip @Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_8fu6gq7z.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 2373175
Using database: database_357d5d93529_n_methyl/minirosetta_database
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
BOINC client no longer exists - exiting
timer handler: client dead, exiting
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 1 starting structures 2423.25 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 0
called boinc_finish(0)

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_8fu6gq7z_929581_12_0_r492840401_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>

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Sid Celery

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Message 96605 - Posted: 18 May 2020, 12:54:23 UTC - in response to Message 96604.  
Last modified: 18 May 2020, 12:59:20 UTC

I was going to do the same for Computation errors on my desktop, but now I realise they're all "split_pass" gzip errors in exactly the same way others have reported.
See here

PS: I've just spotted the new display method in that task list - seems a much easier way to reportlink by selecting Errors, then using that. I like that
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Billy

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Message 96612 - Posted: 18 May 2020, 19:59:57 UTC

WU -- Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_3cm6ew0f_929582_4

<core_client_version>7.16.6</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: rosetta_4.20_x86_64-apple-darwin -run:protocol jd2_scripting -parser:protocol jhr_boinc_v4_cart.xml @flags -in:file:silent Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_3cm6ew0f.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 Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_3cm6ew0f.zip @Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_3cm6ew0f.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 1889263
Using database: database_357d5d93529_n_methyl/minirosetta_database

ERROR: [ERROR] Unable to open constraints file: 661878b62a16b66dd9a610e0aacf01c4_n0_c1_1_0001.MSAcst
ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 457
BOINC:: Error reading and gzipping output datafile: default.out
11:40:10 (9714): called boinc_finish(1)
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Sid Celery

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Message 96619 - Posted: 19 May 2020, 1:40:02 UTC - in response to Message 96604.  

Some errors on my Samsung Galaxy S8 running Android 9.
Note, I've reduced running tasks from 4 at a time to 3 at a time due to repeated restarts.
Do people think I should reduce again to 2 at a time, because I note some use 1.3Mb - and the most recent one over 1.4Mb - I think I've answered my own question

Before I could reduce my concurrent tasks I set NNT to get a WCG OpenPandemics task running and the lower memory footprint allowed my remaining 2 Rosetta tasks to complete successfully and a lot quicker than usual, so I think it's definitely a memory issue. 3 WCG tasks run fine together, but when they've finished I'll only allow 2 Rosetta to run at once - and probably get more done than by running 3 together unsuccessfully
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steve

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Message 96655 - Posted: 20 May 2020, 12:10:07 UTC - in response to Message 96612.  

What file / log are you posting from? I am getting a few errors each day and I would like to diagnose.
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Erich56

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Message 96670 - Posted: 20 May 2020, 19:02:00 UTC

I, too, had 2 tasks today which failed after severl hours, with stderr saying:

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Breakpoint Encountered (0x80000003) at address 0x00007FFB55B60AA2

see here:
https://boinc.bakerlab.org/rosetta/result.php?resultid=1184999275

https://boinc.bakerlab.org/rosetta/result.php?resultid=1184964042

anyone any idea what happened?
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Profile Grant (SSSF)

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Message 96674 - Posted: 20 May 2020, 19:43:56 UTC - in response to Message 96670.  

anyone any idea what happened?
Exit status	202 (0x000000CA) EXIT_ABORTED_BY_PROJECT
No longer need so they were cancelled by the project, although i've no idea why that resulted in an Unhandled Exception error.
Grant
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Profile Grant (SSSF)

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Message 96680 - Posted: 20 May 2020, 21:13:05 UTC - in response to Message 96674.  

anyone any idea what happened?
Exit status	202 (0x000000CA) EXIT_ABORTED_BY_PROJECT
No longer need so they were cancelled by the project, although i've no idea why that resulted in an Unhandled Exception error.
Just had a look at my Task list and the same error occurred when the Server cancelled a couple of Tasks of the same type on my system, but Credit was granted for the work done, so all is well.
Grant
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Message 96685 - Posted: 21 May 2020, 7:49:41 UTC

Name: Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g_929581_20_0
Task 1184606782
Application version Rosetta v4.20 arm-android-linux-gnu

Stderr output
<core_client_version>7.16.3</core_client_version>
<![CDATA[
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu -run:protocol jd2_scripting -parser:protocol jhr_boinc_v4_cart.xml @flags -in:file:silent Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g.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 Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g.zip @Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g.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 2832607
Using database: database_357d5d93529_n_methyl/minirosetta_database
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 1 starting structures 8991.99 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 0
called boinc_finish(0)

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g_929581_20_0_r1500706928_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>

</message>
]]>


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Profile Grant (SSSF)

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Message 96687 - Posted: 21 May 2020, 9:37:29 UTC - in response to Message 96383.  

rb_05_09_24541_24116_ab_t000__robetta_cstwt_5.0_FT_IGNORE_THE_REST_05_10_927507_5_0

<core_client_version>7.6.22</core_client_version>
<![CDATA[
<message>
Incorrect function.
 (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe @rb_05_09_24541_24116_ab_t000__robetta_FLAGS -in::file::fasta t000_.fasta -jumps:pairing_file t000_.fasta.bbcontacts.jumps -jumps:random_sheets 2 -constraints::cst_file t000_.fasta.CB.cst -constraints:cst_weight 5.0 -constraints::cst_fa_file t000_.fasta.MIN.cst -constraints:cst_fa_weight 5.0 -in:file:boinc_wu_zip rb_05_09_24541_24116_ab_t000__robetta.zip -frag3 rb_05_09_24541_24116_ab_t000__robetta.200.3mers.index.gz -fragA rb_05_09_24541_24116_ab_t000__robetta.200.10mers.index.gz -fragB rb_05_09_24541_24116_ab_t000__robetta.200.5mers.index.gz -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 1576447
Using database: database_357d5d93529_n_methylminirosetta_database

[ ERROR ]: Caught exception:


File: C:cygwin64homeboinc4.17Rosettamainsourcesrccore/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306
chi angle must be between -180 and 180: -nan(ind)
 ------------------------ Begin developer's backtrace ------------------------- 
BACKTRACE:
 ------------------------- End developer's backtrace -------------------------- 


AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.



</stderr_txt>
]]>


This is the second time i've had this particular error message- last time it was dodgy WU, the other system that got it also got the same error.
Waiting to see if that's the case again this time around.




Looks like it was another dodgy WU- other system had the same error.




Just got another of these Tasks that error out due to "chi angle must be between -180 and 180: -nan(ind)"

rb_05_20_26052_25617_ab_t000__robetta_cstwt_5.0_FT_IGNORE_THE_REST_06_12_937879_18_0

<core_client_version>7.6.33</core_client_version>
<![CDATA[
<message>
Incorrect function.
 (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe @rb_05_20_26052_25617_ab_t000__robetta_FLAGS -in::file::fasta t000_.fasta -jumps:pairing_file t000_.fasta.bbcontacts.jumps -jumps:random_sheets 2 -constraints::cst_file t000_.fasta.CB.cst -constraints:cst_weight 5.0 -constraints::cst_fa_file t000_.fasta.MIN.cst -constraints:cst_fa_weight 5.0 -in:file:boinc_wu_zip rb_05_20_26052_25617_ab_t000__robetta.zip -frag3 rb_05_20_26052_25617_ab_t000__robetta.200.3mers.index.gz -fragA rb_05_20_26052_25617_ab_t000__robetta.200.12mers.index.gz -fragB rb_05_20_26052_25617_ab_t000__robetta.200.6mers.index.gz -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 3314523
Using database: database_357d5d93529_n_methylminirosetta_database

[ ERROR ]: Caught exception:


File: C:cygwin64homeboinc4.17Rosettamainsourcesrccore/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306
chi angle must be between -180 and 180: -nan(ind)
 ------------------------ Begin developer's backtrace ------------------------- 
BACKTRACE:
 ------------------------- End developer's backtrace -------------------------- 


AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.



</stderr_txt>
]]>

Grant
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steve

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Message 96688 - Posted: 21 May 2020, 10:14:19 UTC
Last modified: 21 May 2020, 10:15:35 UTC

I seem to get 3-4 of these all at the same time

<core_client_version>7.16.1</core_client_version>
<![CDATA[
<message>
process got signal 11</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu -abinitio::fastrelax 1 -ex2aro 1 -frag3 00001.200.3mers.index -in:file:native 00001.pdb -silent_gz 1 -frag9 00001.200.9mers.index -out:file:silent default.out -ex1 1 -abinitio::rsd_wt_loop 0.5 -relax::default_repeats 5 -abinitio::use_filters false -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.5 -beta 1 -abinitio::rg_reweight 0.5 -in:file:boinc_wu_zip rep220_0050_symA_reordered_0008_propagated_0001_A_v2_data.zip -out:file:silent default.out -silent_gz -mute all -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 3604267
Using database: database_357d5d93529_n_methyl/minirosetta_database

</stderr_txt>
]]>


Name rep220_0050_symA_reordered_0008_propagated_0001_A_v2_fold_SAVE_ALL_OUT_937670_111_0
Workunit 1065074881
Created 20 May 2020, 17:18:41 UTC
Sent 20 May 2020, 18:13:58 UTC
Report deadline 23 May 2020, 18:13:58 UTC
Received 20 May 2020, 19:19:41 UTC
Server state Over
Outcome Computation error
Client state Compute error
Exit status 11 (0x0000000B) Unknown error code
Run time 24 sec
CPU time 19 sec
Validate state Invalid
Credit 0.00
Device peak FLOPS 6.07 GFLOPS
Application version Rosetta v4.20
x86_64-pc-linux-gnu
Peak working set size 260.43 MB
Peak swap size 344.57 MB
Peak disk usage 0.02 MB
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Profile Grant (SSSF)

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Message 96690 - Posted: 21 May 2020, 10:44:20 UTC - in response to Message 96688.  
Last modified: 21 May 2020, 10:44:37 UTC

I seem to get 3-4 of these all at the same time
I don't know what, but there is something very wrong with your i7-8809G system. 1 Valid Task and 13 errors is not a good ratio.
It's not overclocked is it? Or overheating?
Grant
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Message 96692 - Posted: 21 May 2020, 11:30:57 UTC - in response to Message 96087.  
Last modified: 21 May 2020, 11:48:17 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.


@michelv

You are comparing me to being the equivalent of a Corona virus carrier because I use Win XP, That because I use an older operating system I don't deserve any support because I might infect the Rosetta database and wipe out all your computers.
Grow up.
Others seeing these notes might think this is a hostile site and no help will be coming to them if they need it because you don't want them to be helped.
I have as much right to get help as any one else, I have been running this project on and of for 15 Years and always been welcome for my help to the project.

You have been here a few months and telling me I don't deserve help.

I doubt I will bother anymore with this project as there are much friendlier projects that need help and Windows XP still works on them (such as TN-Grid).

They also don't jump down my throat and tell me all my gear is crap and you will infect everyone so leave or update.

I have already given my reasons for continuing to use XP in an earlier post. I also use Linux, have a go at me for that if you want I no longer care.

The hostile reaction I have received has surprised and disappointed me.

To the ones that supported me, thank you.

I may come back in the future, but not for time being.

To my detractors you have your wish and you have driven a long term user from the project, live with that, I am sure the project will thank you.

Bye
Conan
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Message 96694 - Posted: 21 May 2020, 12:12:55 UTC - in response to Message 95673.  

OK, so back to the topic of the thread...
Conan, my first instinct when I see process can't start sorts of messages is that there is an authority issue, or anti-virus software in the way.


Thanks Mod Sense,

I have changed nothing in relation to rosetta running on my computer, it has been running this project with the same set up for many years. Something in the more recent updates has changed but I can't work out what it is.

I suspect it is a wget issue as another project (Ibercivis2) and I have narrowed it down to that when trying to run in standalone mode.
Wget dropped support for Win XP with version 1.20.0 or 1.20.1 or something like that, so I suspect that is the issue if Rosetta uses wget.
So I wont be running this XP computer here anymore anyway.

Thanks for offering some possible solutions to my problem, few other did.
No help was forthcoming as all they wanted to do was tell me my computer is crappy and too old so don't run it here.
Nice.

Conan
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Message 96695 - Posted: 21 May 2020, 12:28:55 UTC - in response to Message 96692.  

You are comparing me to being the equivalent of a Corona virus carrier because I use Win XP, That because I use an older operating system I don't deserve any support because I might infect the Rosetta database and wipe out all your computers.

You know me, I also think that XP is obsolete (and i think that, in the future, it's good thing to drop support), but i DON'T think you are like Coronavirus!!!!


Others seeing these notes might think this is a hostile site and no help will be coming to them if they need it because you don't want them to be helped.
I have as much right to get help as any one else, I have been running this project on and of for 15 Years and always been welcome for my help to the project.

I'm also an "old" Rosetta guy and i don't want this site to be hostile to anyone.


They also don't jump down my throat and tell me all my gear is crap and you will infect everyone so leave or update.

Untill project supports XP, you have all reasons to remain here!!


The hostile reaction I have received has surprised and disappointed me.

+1

To the ones that supported me, thank you.
I may come back in the future, but not for time being.

We will see on Ralph!! :-P
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