Rosetta 4.1+ and 4.2+

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James W

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Message 90455 - Posted: 1 Mar 2019, 7:47:57 UTC

Application version Rosetta for Android v4.10
Device 3396190, Task 1059800641, and WU 954742471.
Status: Error while computing.
Exit status: 0 (0x00000000)

CPU type ARM AArch64 Processor rev 3 (aarch64)
Operating System Android 3.18.19-g407ac4f82ff (Android 5.1.1)
Device: Amazon Fire tablet
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu @rb_02_26_1347_1493_ab_t000__h001_robetta_FLAGS -in::file::fasta t000__h001.fasta -psipred_ss2 t000__h001.spider3_ss2 -kill_hairpins t000__h001.nobuformat.spider3_ss2 -abinitio::use_filters true -in:file:boinc_wu_zip rb_02_26_1347_1493_ab_t000__h001_robetta.zip -frag3 rb_02_26_1347_1493_ab_t000__h001_robetta.200.3mers.index.gz -fragA rb_02_26_1347_1493_ab_t000__h001_robetta.200.15mers.index.gz -fragB rb_02_26_1347_1493_ab_t000__h001_robetta.200.5mers.index.gz -nstruct 10000 -cpu_run_time 14400 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1840497

WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x26cc
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu: unused DT entry: type 0x6fffffff arg 0x2
Too many restarts with no progress. Keep application in memory while preempted.

The two warnings above repeat numerous times.
upload failure: <file_xfer_error>
<file_name>rb_02_26_1347_1493_ab_t000__h001_robetta_IGNORE_THE_REST_05_15_818663_8_0_r313824602_0</file_name>
<error_code>-161 (not found)</error_code></file_xfer_error>
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James W

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Message 90456 - Posted: 1 Mar 2019, 8:08:56 UTC

Application version Rosetta for Android v4.10
Device 3396190, Task 1060134981, and WU 955048899
Status: Error while computing.
Errors: Too many errors (may have bug). Too many total results.
Exit status: 0 (0x00000000)

CPU type ARM AArch64 Processor rev 3 (aarch64)
Operating System Android 3.18.19-g407ac4f82ff (Android 5.1.1)
Device: Amazon Fire tablet
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu @rb_02_26_1346_1490_ab_t000__robetta_FLAGS -in::file::fasta t000_.fasta -psipred_ss2 t000_.spider3_ss2 -kill_hairpins t000_.nobuformat.spider3_ss2 -abinitio::use_filters true -in:file:boinc_wu_zip rb_02_26_1346_1490_ab_t000__robetta.zip -frag3 rb_02_26_1346_1490_ab_t000__robetta.200.3mers.index.gz -fragA rb_02_26_1346_1490_ab_t000__robetta.200.16mers.index.gz -fragB rb_02_26_1346_1490_ab_t000__robetta.200.10mers.index.gz -nstruct 10000 -cpu_run_time 14400 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1861768

WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x26cc
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu: unused DT entry: type 0x6fffffff arg 0x2
Too many restarts with no progress. Keep application in memory while preempted.

The two warnings above repeat numerous times.
<message>upload failure: <file_xfer_error>
<file_name>rb_02_26_1346_1490_ab_t000__robetta_IGNORE_THE_REST_10_16_818658_17_0_r1934950353_0</file_name>
<error_code>-161 (not found)</error_code></file_xfer_error>

Mine was the first task as noted above.
Second task failed due to "Error while downloading."
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James W

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Message 90460 - Posted: 2 Mar 2019, 7:41:15 UTC

Application version Rosetta for Android v4.10
Device 3396190, Task 1060169629, and WU 955080582.
Status: Error while computing.
Exit status: 0 (0x00000000)

CPU type ARM AArch64 Processor rev 3 (aarch64)
Operating System Android 3.18.19-g407ac4f82ff (Android 5.1.1)
Device: Amazon Fire tablet
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu @rb_02_26_1338_1483_ab_t000__h001_robetta_FLAGS -in::file::fasta t000__h001.fasta -psipred_ss2 t000__h001.spider3_ss2 -kill_hairpins t000__h001.nobuformat.spider3_ss2 -abinitio::use_filters true -in:file:boinc_wu_zip rb_02_26_1338_1483_ab_t000__h001_robetta.zip -frag3 rb_02_26_1338_1483_ab_t000__h001_robetta.200.3mers.index.gz -fragA rb_02_26_1338_1483_ab_t000__h001_robetta.200.5mers.index.gz -fragB rb_02_26_1338_1483_ab_t000__h001_robetta.200.8mers.index.gz -nstruct 10000 -cpu_run_time 14400 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1934536

WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x26cc
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu: unused DT entry: type 0x6fffffff arg 0x2
Too many restarts with no progress. Keep application in memory while preempted.

The two warnings above repeat numerous times.
upload failure: <file_xfer_error>
<file_name>rb_02_26_1338_1483_ab_t000__h001_robetta_IGNORE_THE_REST_08_05_818648_19_0_r1385013819_0</file_name>
<error_code>-161 (not found)</error_code></file_xfer_error>
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James W

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Message 90465 - Posted: 3 Mar 2019, 1:52:38 UTC

Application version Rosetta for Android v4.10
Device 3396190, Task 1060310226, and WU 955205123.
Status: Error while computing.
Exit status: 0 (0x00000000)

CPU type ARM AArch64 Processor rev 3 (aarch64)
Operating System Android 3.18.19-g407ac4f82ff (Android 5.1.1)
Device: Amazon Fire tablet
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu @rb_02_26_1343_1487_ab_t000__robetta_FLAGS -in::file::fasta t000_.fasta -psipred_ss2 t000_.spider3_ss2 -kill_hairpins t000_.nobuformat.spider3_ss2 -abinitio::use_filters true -in:file:boinc_wu_zip rb_02_26_1343_1487_ab_t000__robetta.zip -frag3 rb_02_26_1343_1487_ab_t000__robetta.200.3mers.index.gz -fragA rb_02_26_1343_1487_ab_t000__robetta.200.18mers.index.gz -fragB rb_02_26_1343_1487_ab_t000__robetta.200.7mers.index.gz -nstruct 10000 -cpu_run_time 14400 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1884457

WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x26cc
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu: unused DT entry: type 0x6fffffff arg 0x2
Too many restarts with no progress. Keep application in memory while preempted.

The two warnings above repeat numerous times.
upload failure: <file_xfer_error>
<file_name>rb_02_26_1343_1487_ab_t000__robetta_IGNORE_THE_REST_07_18_818655_28_0_r238708826_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>
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James W

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Message 90466 - Posted: 3 Mar 2019, 5:39:22 UTC

Application version Rosetta for Android v4.10
Device 3182472, Task 1060286201, and WU 955183565.
Status: Error while computing.
Exit status: 11 (0x0000000B) Unknown error code

CPU type ARM ARMv7 Processor rev 0 (v7l)
Operating System: Android 3.10.49-9411209 (Android 6.0.1)
Device: Samsung SM-S320VL - SDK:23 ABI: armeabi-v7a
process got signal 11
</message><stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.10_arm-android-linux-gnu @rb_02_26_1343_1487_ab_t000__h002_robetta_FLAGS -in::file::fasta t000__h002.fasta -psipred_ss2 t000__h002.spider3_ss2 -kill_hairpins t000__h002.nobuformat.spider3_ss2 -abinitio::use_filters true -in:file:boinc_wu_zip rb_02_26_1343_1487_ab_t000__h002_robetta.zip -frag3 rb_02_26_1343_1487_ab_t000__h002_robetta.200.3mers.index.gz -fragA rb_02_26_1343_1487_ab_t000__h002_robetta.200.14mers.index.gz -fragB rb_02_26_1343_1487_ab_t000__h002_robetta.200.3mers.index.gz -nstruct 10000 -cpu_run_time 14400 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1873660
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Message 90590 - Posted: 28 Mar 2019, 9:23:58 UTC
Last modified: 28 Mar 2019, 9:24:12 UTC

Got new 4 tasks. All completed and validated successfully. Problem that noted previously - did not happen, but only 4 tasks crunched simultaneosuly. Could you generate new bunch of tasks but send 1 or 2 tasks per device, or limit the number of tasks run on device depending on it's RAM?

Thank you for science!
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James W

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Message 91255 - Posted: 12 Oct 2019, 9:51:15 UTC

Application version: Rosetta for Android v4.11
Device 3182472, Task 1098710718, and WU 989434812.
Status: Error while computing.
Errors: Too many errors (may have bug). Too many total results.
Exit status: 194 (0x000000C2) EXIT_ABORTED_BY_CLIENT

CPU type ARM - ARM ARMv7 Processor rev 0 (v7l)
Operating System Android 3.10.49-9411209 (Android 6.0.1)
Device: Samsung SM-S320VL phone
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.11_arm-android-linux-gnu @PJSI28K_android_PJS-I-28K_7_DALA_0001.flags -nstruct 10000 -cpu_run_time 14400 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1618567

<message>finish file present too long</message>
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James W

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Message 91279 - Posted: 17 Oct 2019, 7:57:14 UTC

Application version: Rosetta for Android v4.11
Device: 3182472, Task: 1099197108, and WU: 990066716.
Status: Error while computing.
Exit status: 194 (0x000000C2) EXIT_ABORTED_BY_CLIENT

CPU type ARM - ARM ARMv7 Processor rev 0 (v7l)
Operating System Android 3.10.49-9411209 (Android 6.0.1)
Device: Samsung SM-S320VL phone
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.11_arm-android-linux-gnu @23Dxtlgp_913_2339_0001_d.flags -nstruct 10000 -cpu_run_time 14400 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1330378

<message>finish file present too long</message>
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James W

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Message 91290 - Posted: 20 Oct 2019, 8:41:28 UTC

Application version: Rosetta for Android v4.11
Device: 3182472, Task: 1099197072, and WU: 990066644.
Status: Error while computing.
Exit status: 194 (0x000000C2) EXIT_ABORTED_BY_CLIENT

CPU type ARM - ARM ARMv7 Processor rev 0 (v7l)
Operating System Android 3.10.49-9411209 (Android 6.0.1)
Device: Samsung SM-S320VL phone
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.11_arm-android-linux-gnu @23Dxtlgp_913_2339_0001_d.flags -nstruct 10000 -cpu_run_time 14400 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1330450

<message>finish file present too long</message>
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James W

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Message 91297 - Posted: 22 Oct 2019, 5:45:33 UTC

Application version Rosetta for Android v4.10
Device 3396190, Task 1098727938, and WU 989435867.
Status: Error while computing.
Exit status: 196 (0x000000C4) EXIT_DISK_LIMIT_EXCEEDED
Errors: Too many errors (may have bug) Too many total results

CPU type ARM AArch64 Processor rev 3 (aarch64)
Operating System Android 3.18.19-g1a1ee9cbdeb (Android 5.1.1)
Device: Amazon Fire tablet
<message>Maximum disk usage exceeded</message>
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.11_arm-android-linux-gnu: unused DT entry: type 0x6fffffff arg 0x2
WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_android_4.11_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x26a0

The two warnings above repeat numerous times.
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Profile Bill F
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Message 91362 - Posted: 14 Nov 2019, 3:55:31 UTC

Can we get a response on this Android Ver 4.1 error thread from a moderator or Admin so that we know that someone is working on the issue ?

Thanks
Bill F
In October 1969 I took an oath to support and defend the Constitution of the United States against all enemies, foreign and domestic;
There was no expiration date.

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Message 92856 - Posted: 1 Apr 2020, 3:31:34 UTC

Please report issues and/or bugs regarding the new 4.12 versions of Rosetta in this thread. We removed the android app versions and created a new "Rosetta for devices" app version. This includes Android ARM and Linux ARM (aarch64) platforms. We will post an official news update tomorrow with more details. Please be patient as our servers are quite busy trying to push out the new apps and jobs.
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Klimax

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Message 92859 - Posted: 1 Apr 2020, 6:08:24 UTC - in response to Message 92856.  

Would it be possible to support Windows on ARM (WOA) too?
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Message 92962 - Posted: 1 Apr 2020, 18:01:14 UTC - in response to Message 92931.  
Last modified: 1 Apr 2020, 18:27:23 UTC

Rosetta v4.12 x86_64-apple-darwin task crashed due to

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<message>
process got signal 11</message>
<stderr_txt>
etta_4.12_x86_64-apple-darwin(74386,0x7fffac05d380) malloc: *** error for object 0x10dbc2000: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
rosetta_4.12_x86_64-apple-darwin(74386,0x7fffac05d380) malloc: *** error for object 0x10dbc2000: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
rosetta_4.12_x86_64-apple-darwin(74386,0x7fffac05d380) malloc: *** error for object 0x10dbc2000: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
rosetta_4.12_x86_64-apple-darwin(74386,0x7fffac05d380) malloc: *** error for object 0x10dbc2000: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
[snip]

https://boinc.bakerlab.org/rosetta/result.php?resultid=1138137769


Update: all my Rosetta v4.12 tasks fail after 10-20 seconds with similar stderr output. One of the non-corrupted messages points to a corrupt zip file:

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: rosetta_4.12_x86_64-apple-darwin -run:protocol jd2_scripting -parser:protocol jhr_boinc.xml @flags -in:file:silent 8yo4kt0l_jhr_design1_COVID-19.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 8yo4kt0l_jhr_design1_COVID-19.zip -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 2253607
Starting watchdog...
Watchdog active.
error: zipfile probably corrupt (illegal instruction)
rosetta_4.12_x86_64-apple-darwin(97934,0x7fffac05d380) malloc: *** error for object 0x111b64000: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug

</stderr_txt>
]]>

(The Rosetta v4.09 and Rosetta Mini v3.78 task continue to run fine)

Crash reports available on request if any of the developers wants to look
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Message 92974 - Posted: 1 Apr 2020, 20:05:54 UTC

I had a successful 4.12 Linux on ARM task at Ralph last night on my Odroid N2.
However, just one is enough to almost fill up the tiny eMMC based root file system of 7GB (I was cheap, bigger eMMC are available and supported). The project directory is 506MB, each Rosetta slot is 863MB, its the minirosetta_database consuming 99% of the space there, over and over again, if running multiple WUs.
So a starting WU hammers the SD card for some minutes, even eMMC break out in sweat.

Right now I'm running just one per Odroid N2, I'd need to remove the GUI to free up space or add an SD card for /var/lib/boinc-client but am not eager to do either :-)
SBC booting from SSD or eg. ARM cloud servers will be able to run more work units without problems.
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Message 92982 - Posted: 1 Apr 2020, 21:33:20 UTC

I snuck in 3 v4.12 tasks overnight. Only just remembered. All completed successfully.
Nice credit levels too.
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Message 92984 - Posted: 1 Apr 2020, 22:10:09 UTC
Last modified: 1 Apr 2020, 22:10:52 UTC

hi!

I've a lot of tasks (60) in error with that stderr:

Exemple for task 1025095366

<core_client_version>7.16.3</core_client_version>
<![CDATA[
<message>
process got signal 4</message>
<stderr_txt>

</stderr_txt>
]]>

On a Mac Pro 4,1 with MacOs 10.11.6
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Message 93003 - Posted: 2 Apr 2020, 0:59:50 UTC

I'm now running my first 5 Rosetta 4.12 tasks, under Windows 10 64 bits, BOINC 7.14.2.

They all share a VERY big database file, 371.81 MB, which probably took over an hour to download.

Is there anything available on what features 4.12 has that 4.0+ didn't have?
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Gorgan Stefan

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Message 93055 - Posted: 2 Apr 2020, 11:32:50 UTC
Last modified: 2 Apr 2020, 12:18:49 UTC

I received 9 tasks on rosetta 4.12 a few hours ago. They seem to use a lot of RAM compared to the older tasks (over 1.5 GB after 15 minutes of working on them).
After a while I noticed one of the task was 'Waiting to run", probably due to the fact that all my RAM was used. And then all tasks started getting this error:
2/4/2020 13:04:58 | Rosetta@home | Task rb_04_01_20072_19955__t000__2_C1_SAVE_ALL_OUT_IGNORE_THE_REST_904939_93_0 exited with zero status but no 'finished' file
2/4/2020 13:04:58 | Rosetta@home | If this happens repeatedly you may need to reset the project.
Now I'm resetting the project hoping this doesn't happen again when I get new tasks.

EDIT:
I done a reset and now I'm getting new errors besides the previous one:
2/4/2020 15:06:19 | Rosetta@home | Output file rb_04_02_17128_19982_ab_t000__h001_robetta_IGNORE_THE_REST_04_13_904952_11_0_r1478835244_0 for task rb_04_02_17128_19982_ab_t000__h001_robetta_IGNORE_THE_REST_04_13_904952_11_0 absent

Any idea what's the problem or how can I stop getting 4.12 tasks? If I can't run them on my system I want at least to stop receiving them so someone else can complete them.
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Message 93075 - Posted: 2 Apr 2020, 14:08:06 UTC - in response to Message 93055.  

I received 9 tasks on rosetta 4.12 a few hours ago. They seem to use a lot of RAM compared to the older tasks (over 1.5 GB after 15 minutes of working on them).
After a while I noticed one of the task was 'Waiting to run", probably due to the fact that all my RAM was used. And then all tasks started getting this error:
2/4/2020 13:04:58 | Rosetta@home | Task rb_04_01_20072_19955__t000__2_C1_SAVE_ALL_OUT_IGNORE_THE_REST_904939_93_0 exited with zero status but no 'finished' file
2/4/2020 13:04:58 | Rosetta@home | If this happens repeatedly you may need to reset the project.
Now I'm resetting the project hoping this doesn't happen again when I get new tasks.

EDIT:
I done a reset and now I'm getting new errors besides the previous one:
2/4/2020 15:06:19 | Rosetta@home | Output file rb_04_02_17128_19982_ab_t000__h001_robetta_IGNORE_THE_REST_04_13_904952_11_0_r1478835244_0 for task rb_04_02_17128_19982_ab_t000__h001_robetta_IGNORE_THE_REST_04_13_904952_11_0 absent

Any idea what's the problem or how can I stop getting 4.12 tasks? If I can't run them on my system I want at least to stop receiving them so someone else can complete them.

The most obvious answer is to get more RAM. The tasks here are very demanding - more than ever.
You should expect to need 2Gb per task you run simultaneously. I see you have a 6-core, 12 thread CPU but "only" 16Gb RAM

A quick solution is to change the number of CPUs you have running at once to 8 by going into Boinc, Options menu, Computing Preferences, Computing tab and enter 67% of CPUs to run. This ought to allow you to run 8 tasks without RAM errors. If you buy more RAM you'll be able to run all 12 threads again when you're able to.
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Message boards : Number crunching : Rosetta 4.1+ and 4.2+



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