Rosetta 4.1+ and 4.2+
Message boards : Number crunching : Rosetta 4.1+ and 4.2+
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 Grant (SSSF)Send message Joined: 28 Mar 20 Posts: 1673 Credit: 17,596,129 RAC: 22,414 
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The problem is that revised Estimated time doesn't get sent back to the Servers until the Task is finished, by which time more work has already been sent based on the lower Estimated completion time. And with the Runtimes of these Tasks, it takes a week (or more or less depending on how many cores & threads your system has) for the Estimates to match the actual Runtime.It looks like there's going to be some problems with v 4.15- Estimated completion times are 39min 18sec; that's going to lead to a lot of overfilled caches & Tasks timing out....The first v4.15 tasks I got were also noted to be in the 39 min. range. However, my BOINC manager revised their completion times to 01:14:54, almost twice as long. Will see if I get same results as you did. I'd suggest you check your cache size & settings for when Rosetta can run as you have more Tasks that have timed out & missed the deadlines than ones that you have in your Valid list (and your i3 may run in to memory issues when larger RAM requirement Tasks make their return). A very small cache & giving BOINC more memory if it needs it should stop the missed deadlines, & help avoid RAM issues with the i3 in the future. Your Account page, Computing Settings, Computing
Usage limits
Use at most 100% of the CPUs
Use at most 100% of CPU time
When to suspend
Suspend when computer is on battery (not selected)
Suspend when computer is in use (not selected)
Suspend GPU computing when computer is in use (not selected)
'In use' means mouse/keyboard input in last 3 minutes
Suspend when no mouse/keyboard input in last --- minutes
Suspend when non-BOINC CPU usage is above --- %
Compute only between ---
Other
Store at least 1 days of work
Store up to an additional 0.02 days of work
Switch between tasks every 60 minutes
Request tasks to checkpoint at most every 60 seconds
Disk
Use no more than 20 GB
Leave at least 2 GB free
Use no more than 60 % of total
Memory
When computer is in use, use at most 95 %
When computer is not in use, use at most 95 %
Leave non-GPU tasks in memory while suspended (not selected)
Page/swap file: use at most 75 %Grant Darwin NT |
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James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Thanks for the setup suggestions. I hadn't changed configuration since I set up BOINC and began working on Seti. Started with a Pentium II, then III, and up to Pentium IV with XP before getting my Optiplex over 6 yrs ago. How "state-of-the-art" does change! I mainly used my Optiplex (i5) for working as a medical transcriptionist, so didn't want BOINC getting in the way. Rosetta was just a backup project at the time. I boosted RAM from 4 to 8G, which made a major difference. Motherboard only has 2 RAM slots, however. (I remember how RAM used to cost a mint.) With Rosetta's current short deadlines as a regular thing of late, and its being a memory glutton, can be a challenge keeping a moderate desktop unit able to keep pace. Thanks again! :-) PS: for v4.15 apps, my estimated completion time is now up to 4 hrs. |
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Grant (SSSF) Send message Joined: 28 Mar 20 Posts: 1673 Credit: 17,596,129 RAC: 22,414
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PS: for v4.15 apps, my estimated completion time is now up to 4 hrs.It'll take a while for it to match reality (being the default Target CPU runtime of 8hrs, or whatever you select in the Rosetta preferences.). Grant Darwin NT |
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Greger Send message Joined: 3 May 14 Posts: 10 Credit: 114,865,773 RAC: 109,185
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<core_client_version>7.16.1</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255)</message> <stderr_txt> command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.12_x86_64-pc-linux-gnu -silent_gz -mute all -s chainA_chainB_20_04_15_28_13.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol local_docking_20_04_15_28_13.xml -out:nstruct 10000 -jd2:ntrials 100 -ex1 -ex2aro -beta -use_input_sc -in:file:native chainA_chainB_20_04_15_28_13.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1004427 ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 380 BOINC:: Error reading and gzipping output datafile: default.out 15:03:18 (67461): called boinc_finish(1) </stderr_txt> ]]> Task: https://boinc.bakerlab.org/rosetta/result.php?resultid=1147139880 Unsupported file? any solution for this? Worked well but recently got this issue and host got 4 valid with application Rosetta v4.12 x86_64-pc-linux-gnu. |
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Tomcat雄猫 Send message Joined: 20 Dec 14 Posts: 180 Credit: 5,386,173 RAC: 0 |
I got two of the same errors on my Android devices running Rosetta v4.15 arm-android-linux-gnu. Rosetta for Portable Devices v4.12 arm-android-linux-gnu tasks run fine. <core_client_version>7.4.39</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu -silent_gz -mute all -s chainA_chainB_20_04_15_28_11.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol local_docking_20_04_15_28_11.xml -out:nstruct 10000 -jd2:ntrials 100 -ex1 -ex2aro -beta -use_input_sc -in:file:native chainA_chainB_20_04_15_28_11.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3981396 ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 380 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish(1) </stderr_txt> ]]> |
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Millenium Send message Joined: 20 Sep 05 Posts: 68 Credit: 184,283 RAC: 0 |
Just had this with a 4.15 WU <core_client_version>7.14.2</core_client_version> <![CDATA[ <message> Funzione non corretta. (0x1) - exit code 1 (0x1)</message> <stderr_txt> command: projects/boinc.bakerlab.org_rosetta/rosetta_4.15_windows_x86_64.exe -silent_gz -mute all -s chainA_chainB_20_04_15_28_12.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol local_docking_20_04_15_28_12.xml -out:nstruct 10000 -jd2:ntrials 100 -ex1 -ex2aro -beta -use_input_sc -in:file:native chainA_chainB_20_04_15_28_12.pdb -out:file:silent default.out -out:file:silent_struct_type protein -run:write_failures false -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3986571 ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF ERROR:: Exit from: ......srccoreimport_poseimport_pose.cc line: 380 BOINC:: Error reading and gzipping output datafile: default.out 20:41:28 (3556): called boinc_finish(1) </stderr_txt> ]]> Task: https://boinc.bakerlab.org/rosetta/result.php?resultid=1147880898 All the others are running fine, just reporting this particular one, another user too received it and had the same error so it is a bugged WU. |
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James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Name: 2d1014c00c014fc0ae96dda2d79baef5_dock_ens3_20_04_15_58_03_localDocking_8_SAVE_ALL_OUT_912589_8_0 Application: Rosetta v4.15 arm-android-linux-gnu Device: 3396190--an Amazon Fire tablet running Android 3.18.19-g4bb6ac47eed (Android 5.1.1). Task: 1148219229, and WU: 1033312411. Status: Completed and validated. Exit status: 0 (0x00000000) Stderr output: WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x28ac My first task on my Amazon Fire. Small credit number (5+) with 1000 decoys, but doing something. Hopefully result would be of use. Worth keeping this device available to crunch? |
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James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
27bc1069693f209043a6da29aa50df68_dock_ens3_20_04_15_58_39_globalDocking_1_SAVE_ALL_OUT_912570_8_0 Application: Rosetta v4.15 arm-android-linux-gnu Device: 3396190--an Amazon Fire tablet running Android 3.18.19-g4bb6ac47eed (Android 5.1.1). Task: 1148219018, and WU: 1033312234. Status: Completed and validated. Exit status: 0 (0x00000000) Stderr output: WARNING: linker: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu: unused DT entry: type 0x6ffffffe arg 0x28acNote that the above WARNINGs repeat multiple times. Previous task on this Amazon Fire was "....localDocking...." This task was for "....globalDocking...." with 26+ credit versus 5+. Just a bit better. |
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James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Name: 1b539b9096d09aa7756c5d884dd3ad0d_dock_ens_20_04_15_28_11_localDocking_0_SAVE_ALL_OUT_910393_35_0 Application: Rosetta v4.15 windows_x86_64 Device: 1759960, Task: 1147167016, and WU: 1032418450. Status: Error while computing. Exit status: 1 (0x00000001) Unknown error code Stderr output: Incorrect function. (0x1) - exit code 1 (0x1)This is an error seen in a number of reports from different users involving the "localDocking" tasks (and Windows in my case). Able to crunch using my Amazon tablet however. |
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juan BFP Send message Joined: 26 Dec 08 Posts: 5 Credit: 322,924 RAC: 0 |
https://boinc.bakerlab.org/rosetta/result.php?resultid=1147882702 Credit 20.00 Run this Wu for >12 Hrs, exit normally and receive only 20 credits. If that right or i miss something? |
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Mod.Sense Volunteer moderator Send message Joined: 22 Aug 06 Posts: 4018 Credit: 0 RAC: 0 |
The task was ended by the watchdog. There is currently an issue with the i686 Linux version of the application. See discussion here. Rosetta Moderator: Mod.Sense |
Keith Myers Send message Joined: 29 Mar 20 Posts: 97 Credit: 332,473 RAC: 825 |
https://boinc.bakerlab.org/rosetta/result.php?resultid=1147882702 Don't run any of the i686 applications. Only the x86_64 applications work. Use the <no_alt_platform>1</no_alt_platform> in the cc_config.xml file to only run native x86_64 applications. |
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robertmiles Send message Joined: 16 Jun 08 Posts: 1232 Credit: 14,269,631 RAC: 2,588 
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It looks like there's going to be some problems with v 4.15- Estimated completion times are 39min 18sec; that's going to lead to a lot of overfilled caches & Tasks timing out....The first v4.15 tasks I got were also noted to be in the 39 min. range. However, my BOINC manager revised their completion times to 01:14:54, almost twice as long. Will see if I get same results as you did. It is typical for any new versions of BOINC apps running on your computer to have initial estimated completion fairly far off their actual completion times. It typically takes about ten successful tasks with the new version for BOINC to work out how to correct those initial completion time estimates for your computer. |
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robertmiles Send message Joined: 16 Jun 08 Posts: 1232 Credit: 14,269,631 RAC: 2,588
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Thanks for the setup suggestions. I hadn't changed configuration since I set up BOINC and began working on Seti. Started with a Pentium II, then III, and up to Pentium IV with XP before getting my Optiplex over 6 yrs ago. How "state-of-the-art" does change! I mainly used my Optiplex (i5) for working as a medical transcriptionist, so didn't want BOINC getting in the way. Rosetta was just a backup project at the time. I boosted RAM from 4 to 8G, which made a major difference. Motherboard only has 2 RAM slots, however. (I remember how RAM used to cost a mint.) These days, many memory boards have more memory per board. If you know enough information about what motherboard you are using, this site offers help determining whether you can get boards that are compatible but have more and faster memory per board: https://www.crucial.com/ |
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James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Name: xxxxx_dock_ens_20_04_15_28_XX_localDocking_0_SAVE_ALL_OUT_xxxxx Application: Rosetta v4.15 windows_x86_64 Device: 3710630 Status: Error while computing. Exit status: 1 (0x00000001) Unknown error code Stderr output: Incorrect function. (0x1) - exit code 1 (0x1)I rec'd the following batch of 5 tasks for above device which all errored as noted. They errored between 1 and 2 minutes into their run. They were all "localDocking" tasks as I've noted earlier for both of my PCs. "GlobalDocking" tasks work okay. Also, I got the "luck of the draw" to receive them all after they'd failed for other hosts! I'm going to just abort these "localDocking" tasks until I hear of a fix. https://boinc.bakerlab.org/rosetta/result.php?resultid=1148949326 https://boinc.bakerlab.org/rosetta/result.php?resultid=1148949325 https://boinc.bakerlab.org/rosetta/result.php?resultid=1148949291 https://boinc.bakerlab.org/rosetta/result.php?resultid=1148950274 https://boinc.bakerlab.org/rosetta/result.php?resultid=1148950273 |
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nexiagsi16v Send message Joined: 23 Feb 14 Posts: 1 Credit: 507,041 RAC: 0 |
Hi, Linux Mint 19.3 on a i3 8300 with 8GB Ram. Rosetta v4.15 i686-pc-linux-gnu runs 16h for 20 Points. stdrr out: ====================================================== DONE :: 1 starting structures 57613 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== The WUs should run 12h (Rosetta mini do it so and get good Point with a lot more than 1 decoys from 1 attempts). Another member of Seti Germany use Ryzen with Linux an the same Problem. His preference is 6h for a WU. Rosetta mini do it well, but the Rosetta v4.15 i686-pc-linux-gnu go up to 10h. Yes, the same 4h more like at mine 12h to 16h. Is it normal, that Rosetta stoppt crunching at 4h over the given time at Rosetta preferences? I believe we wastet CPU-time here? Under Windows noch Problem with that...i think. Tschau Norman |
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Mod.Sense Volunteer moderator Send message Joined: 22 Aug 06 Posts: 4018 Credit: 0 RAC: 0 |
To any that have found this thread because they are having Linux i686 issues, please join Ralph (project url is: http://ralph.bakerlab.org/) with your machine. This will help with testing when changes are made to address this, and confirm they are working. No promises on when a new version will be available there. It may take some time. If you would like to try creating a simple cc_config.xml file, you can get BOINC to use the x86_64 version instead of the i686 version that is having trouble. There is an example here. Rosetta Moderator: Mod.Sense |
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kksplace Send message Joined: 12 May 19 Posts: 7 Credit: 5,303,601 RAC: 0 |
Will creating the cc_config.xml file input that is recommended also limit Rosetta Mini WUs that are also i686? They seem to be working fine (actually working quite well based on RAC) on my Linux rigs. It is only the 4.12 and now 4.15 i686 WUs that are having problems. (...and I got signed up on Ralph, awaiting test WUs when they are available for one of my Linux rigs.) |
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James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Name: xxxxx_dock_ens_20_04_15_28_XX_localDocking_0_SAVE_ALL_OUT_xxxxx Application: Rosetta v4.15 windows_x86_64 Device: 1759960 Task: 1150250651. WU: 1032321020 Status: Error while computing. Exit status: 1 (0x00000001) Unknown error code Errors: Too many errors (may have bug) Too many total results. Stderr output: Incorrect function. (0x1) - exit code 1 (0x1)Errored with run time 1 minute & 5 seconds. Again was a "localDocking" task as I've noted earlier for both of my PCs. See my previous message 94424 "GlobalDocking" tasks work okay. This type of task should not be distributed for Rosetta v4.15 windows_x86_64 as they will fail and are a waste of time and energy. |
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[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,523,781 RAC: 8,309 
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Some problems with "12v1n_" wus. I have 4hs wus (in my profile), but these are crunching over 10hs and with NO checkpoint This is and example 1152133806: Unhandled Exception Detected... |
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Number crunching :
Rosetta 4.1+ and 4.2+
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