Posts by James Adrian

1) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93562)
Posted 5 Apr 2020 by Profile James Adrian
Post:
Thanks Robert, appreciate the reply. I've since discovered there is a problem with 4.12 Rosetta on macs.
I found it over in Questions and Answers: Macintosh
under
Computations Errors on 7.14.4.
So for those having this problem there is info there.
2) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93550)
Posted 5 Apr 2020 by Profile James Adrian
Post:
I'm running a mac, cpu only. I received three work units and all three ran for about 20 seconds and then returned computation error.
Mac OS version 10.15.4, Boinc version 7.14.14, and Rosetta version 4.12. These are the first 4.12's I've gotten, so I'm just curious if anyone else is seeing this as well. I've had no problem with earlier versions. Here's a snippet from the logs:

Sun Apr 5 15:31:22 2020 | Rosetta@home | update requested by user
Sun Apr 5 15:31:25 2020 | Rosetta@home | Sending scheduler request: Requested by user.
Sun Apr 5 15:31:25 2020 | Rosetta@home | Requesting new tasks for CPU
Sun Apr 5 15:31:26 2020 | Rosetta@home | Scheduler request completed: got 3 new tasks
Sun Apr 5 15:31:28 2020 | Rosetta@home | Started download of rosetta_4.12_x86_64-apple-darwin
Sun Apr 5 15:31:28 2020 | Rosetta@home | Started download of rosetta_graphics_4.12_x86_64-apple-darwin
Sun Apr 5 15:31:37 2020 | Rosetta@home | Finished download of rosetta_4.12_x86_64-apple-darwin
Sun Apr 5 15:31:37 2020 | Rosetta@home | Started download of minirosetta_database_357d5d93529_n_methyl.zip
Sun Apr 5 15:31:40 2020 | Rosetta@home | Finished download of rosetta_graphics_4.12_x86_64-apple-darwin
Sun Apr 5 15:31:40 2020 | Rosetta@home | Started download of flags_il1r2
Sun Apr 5 15:31:41 2020 | Rosetta@home | Finished download of flags_il1r2
Sun Apr 5 15:31:41 2020 | Rosetta@home | Started download of 2qq4ew9m_Mini_Protein_binds_IL1R_COVID-19_design0.zip
Sun Apr 5 15:31:44 2020 | Rosetta@home | Finished download of 2qq4ew9m_Mini_Protein_binds_IL1R_COVID-19_design0.zip
Sun Apr 5 15:31:44 2020 | Rosetta@home | Started download of 2qq4ew9m_Mini_Protein_binds_IL1R_COVID-19_design0.flags
Sun Apr 5 15:31:45 2020 | Rosetta@home | Finished download of 2qq4ew9m_Mini_Protein_binds_IL1R_COVID-19_design0.flags
Sun Apr 5 15:31:45 2020 | Rosetta@home | Started download of 4ah5oy5y_Mini_Protein_binds_IL1R_COVID-19_design0.zip
Sun Apr 5 15:31:47 2020 | Rosetta@home | Finished download of 4ah5oy5y_Mini_Protein_binds_IL1R_COVID-19_design0.zip
Sun Apr 5 15:31:47 2020 | Rosetta@home | Started download of 4ah5oy5y_Mini_Protein_binds_IL1R_COVID-19_design0.flags
Sun Apr 5 15:31:48 2020 | Rosetta@home | Finished download of 4ah5oy5y_Mini_Protein_binds_IL1R_COVID-19_design0.flags
Sun Apr 5 15:31:48 2020 | Rosetta@home | Started download of 5kp3uc9q_Mini_Protein_binds_IL1R_COVID-19_design0.zip
Sun Apr 5 15:31:52 2020 | Rosetta@home | Finished download of 5kp3uc9q_Mini_Protein_binds_IL1R_COVID-19_design0.zip
Sun Apr 5 15:31:52 2020 | Rosetta@home | Started download of 5kp3uc9q_Mini_Protein_binds_IL1R_COVID-19_design0.flags
Sun Apr 5 15:31:53 2020 | Rosetta@home | Finished download of 5kp3uc9q_Mini_Protein_binds_IL1R_COVID-19_design0.flags
Sun Apr 5 15:32:05 2020 | Rosetta@home | Finished download of minirosetta_database_357d5d93529_n_methyl.zip
Sun Apr 5 15:32:09 2020 | Rosetta@home | Starting task 5kp3uc9q_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0
Sun Apr 5 15:33:25 2020 | Rosetta@home | Computation for task 5kp3uc9q_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0 finished
Sun Apr 5 15:33:25 2020 | Rosetta@home | Output file 5kp3uc9q_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0_r1019687941_0 for task 5kp3uc9q_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0 absent
Sun Apr 5 15:33:28 2020 | Rosetta@home | Starting task 2qq4ew9m_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0
Sun Apr 5 15:34:42 2020 | Rosetta@home | Computation for task 2qq4ew9m_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0 finished
Sun Apr 5 15:34:42 2020 | Rosetta@home | Output file 2qq4ew9m_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0_r1625578171_0 for task 2qq4ew9m_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0 absent
Sun Apr 5 15:34:44 2020 | Rosetta@home | Starting task 4ah5oy5y_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0
Sun Apr 5 15:36:06 2020 | Rosetta@home | Computation for task 4ah5oy5y_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0 finished
Sun Apr 5 15:36:06 2020 | Rosetta@home | Output file 4ah5oy5y_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0_r1915284257_0 for task 4ah5oy5y_Mini_Protein_binds_IL1R_COVID-19_design0_SAVE_ALL_OUT_905220_3_0 absent
3) Message boards : Number crunching : Minirosetta 3.73-3.78 (Message 79805)
Posted 27 Mar 2016 by Profile James Adrian
Post:
rls5 thanks for all the info!

I checked the logs and didn't find any errors and prefs show 6 hours as you mentioned below. If it happens again I'll wait for the 6 hour mark, just so I can see what happens. (:-)


Rosetta appear OK.

I just set my Rosetta PREFERENCES: CPU TARGET RUNTIME = 14 hours, enabled Rosetta computing on one of my Linux 64-bit systems and Rosetta downloaded 50 14-hour jobs. I think the only difference in a default 6-hour job and a 14-hour job is what Rosetta sets in the "-cpu_run_time 21600" as a command line option. I don't think Rosetta jobs care what system they execute on .... MACOS, Windows, Linux86/64.

I think ALL Rosetta jobs are set up to just try 99 decoys. The cpu_run_time limit set by the user is checked after every decoy. If that time is exceeded, Rosetta wraps up the job and it is completed early, before the 99 decoy limit is reached.

NOTE: THIS is one reason why it is very, very tough to compare system performances. Jobs will only stop before the preference time IF and ONLY IF they complete the 99 decoys.

I would guess that your event log is showing some problem with DISK SPACE available for Rosetta. BOINC has 3 possible limits on disk and I always seem to hit them accidently:

1. maximum amount used
2. amount to leave free
3. maximum % of disk


SAMPLE command line will only differ in the leading OS name and is added by the Rosetta server when it dispatches the job to a system.

command: minirosetta_3.71_x86_64-apple-darwin -abinitio::fastrelax 1 -ex2aro 1 -frag3 00001.200.3mers -in:file:native 00001.pdb -silent_gz 1 -frag9 00001.200.9mers -out:file:silent default.out -ex1 1 -abinitio::rsd_wt_loop 0.5 -relax::default_repeats 15 -abinitio::use_filters false -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.5 -abinitio::rg_reweight 0.5 -in:file:boinc_wu_zip NTF2_215_N90N92K61_4_9_1_data.zip -out:file:silent default.out -silent_gz -mute all -nstruct 10000
-cpu_run_time 21600
-checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3415526



4) Message boards : Number crunching : Minirosetta 3.73-3.78 (Message 79800)
Posted 26 Mar 2016 by Profile James Adrian
Post:
ArcSedna,

I just saw your post, once I sorted to see newest first. My problem seems slightly different but like you I see the problem with work units named as in your post. One other observation: I have a newer Mac laptop but so far I have not seen the problem with the work units on it, just on my older iMac.
5) Message boards : Number crunching : Minirosetta 3.73-3.78 (Message 79799)
Posted 26 Mar 2016 by Profile James Adrian
Post:
Has anyone else gotten work units for Minirosetta 3.71 that are estimated to run 14 days? I'm running on an old (2009) Mac with 8GB of memory and lately I've gotten these here and there.

Thanks

Boinc 7.6.22
Mac OS 10.11.4






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