Message boards : Number crunching : Rosetta 4.1+ and 4.2+
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![]() Send message Joined: 28 Mar 20 Posts: 1611 Credit: 16,521,941 RAC: 3,372 ![]() |
Is not the first..Looks like it suffered from the same problem as mine, Starting watchdog... Watchdog active. Starting watchdog... Watchdog active.Looks like they failed after restarting. A problem with the checkpoint? From the system that processed the same WU as me, Starting watchdog... Watchdog active. Grant Darwin NT |
svincent Send message Joined: 30 Dec 05 Posts: 219 Credit: 12,120,035 RAC: 8 |
I've had a couple of tasks fail on Ubuntu 19.10. They appeared to run for the full 8 hours but the upload failed. <error_code>-131 (file size too big)</error_code> https://boinc.bakerlab.org/rosetta/result.php?resultid=1157342448 </stderr_txt> <message> upload failure: <file_xfer_error> <file_name>Mini_Protein_binds_IL6R_COVID-19_1p9m_3_SAVE_ALL_OUT_IGNORE_THE_REST_3fg6zc0o_924138_1_0_r441246010_0</file_name> <error_code>-131 (file size too big)</error_code> </file_xfer_error> </ and https://boinc.bakerlab.org/rosetta/result.php?resultid=1157317275 </stderr_txt> <message> upload failure: <file_xfer_error> <file_name>Mini_Protein_binds_IL6R_COVID-19_1p9m_2_SAVE_ALL_OUT_IGNORE_THE_REST_2pn8jf2i_924136_1_0_r712855490_0</file_name> <error_code>-131 (file size too big)</error_code> </file_xfer_error> </message> Any settings I need to change? |
Nick Name Send message Joined: 12 Aug 09 Posts: 3 Credit: 2,487,614 RAC: 0 |
The size has been set incorrectly. I have some with the same thing on Windows 10 that ended with a computation error. Rosetta@home 4/22/2020 1:51:16 PM Computation for task Mini_Protein_binds_IL6R_COVID-19_1bqu_1_SAVE_ALL_OUT_IGNORE_THE_REST_5wl5hq6z_924127_1_0 finished Rosetta@home 4/22/2020 1:51:16 PM Output file Mini_Protein_binds_IL6R_COVID-19_1bqu_1_SAVE_ALL_OUT_IGNORE_THE_REST_5wl5hq6z_924127_1_0_r251659771_0 for task Mini_Protein_binds_IL6R_COVID-19_1bqu_1_SAVE_ALL_OUT_IGNORE_THE_REST_5wl5hq6z_924127_1_0 exceeds size limit. Rosetta@home 4/22/2020 1:51:16 PM File size: 100258133.000000 bytes. Limit: 100000000.000000 bytes These should be canceled server-side and reissued when fixed. Team USA page | Team USA forum Follow us on Twitter |
benknobi89 Send message Joined: 24 Mar 20 Posts: 1 Credit: 1,274,155 RAC: 2 |
I'm having the same issue: Wed Apr 22 12:26:16 2020 | Rosetta@home | Output file Mini_Protein_binds_IL6R_COVID-19_1p9m_3_SAVE_ALL_OUT_IGNORE_THE_REST_3fb2sj8a_924138_1_0_r1088028856_0 for task Mini_Protein_binds_IL6R_COVID-19_1p9m_3_SAVE_ALL_OUT_IGNORE_THE_REST_3fb2sj8a_924138_1_0 exceeds size limit. Wed Apr 22 12:26:16 2020 | Rosetta@home | File size: 108086503.000000 bytes. Limit: 100000000.000000 byte Wed Apr 22 12:59:20 2020 | Rosetta@home | Computation for task Mini_Protein_binds_IL6R_COVID-19_1p9m_3_SAVE_ALL_OUT_IGNORE_THE_REST_6uj1ab9u_924138_1_0 finished Wed Apr 22 12:59:20 2020 | Rosetta@home | Output file Mini_Protein_binds_IL6R_COVID-19_1p9m_3_SAVE_ALL_OUT_IGNORE_THE_REST_6uj1ab9u_924138_1_0_r667199254_0 for task Mini_Protein_binds_IL6R_COVID-19_1p9m_3_SAVE_ALL_OUT_IGNORE_THE_REST_6uj1ab9u_924138_1_0 exceeds size limit. Wed Apr 22 12:59:20 2020 | Rosetta@home | File size: 118056626.000000 bytes. Limit: 100000000.000000 bytes Although I would point out that 100 mb is a pretty large file for rosetta so I wonder if its indicative of some other sort of error in the analysis itself. |
James W Send message Joined: 25 Nov 12 Posts: 130 Credit: 1,766,254 RAC: 0 |
Name: 04209mer_stapler_stub366_1-6_53_2449252_3mers_0001_0001_SAVE_ALL_OUT_924092_311_0 Application: Rosetta v4.15 windows_x86_64 Device: 3710630 Task: 1157048481. WU: 1040740292 Status: Error while computing. Exit status: -1073741819 (0xC0000005) STATUS_ACCESS_VIOLATION Stderr output: (unknown error) - exit code -1073741819 (0xc0000005)Same as error quoted in Message ID 95024. |
Mod.Sense Volunteer moderator Send message Joined: 22 Aug 06 Posts: 4018 Credit: 0 RAC: 0 |
The Project Team is aware of, and working on the file size issues. Rosetta Moderator: Mod.Sense |
Admin Project administrator Send message Joined: 1 Jul 05 Posts: 4805 Credit: 0 RAC: 0 |
We had to cancel these work units. Unfortunately they slipped past our quality checks. We are working on a fix and will hopefully have these important COVID-19 jobs out asap. Sorry for these recent issues. These are relatively new tasks and protocols so it's a learning process for us also. On a positive note, these large sampling runs are producing great results that otherwise were never practically possible to obtain. |
Tomcat雄猫 Send message Joined: 20 Dec 14 Posts: 180 Credit: 5,386,173 RAC: 0 |
Got this error on my Mac, never seen this before. Are these the same as the ones above? It ran until completion and got reported normally. https://boinc.bakerlab.org/rosetta/result.php?resultid=1156715070 <core_client_version>7.14.4</core_client_version> <![CDATA[ <stderr_txt> command: rosetta_4.16_x86_64-apple-darwin -score:weights hugh2020_HHH_rd4_0628_A9V__beta16.nostab-refit.wts -beta_nov16 -corrections:beta_nov16 -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 hugh2020_HHH_rd4_0628_A9V__beta16.nostab-refit_fragments_fold_data.zip -out:file:silent default.out -silent_gz -mute all -in:file:fasta 00001.fasta -out:file:silent_struct_type binary -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 5000 -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 1818959 Starting watchdog... Watchdog active. ====================================================== DONE :: 1 starting structures 129556 cpu seconds This process generated 962 decoys from 962 attempts ====================================================== BOINC :: WS_max 3.59453e+08 BOINC :: Watchdog shutting down... 22:48:28 (1040): called boinc_finish(0) </stderr_txt> <message> finish file present too long</message> ]]> |
Tomcat雄猫 Send message Joined: 20 Dec 14 Posts: 180 Credit: 5,386,173 RAC: 0 |
Also got these four validation errors on my main rig. Is the only issue with them the WU got cancelled (presumably after they were reported)? https://boinc.bakerlab.org/rosetta/result.php?resultid=1158001484 https://boinc.bakerlab.org/rosetta/result.php?resultid=1157903020 https://boinc.bakerlab.org/rosetta/result.php?resultid=1157900936 https://boinc.bakerlab.org/rosetta/result.php?resultid=1156662934 Also, why is there such a comically large number of "decoys" generated? |
![]() Send message Joined: 28 Mar 20 Posts: 1611 Credit: 16,521,941 RAC: 3,372 ![]() |
Got this error on my Mac, never seen this before. Are these the same as the ones above?Nope. It's a problem that has been around for years- a lot of disk I/O and resource contention resulting in the cleanup after the Task was finished not happening fast enough for the Manager's liking, so it gets clobbered. Even if the Task finished without error, it still becomes one.</stderr_txt> <message> finish file present too long</message> ]]> The latest version of BOINC (7.16.5) is meant to have the fix for it. Grant Darwin NT |
Erich56 Send message Joined: 11 Jan 16 Posts: 35 Credit: 1,437,503 RAC: 0 |
last night, I had several tasks which after several hours failed with 202 (0x000000CA) EXIT_ABORTED_BY_PROJECT Unhandled Exception Detected... - Unhandled Exception Record - Reason: Breakpoint Encountered (0x80000003) at address 0x00007FF93AADC302 for more Details see: https://boinc.bakerlab.org/rosetta/result.php?resultid=1157856714 what's the problem behind it? |
![]() Send message Joined: 28 Mar 20 Posts: 1611 Credit: 16,521,941 RAC: 3,372 ![]() |
what's the problem behind it?A batch of dodgy Work Units. Grant Darwin NT |
Tomcat雄猫 Send message Joined: 20 Dec 14 Posts: 180 Credit: 5,386,173 RAC: 0 |
Got this error on my Mac, never seen this before. Are these the same as the ones above?Nope. Welp, I AM using the lastest BOINC version for MAC. Good to know it hasn't been fixed for MacOS. That's odd, my Mac is not new, but its SSD still offers top-notch performance. |
![]() Send message Joined: 28 Mar 20 Posts: 1611 Credit: 16,521,941 RAC: 3,372 ![]() |
Welp, I AM using the lastest BOINC version for MAC. Good to know it hasn't been fixed for MacOS. That's odd, my Mac is not new, but its SSD still offers top-notch performance.? From the BOINC download page. Mac OS X (64-bit Intel) Version 10.6.0+ 7.16.6 Recommended versionYou've got v7.14.4 according to your system info here. Grant Darwin NT |
Admin Project administrator Send message Joined: 1 Jul 05 Posts: 4805 Credit: 0 RAC: 0 |
There are a lot of models because of the filtering criteria being used. We are trying to find needles in a haystack and each search step can be short or long depending on the modeling problem at hand. We are looking into ways to decrease the size of these filtered models to take care of this issue but the underlying goal of sampling a very large space is still necessary. |
![]() ![]() Send message Joined: 30 May 06 Posts: 2 Credit: 8,465,106 RAC: 0 |
We had to cancel these work units. Unfortunately they slipped past our quality checks. We are working on a fix and will hopefully have these important COVID-19 jobs out asap. Sorry for these recent issues. These are relatively new tasks and protocols so it's a learning process for us also. On a positive note, these large sampling runs are producing great results that otherwise were never practically possible to obtain. Good to hear about the great results. Thanks for all the hard work. Everyone's peddling about as fast as they can right now. :-) |
Dr Who Fan![]() Send message Joined: 28 May 06 Posts: 64 Credit: 245,041 RAC: 44 |
https://boinc.bakerlab.org/rosetta/result.php?resultid=1157960758 Name 0yx8rt2q_24HGBAB0HM2HGABB24H_build_COVID-19_binder_build1_SAVE_ALL_OUT_924149_47_0 Application version Rosetta v4.15 arm-android-linux-gnu Peak working set size 688.89 MB Peak swap size 972.25 MB Peak disk usage 1,098.00 MB Stderr output ![]() ![]() |
CIA Send message Joined: 3 May 07 Posts: 100 Credit: 21,059,812 RAC: 0 |
According to your user page you are still on BONIC 17.14.4 for your one Mac computer. The latest OS X version of BONIC is 7.16.16. Head over the the main BONIC page and download/install the latest version. /edit Really everyone should take a few moments regardless of OS and check that you are running the most recent version for your rigs. |
Tomcat雄猫 Send message Joined: 20 Dec 14 Posts: 180 Credit: 5,386,173 RAC: 0 |
Welp, I AM using the lastest BOINC version for MAC. Good to know it hasn't been fixed for MacOS. That's odd, my Mac is not new, but its SSD still offers top-notch performance.? Oops... I remember just having just updated to 7.16.x a few days prior due to "suspend when CPU is above XX" not working properly on a previous version. I guess i forgot to actually install the thing. |
Plomos Send message Joined: 4 Mar 11 Posts: 11 Credit: 439,043 RAC: 0 |
Am noticing with tasks marked as Mini_Protein_binds_IL6R_COVID-19_1p9m_v2_3_SAVE_ALL_OUT_IGNORE_THE_REST_6vq3dw3t_924614_2 do end up creating decoys, but according to the windows graphics output they spend a lot of time with Stage: unknown and then eventually run 2 or 3 steps before going to the next model. Is this normal behavior? Have seen this with quite a few of the Mini_Protein_binds units. Example https://boinc.bakerlab.org/rosetta/result.php?resultid=1159847678 |
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Number crunching :
Rosetta 4.1+ and 4.2+
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