1)
Message boards :
Number crunching :
New kind of app on Ralph
(Message 102011)
Posted 3 Jun 2021 by biodoc Post: I wonder if the the "rosetta python projects" app is an implementation of PyRosetta for boinc. |
2)
Message boards :
Number crunching :
New kind of app on Ralph
(Message 101977)
Posted 31 May 2021 by biodoc Post: Apparently, when i got one and another one is in waiting the CPU crunches one of the pythons ones and nothing else. An alternative to uninstalling VBOX is to add this line to the "options" section of your cc_config.xml file and then restart the boinc client. <dont_use_vbox>1</dont_use_vbox> |
3)
Message boards :
Number crunching :
"Rosetta v4.12 i686-pc-linux-gnu" : fixed 20 h CPU time, fixed 20 credits
(Message 93890)
Posted 8 Apr 2020 by biodoc Post: @xii5ku, thank you for tracking this problem down. My caches are full of the linux i686 tasks. I would think it would be a good idea to stop the server from sending this work until the bug in the app is fixed. |
4)
Message boards :
Number crunching :
Computation errors: rb_02_25_16883_16706_ab_t000__robetta_cstwt_5.0_xxxx
(Message 91793)
Posted 27 Feb 2020 by biodoc Post: I've had ~20 of these tasks fail after 8 hours of computation time: rb_02_25_16883_16706_ab_t000__robetta_cstwt_5.0_FT_IGNORE_THE_REST_07_04_900260_6_0. Example: https://boinc.bakerlab.org/rosetta/result.php?resultid=1124284684 I've aborted the others in my que. linux 3900x processor 64 GB RAM |
5)
Message boards :
Number crunching :
Validators not running
(Message 90700)
Posted 21 Apr 2019 by biodoc Post: Both mini-R and R validators need a kick start. Also the mini-R assimilator is not running. |
6)
Message boards :
News :
Another publication in Nature describing the first de novo designed proteins with anti-cancer activity
(Message 90406)
Posted 22 Feb 2019 by biodoc Post: Congratulations! Unfortunately I'd have to pay for the article to read it but based on the abstract, it sounds very cool. |
7)
Message boards :
Number crunching :
Rosetta 4.0+
(Message 89188)
Posted 29 Jun 2018 by biodoc Post: I'm seeing quite a number of identical computation errors on 2 of my machines. They seem to occur in "bunches". For example, the ryzen had no errors for a couple of days and then I got about 180 of them within a few minutes. My other 2 machines are error free but they are running older kernels (mint 7.3 and 18.3) computer 1 https://boinc.bakerlab.org/rosetta/results.php?hostid=3420461&offset=0&show_names=0&state=6&appid= CPU type: 2 x Intel(R) Xeon(R) CPU E5-2690 v2 @ 3.00GHz [Family 6 Model 62 Stepping 4] Number of processors: 40 Coprocessors: NVIDIA Quadro FX 4800 (1535MB) driver: 340.10 OpenCL: 1.0 Operating System: Linux Mint 19 Tara [4.15.0-23-generic|libc 2.27 (Ubuntu GLIBC 2.27-3ubuntu1)] BOINC version: 7.9.3 Memory: 96602.15 MB Error: <core_client_version>7.9.3</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63)</message> <stderr_txt> command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.07_x86_64-pc-linux-gnu -run:protocol jd2_scripting @flags_rb_06_28_403_572__t000__0_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_06_28_403_572__t000__0_C1_robetta.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 3482852 rosetta_4.07_x86_64-pc-linux-gnu: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed. SIGABRT: abort called Stack trace (17 frames): [0x5efead0] [0x5ffe380] [0x607e517] [0x60083a8] [0x6002794] [0x60027ee] [0x6000f73] [0x6001996] [0x60007df] [0x600020e] [0x5f1d10e] [0x5f1d73e] [0x5f1707a] [0x5f17202] [0x412631] [0x5fff8cc] [0x610b97] Exiting... </stderr_txt> ]]> Computer 2 CPU type: AMD Ryzen 7 2700X Eight-Core Processor [Family 23 Model 8 Stepping 2] Number of processors: 16 Coprocessors: NVIDIA GeForce GTX 780 Ti (3015MB) driver: 390.67 OpenCL: 1.2 Operating System: Antergos Linux [4.17.2-1-ARCH] BOINC version: 7.8.6 Memory: 16037.01 MB <core_client_version>7.8.6</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63)</message> <stderr_txt> command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.07_x86_64-pc-linux-gnu -relax::minimize_bond_lengths 1 -out:file:silent_struct_type binary -ignore_unrecognized_res 1 -abinitio::rsd_wt_loop 0.5 -abinitio::use_filters false -abinitio::rg_reweight 0.5 -relax::default_repeats 2 -beta 1 -abinitio::increase_cycles 10 -ex2aro 1 -frag9 00001.200.9mers -abinitio::fastrelax 1 -abinitio::detect_disulfide_before_relax 1 -ex1 1 -relax::minimize_bond_angles 1 -beta_cart 1 -in:file:native 00001.pdb -relax::dualspace 1 -optimization::default_max_cycles 200 -abinitio::rsd_wt_helix 0.5 -frag3 00001.200.3mers -in:file:boinc_wu_zip DRH_curve_X_h21_l4_h29_l2_09658_4_loop_11_0001_one_capped_0001_fragments_data.zip -out:file:silent default.out -silent_gz 1 -mute all -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 1195778 rosetta_4.07_x86_64-pc-linux-gnu: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed. SIGABRT: abort called Stack trace (17 frames): [0x5efead0] [0x5ffe380] [0x607e517] [0x60083a8] [0x6002794] [0x60027ee] [0x6000f73] [0x6001996] [0x60007df] [0x600020e] [0x5f1d10e] [0x5f1d73e] [0x5f1707a] [0x5f17202] [0x412631] [0x5fff8cc] [0x610b97] Exiting... </stderr_txt> ]]> |
8)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 77196)
Posted 1 Aug 2014 by biodoc Post: Perhaps the Baker lab use of University Network bandwith is affecting student access to facebook, youtube and Netflix? Sad, science no longer rules these days. |
9)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 77103)
Posted 29 Jul 2014 by biodoc Post: Similar problems with my 4 computers: 7/29/2014 4:56:43 PM | rosetta@home | Started upload of tube9_26_A_tube9_26_B_patchdock_split_03_140727_SAVE_ALL_OUT__179886_89_0_0 7/29/2014 4:57:01 PM | rosetta@home | Temporarily failed upload of hc_centroids_1tsf_234_0.5_06-01-14_SAVE_ALL_OUT_168123_4458_0_0: transient HTTP error 7/29/2014 4:57:01 PM | rosetta@home | Backing off 00:06:23 on upload of hc_centroids_1tsf_234_0.5_06-01-14_SAVE_ALL_OUT_168123_4458_0_0 7/29/2014 4:57:04 PM | rosetta@home | Temporarily failed upload of tube9_26_A_tube9_26_B_patchdock_split_03_140727_SAVE_ALL_OUT__179886_89_0_0: connect() failed 7/29/2014 4:57:04 PM | rosetta@home | Backing off 00:05:20 on upload of tube9_26_A_tube9_26_B_patchdock_split_03_140727_SAVE_ALL_OUT__179886_89_0_0 |
10)
Message boards :
Number crunching :
Report stuck & aborted 5.01 WU here please - III
(Message 14528)
Posted 24 Apr 2006 by biodoc Post: I just aborted a WU (details below). It was running 8+ hours at 2% complete and I have a 2 hr runtime pref. set. The behavior of this WU was similar to the FACONTACT & HBLR_1.0 WUs that I've seen posted here & experienced myself as "long runners". They seem to run normally through the "model 1" process (# of steps in the 6 figure range) & instead of moving on to "model 2, step 1", they start over as model 1, step1. Perhaps it could be described as a "model 1 loop" bug? Anyone else seen this? I'm only running Rosetta & I have "leave in memory" checked as a pref. Could this be Accepted RMSD & Accepted energy parameters or "goals" are not met during the Model 1 calculation & thus does not move on to a model 2 calculation & just starts the model 1 calculation over again? Result ID 18037907 Name FARELAX_NOFILTERS_1scjB_417_302_3 Workunit 13208951 |
11)
Message boards :
Number crunching :
Report stuck & aborted 5.01 WU here please - III
(Message 14310)
Posted 21 Apr 2006 by biodoc Post: I just abort 2 "long runners" (17+ hours; about 2% complete) Result ID 17758781 Name FACONTACTS_RECENTER_NOFILTERS_1scjB_448_993_1 Result ID 17757908 Name FACONTACTS_RECENTER_NOFILTERS_1tit__448_560_1 |
12)
Message boards :
Number crunching :
Report stuck & aborted WU here please - II
(Message 13485)
Posted 11 Apr 2006 by biodoc Post: Iv'e got a stuck work unit at 1.042% complete (4h 50min) w/ 2 hr runtime preference. No activity in graphics mode. I've aborted this work unit after six hours. http://boinc.bakerlab.org/rosetta/result.php?resultid=17002591 |
13)
Message boards :
Number crunching :
Report stuck & aborted WU here please - II
(Message 13478)
Posted 11 Apr 2006 by biodoc Post: Iv'e got a stuck work unit at 1.042% complete (4h 50min) w/ 2 hr runtime preference. No activity in graphics mode. http://boinc.bakerlab.org/rosetta/workunit.php?wuid=13936782 Please advise; should I terminate? |
14)
Message boards :
Number crunching :
Miscellaneous Work Unit Errors
(Message 13231)
Posted 8 Apr 2006 by biodoc Post: Since the upgrade to version 4.97, I've had most of the WU's failing with client errors on my 4 windoze boxes (42 failures & counting!). My linux box is OK. FYI, I had absolutely no errors with 4.83 since it was released. These are the errors I'm seeing: ***UNHANDLED EXCEPTION**** Reason: Access Violation (0xc0000005) at address 0x00599FF4 read attempt to address 0x06C2FFF0 ***UNHANDLED EXCEPTION**** Reason: Access Violation (0xc0000005) at address 0x00599FF4 read attempt to address 0x06C2FC8C ***UNHANDLED EXCEPTION**** Reason: Access Violation (0xc0000005) at address 0x007022EA read attempt to address 0x06AAFF34 ***UNHANDLED EXCEPTION**** Reason: Access Violation (0xc0000005) at address 0x00599FF4 read attempt to address 0x06CBFA98 ***UNHANDLED EXCEPTION**** Reason: Access Violation (0xc0000005) at address 0x007022EA read attempt to address 0x0EB4FF90 |
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