Posts by svincent

21) Message boards : Number crunching : "Rosetta Mini for Android is not available for your type of computer" (Message 81013) Posted 12 Jan 2017 by svincent Post: I'm seeing the same thing on Ubuntu 16.04: a project backoff of 24 hours accompanied by the message "Rosetta Mini for Android is not available for your type of computer." when attempting to get new tasks via Update. Before the recent hiccups this machine crunched Rosetta without any problems.
22) Message boards : Rosetta@home Science : New article in Nature co-authored by Dr. Baker (Message 80792) Posted 26 Oct 2016 by svincent Post: More commentary in Derek Lowe's blog here: http://blogs.sciencemag.org/pipeline/archives/2016/10/24/nailing-down-small-proteins
23) Message boards : Number crunching : Compute error (Message 80426) Posted 23 Jul 2016 by svincent Post: Task 851611490 14h2ld25newC8104_fold_and_dock_SAVE_ALL_OUT_401627_570_0) failed with this error message ERROR: get_jump_that_builds_residue: not build by a jump! ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 394 Not quite sure why the exclamation mark is warranted but there you go.
24) Message boards : Number crunching : Minirosetta 3.73-3.78 (Message 80107) Posted 19 May 2016 by svincent Post: 825724761 ERROR: in::file::boinc_wu_zip 5H2LD-13_tj58_5_054307_0014_I_0001_data.zip does not exist! ERROR:: Exit from: ......srcappspublicboincminirosetta.cc line: 226 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish I see the same error: seems to happen with all tasks named yh_*. Boinc 7.2.42/Ubuntu 14.04
25) Message boards : Number crunching : Minirosetta 3.73-3.78 (Message 79954) Posted 28 Apr 2016 by svincent Post: Thanks for the suggestions. I don't think it's disk space: I'm using 1.5GB out of 100GB available to Boinc. In fact I don't think it's anything local to my machine at all since those tasks were given out again to a couple of wingmen: they failed in what seems to be the same fashion. (I tried the ldd command you suggested: output below) svincent@svincent-desktop:~/BOINC/projects/boinc.bakerlab.org_rosetta$ ldd minirosetta_graphics_3.73_x86_64-pc-linux-gnu linux-vdso.so.1 => (0x00007ffc460a5000) libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1 (0x00007f102c488000) libGL.so.1 => /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1 (0x00007f102c222000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f102bf1e000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f102bc18000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f102ba02000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f102b63d000) libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f102b308000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f102b0ea000) libglapi.so.0 => /usr/lib/x86_64-linux-gnu/libglapi.so.0 (0x00007f102aec3000) libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f102acb1000) libXdamage.so.1 => /usr/lib/x86_64-linux-gnu/libXdamage.so.1 (0x00007f102aaae000) libXfixes.so.3 => /usr/lib/x86_64-linux-gnu/libXfixes.so.3 (0x00007f102a8a8000) libX11-xcb.so.1 => /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1 (0x00007f102a6a6000) libxcb-glx.so.0 => /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0 (0x00007f102a48f000) libxcb-dri2.so.0 => /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0 (0x00007f102a28a000) libxcb-dri3.so.0 => /usr/lib/x86_64-linux-gnu/libxcb-dri3.so.0 (0x00007f102a087000) libxcb-present.so.0 => /usr/lib/x86_64-linux-gnu/libxcb-present.so.0 (0x00007f1029e84000) libxcb-sync.so.1 => /usr/lib/x86_64-linux-gnu/libxcb-sync.so.1 (0x00007f1029c7e000) libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f1029a5f000) libxshmfence.so.1 => /usr/lib/x86_64-linux-gnu/libxshmfence.so.1 (0x00007f102985d000) libXxf86vm.so.1 => /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1 (0x00007f1029657000) libdrm.so.2 => /usr/lib/x86_64-linux-gnu/libdrm.so.2 (0x00007f102944a000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f1029246000) /lib64/ld-linux-x86-64.so.2 (0x00007f102c6f6000) libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f1029042000) libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f1028e3c000)
26) Message boards : Number crunching : Minirosetta 3.73-3.78 (Message 79950) Posted 27 Apr 2016 by svincent Post: I'm seeing a lot of robetta tasks crash immediately : the relevant line in the task log seems to be: ERROR: Unable to open weights/patch file. None of (./)beta_cart or (./)beta_cart.wts or minirosetta_database/scoring/weights/beta_cart or minirosetta_database/scoring/weights/beta_cart.wts exist ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 2884 [0x4485e82] Sample tasks: 815715361 815591894 Boinc 7.2.42 Ubuntu 14.04
27) Message boards : Number crunching : Minirosetta 3.73-3.78 (Message 79931) Posted 25 Apr 2016 by svincent Post: I'm seeing the same issue that's been reported above: an intermittent failure to get new workunits accompanied by this message in the event log. Rosetta Mini for Android is not available for your type of computer. Do Network Communication successfully reports the task. I'm running 2 R@h workunits/Ubuntu 14.04 LTS/Boinc 7.2.42/No workbuffer
28) Message boards : Number crunching : validate errors (Message 79005) Posted 29 Oct 2015 by svincent Post: Task 768264227 gave Validate Error. 6H_TUBE8_AB_6H_TUBE_07.pdb_15_10_12_32_13_globalDocking_1_SAVE_ALL_OUT_309429_46_0
29) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 78622) Posted 30 Aug 2015 by svincent Post: There was a big windstorm in the Pacific Northwest yesterday. Power was cut to the University of Washington: I believe it's been restored but would assume Rosetta@home is in recovery mode. If that's the case, do you have any idea why I have still been able to download new tasks the entire time--just unable to upload? I'm not affiliated with the project and was really just speculating. But there are multiple servers: perhaps the file system of one but not the rest became corrupt and needs to be restored. Or something.
30) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 78617) Posted 30 Aug 2015 by svincent Post: There was a big windstorm in the Pacific Northwest yesterday. Power was cut to the University of Washington: I believe it's been restored but would assume Rosetta@home is in recovery mode.
31) Message boards : Number crunching : Minirosetta 3.59 (Message 78545) Posted 6 Aug 2015 by svincent Post: FFD__5strand14helixWYY_filteredloops_321_0001_dock_PD1CancerImmunotherapy_15_08_07_40_34_globalDocking_4_SAVE_ALL_OUT_277259_19 crashed immediately on Linux (nothing useful in stderr): it also crashed on a Windows machine
32) Message boards : Rosetta@home Science : Graphene (Message 78214) Posted 18 May 2015 by svincent Post: http://boinc.bakerlab.org/rosetta/rah_graphics.php only in German , maybe it is somewhere in English? regards Tx Rico but perhaps there is a translation issue here: I was referring to the single hexagonal sheet carbon structure rather than Rosetta's graphics.
33) Message boards : Rosetta@home Science : Graphene (Message 78208) Posted 17 May 2015 by svincent Post: I've got a task 735267454 named WY2RL95I_asym_LargeGrapheneWithVirtAtoms_Squashed.pdb_DHR10.pdb_0069__v6_0003_relax_SAVE_ALL_OUT_267837_75_0 I'm intrigued: fascinating material though graphene is, I don't quite see its relevance to protein folding. Could someone please explain?
34) Message boards : Number crunching : Minirosetta 3.54 (Message 78145) Posted 21 Apr 2015 by svincent Post: Task 731275755 ( R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0005_fold_and_dock_SAVE_ALL_OUT_263848_834_0 ) got stuck getting no CPU time and I aborted it. Properties were: CPU time at last checkpoint : 8:06 CPU time : 8.39 Elapsed time : 11:55:19
35) Message boards : Number crunching : dock_placestub_* tasks failing (Message 78006) Posted 7 Mar 2015 by svincent Post: I'm seeing tasks with names starting with dock_placestub_ (e.g. task 722107660 ) fail early with a Validate Error: the following error message is repeated many times. ERROR: Cannot open patchdock file: 3_input_0109_0001_ss1_3_ss2_1_ss3_3_0001_0001_vegf.patchdock ERROR:: Exit from: src/protocols/protein_interface_design/read_patchdock.cc line: 112 Boinc 7.2.42 on Ubuntu 14.04
36) Message boards : Rosetta@home Science : Azurin, rb_, zibochen (Message 77730) Posted 11 Dec 2014 by svincent Post: Azurin is a small copper-containing protein found in bacteria where it's involved in electron transport processes. Jobs starting with rb_ are indeed robetta jobs.The first two numbers are the month and day of the submitted job: the third indicates its identifier in the robetta queue. You can look up the details of each individual job at http://robetta.bakerlab.org/queue.jsp . No idea about zibochen
37) Message boards : Number crunching : Assertion failure in FragmentMover (Message 77527) Posted 30 Sep 2014 by svincent Post: Task 694186107 ( ebob1_3_1348_fold_SAVE_ALL_OUT_212831_44_0 ) failed with the following assertion failure: a wingman had the same problem. ERROR: Assertion failure: runtime_assert( ( begin + size - 1 ) <= pose.total_residue() ); ERROR:: Exit from: ......srcprotocolssimple_movesFragmentMover.cc line: 307 std::cerr: Exception was thrown: [ERROR] EXCN_utility_exit has been thrown from: ......srcprotocolssimple_movesFragmentMover.cc line: 307 ERROR: Assertion failure: runtime_assert( ( begin + size - 1 ) <= pose.total_residue() );
38) Message boards : Rosetta@home Science : Rosetta@home Research Updates (Message 77001) Posted 12 Jul 2014 by svincent Post: I hope the idea of a monthly newsletter hasn't fallen by the wayside: I'd certainly enjoy reading it.
39) Message boards : Number crunching : Minirosetta 3.52 (Message 77000) Posted 12 Jul 2014 by svincent Post: I'm also seeing the occasional failure "bad_alloc" failure on Ubuntu 14.04. Sample: Task 673942668 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc </stderr_txt>
40) Message boards : Number crunching : Minirosetta 3.52 (Message 76819) Posted 10 Jun 2014 by svincent Post: I'm seeing failures on Linux with tasks named T0763*. See 666899120 ERROR: HybridizeFoldtreeDynamic: failed to build fold tree from cuts and jumps ERROR:: Exit from: src/protocols/hybridization/HybridizeFoldtreeDynamic.cc line: 676 SIGSEGV: segmentation violation Stack trace (20 frames): [0xbb009c7]

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