Posts by Conan

21) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6070) Posted 19 Mar 2016 by Conan Post: With 3.72, no successful work units on any Linux hosts. Tested across multiple distributions (all 64-bit). They are running to completion, but then reporting output file missing. I am seeing the same thing, NO successful work units at all. Most run to completion (for me that is a 6 hour run time) but a number are also failing in less than an hour. This is on a 64 bit Linux host. Conan
22) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 5959) Posted 5 Jan 2016 by Conan Post: Got this error but the work unit was valid <stderr_txt> or/Parser should have replaced DummyMover.) ERROR: false ERROR:: Exit from: ......srcappspublicboincminirosetta.cc line: 96 DummyMover::apply() should never have been called! (JobDistributor/Parser should have replaced DummyMover.) This line was repeated dozens of times See Result 3473010 Conan
23) Message boards : Cafe RALPH : GEN_ADMIN_EMAIL (Message 5914) Posted 13 Oct 2015 by Conan Post: The block was put in a number of years ago to stop people hi-jacking teams and dumping existing members just to gain the points of that team by merging them with their existing team. It would appear that it is still in place which is why you can't request the team founder transfer function. I found this e-mail on the Rosetta web site to the project leader David Baker Email: dabaker@u.washington.edu. Also you can send a PM to dekim, the only Project person to visit RALPH with any regularity, this could be quicker than the e-mail. Conan
24) Message boards : RALPH@home bug list : Rosetta mini beta 3.60 (Message 5856) Posted 15 Jul 2015 by Conan Post: Well for me I received 22 work units and had 22 failures all with same error <message> process exited with code 193 (0xc1, -63) </message> <stderr_txt> [2015- 7-15 13:31: 0:] :: BOINC:: Initializing ... ok. [2015- 7-15 13:31: 0:] :: BOINC :: boinc_init() BOINC:: Setting up shared resources ... ok. BOINC:: Setting up semaphores ... ok. BOINC:: Updating status ... ok. BOINC:: Registering timer callback... ok. BOINC:: Worker initialized successfully. command: ../../projects/ralph.bakerlab.org/minirosetta_beta_3.60_x86_64-pc-linux-gnu -run:protocol jd2_scripting @flags_rb_09_11_41907_80823__t000__2_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_09_11_41907_80823__t000__2_C1_robetta.zip -nstruct 10000 -cpu_run_time 3600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3220592 Registering options.. Registered extra options. Initializing broker options ... Registered extra options. Initializing core... Initializing options.... ok Options::initialize() Options::adding_options() Options::initialize() Check specs. Options::initialize() End reached Loaded options.... ok Processed options.... ok Initializing random generators... ok Initialization complete. Setting WU description ... Unpacking zip data: ../../projects/ralph.bakerlab.org/minirosetta_database_14d5f91.zip Unpacking WU data ... Unpacking data: ../../projects/ralph.bakerlab.org/input_rb_09_11_41907_80823__t000__2_C1_robetta.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. SIGILL: illegal instruction Stack trace (18 frames): [0x3c04cbd] [0x409f10] [0x35b0473] [0x376a461] [0x37343a8] [0x373498c] [0x2f6f8a7] [0x2f6fe1f] [0x2f7017b] [0x19d80ef] [0x104699d] [0x1fc3b7e] [0x1fc556b] [0x202cc6d] [0x202bbc0] [0x40de78] [0x3cbb84b] [0x4003e9] Exiting... As soon as the application has unpacked and begins to run via BOINC it fails I am using AMD Phenom CPUs running 64 Bit Fedora Linux. Conan
25) Message boards : RALPH@home bug list : Minirosetta beta 3.56-3.58 (Message 5846) Posted 7 Jun 2015 by Conan Post: We should start up testing again with the recent 3.58 update. This version adds support for cyclic peptide modeling. We put testing on hold until we got this feature added. So why did we get 3.54 work units over the past few days? Should we not be testing the 3.58 work? Conan
26) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5817) Posted 26 Feb 2015 by Conan Post: New record for me I think, 100% failures with no successes after many dozens of tasks. This batch is fundamentally flawed and the parameters need resetting. Conan
27) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5812) Posted 25 Feb 2015 by Conan Post: Received this error on Task 3335547 ERROR: Error: can't read sequence! Use -in::file::fasta sequence.fasta or -in::file::native native.pdb! ERROR:: Exit from: src/protocols/abinitio/AbrelaxApplication.cc line: 488 std::cerr: Exception was thrown: [ERROR] EXCN_utility_exit has been thrown from: src/protocols/abinitio/AbrelaxApplication.cc line: 488 ERROR: Error: can't read sequence! Use -in::file::fasta sequence.fasta or -in::file::native native.pdb! Conan
28) Message boards : RALPH@home bug list : Rosetta Mini Beta 3.53 (Message 5794) Posted 4 Sep 2014 by Conan Post: New message on my manager on Windows 8.1 64 bit Rosetta Mini Beta is not available for your type of computer. I am also getting this message on my Windows XP 32 Bit computers, and can't get any work. Conan
29) Message boards : RALPH@home bug list : Rosetta Mini Beta 3.53 (Message 5793) Posted 4 Sep 2014 by Conan Post: Had 3 failed work units on Linux 64 Bit This error on Result 3296207 ERROR: Can't create a polymer bond after residue 9 due to incompatible type: ASP_p:CtermTruncation ERROR:: Exit from: src/core/conformation/Conformation.cc line: 643 std::cerr: Exception was thrown: [ERROR] EXCN_utility_exit has been thrown from: src/core/conformation/Conformation.cc line: 643 ERROR: Can't create a polymer bond after residue 9 due to incompatible type: ASP_p:CtermTruncation This error on Result 3300622 ERROR: Can't create a polymer bond after residue 52 due to incompatible type: VAL_p:CtermTruncation ERROR:: Exit from: src/core/conformation/Conformation.cc line: 643 std::cerr: Exception was thrown: [ERROR] EXCN_utility_exit has been thrown from: src/core/conformation/Conformation.cc line: 643 ERROR: Can't create a polymer bond after residue 52 due to incompatible type: VAL_p:CtermTruncation This error on Result 3304866 ERROR: Can't create a polymer bond after residue 73 due to incompatible type: ALA_p:CtermTruncation ERROR:: Exit from: src/core/conformation/Conformation.cc line: 643 std::cerr: Exception was thrown: [ERROR] EXCN_utility_exit has been thrown from: src/core/conformation/Conformation.cc line: 643 ERROR: Can't create a polymer bond after residue 73 due to incompatible type: ALA_p:CtermTruncation All to do with "relax_xxxx.x_ralph_test_bbonly_" type work units (where xxxx.x changes). Conan
30) Message boards : RALPH@home bug list : Rosetta Mini Beta 3.53 (Message 5785) Posted 17 Aug 2014 by Conan Post: Had this one fail with this error message WU 3128681 ERROR: Fullatom mismatch in checkpointer. ERROR:: Exit from: ......srcprotocolscheckpointCheckPointer.cc line: 379 ERROR: core::pose::symmetry::is_symmetric( native_pose ) \|\| core::pose::symmetry::is_symmetric( pose ) ERROR:: Exit from: ......srccorescoringrms_util.cc line: 1217 std::cerr: Exception was thrown: [ERROR] EXCN_utility_exit has been thrown from: ......srccorescoringrms_util.cc line: 1217 ERROR: core::pose::symmetry::is_symmetric( native_pose ) \|\| core::pose::symmetry::is_symmetric( pose ) Conan
31) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5756) Posted 20 Jul 2014 by Conan Post: Wus with names Tc794_hybrid... Tc804_summ_hybrid... Have problems with checkpointing (usual not working at all - reset to 0% progress if restart). And usual run much longer to target time (my target time set to 2 hour, but usual run 5-6 hours) Also some of this Wus grant only 20 Cr and have "InternalDecoyCount: 0 (GZ)" in logs AFAIK it is mean what no any usuful work was done and 5-6 hours of CPU time wasted at each such WU Each work unit will run until at least 1 Decoy has been run. If it takes longer than your set preferences then it keeps going till at least 1 Decoy finishes. Setting to 2 hours will work most of the time. The 5-6 hour run times happen to suit my 6 hour preference setting, but even then I have had some go over 7 hours. I have not tested the check-pointing so I can't test if the work units restart from zero like you are seeing. Conan
32) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5751) Posted 19 Jul 2014 by Conan Post: Every work unit on my Windows computers of the Tc804_Symm_hybrid_20174_xxxx_0 type only grants from 46 to 48 points per work unit no matter what the run time or the claimed credit. I have processed 8 of these so far and they all show the same behaviour. Times range from 17,895 seconds to 29,299 seconds but the credit granted is always 46-48 points. This only affects my Windows 32 bit computers as my 64 bit Linux machines don't have this issue and have normal points granted for the same work unit type. The Windows work units also only process 1 Decoy, yet the Linux work units process 3-4 Decoys. All other work units grant normal credits just the Tc804_Symm_hybrid_20174_xxxx_0 types on Windows grant the very low credit. Example Result 3000573 Result 3004229 Result 2989819 Conan
33) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5732) Posted 19 May 2014 by Conan Post: Had this TASK 2939795 that got to just over 17% and then stayed there and ran up time to over 12 hours run time (my preferences are set to 6 hours). I suspended the task and resumed it and it had now dropped back to normal processing with the percent done moving forward again and the time has dropped back to as well showing 1 1/2 hours so far and 3 1/5 to go. Will see if it processes successfully. Conan
34) Message boards : Number crunching : Export of Statistics (Message 5728) Posted 16 May 2014 by Conan Post: Stat Export still not working. Can this be fixed please? Conan
35) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5727) Posted 15 May 2014 by Conan Post: Your Server Status on the front page is at least 353 DAYS behind time. It shows the 17th May 2013 and today is the 15th May 2014. (Shown in top right corner) The actual Server time is correct on the Server Status page. Conan
36) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5726) Posted 9 May 2014 by Conan Post: Stat exports not working still. Conan
37) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5724) Posted 3 May 2014 by Conan Post: Export of Stats not working. Conan
38) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5723) Posted 2 May 2014 by Conan Post: Have had one WU play up by stopping at 35% but keep running the time up to over 14 Hours (my preferences are set to 6 hours). I suspended the WU then resumed it, and now it has reset itself back to just 2 Hours run time and progressing normally. Will see how it pans out as it is still running. This Result Conan Completed successfully, as has all other tasks. Conan
39) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5722) Posted 1 May 2014 by Conan Post: Have had one WU play up by stopping at 35% but keep running the time up to over 14 Hours (my preferences are set to 6 hours). I suspended the WU then resumed it, and now it has reset itself back to just 2 Hours run time and progressing normally. Will see how it pans out as it is still running. This Result Conan
40) Message boards : RALPH@home bug list : Minirosetta 3.49 (Message 5693) Posted 16 Nov 2013 by Conan Post: These new Rosetta Mini Beta types are we going to get some more to test? Conan

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