Posts by Peti

1) Message boards : Number crunching : Rosetta 4.0+ (Message 92434) Posted 28 Mar 2020 by Peti Post: "ERROR: Assertion `copy_pose.size() == native.size()` failed. MSG:the reference pose must be the same size as the working pose ERROR:: Exit from: ......srcprotocolsprotein_interface_designfiltersRmsdFilter.cc line: 323 22:47:47 (7828): called boinc_finish(0)" https://boinc.bakerlab.org/rosetta/result.php?resultid=1134099093 Is this an error? The work unit is validated. Is the result usable? I see this across 2 Ryzen hosts. Hi, I'd think it's an error if it says so. But it's inside the Rosetta software or data, some tasks are getting this very same error message at my PC, too. for example, this: https://boinc.bakerlab.org/rosetta/result.php?resultid=1134374428 ERROR: Assertion `copy_pose.size() == native.size()` failed. MSG:the reference pose must be the same size as the working pose ERROR:: Exit from: src/protocols/protein_interface_design/filters/RmsdFilter.cc line: 323 And to note, my PC was not overclocked at that time, and I did not reboot the PC or stop boinc in any way around that time. so it must be the software....
2) Message boards : Number crunching : Rosetta 4.0+ (Message 92319) Posted 26 Mar 2020 by Peti Post: No need to worry about it. The ProjectTeam can identify any bad results. Thank you, then I don't worry.
3) Message boards : Number crunching : Rosetta 4.0+ (Message 92308) Posted 26 Mar 2020 by Peti Post: Hi everyone, I am sometimes seeing very similar error messages. ERROR: std::abs( coordsys_rot.det() - 1.0 ) < 1e-6 ERROR:: Exit from: src/core/pose/symmetry/util.cc line: 884 and ERROR: Assertion `copy_pose.size() == native.size()` failed. MSG:the reference pose must be the same size as the working pose ERROR:: Exit from: src/protocols/protein_interface_design/filters/RmsdFilter.cc line: 323 and https://boinc.bakerlab.org/rosetta/result.php?resultid=1131649536 _64-pc-linux-gnu': free(): invalid pointer: 0x00000000080e29a8 * * Error in `../../projects/boinc.bakerlab.org_rosetta/rosetta_4.08_x86_64-pc-linux-gnu': free(): invalid pointer: 0x00000000080e29a8 * and https://boinc.bakerlab.org/rosetta/result.php?resultid=1131646232 _64-pc-linux-gnu': double free or corruption (!prev): 0x00000000060b5a60 * * Error in `../../projects/boinc.bakerlab.org_rosetta/rosetta_4.08_x86_64-pc-linux-gnu': double free or corruption (!prev): 0x00000000060b5a60 * (maybe these last two were due to bad cpu overclock? or maybe not?) I just found this thread, after I already posted my problems here https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13629&postid=92306#92306 The tasks seems "Completed and validated" on the webpage. Why is that, if there is error? Whom should I tell that my PC might have made mistakes that are unnoticed? I don't want to mix bad results into good data...
4) Questions and Answers : Getting started : Completed and validated task but early reporting and error message in the Stderr output? (Message 92306) Posted 26 Mar 2020 by Peti Post: Update: I have a handful of new tasks finished and no error. This time: no overclock & not touching the Boinc manager after the start. (also, I have reset the project yesterday, and downloaded all the tasks and necessary files again, so it's clean start.) I'm still not sure if my overclock was bad or there was a bug / problem in the stop and restart... (I exited boinc manager and stopped tasks before reboot, it should have checkpoints so it should not matter, should it? I guess it should properly restart from checkpoint even in case of power blackout ?) my overclock was looking stable, passed memtest and stress tests (a program calculating pi to lots of digits) and it also reported some of the rosetta tasks without problems. (I'm running Folding at home in parallel , I had no calculation errors in that neither cpu not GPU work units) So I don't know if it's some random hardware error happening rarely, or it's a software bug) By the way, why the Boinc manager does not suspend calculation when Folding manages to receive a cpu workunit and starts to calculate? There is this setting that says "suspend when no boinc cpu usage is >25%" but it just does nothing, and I have to manually pause it. (I cannot have CPU at 100% since I need one cpu core for the GPU folding@home, so I set rosetta to use 88%) edit: there are some other people here, who had some similar error messages here too: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=12242&postid=92152#92152
5) Questions and Answers : Getting started : Completed and validated task but early reporting and error message in the Stderr output? (Message 92281) Posted 25 Mar 2020 by Peti Post: Hi everyone! I'm new to this topic, and I'm confused a little. So, my PC has calculated some tasks. Sometimes I see early reporting (few hours remaining) after rebooting the PC and restarting boinc manager, and I also had some computation error (I guess incorrect setting while trying to overclock cpu, now it's back to normal settings) When I browse the reported tasks on the webpage, I still see errors in the "Stderr output" text. and the task seems "Completed and validated" on the webpage. Why is that, if there is error? for example this:https://boinc.bakerlab.org/rosetta/result.php?resultid=1132408641 ERROR: std::abs( coordsys_rot.det() - 1.0 ) < 1e-6 ERROR:: Exit from: src/core/pose/symmetry/util.cc line: 884 And runtime is much less than expected. (1 hours 19 min 56 sec instead of >7 hours) another example: https://boinc.bakerlab.org/rosetta/result.php?resultid=1131638832 run time 2 hours 59 min 50 sec instead of >7 hours, the same error in stderr. and this: https://boinc.bakerlab.org/rosetta/result.php?resultid=1131616913 ERROR: Assertion `copy_pose.size() == native.size()` failed. MSG:the reference pose must be the same size as the working pose ERROR:: Exit from: src/protocols/protein_interface_design/filters/RmsdFilter.cc line: 323 (also early reporting, 4 hours 16 min 49 sec) then how is this "valid"? Whom should I tell that my PC might have made mistakes that are unnoticed? (just to note, I have overclocked the PC and was running Rosetta@home like that, but PC did not crash, seemed stable for a day of 90% cpu load, now I reset CPU clock to normal and reset project in boinc manager, I'm curious if the computer will keep making mistakes, if this is a bug in software or due to overclock) (By the way, Linux Mint 19.3 system, 7.9.3 X64 boinc manager, EVGA SR2 with dual xeon x5670, 64GB ECC memory)