cryptic error “Got some signal… It is:15” — an issue with ‘fixbb’, or something else?

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    • October 16, 2019 at 9:59 pm #3285
      Anonymous

        Hello Forum

        I’m trying to run fixbb on my cluster here, and everything seems to have been going well for a while, but it suddenly stopped and spit out the following in the log file: 


        
^[[0mcore.pack.interaction_graph.interaction_graph_factory: (0) ^[[0mInstantiating PDInteractionGraph
        
Got some signal... It is:15
        
Process was terminated!
        
Got some signal... It is:15
        
Process was terminated!
        
Got some signal... It is:15
        
Process was terminated!
        
Got some signal... It is:15
        
Process was terminated!
        
Got some signal... It is:15
        
Process was terminated!
        
Got some signal... It is:15
        
Process was terminated!
        
Got some signal... It is:15
        
Process was terminated!
        


        
mpiexec noticed that process rank 7 with PID 20123 on node baldr-3 exited on signal 9 (Killed).

         

        now i’m not sure what this signal means or what the source of it is (e.g., something wrong with how I called fixbb, or mpiexec, or missing libraries).  Any insights would be most appreciated.

        Thanks! 

      • October 16, 2019 at 10:03 pm #15014
        Anonymous

          Signal 15 is SIGTERM.  This is a Linux/unix thing not a Rosetta thing.  It means something outside of Rosetta issued a command to Rosetta to stop running. 

          One of your processed got signal 9, which is SIGKILL, which again means something external to rosetta killed it.  9 is a “harder kill” than 15.

          If you are on a cluster I’d guess the most likely thing is you ran out your allocation of computer time, but there’s not enough data here to know.  

          • October 16, 2019 at 10:05 pm #15015
            Anonymous

              fantastic thanks!  that was easy enough to solve :) 

              I was worried it was something more complicated 

               

          • October 16, 2019 at 11:36 pm #15016
            Anonymous

              Neverthless, that error message is pretty awful and confusing for users.  I’m going to open a pull request to add a clearer error message.

            • October 18, 2019 at 7:49 pm #15019
              Anonymous

                OK.  So the bad news is, I don’t know why your crash occurs.  The good news is, the next time it happens, if you use the next pu blic release of Rosetta, the error emssage will be less cryptic!

                • October 30, 2019 at 4:29 pm #15029
                  Anonymous

                    thanks! 

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