I'm running some modeling with symmetry docking protocol (SymDock.mpi.macosgccrelease). I noticed that some of my runs ended with an error message such as this (the exact of seconds of timeout varies):
ERROR: quick exit from job-distributor due to flag jd2::XXX and timeout of 104.5 seconds
ERROR:: Exit from: src/protocols/jd2/MPIFileBufJobDistributor.cc line: 318
This error appeared to be random that it could happen at any point of the computation and if I re-ran the computation with the same inputs and flags, the error could just go away or happen at a different point.
This error also does not affect the decoys created.
My question is if there is a flag I can set to ignore the timeout?
This error occurs when using silent file output with MPI, and is due to an overzealous termination when MPI communication takes longer than expected. You can remove this timeout by adding the following option to your command line: -jd2:mpi_timeout_factor 0.0
I followed your suggestion and the issue is solved. Thank you very much!