mpirun docking_protocol

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    • August 3, 2020 at 6:38 pm #3523
      Anonymous

        Hi all,

        I was running mpi docking_protocol (docking_protocol.cxx11threadmpiserialization.linuxgccrelease) to generate 500 decoys. I got this error and only 470 decoys as output:

        [ ERROR ]: Error(s) were encountered when running jobs.

        12 jobs failed;

        Check the output further up for additional error messages.

        Primary job  terminated normally, but 1 process returned

        a non-zero exit code. Per user-direction, the job has been aborted.

        mpirun detected that one or more processes exited with non-zero status, thus causing

        the job to be terminated. The first process to do so was:

          Process name: [[24734,1],19]

          Exit code:    255

        I then went to the output file and saw this:

        core.optimization.LineMinimizer: (13){0} [ ERROR ] Inaccurate G! step= 3.8147e-06 Deriv= -3.24745e-07 Finite Diff= 2.44379e-06

        core.optimization.LineMinimizer: (27){0} [ ERROR ] Inaccurate G! step= 1.90735e-06 Deriv= -0.0566125 Finite Diff= 0.440445

        core.optimization.LineMinimizer: (6){0} [ ERROR ] Inaccurate G! step= 3.8147e-06 Deriv= -3.74618e-08 Finite Diff= 0

        core.optimization.LineMinimizer: (25){0} [ ERROR ] Inaccurate G! step= 3.8147e-06 Deriv= -0.0324837 Finite Diff= 0.0853026

        core.optimization.LineMinimizer: (7){0} [ ERROR ] Inaccurate G! step= 9.53674e-07 Deriv= -0.104392 Finite Diff= 0.358539

        core.optimization.LineMinimizer: (11){0} [ ERROR ] Inaccurate G! step= 1.90735e-06 Deriv= -0.14514 Finite Diff= 0.194866

        core.optimization.LineMinimizer: (22){0} [ ERROR ] Inaccurate G! step= 3.8147e-06 Deriv= -0.0539229 Finite Diff= 0.000939131

        core.optimization.LineMinimizer: (10){0} [ ERROR ] Inaccurate G! step= 1.90735e-06 Deriv= -0.198693 Finite Diff= 0.590045

        core.optimization.LineMinimizer: (22){0} [ ERROR ] Inaccurate G! step= 3.8147e-06 Deriv= -486138 Finite Diff= 5.05403e+08

        core.optimization.LineMinimizer: (5){0} [ ERROR ] Inaccurate G! step= 6.10352e-07 Deriv= -1.41346e-08 Finite Diff= 1.49012e-06

        core.optimization.LineMinimizer: (24){0} [ ERROR ] Inaccurate G! step= 3.8147e-06 Deriv= -1.22603e+06 Finite Diff= 5.16252e+06

        The score file looks fine and it run well with normal docking_protocol (docking_protocol.linuxgccrelease) but not mpi (docking_protocol.cxx11threadmpiserialization.linuxgccrelease). Could anyone please help?

        Thank you very much!

        Nan

         

      • August 14, 2020 at 4:18 pm #15453
        Anonymous

          Hi Nan,

          This is not a docking problem per se. You seem to be in a bad place in the energy landscape, so the minimizer is not meeting its tolerance limits. Usually these turn up as warnings and we ignore them, but your compiler seems to throw them up as errors. That’s why you don’t see the protocol stopping without mpi. When you compiled using mpi, there was some setting that turned all warnings into errors. You need to figure out what that setting was and recompile it.

          Best,

          Shourya

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