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Coupling with external code

  cd build
  make tmcmc_theta_external use_torc=1

This version creates intermediate folders of the form tmpdir.*.*.*.* where the external code is running on a set of parameters saved in params.txt. After the execution the directory is deleted. If you want to keep the directories set REMOVEDIRS 0 in source/likelihoods/loglike_theta.c.

To setup the example:

    cd examples/sampling/external/tmcmc
    ./setup_tmcmc.sh
    cd runs/run_001

Contents of runs/run_001:

  • The Π4U executable: tmcmc_theta_external

  • The files priors.par and tmcmc.par. These files contain information about the choice of the prior distributions and the TMCMC parameters respectively.

  • A directory named model. Inside this directory, Π4U expects to find:

    • a file with the experimental data named data.txt
    • a user-provided script named doall.sh, which (i) runs the external simulation, (ii) compares the output with the experimental data, and (iii) saves the log-likelihood inside a file called loglike.txt. The value inside loglike.txt is then read from Π4U.

To run the example: 

    mpirun -np 4 ./tmcmc_theta_external

or

    export TORC_WORKERS=4
    mpirun -np 1 ./tmcmc_theta_external