file frontends/MontePythonLike_3_3_0.cpp

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Detailed Description



  • 2019 June, 2020 May
  • 2019 June
  • 2020 Apr

Frontend source for the MontePython backend.

Authors (add name and date if you modify):

Source code

//   GAMBIT: Global and Modular BSM Inference Tool
//   *********************************************
///  \file
///  Frontend source for the MontePython backend.
///  *********************************************
///  Authors (add name and date if you modify):
///  \author Janina Renk
///          (
///  \date 2019 June, 2020 May
///  \author Sanjay Bloor
///          (
///  \date 2019 June
///  \author Pat Scott
///          (
///  \date 2020 Apr
///  *********************************************

#include "gambit/Backends/frontend_macros.hpp"
#include "gambit/Backends/frontends/MontePythonLike_3_3_0.hpp"

#ifdef HAVE_PYBIND11

  #include "gambit/Utils/begin_ignore_warnings_pybind11.hpp"
  #include <pybind11/stl.h>
  #include <pybind11/stl_bind.h>
  #include <pybind11/functional.h>
  #include "gambit/Utils/end_ignore_warnings.hpp"

    using namespace pybind11::literals; // to bring in the `_a` literal to initialise python dictionaries with pybind11

    static map_str_dbl chached_likelihoods; // string double map to save likelihood calculation from previous param point

    /// calls the function "get_available_likelihoods" in the patched file of MontePython backend.
    /// This returns a list containing strings with the names of all likelihoods available in the MontePythonLike backend
    std::vector<str> get_MP_available_likelihoods()
      pybind11::list avail_likes = MontePythonLike.attr("get_available_likelihoods")(backendDir);
      return avail_likes.cast<std::vector<str>>();

    /// convenience function to check compatibility of likelihoods and CLASS version in use
    /// add further rules for incompatibilities here.
    void check_likelihood_classy_combi(std::string& likelihood, std::string& classy_backendDir)

      // add all combinations that are not compatible here.
      // example for such an incompatibility: an update in CLASS 2.7 enables the separation
      // of the matter power spectrum into the baryonic and CDM components separated from
      // other non-CDM species (e.g. massive neutrinos). Likelihoods that rely on the
      // baryon+CDM matter power spectrum can't be used with a CLASS version below 2.7
      map_str_str incompatible_combi = {{"bao_correlations", "2.6.3"},{"euclid_pk", "2.6.3"},
          {"ska1_IM_band1", "2.6.3"},{"ska1_IM_band2", "2.6.3"},{"ska2_pk", "2.6.3"},{"Lya_abg", "2.6.3"}};

      // check if incompatible CLASS version exists for given likelihood
      if (incompatible_combi.count(likelihood))
        // if incompatible version in use throw a fatal error
        if (classy_backendDir.find(incompatible_combi[likelihood]) != std::string::npos)
          std::string classy_version = classy_backendDir.substr(classy_backendDir.find("classy/"),classy_backendDir.find("/lib"));
          classy_version = classy_version.substr(7, classy_version.size() - 11);

          std::ostringstream ss;
            ss << "You requested the MontePython likelihood '"<< likelihood<<"'." << endl
               << "The CLASS version "<< classy_version << " is not compatible with that likelihood"<< endl
               << "You need to install a later version of CLASS. To do so you can execute" << endl
               << "\ncd build; make nuke-classy_"<< classy_version <<"; make classy_<version_name>; cd ..\n" << endl
               << "where <version_name> is the version greater than "<< classy_version <<" of the CLASS backend." << endl
               << "Type \n\n./gambit backends\n\nto see which versions are available to install." << endl;
            backend_error().raise(LOCAL_INFO, ss.str());

    /// convenience function to check if the chosen likelihood is supported
    /// add further rules for incompatibilities here.
    void check_likelihood_support(std::string& likelihood)
      // There are two different reasons why the support for a likelihood is
      // switched off:
      // 1) python version that GAMBIT is configured with is not compatible with the likelihood
      // 2) likelihood implementation does not follow MontePython guidelines

      // case 1): python version that GAMBIT is configured with is not compatible with the
      // python version the likelihood works with.
      // Currently the likelihoods 'euclid_lensing' and 'euclid_pk' will not work with Python 3, nor will many SKA likelihoods.
      // Throw a fatal error when any of these likelihoods is in use and GAMBIT is configured with Python 3.

      // Get the python major version in use
      pybind11::module sys = pybind11::module::import("sys");
      int pyMajorVersion = sys.attr("version_info").attr("major").cast<int>();
      std::set<std::string> python3_incomp { "euclid_lensing", "euclid_pk", "ska1_pk", "ska2_pk",
          "ska1_lensing", "ska2_lensing", "ska1_IM_band2"};

      // check for incompatible combinations
      if ( (pyMajorVersion == 3) && python3_incomp.count(likelihood))
        std::ostringstream err;
        err << "You requested the MontePython likelihood '" << likelihood << "', ";
        err << "but you are using Python 3. In MontePython" << STRINGIFY(VERSION);
        err << "this likelihood only works with Python 2.\n";
        err << "Please reconfigure GAMBIT with Python 2, if you want to use this likelihood.";
        backend_error().raise(LOCAL_INFO, err.str());

      // case 2) likelihood implementation does not follow MontePython guidelines,
      // examples could be
      //  * quantities derived by CLASS are not called directly through the CLASS python
      //    object but through MontePython data.get_mcmc_parameters(['derived'])
      //  * parameters setting the obsevables that CLASS has to compute are not specified
      //    correctly with 'need_cosmo_arguments' function
      // If you fix these issues, you can use the likelihood; in that case, remove it from the list
      // 'unsupported_likes'
      std::set<std::string> unsupported_likes { "Lya_abg", "gunn_peterson" };

        std::ostringstream err;
        err << "You requested the MontePython likelihood '" << likelihood << "'' ";
        err << "which is currently not supported by MontePython" << STRINGIFY(VERSION);
        err << ". For information on why this could be the case, type \n";
        err << "./gambit check_likelihood_support";
        backend_error().raise(LOCAL_INFO, err.str());

    /// convenience function to compute the loglike from a given experiment, given a MontePython likelihood-data container
    /// mplike, using the CLASS Python object cosmo.
    double get_MP_loglike(const MPLike_data_container& mplike, pybind11::object& cosmo, std::string& experiment)

      double result;

      //static const bool first_run
      // check if likelihood needs to be re-evaluated:
      // => if CLASS re-ran likelihood needs updating in any case
      bool needs_update = cosmo.attr("recomputed").cast<bool>();

      // => if CLASS did not re-compute: check if likelihood has nuisance parameters
      if(not needs_update)
          // get list of nuisance parameter needed for likelihood calculation from MP
          // => if the list is not empty, there are nuisance parameters, hence we need to update MP likelihood
          //   (note: pybind11::bool_(list) = True if list contains entries, False if list is empty)
          pybind11::list nuisance_list  ="use_nuisance");
          needs_update = pybind11::bool_(nuisance_list);
        catch(const std::exception&)
          // if for some reason the MP likelihood object does not have the attribute "use_nuisance" (even though all of them
          //  should, but let's not count on it...) there are no nuisance parameters. So calculation can be skipped.
          needs_update = false;

      // calculate likelihood if check above concluded that it needs updating
      // (CLASS rerun and/or likelihood has nuisance parameters)

        logger() << LogTags::info << "[MontePythonLike_" << STRINGIFY(VERSION) << "]:  Start evaluation for -> " << experiment << " <-" << EOM;
        // need to use since it is a const map -> [] can create entry & can't be used on const object
        result ="loglkl")(cosmo,<double>();

        logger() << LogTags::info << "[MontePythonLike_" << STRINGIFY(VERSION) << "]:  Finished evaluation for -> " << experiment << " <-";
        logger() << " and got: " << result <<  EOM;

        // save likelihood result
        chached_likelihoods[experiment] = result;
      // use cached likelihood value if the cosmology has not changed w.r.t. previously calculated point
        // get cached result
        result = chached_likelihoods[experiment];
        logger() << LogTags::info << "[MontePythonLike_" << STRINGIFY(VERSION) << "]:  Using cached LogLike value for -> " << experiment << " <-";
        logger() << " which is: " << result <<  EOM;

      return result;

    /// Creates a MontePython 'Data' object.
    /// This is initialised with a list of the relevant experimental limits to import.
    pybind11::object create_MP_data_object(map_str_str& experiments)

      static bool first_run = true;

      pybind11::dict path_dict = pybind11::dict("MontePython"_a=backendDir,
          "cosmo"_a=backendDir+"",  // we never want to class CLASS from MP so there is no need to pass anything here

      // Cast the list of experiments to a tuple, for MP to fire up...
      // note that experiments is a str to str map where the key is the likelihood name.
      // This is the only thing we need here when creating the data object
      // The value of the keys (data files to use) will be needed when initialising the likelihood objects
      // in the function 'create_MP_likelihood_objects'
      pybind11::list MP_experiments;
      for (auto const & it : experiments)
        std::string exp_name = it.first;

        // run test if likelihoods are supported
        if(first_run) check_likelihood_support(exp_name);

        // If everything is fine, add the experiment to the list.
        MP_experiments.attr("append")( exp_name.c_str() );

      // Import Data object from MontePython
      // (pass empty string as "command_line" since we do not need this information as sampling is taken care
      // of by GAMBIT)
      pybind11::object data = MontePythonLike.attr("Data")("", path_dict, MP_experiments);

      first_run = false;

      return data;

    /// Returns a map of string to Python objects. These Python objects from MontePython are the initialised
    /// "Likelihood" objects used internal to MontePython. GAMBIT interfaces to these by requesting the
    /// loglike methods of these Python objects.
    /// Note that this is only executed once before the likelihoods for the first point in parameter space
    /// are calculated. -> time expensive loading up of all modules and data files is just done once.
    map_str_pyobj create_MP_likelihood_objects(pybind11::object& data, map_str_str& experiments)
      // in stand-alone MP the command line contains some information for the sampler (how many points, restart..)
      // since the scanner module of GAMBIT is taking care of these things we do not need to pass anything here
      pybind11::str command_line = "";

      // Root likelihood path.
      std::string like_path = backendDir+"/likelihoods/";

      // Add the Likelihood path to sys so we can import it in Python
      pybind11::module sys = pybind11::module::import("sys");
      sys.attr("path").attr("insert")(0, like_path);

      map_str_pyobj likelihoods;

      // Now go through each experiment one by one, and initialise the Likelihood containers in
      // MontePython, then add them to a dictionary to pass back to CosmoBit.
      for (auto const& it : experiments)

        std::string exp_name = it.first;
        std::string data_file = it.second;

        pybind11::str exp_path;
        // set path to .data file to the default one in MP if the "default" option is choosen
        // if not use the data file that has been chossen in the yaml file
        if(data_file == "default")  {exp_path = like_path + "/" + exp_name + "/" + exp_name + ".data";}
        else                        {exp_path = data_file;}

        pybind11::module  exp_module = pybind11::module::import(exp_name.c_str());
        pybind11::object  EXP_MODULE = exp_module.attr(exp_name.c_str())(exp_path, data, command_line);

        likelihoods[exp_name] = EXP_MODULE;

        // store likelihood objects in data object
        // this is needed to be able to get a list with
        // all nuisance parameters that need to be included
        // in the scan. This is done in the function 'create_MP_objects'
        // by calling data.check_nuisance_params()

      // Remove "like_path" from sys.path (The likelihoods are now loaded)

      return likelihoods;



Updated on 2023-06-26 at 21:36:57 +0000