file polychord_1.20.1/polychord_1.20.1/polychord.cpp
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Namespaces
| Name |
|---|
| Gambit TODO: see if we can use this one: |
| Gambit::PolyChord_1_20_1 |
Types
| Name | |
|---|---|
| typedef Gambit::Scanner::like_ptr | scanPtr Typedef for the ScannerBit pointer to the external loglikelihood function. |
Functions
| Name | |
|---|---|
| scanner_plugin(polychord , version(1, 20, 1) ) |
Detailed Description
ScannerBit interface to PolyChord 1.20.1
Authors (add name and date if you modify):
Types Documentation
typedef scanPtr
typedef Gambit::Scanner::like_ptr scanPtr;
Typedef for the ScannerBit pointer to the external loglikelihood function.
Functions Documentation
function scanner_plugin
scanner_plugin(
polychord ,
version(1, 20, 1)
)
=================================================
Interface to ScannerBit
The constructor to run when the PolyChord plugin is loaded.
The main routine to run for the PolyChord scanner.
TODO: Replace with some wrapper? Maybe not, this is already pretty straightforward, though perhaps a little counterintuitive that the printer is the place to get this information.
Source code
// GAMBIT: Global and Modular BSM Inference Tool
// *********************************************
/// \file
///
/// ScannerBit interface to PolyChord 1.20.1
///
/// *********************************************
///
/// Authors (add name and date if you modify):
//
/// \author Ben Farmer
/// (ben.farmer@gmail.com)
/// \date October 2013 - Aug 2016
///
/// \author Will Handley
/// (wh260@cam.ac.uk)
/// \date May 2018, June 2021, Mar 2022
///
/// \author Patrick Stoecker
/// (stoecker@physik.rwth-aachen.de)
/// \date May 2020
///
/// \author Anders Kvellestad
/// (anders.kvellestad@fys.uio.no)
/// \date June 2022
///
/// *********************************************
#include <vector>
#include <string>
#include <cmath>
#include <iostream>
#include <fstream>
#include <map>
#include <sstream>
#include <iomanip> // For debugging only
#include <algorithm>
#include <numeric>
#include "gambit/ScannerBit/scanner_plugin.hpp"
#include "gambit/ScannerBit/scanners/polychord/1.20.1/polychord.hpp"
#include "gambit/Utils/yaml_options.hpp"
#include "gambit/Utils/util_functions.hpp"
namespace Gambit
{
namespace PolyChord_1_20_1
{
/// Global pointer to loglikelihood wrapper object, for use in the PolyChord callback functions
LogLikeWrapper *global_loglike_object;
}
}
/// Typedef for the ScannerBit pointer to the external loglikelihood function
typedef Gambit::Scanner::like_ptr scanPtr;
/// =================================================
/// Interface to ScannerBit
/// =================================================
scanner_plugin(polychord, version(1, 20, 1))
{
// Access PolyChord stuff and standard Gambit things
using namespace Gambit;
using namespace Gambit::PolyChord_1_20_1;
// An error is thrown if any of the following entries are not present in the inifile (none absolutely required for PolyChord).
reqd_inifile_entries();
// Tell cmake system to search known paths for these libraries; any not found must be specified in config/scanner_locations.yaml.
reqd_libraries("chord");
// Pointer to the (log)likelihood function
scanPtr LogLike;
/// The constructor to run when the PolyChord plugin is loaded.
plugin_constructor
{
// Retrieve the external likelihood calculator
LogLike = get_purpose(get_inifile_value<std::string>("like"));
if (LogLike->getRank() == 0) std::cout << "Loading PolyChord nested sampling plugin for ScannerBit." << std::endl;
}
/// The main routine to run for the PolyChord scanner.
int plugin_main (void)
{
/// ************
/// TODO: Replace with some wrapper? Maybe not, this is already pretty straightforward,
/// though perhaps a little counterintuitive that the printer is the place to get this
/// information.
bool resume_mode = get_printer().resume_mode();
/// ************
// Retrieve the dimensionality of the scan.
int ma = get_dimension();
// Retrieve the global option specifying the minimum interesting likelihood
double gl0 = get_inifile_value<double>("likelihood: model_invalid_for_lnlike_below");
// Retrieve the global option specifying the likelihood offset to use
double offset = get_inifile_value<double>("likelihood: lnlike_offset", 0.);
// Make sure the likleihood functor knows to apply the offset internally in ScannerBit
LogLike->setPurposeOffset(offset);
// Offset the minimum interesting likelihood by the offset
gl0 = gl0 + offset;
// Retrieve whether the scanned parameters should be added to the native output and determine nderived
int nderived = 2;
if (get_inifile_value<bool>("print_parameters_in_native_output", false)) nderived += ma;
// Initialise polychord settings
Settings settings(ma, nderived);
// Create the object that interfaces to the PolyChord LogLike callback function
LogLikeWrapper loglwrapper(LogLike, get_printer());
global_loglike_object = &loglwrapper;
// ---------- Compute an ordering for fast and slow parameters
// Read list of fast parameters from file
std::vector<std::string> fast_params = get_inifile_value<std::vector<std::string>>("fast_params", {});
// Get list of parameters used from loglikelihood
std::vector<std::string> varied_params = LogLike->getShownParameters();
std::vector<std::string> all_params = LogLike->getParameters();
// Compute the set difference between fast_params and all_params to check if there are any fast_params not included in all_params
std::set<std::string> set_fast_params(fast_params.begin(), fast_params.end()), set_params(all_params.begin(), all_params.end()), diff;
std::set_difference(set_fast_params.begin(), set_fast_params.end(), set_params.begin(), set_params.end(),std::inserter(diff,diff.begin()));
if (diff.size())
{
// Raise an error if any specified fast_params are not actually being sampled over.
std::string error_message = "You have specified:\n";
for (auto param : diff) error_message += param + "\n" ;
error_message += "as fast param(s), but the list of params is:\n";
for (auto param : all_params) error_message += param + "\n";
scan_error().raise(LOCAL_INFO,error_message);
}
// Compute the locations in PolyChord's unit hypercube, ordering from slow to fast
// This defaults to nDims if there are no fast parameters, or if all parameters are fast.
// grade_dims is a vector of integers that indicates the number of slow and fast parameters
settings.grade_dims.clear();
unsigned int i = 0;
// Run through all the parameters, and if they're slow parameters
// give them an index i, then increment i
for (auto param : varied_params)
if (std::find(fast_params.begin(), fast_params.end(),param) == fast_params.end())
global_loglike_object->index_map[param] = (i++);
unsigned int nslow = i;
if(nslow!=0) settings.grade_dims.push_back(nslow);
// Do the same for the fast parameters
for (auto param : varied_params)
if (std::find(fast_params.begin(), fast_params.end(),param) != fast_params.end())
global_loglike_object->index_map[param] = (i++);
unsigned int nfast = i-nslow;
if (nfast>0) settings.grade_dims.push_back(nfast);
// In the unusual case of all fast parameters, there's only one grade.
if (nslow==0) {nslow = nfast; nfast=0;}
// ---------- End computation of ordering for fast and slow parameters
// PolyChord algorithm options.
settings.nlive = get_inifile_value<int>("nlive", settings.nDims*25); // number of live points
settings.num_repeats = get_inifile_value<int>("num_repeats", nslow*2); // length of slice sampling chain
settings.nprior = get_inifile_value<int>("nprior", settings.nlive*10); // number of prior samples to begin algorithm with
settings.do_clustering = get_inifile_value<bool>("do_clustering", true); // Whether or not to perform clustering
settings.feedback = get_inifile_value<int>("fb", 1); // Feedback level
settings.precision_criterion = get_inifile_value<double>("tol", 0.5); // Stopping criterion (consistent with multinest)
settings.logzero = get_inifile_value<double>("logzero",gl0);
settings.max_ndead = get_inifile_value<double>("maxiter", -1); // Max no. of iterations, a negative value means infinity (different in comparison with multinest).
settings.maximise = get_inifile_value<bool>("maximise", false); // Whether to run a maximisation algorithm once the run is finished
settings.boost_posterior = 0; // Increase the number of posterior samples produced
bool outfile (get_inifile_value<bool>("outfile", true)); // write output files?
settings.posteriors = outfile;
settings.equals = outfile;
settings.cluster_posteriors = outfile;
settings.write_paramnames = outfile;
settings.write_stats = outfile;
settings.write_live = outfile;
settings.write_dead = outfile;
settings.write_prior = outfile;
settings.write_resume = outfile;
settings.read_resume = resume_mode;
settings.compression_factor = get_inifile_value<double>("compression_factor",0.36787944117144233);
settings.synchronous = get_inifile_value<bool>("synchronous", true); // Whether to run in synchronous parallelisation mode
settings.base_dir = get_inifile_value<std::string>("default_output_path")+"PolyChord";
settings.file_root = get_inifile_value<std::string>("root", "native");
settings.seed = get_inifile_value<int>("seed",-1);
if (nslow>0 and nfast>0)
{
// Specify the fraction of time to spend in the slow parameters.
//double frac_slow = get_inifile_value<double>("frac_slow",0.75);
//settings.grade_frac = std::vector<double>({frac_slow, 1-frac_slow});
double oversample_fast = get_inifile_value<double>("oversample_fast",30.0);
settings.grade_frac = std::vector<double>({settings.num_repeats*1.0, oversample_fast*nfast});
}
Utils::ensure_path_exists(settings.base_dir);
Utils::ensure_path_exists(settings.base_dir + "/clusters/");
// Point the boundSettings to the settings in use
global_loglike_object->boundSettings = settings;
// Set the speed threshold for the printer.
// Evaluations of speeds >= threshold are not printed
// Speeds start at 0
global_loglike_object->printer_speed_threshold =
get_inifile_value<int>("printer_speed_threshold",settings.grade_dims.size());
if(resume_mode==1 and outfile==0)
{
// It is stupid to be in resume mode while not writing output files.
// Means subsequent resumes will be impossible. Throw an error.
scan_error().raise(LOCAL_INFO,"Error from PolyChord ScannerBit plugin! Resume mode is activated, however "
"PolyChord native output files are set to not be written. These are needed "
"for resuming; please change this setting in your yaml file (set option \"outfile: 1\")");
}
// Setup auxilliary streams. These are only needed by the master process,
// so let's create them only for that process
int myrank = get_printer().get_stream()->getRank(); // MPI rank of this process
if(myrank==0)
{
// Get inifile options for each print stream
Options txt_options = get_inifile_node("aux_printer_txt_options");
//Options stats_options = get_inifile_node("aux_printer_stats_options"); //FIXME
Options live_options = get_inifile_node("aux_printer_live_options");
// Options to desynchronise print streams from the main Gambit iterations. This allows for random access writing, or writing of global scan data.
//stats_options.setValue("synchronised",false); //FIXME
txt_options.setValue("synchronised",false);
live_options.setValue("synchronised",false);
// Initialise auxiliary print streams
get_printer().new_stream("txt",txt_options);
//get_printer().new_stream("stats",stats_options); //FIXME
get_printer().new_stream("live",live_options);
}
// Ensure that MPI processes have the same IDs for auxiliary print streams;
Scanner::assign_aux_numbers("Posterior","LastLive");
//Run PolyChord, passing callback functions for the loglike and dumper.
if(myrank == 0) std::cout << "Starting PolyChord run..." << std::endl;
run_polychord(callback_loglike, callback_dumper, settings);
if(myrank == 0) std::cout << "PolyChord run finished!" << std::endl;
return 0;
}
}
/// =================================================
/// Function definitions
/// =================================================
namespace Gambit {
namespace PolyChord_1_20_1 {
///@{ Plain-vanilla functions to pass to PolyChord for the callback
// Note: we are using the c interface from cwrapper.f90, so the function
// signature is a little different than in the polychord examples.
double callback_loglike(double *Cube, int ndim, double* phi, int nderived)
{
// Call global interface to ScannerBit loglikelihood function
// Could also pass this object in via context pointer, but that
// involves some casting and could risk a segfault.
return global_loglike_object->LogLike(Cube, ndim, phi, nderived);
}
void callback_dumper(int ndead, int nlive, int npars,
double *live, double *dead, double* logweights,
double logZ, double logZerr)
{
global_loglike_object->
dumper(ndead, nlive, npars, live, dead, logweights, logZ, logZerr);
}
///@}
/// LogLikeWrapper Constructor
LogLikeWrapper::LogLikeWrapper(scanPtr loglike, printer_interface& printer)
: boundLogLike(loglike), boundPrinter(printer)
{ }
/// Main interface function from PolyChord to ScannerBit-supplied loglikelihood function
/// This is the function that will be passed to PolyChord as the
/// loglike callback routine
///
/// Input arguments
/// ndim = dimensionality (total number of free parameters) of the problem
/// nderived = total number of derived parameters
/// Cube[ndim] = ndim parameters
///
/// Output arguments
/// phi[nderived] = nderived devired parameters
/// lnew = loglikelihood
///
double LogLikeWrapper::LogLike(double *Cube, int ndim, double* phi, int nderived)
{
// Cached "below threshold" unitcube parameters of the previous point.
static int ndim_threshold =
std::accumulate( boundSettings.grade_dims.begin(),
boundSettings.grade_dims.begin() + printer_speed_threshold,
0);
static std::vector<double> prev_slow_unit(ndim_threshold);
//convert C style array to C++ vector class, reordering parameters slow->fast
std::vector<std::string> params = boundLogLike->getShownParameters();
std::vector<double> unitpars(ndim);
for (auto i=0; i<ndim; i++)
unitpars[i] = Cube[index_map[params[i]]];
std::vector<double> derived(phi, phi + nderived);
// Disable the printer when the unitcube parameters with speeds below
// the threshold have not changed and enable it otherwise
// (It might be probably already enabled again at that point)
if ( ndim_threshold < ndim
&& std::equal(prev_slow_unit.begin(),prev_slow_unit.end(),Cube) )
{
boundLogLike->getPrinter().disable();
}
else
{
boundLogLike->getPrinter().enable();
}
prev_slow_unit = std::vector<double>(Cube,Cube+ndim_threshold);
double lnew = boundLogLike(unitpars);
// Done! (lnew will be used by PolyChord to guide the search)
// Get the transformed parameters and add them as derived parameters
if (nderived > 2)
{
std::unordered_map<std::string,double> param_map;
boundLogLike->getPrior().transform(unitpars, param_map);
for (auto& param: param_map)
{
// param_map contains ALL parameters.
// We just need the ones which are varied (i.e. the keys of index_map)
if (index_map.find(param.first) != index_map.end())
phi[index_map[param.first]] = param.second;
}
}
// Get, set and ouptut the process rank and this point's ID
int myrank = boundLogLike->getRank(); // MPI rank of this process
int pointID = boundLogLike->getPtID(); // point ID number
phi[nderived - 2] = myrank;
phi[nderived - 1] = pointID;
return lnew;
}
/// Main interface to PolyChord dumper routine
/// The dumper routine will be called every time the live points compress by a factor compression_factor
/// PolyChord does not need to the user to do anything. User can use the arguments in whichever way they want
///
/// Arguments:
///
/// ndead = total number of discarded points for posterior usage
/// nlive = total number of live points
/// nPar = total number of parameters + 2 (free + derived + 2)
/// live[nlive*npars] = 2D array containing the last set of live points
/// (physical parameters plus derived parameters + birth contour + death contour)
/// dead[ndead*npars] = posterior distribution containing nSamples points.
/// Each sample has nPar parameters (physical + derived)
/// along with the their loglike value & posterior probability
/// logweights[ndead] = log of posterior weighting of dead points. Use this to turn them into posterior weighted samples
/// logZ = log evidence value
/// logZerr = error on log evidence value
void LogLikeWrapper::dumper(int ndead, int nlive, int npars,
double *live, double *dead, double* logweights,
double /*logZ*/, double /*logZerr*/)
{
int thisrank = boundPrinter.get_stream()->getRank(); // MPI rank of this process
if(thisrank!=0)
{
scan_err <<"Error! ScannerBit PolyChord plugin attempted to run 'dumper' function on a worker process "
<<"(thisrank=="<<thisrank<<")! PolyChord should only try to run this function on the master "
<<"process. Most likely this means that your PolyChord installation is not running in MPI mode "
<<"correctly, and is actually running independent scans on each process. Alternatively, the "
<<"version of PolyChord you are using may be too far ahead of what this plugin can handle, "
<<"if e.g. the described behaviour has changed since this plugin was written."
<< scan_end;
}
// Write a file at first run of dumper to specify the index of a given dataset.
static bool first = true;
if (first)
{
int ndim = boundSettings.nDims;
int nderived = boundSettings.nDerived;
// Construct the inversed index map
// map[polychord_hypercube] = {name, gambit_hypercube}
std::vector<std::string> params = boundLogLike->getShownParameters();
std::map<int,std::pair<std::string,int>> inversed_map;
for (int i=0; i<ndim; ++i)
inversed_map[index_map[params[i]]] = {params[i],i};
std::ostringstream fname;
fname << boundSettings.base_dir << "/" <<boundSettings.file_root << ".indices";
std::ofstream ofs(fname.str());
int index = 0;
ofs << index++ << "\t" << "Posterior" << std::endl;
ofs << index++ << "\t" << "-2*(" << boundLogLike->getPurpose() << ")" << std::endl;
for (int i=0; i<ndim; ++i)
ofs << index++ << "\t" << "unitCubeParameters[" << inversed_map[i].second <<"]" << std::endl;
for (int i=0; i<nderived -2; ++i)
ofs << index++ << "\t" << inversed_map[i].first << std::endl;
ofs << index++ << "\t" << "MPIrank" << std::endl;
ofs << index++ << "\t" << "pointID" << std::endl;
ofs.close();
}
first = false;
// Get printers for each auxiliary stream
printer* txt_stream( boundPrinter.get_stream("txt") );
printer* live_stream( boundPrinter.get_stream("live") );
// Reset the print streams. WARNING! This potentially deletes the old data (here we overwrite it on purpose)
txt_stream->reset();
live_stream->reset();
// Ensure the "quantity" IDcode is UNIQUE across all printers! This way fancy printers
// have the option of ignoring duplicate writes and doing things like combine all the
// auxiliary streams into a single database. But must be able to assume IDcodes are
// unique for a given quanity to do this.
// Negative numbers not used by functors, so those are 'safe' to use here
// The discarded live points (and rejected candidate live points if IS = 1)
for( int i_dead = 0; i_dead < ndead; i_dead++ )
{
int myrank = dead[npars*i_dead + npars-4]; //MPI rank stored in fourth last column
int pointID = dead[npars*i_dead + npars-3]; //pointID stored in third last column
double logw = logweights[i_dead]; //posterior weight stored in logweights
double birth = dead[npars*i_dead + npars-2]; // birth contours
double death = dead[npars*i_dead + npars-1]; // death contours
txt_stream->print( std::exp(logw), "Posterior", myrank, pointID);
txt_stream->print( birth, "LogLike_birth", myrank, pointID);
txt_stream->print( death, "LogLike_death", myrank, pointID);
}
// The last set of live points
for( int i_live = 0; i_live < nlive; i_live++ )
{
int myrank = live[npars*i_live + npars-4]; //MPI rank stored in fourth last column
int pointID = live[npars*i_live + npars-3]; //pointID stored in third last column
live_stream->print( true, "LastLive", myrank, pointID); // Flag which points were the last live set
}
}
}
}
Updated on 2023-06-26 at 21:36:54 +0000