cdec cleanup, remove bayesian stuff, parsing stuff

1 files changed, 0 insertions, 447 deletions

diff --git a/gi/pyp-topics/src/mpi-pyp.hh b/gi/pyp-topics/src/mpi-pyp.hh
deleted file mode 100644
index c2341b9e..00000000
--- a/gi/pyp-topics/src/mpi-pyp.hh
+++ /dev/null
@@ -1,447 +0,0 @@
-#ifndef _mpipyp_hh
-#define _mpipyp_hh
-
-#include <math.h>
-#include <map>
-#include <tr1/unordered_map>
-//#include <google/sparse_hash_map>
-
-#include <boost/random/uniform_real.hpp>
-#include <boost/random/variate_generator.hpp>
-#include <boost/random/mersenne_twister.hpp>
-#include <boost/tuple/tuple.hpp>
-#include <boost/serialization/map.hpp>
-#include <boost/mpi.hpp>
-#include <boost/mpi/environment.hpp>
-#include <boost/mpi/communicator.hpp>
-#include <boost/mpi/operations.hpp>
-
-
-#include "pyp.hh"
-
-//
-// Pitman-Yor process with customer and table tracking
-//
-
-template <typename Dish, typename Hash=std::tr1::hash<Dish> >
-class MPIPYP : public PYP<Dish, Hash> {
-public:
-  typedef std::map<Dish, int> dish_delta_type;
-
-  MPIPYP(double a, double b, Hash hash=Hash());
-
-  template < typename Uniform01 >
-    int increment(Dish d, double p0, Uniform01& rnd);
-  template < typename Uniform01 >
-    int decrement(Dish d, Uniform01& rnd);
-
-  void clear();
-  void reset_deltas();
-
-  void synchronise(dish_delta_type* result);
-
-private:
-  typedef std::map<Dish, typename PYP<Dish,Hash>::TableCounter> table_delta_type;
-
-  dish_delta_type m_count_delta;
-  table_delta_type m_table_delta;
-};
-
-template <typename Dish, typename Hash>
-MPIPYP<Dish,Hash>::MPIPYP(double a, double b, Hash h)
-: PYP<Dish,Hash>(a, b, 0, h) {}
-
-template <typename Dish, typename Hash>
-  template <typename Uniform01>
-int 
-MPIPYP<Dish,Hash>::increment(Dish dish, double p0, Uniform01& rnd) {
-  //std::cerr << "-----INCREMENT DISH " << dish << std::endl;
-  int delta = 0;
-  int table_joined=-1;
-  typename PYP<Dish,Hash>::TableCounter &tc = PYP<Dish,Hash>::_dish_tables[dish];
-
-  // seated on a new or existing table?
-  int c = PYP<Dish,Hash>::count(dish); 
-  int t = PYP<Dish,Hash>::num_tables(dish); 
-  int T = PYP<Dish,Hash>::num_tables();
-  double& a = PYP<Dish,Hash>::_a;
-  double& b = PYP<Dish,Hash>::_b;
-  double pshare = (c > 0) ? (c - a*t) : 0.0;
-  double pnew = (b + a*T) * p0;
-  if (pshare < 0.0) {
-    std::cerr << pshare << " " << c << " " << a << " " << t << std::endl;
-    assert(false);
-  }
-
-  if (rnd() < pnew / (pshare + pnew)) {
-    // assign to a new table
-    tc.tables += 1;
-    tc.table_histogram[1] += 1;
-    PYP<Dish,Hash>::_total_tables += 1;
-    delta = 1;
-    table_joined = 1;
-  }
-  else {
-    // randomly assign to an existing table
-    // remove constant denominator from inner loop
-    double r = rnd() * (c - a*t);
-    for (std::map<int,int>::iterator
-         hit = tc.table_histogram.begin();
-         hit != tc.table_histogram.end(); ++hit) {
-      r -= ((hit->first - a) * hit->second);
-      if (r <= 0) {
-        tc.table_histogram[hit->first+1] += 1;
-        hit->second -= 1;
-        table_joined = hit->first+1;
-        if (hit->second == 0)
-          tc.table_histogram.erase(hit);
-        break;
-      }
-    }
-    if (r > 0) {
-      std::cerr << r << " " << c << " " << a << " " << t << std::endl;
-      assert(false);
-    }
-    delta = 0;
-  }
-
-  std::tr1::unordered_map<Dish,int,Hash>::operator[](dish) += 1;
-  //google::sparse_hash_map<Dish,int,Hash>::operator[](dish) += 1;
-  PYP<Dish,Hash>::_total_customers += 1;
-
-  // MPI Delta handling
-  // track the customer entering
-  typename dish_delta_type::iterator customer_it; 
-  bool customer_insert_result; 
-  boost::tie(customer_it, customer_insert_result) 
-    = m_count_delta.insert(std::make_pair(dish,0)); 
-
-  customer_it->second += 1;
-  if (customer_it->second == 0)
-    m_count_delta.erase(customer_it);
-
-  // increment the histogram bar for the table joined
-  /*
-  typename PYP<Dish,Hash>::TableCounter &delta_tc = m_table_delta[dish];
-
-  std::map<int,int> &histogram = delta_tc.table_histogram;
-  assert (table_joined > 0);
-
-  typename std::map<int,int>::iterator table_it; bool table_insert_result; 
-  boost::tie(table_it, table_insert_result) = histogram.insert(std::make_pair(table_joined,0)); 
-  table_it->second += 1;
-  if (delta == 0) {
-    // decrement the histogram bar for the table left 
-    typename std::map<int,int>::iterator left_table_it; 
-    boost::tie(left_table_it, table_insert_result) 
-      = histogram.insert(std::make_pair(table_joined-1,0)); 
-    left_table_it->second -= 1;
-    if (left_table_it->second == 0) histogram.erase(left_table_it);
-  }
-  else delta_tc.tables += 1;
-
-  if (table_it->second == 0) histogram.erase(table_it);
-
-    //std::cerr << "Added (" << delta << ") " << dish << " to table " << table_joined << "\n"; 
-    //std::cerr << "Dish " << dish << " has " << count(dish) << " customers, and is sitting at " << PYP<Dish,Hash>::num_tables(dish) << " tables.\n"; 
-    //for (std::map<int,int>::const_iterator 
-    //     hit = delta_tc.table_histogram.begin();
-    //     hit != delta_tc.table_histogram.end(); ++hit) {
-    //  std::cerr << "    " << hit->second << " tables with " << hit->first << " customers." << std::endl; 
-    //}
-    //std::cerr << "Added (" << delta << ") " << dish << " to table " << table_joined << "\n"; 
-    //std::cerr << "Dish " << dish << " has " << count(dish) << " customers, and is sitting at " << PYP<Dish,Hash>::num_tables(dish) << " tables.\n"; 
-    int x_num_customers=0, x_num_table=0;
-    for (std::map<int,int>::const_iterator 
-         hit = delta_tc.table_histogram.begin();
-         hit != delta_tc.table_histogram.end(); ++hit) {
-      x_num_table += hit->second;
-      x_num_customers += (hit->second*hit->first);
-    }
-    int tmp_c = PYP<Dish,Hash>::count(dish);
-    int tmp_t = PYP<Dish,Hash>::num_tables(dish);
-    assert (x_num_customers <= tmp_c); 
-    assert (x_num_table <= tmp_t); 
-
-  if (delta_tc.table_histogram.empty()) {
-    assert (delta_tc.tables == 0);
-    m_table_delta.erase(dish);
-  }
-  */
-
-  //PYP<Dish,Hash>::debug_info(std::cerr);
-  //std::cerr << "   Dish " << dish << " has count " << PYP<Dish,Hash>::count(dish) << " tables " << PYP<Dish,Hash>::num_tables(dish) << std::endl;
-
-  return delta;
-}
-
-template <typename Dish, typename Hash>
-  template <typename Uniform01>
-int 
-MPIPYP<Dish,Hash>::decrement(Dish dish, Uniform01& rnd)
-{
-  //std::cerr << "-----DECREMENT DISH " << dish << std::endl;
-  typename std::tr1::unordered_map<Dish, int>::iterator dcit = find(dish);
-  //typename google::sparse_hash_map<Dish, int>::iterator dcit = find(dish);
-  if (dcit == PYP<Dish,Hash>::end()) {
-    std::cerr << dish << std::endl;
-    assert(false);
-  } 
-
-  int delta = 0, table_left=-1;
-
-  typename std::tr1::unordered_map<Dish, typename PYP<Dish,Hash>::TableCounter>::iterator dtit 
-    = PYP<Dish,Hash>::_dish_tables.find(dish);
-  //typename google::sparse_hash_map<Dish, TableCounter>::iterator dtit = _dish_tables.find(dish);
-  if (dtit == PYP<Dish,Hash>::_dish_tables.end()) {
-    std::cerr << dish << std::endl;
-    assert(false);
-  } 
-  typename PYP<Dish,Hash>::TableCounter &tc = dtit->second;
-
-  double r = rnd() * PYP<Dish,Hash>::count(dish);
-  for (std::map<int,int>::iterator hit = tc.table_histogram.begin();
-       hit != tc.table_histogram.end(); ++hit) {
-    r -= (hit->first * hit->second);
-    if (r <= 0) {
-      table_left = hit->first;
-      if (hit->first > 1) {
-        tc.table_histogram[hit->first-1] += 1;
-      }
-      else {
-        delta = -1;
-        tc.tables -= 1;
-        PYP<Dish,Hash>::_total_tables -= 1;
-      }
-
-      hit->second -= 1;
-      if (hit->second == 0) tc.table_histogram.erase(hit);
-      break;
-    }
-  }
-  if (r > 0) {
-    std::cerr << r << " " << PYP<Dish,Hash>::count(dish) << " " << PYP<Dish,Hash>::_a << " " 
-      << PYP<Dish,Hash>::num_tables(dish) << std::endl;
-    assert(false);
-  }
-
-  // remove the customer
-  dcit->second -= 1;
-  PYP<Dish,Hash>::_total_customers -= 1;
-  assert(dcit->second >= 0);
-  if (dcit->second == 0) {
-    PYP<Dish,Hash>::erase(dcit);
-    PYP<Dish,Hash>::_dish_tables.erase(dtit);
-  }
-
-  // MPI Delta processing
-  typename dish_delta_type::iterator it; 
-  bool insert_result; 
-  boost::tie(it, insert_result) = m_count_delta.insert(std::make_pair(dish,0)); 
-  it->second -= 1;
-  if (it->second == 0) m_count_delta.erase(it);
-
-  assert (table_left > 0);
-  typename PYP<Dish,Hash>::TableCounter& delta_tc = m_table_delta[dish];
-  if (table_left > 1) {
-    std::map<int,int>::iterator tit;
-    boost::tie(tit, insert_result) = delta_tc.table_histogram.insert(std::make_pair(table_left-1,0));
-    tit->second += 1;
-    if (tit->second == 0) delta_tc.table_histogram.erase(tit);
-  }
-  else delta_tc.tables -= 1;
-
-  std::map<int,int>::iterator tit;
-  boost::tie(tit, insert_result) = delta_tc.table_histogram.insert(std::make_pair(table_left,0));
-  tit->second -= 1;
-  if (tit->second == 0) delta_tc.table_histogram.erase(tit);
-
-  //  std::cerr << "Dish " << dish << " has " << count(dish) << " customers, and is sitting at " << PYP<Dish,Hash>::num_tables(dish) << " tables.\n"; 
-  //  for (std::map<int,int>::const_iterator 
-  //       hit = delta_tc.table_histogram.begin();
-  //       hit != delta_tc.table_histogram.end(); ++hit) {
-  //    std::cerr << "    " << hit->second << " tables with " << hit->first << " customers." << std::endl; 
-  //  }
-    int x_num_customers=0, x_num_table=0;
-    for (std::map<int,int>::const_iterator 
-         hit = delta_tc.table_histogram.begin();
-         hit != delta_tc.table_histogram.end(); ++hit) {
-      x_num_table += hit->second;
-      x_num_customers += (hit->second*hit->first);
-    }
-    int tmp_c = PYP<Dish,Hash>::count(dish);
-    int tmp_t = PYP<Dish,Hash>::num_tables(dish);
-    assert (x_num_customers <= tmp_c); 
-    assert (x_num_table <= tmp_t); 
-
-  if (delta_tc.table_histogram.empty()) {
-  //  std::cerr << "   DELETING " << dish << std::endl;
-    assert (delta_tc.tables == 0);
-    m_table_delta.erase(dish);
-  }
-
-  //PYP<Dish,Hash>::debug_info(std::cerr);
-  //std::cerr << "   Dish " << dish << " has count " << PYP<Dish,Hash>::count(dish) << " tables " << PYP<Dish,Hash>::num_tables(dish) << std::endl;
-  return delta;
-}
-
-template <typename Dish, typename Hash>
-void 
-MPIPYP<Dish,Hash>::clear() {
-  PYP<Dish,Hash>::clear();
-  reset_deltas();
-}
-
-template <typename Dish, typename Hash>
-void 
-MPIPYP<Dish,Hash>::reset_deltas() { 
-  m_count_delta.clear(); 
-  m_table_delta.clear();
-}
-
-template <typename Dish>
-struct sum_maps {
-  typedef std::map<Dish,int> map_type;
-  map_type& operator() (map_type& l, map_type const & r) const {
-    for (typename map_type::const_iterator it=r.begin(); it != r.end(); it++)
-      l[it->first] += it->second;
-    return l;
-  }
-};
-
-template <typename Dish>
-struct subtract_maps {
-  typedef std::map<Dish,int> map_type;
-  map_type& operator() (map_type& l, map_type const & r) const {
-    for (typename map_type::const_iterator it=r.begin(); it != r.end(); it++)
-      l[it->first] -= it->second;
-    return l;
-  }
-};
-
-// Needed Boost definitions
-namespace boost { 
-  namespace mpi {
-    template <>
-    struct is_commutative< sum_maps<int>, std::map<int,int> > : mpl::true_ {};
-  }
-
-  namespace serialization {
-    template<class Archive>
-    void serialize(Archive & ar, PYP<int>::TableCounter& t, const unsigned int version) {
-      ar & t.table_histogram;
-      ar & t.tables;
-    }
-
-  } // namespace serialization
-} // namespace boost
-
-template <typename A, typename B, typename C>
-struct triple {
-  triple() {}
-  triple(const A& a, const B& b, const C& c) : first(a), second(b), third(c) {}
-  A first;
-  B second;
-  C third;
-
-  template<class Archive>
-  void serialize(Archive &ar, const unsigned int version){
-      ar & first;
-      ar & second;
-      ar & third;
-  }
-};
-
-BOOST_IS_BITWISE_SERIALIZABLE(MPIPYP<int>::dish_delta_type)
-BOOST_CLASS_TRACKING(MPIPYP<int>::dish_delta_type,track_never)
-
-template <typename Dish, typename Hash>
-void 
-MPIPYP<Dish,Hash>::synchronise(dish_delta_type* result) {
-  boost::mpi::communicator world; 
-  //int rank = world.rank(), size = world.size();
-
-  boost::mpi::all_reduce(world, m_count_delta, *result, sum_maps<Dish>());
-  subtract_maps<Dish>()(*result, m_count_delta);
- 
-/*
-  // communicate the customer count deltas
-  dish_delta_type global_dish_delta;
-  boost::mpi::all_reduce(world, m_count_delta, global_dish_delta, sum_maps<Dish>());
-
-  // update this restaurant
-  for (typename dish_delta_type::const_iterator it=global_dish_delta.begin(); 
-       it != global_dish_delta.end(); ++it) {
-    int global_delta = it->second - m_count_delta[it->first];
-    if (global_delta == 0) continue;
-    typename std::tr1::unordered_map<Dish,int,Hash>::iterator dit; bool inserted;
-    boost::tie(dit, inserted) 
-      = std::tr1::unordered_map<Dish,int,Hash>::insert(std::make_pair(it->first, 0));
-    dit->second += global_delta;
-    assert(dit->second >= 0);
-    if (dit->second == 0) {
-      std::tr1::unordered_map<Dish,int,Hash>::erase(dit);
-    }
-
-    PYP<Dish,Hash>::_total_customers += (it->second - m_count_delta[it->first]);
-    int tmp = PYP<Dish,Hash>::_total_customers;
-    assert(tmp >= 0);
-    //std::cerr << "Process " << rank << " adding " <<  (it->second - m_count_delta[it->first]) << " of customer " << it->first << std::endl;
-  }
-*/
-/*
-  // communicate the table count deltas
-  for (int process = 0; process < size; ++process) {
-    typename std::vector< triple<Dish, int, int> > message;
-    if (rank == process) {
-      // broadcast deltas
-      for (typename table_delta_type::const_iterator dish_it=m_table_delta.begin(); 
-           dish_it != m_table_delta.end(); ++dish_it) {
-        //assert (dish_it->second.tables > 0);
-        for (std::map<int,int>::const_iterator it=dish_it->second.table_histogram.begin(); 
-             it != dish_it->second.table_histogram.end(); ++it) {
-          triple<Dish, int, int> m(dish_it->first, it->first, it->second);
-          message.push_back(m);
-        }
-        // append a special message with the total table delta for this dish
-        triple<Dish, int, int> m(dish_it->first, -1, dish_it->second.tables);
-        message.push_back(m);
-      }
-      boost::mpi::broadcast(world, message, process);
-    }
-    else {
-      // receive deltas
-      boost::mpi::broadcast(world, message, process);
-      for (typename std::vector< triple<Dish, int, int> >::const_iterator it=message.begin(); it != message.end(); ++it) {
-        typename PYP<Dish,Hash>::TableCounter& tc = PYP<Dish,Hash>::_dish_tables[it->first];
-        if (it->second >= 0) {
-          std::map<int,int>::iterator tit; bool inserted;
-          boost::tie(tit, inserted) = tc.table_histogram.insert(std::make_pair(it->second, 0));
-          tit->second += it->third;
-          if (tit->second < 0) {
-            std::cerr << tit->first << " " << tit->second << " " << it->first << " " << it->second << " " << it->third << std::endl;
-            assert(tit->second >= 0);
-          }
-          if (tit->second == 0) {
-            tc.table_histogram.erase(tit);
-          }
-        }
-        else {
-          tc.tables += it->third;
-          PYP<Dish,Hash>::_total_tables += it->third;
-          assert(tc.tables >= 0);
-          if (tc.tables == 0) assert(tc.table_histogram.empty());
-          if (tc.table_histogram.empty()) {
-            assert (tc.tables == 0);
-            PYP<Dish,Hash>::_dish_tables.erase(it->first);
-          }
-        }
-      }
-    }
-  }
-*/
-
-//  reset_deltas();
-}
-
-#endif