diff options
Diffstat (limited to 'gi')
| -rw-r--r-- | gi/pyp-topics/src/makefile.depend | 8102 | ||||
| -rw-r--r-- | gi/pyp-topics/src/mpi-pyp-topics.cc | 99 | ||||
| -rw-r--r-- | gi/pyp-topics/src/mpi-pyp-topics.hh | 10 | ||||
| -rw-r--r-- | gi/pyp-topics/src/mpi-pyp.hh | 277 | ||||
| -rw-r--r-- | gi/pyp-topics/src/mpi-train-contexts.cc | 113 | ||||
| -rw-r--r-- | gi/pyp-topics/src/pyp-topics.cc | 6 | ||||
| -rw-r--r-- | gi/pyp-topics/src/pyp.hh | 45 |
7 files changed, 4389 insertions, 4263 deletions
diff --git a/gi/pyp-topics/src/makefile.depend b/gi/pyp-topics/src/makefile.depend index 88bc73c1..d8ef78d8 100644 --- a/gi/pyp-topics/src/makefile.depend +++ b/gi/pyp-topics/src/makefile.depend @@ -1,4089 +1,4037 @@ contexts_corpus.o: contexts_corpus.cc contexts_corpus.hh \ - /Users/pblunsom/packages/include/boost/ptr_container/ptr_vector.hpp \ - /Users/pblunsom/packages/include/boost/ptr_container/ptr_sequence_adapter.hpp \ - /Users/pblunsom/packages/include/boost/ptr_container/detail/reversible_ptr_container.hpp \ - /Users/pblunsom/packages/include/boost/ptr_container/detail/throw_exception.hpp \ - /Users/pblunsom/packages/include/boost/assert.hpp \ - /Users/pblunsom/packages/include/boost/config.hpp \ - /Users/pblunsom/packages/include/boost/config/user.hpp \ - /Users/pblunsom/packages/include/boost/config/select_compiler_config.hpp \ - /Users/pblunsom/packages/include/boost/config/compiler/gcc.hpp \ - /Users/pblunsom/packages/include/boost/config/select_stdlib_config.hpp \ - 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/home/pblunsom/packages/include/boost/type_traits/is_fundamental.hpp \ + /home/pblunsom/packages/include/boost/thread/condition.hpp timing.h \ + clock_gettime_stub.c contexts_corpus.hh contexts_lexer.h \ + ../../../decoder/dict.h \ + /home/pblunsom/packages/include/boost/functional/hash.hpp \ + /home/pblunsom/packages/include/boost/functional/hash/hash.hpp \ + /home/pblunsom/packages/include/boost/functional/hash/hash_fwd.hpp \ + /home/pblunsom/packages/include/boost/functional/hash/detail/hash_float.hpp \ + /home/pblunsom/packages/include/boost/functional/hash/detail/float_functions.hpp \ + /home/pblunsom/packages/include/boost/functional/hash/detail/limits.hpp \ + /home/pblunsom/packages/include/boost/integer/static_log2.hpp \ + /home/pblunsom/packages/include/boost/functional/hash/detail/hash_float_generic.hpp \ + /home/pblunsom/packages/include/boost/functional/hash/extensions.hpp \ + /home/pblunsom/packages/include/boost/detail/container_fwd.hpp \ + ../../../decoder/wordid.h gzstream.hh clock_gettime_stub.o: clock_gettime_stub.c gammadist.o: gammadist.c gammadist.h mt19937ar.h mt19937ar.o: mt19937ar.c mt19937ar.h diff --git a/gi/pyp-topics/src/mpi-pyp-topics.cc b/gi/pyp-topics/src/mpi-pyp-topics.cc index 4525302e..50db61c1 100644 --- a/gi/pyp-topics/src/mpi-pyp-topics.cc +++ b/gi/pyp-topics/src/mpi-pyp-topics.cc @@ -8,7 +8,6 @@ void MPIPYPTopics::sample_corpus(const Corpus& corpus, int samples, int freq_cutoff_start, int freq_cutoff_end, int freq_cutoff_interval, int max_contexts_per_document) { - std::cout << "I am process " << m_rank << " of " << m_size << "." << std::endl; Timer timer; std::cout << m_am_root << std::endl; @@ -85,7 +84,7 @@ void MPIPYPTopics::sample_corpus(const Corpus& corpus, int samples, F p0 = m_topic_pyp.prob(new_topic, m_topic_p0); int table_delta = m_document_pyps.at(i).increment(new_topic, p0); if (table_delta) - m_topic_pyp.increment(new_topic, m_topic_p0); + m_topic_pyp.increment(new_topic, m_topic_p0, rnd); } else m_document_pyps.at(i).increment(new_topic, m_topic_p0); } @@ -95,23 +94,7 @@ void MPIPYPTopics::sample_corpus(const Corpus& corpus, int samples, } // Synchronise the topic->word counds across the processes. - for (std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin(); - levelIt != m_word_pyps.end(); ++levelIt) { - for (MPIPYPs::iterator pypIt=levelIt->begin(); - pypIt != levelIt->end(); ++pypIt) { - if (!m_am_root) boost::mpi::communicator().barrier(); - std::cerr << "Before Sync Process " << m_rank << ":"; - pypIt->debug_info(std::cerr); std::cerr << std::endl; - if (m_am_root) boost::mpi::communicator().barrier(); - - pypIt->synchronise(); - - if (!m_am_root) boost::mpi::communicator().barrier(); - std::cerr << "After Sync Process " << m_rank << ":"; - pypIt->debug_info(std::cerr); std::cerr << std::endl; - if (m_am_root) boost::mpi::communicator().barrier(); - } - } + synchronise(); if (m_am_root) std::cerr << " Initialized in " << timer.Elapsed() << " seconds\n"; @@ -172,7 +155,7 @@ void MPIPYPTopics::sample_corpus(const Corpus& corpus, int samples, int table_delta = m_document_pyps.at(doc_index).decrement(current_topic); if (m_use_topic_pyp && table_delta < 0) - m_topic_pyp.decrement(current_topic); + m_topic_pyp.decrement(current_topic, rnd); } // sample a new_topic @@ -186,7 +169,7 @@ void MPIPYPTopics::sample_corpus(const Corpus& corpus, int samples, F p0 = m_topic_pyp.prob(new_topic, m_topic_p0); int table_delta = m_document_pyps.at(doc_index).increment(new_topic, p0); if (table_delta) - m_topic_pyp.increment(new_topic, m_topic_p0); + m_topic_pyp.increment(new_topic, m_topic_p0, rnd); } else m_document_pyps.at(doc_index).increment(new_topic, m_topic_p0); } @@ -194,19 +177,10 @@ void MPIPYPTopics::sample_corpus(const Corpus& corpus, int samples, if (m_am_root) std::cerr << "."; std::cerr.flush(); } } - m_world.barrier(); + std::cerr << "|"; std::cerr.flush(); + // Synchronise the topic->word counds across the processes. - for (std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin(); - levelIt != m_word_pyps.end(); ++levelIt) { - for (MPIPYPs::iterator pypIt=levelIt->begin(); - pypIt != levelIt->end(); ++pypIt) { - std::cerr << "Before Sync Process " << m_rank << ":"; - pypIt->debug_info(std::cerr); std::cerr << std::endl; - pypIt->synchronise(); - std::cerr << "After Sync Process " << m_rank << ":"; - pypIt->debug_info(std::cerr); std::cerr << std::endl; - } - } + synchronise(); if (m_am_root) std::cerr << " ||| sampled " << processed_terms << " terms."; @@ -221,19 +195,19 @@ void MPIPYPTopics::sample_corpus(const Corpus& corpus, int samples, levelIt != m_word_pyps.end(); ++levelIt) { for (MPIPYPs::iterator pypIt=levelIt->begin(); pypIt != levelIt->end(); ++pypIt) { - pypIt->resample_prior(); + pypIt->resample_prior(rnd); log_p += pypIt->log_restaurant_prob(); } } for (PYPs::iterator pypIt=m_document_pyps.begin(); pypIt != m_document_pyps.end(); ++pypIt) { - pypIt->resample_prior(); + pypIt->resample_prior(rnd); log_p += pypIt->log_restaurant_prob(); } if (m_use_topic_pyp) { - m_topic_pyp.resample_prior(); + m_topic_pyp.resample_prior(rnd); log_p += m_topic_pyp.log_restaurant_prob(); } @@ -257,10 +231,44 @@ void MPIPYPTopics::sample_corpus(const Corpus& corpus, int samples, delete [] randomDocIndices; } +void MPIPYPTopics::synchronise() { + // Synchronise the topic->word counds across the processes. + //for (std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin(); + // levelIt != m_word_pyps.end(); ++levelIt) { +// std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin(); +// { +// for (MPIPYPs::iterator pypIt=levelIt->begin(); pypIt != levelIt->end(); ++pypIt) { + for (size_t label=0; label < m_word_pyps.at(0).size(); ++label) { + MPIPYP<int>& pyp = m_word_pyps.at(0).at(label); + + //if (!m_am_root) boost::mpi::communicator().barrier(); + //std::cerr << "Before Sync Process " << m_rank << ":"; + //pyp.debug_info(std::cerr); std::cerr << std::endl; + //if (m_am_root) boost::mpi::communicator().barrier(); + + MPIPYP<int>::dish_delta_type delta; + pyp.synchronise(&delta); + + for (MPIPYP<int>::dish_delta_type::const_iterator it=delta.begin(); it != delta.end(); ++it) { + int count = it->second; + if (count > 0) + for (int i=0; i < count; ++i) increment(it->first, label); + if (count < 0) + for (int i=0; i > count; --i) decrement(it->first, label); + } + pyp.reset_deltas(); + + //if (!m_am_root) boost::mpi::communicator().barrier(); + //std::cerr << "After Sync Process " << m_rank << ":"; + //pyp.debug_info(std::cerr); std::cerr << std::endl; + //if (m_am_root) boost::mpi::communicator().barrier(); + } +// } +} void MPIPYPTopics::decrement(const Term& term, int topic, int level) { //std::cerr << "MPIPYPTopics::decrement(" << term << "," << topic << "," << level << ")" << std::endl; - m_word_pyps.at(level).at(topic).decrement(term); + m_word_pyps.at(level).at(topic).decrement(term, rnd); if (m_backoff.get()) { Term backoff_term = (*m_backoff)[term]; if (!m_backoff->is_null(backoff_term)) @@ -270,7 +278,7 @@ void MPIPYPTopics::decrement(const Term& term, int topic, int level) { void MPIPYPTopics::increment(const Term& term, int topic, int level) { //std::cerr << "MPIPYPTopics::increment(" << term << "," << topic << "," << level << ")" << std::endl; - m_word_pyps.at(level).at(topic).increment(term, word_pyps_p0(term, topic, level)); + m_word_pyps.at(level).at(topic).increment(term, word_pyps_p0(term, topic, level), rnd); if (m_backoff.get()) { Term backoff_term = (*m_backoff)[term]; @@ -301,6 +309,7 @@ int MPIPYPTopics::sample(const DocumentId& doc, const Term& term) { if (cutoff <= sums[k]) return k; } + std::cerr << cutoff << " " << sum << std::endl; assert(false); } @@ -355,10 +364,11 @@ int MPIPYPTopics::max_topic() const { return current_topic; } -int MPIPYPTopics::max(const DocumentId& doc) const { +int MPIPYPTopics::max(const DocumentId& true_doc) const { //std::cerr << "MPIPYPTopics::max(" << doc << "," << term << ")" << std::endl; // collect probs F current_max=0.0; + DocumentId local_doc = true_doc - m_mpi_start; int current_topic=-1; for (int k=0; k<m_num_topics; ++k) { //F p_w_k = prob(term, k); @@ -368,8 +378,8 @@ int MPIPYPTopics::max(const DocumentId& doc) const { topic_prob = m_topic_pyp.prob(k, m_topic_p0); F prob = 0; - if (doc < 0) prob = topic_prob; - else prob = m_document_pyps[doc].prob(k, topic_prob); + if (local_doc < 0) prob = topic_prob; + else prob = m_document_pyps.at(local_doc).prob(k, topic_prob); if (prob > current_max) { current_max = prob; @@ -380,10 +390,11 @@ int MPIPYPTopics::max(const DocumentId& doc) const { return current_topic; } -int MPIPYPTopics::max(const DocumentId& doc, const Term& term) const { +int MPIPYPTopics::max(const DocumentId& true_doc, const Term& term) const { //std::cerr << "MPIPYPTopics::max(" << doc << "," << term << ")" << std::endl; // collect probs F current_max=0.0; + DocumentId local_doc = true_doc - m_mpi_start; int current_topic=-1; for (int k=0; k<m_num_topics; ++k) { F p_w_k = prob(term, k); @@ -393,8 +404,8 @@ int MPIPYPTopics::max(const DocumentId& doc, const Term& term) const { topic_prob = m_topic_pyp.prob(k, m_topic_p0); F p_k_d = 0; - if (doc < 0) p_k_d = topic_prob; - else p_k_d = m_document_pyps[doc].prob(k, topic_prob); + if (local_doc < 0) p_k_d = topic_prob; + else p_k_d = m_document_pyps.at(local_doc).prob(k, topic_prob); F prob = (p_w_k*p_k_d); if (prob > current_max) { diff --git a/gi/pyp-topics/src/mpi-pyp-topics.hh b/gi/pyp-topics/src/mpi-pyp-topics.hh index a85a776d..4a4433e6 100644 --- a/gi/pyp-topics/src/mpi-pyp-topics.hh +++ b/gi/pyp-topics/src/mpi-pyp-topics.hh @@ -8,9 +8,13 @@ #include <boost/random/uniform_real.hpp> #include <boost/random/variate_generator.hpp> #include <boost/random/mersenne_twister.hpp> +#include <boost/random/inversive_congruential.hpp> +#include <boost/random/linear_congruential.hpp> +#include <boost/random/lagged_fibonacci.hpp> #include <boost/mpi/environment.hpp> #include <boost/mpi/communicator.hpp> + #include "mpi-pyp.hh" #include "corpus.hh" @@ -62,6 +66,8 @@ public: std::ostream& print_document_topics(std::ostream& out) const; std::ostream& print_topic_terms(std::ostream& out) const; + void synchronise(); + private: F word_pyps_p0(const Term& term, int topic, int level) const; @@ -78,7 +84,9 @@ private: unsigned long m_seed; - typedef boost::mt19937 base_generator_type; + //typedef boost::mt19937 base_generator_type; + //typedef boost::hellekalek1995 base_generator_type; + typedef boost::lagged_fibonacci607 base_generator_type; typedef boost::uniform_real<> uni_dist_type; typedef boost::variate_generator<base_generator_type&, uni_dist_type> gen_type; diff --git a/gi/pyp-topics/src/mpi-pyp.hh b/gi/pyp-topics/src/mpi-pyp.hh index 65358d20..0328b387 100644 --- a/gi/pyp-topics/src/mpi-pyp.hh +++ b/gi/pyp-topics/src/mpi-pyp.hh @@ -26,18 +26,21 @@ 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()); - virtual int increment(Dish d, double p0); - virtual int decrement(Dish d); + 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(); + void synchronise(dish_delta_type* result); private: - typedef std::map<Dish, int> dish_delta_type; typedef std::map<Dish, typename PYP<Dish,Hash>::TableCounter> table_delta_type; dish_delta_type m_count_delta; @@ -49,8 +52,10 @@ 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) { +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]; @@ -63,19 +68,23 @@ MPIPYP<Dish,Hash>::increment(Dish dish, double p0) { double& b = PYP<Dish,Hash>::_b; double pshare = (c > 0) ? (c - a*t) : 0.0; double pnew = (b + a*T) * p0; - assert (pshare >= 0.0); + if (pshare < 0.0) { + std::cerr << pshare << " " << c << " " << a << " " << t << std::endl; + assert(false); + } - if (mt_genrand_res53() < pnew / (pshare + pnew)) { + 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 = mt_genrand_res53() * (c - a*t); + double r = rnd() * (c - a*t); for (std::map<int,int>::iterator hit = tc.table_histogram.begin(); hit != tc.table_histogram.end(); ++hit) { @@ -83,9 +92,9 @@ MPIPYP<Dish,Hash>::increment(Dish dish, double p0) { 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); - table_joined = hit->first+1; break; } } @@ -112,32 +121,66 @@ MPIPYP<Dish,Hash>::increment(Dish dish, double p0) { m_count_delta.erase(customer_it); // increment the histogram bar for the table joined - if (!delta) { - assert (table_joined >= 0); - std::map<int,int> &histogram = m_table_delta[dish].table_histogram; - 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 (table_it->second == 0) histogram.erase(table_it); + /* + 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 - boost::tie(table_it, table_insert_result) = histogram.insert(std::make_pair(table_joined-1,0)); - table_it->second -= 1; - if (table_it->second == 0) histogram.erase(table_it); + 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 { - typename PYP<Dish,Hash>::TableCounter &delta_tc = m_table_delta[dish]; - delta_tc.tables += 1; - delta_tc.table_histogram[1] += 1; + 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) +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()) { @@ -156,7 +199,7 @@ MPIPYP<Dish,Hash>::decrement(Dish dish) } typename PYP<Dish,Hash>::TableCounter &tc = dtit->second; - double r = mt_genrand_res53() * PYP<Dish,Hash>::count(dish); + 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); @@ -191,26 +234,54 @@ MPIPYP<Dish,Hash>::decrement(Dish dish) 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); - if (it->second == 0) - m_count_delta.erase(it); - - assert (table_left >= 0); + assert (table_left > 0); typename PYP<Dish,Hash>::TableCounter& delta_tc = m_table_delta[dish]; - if (table_left > 1) - delta_tc.table_histogram[table_left-1] += 1; + 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 = delta_tc.table_histogram.find(table_left); - //assert (tit != delta_tc.table_histogram.end()); + 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; } @@ -238,6 +309,16 @@ struct sum_maps { } }; +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 { @@ -255,60 +336,110 @@ namespace boost { } // 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; + } +}; + template <typename Dish, typename Hash> void -MPIPYP<Dish,Hash>::synchronise() { +MPIPYP<Dish,Hash>::synchronise(dish_delta_type* result) { boost::mpi::communicator world; - int rank = world.rank(), size = world.size(); + //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; // the “merged” map + 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) { - std::tr1::unordered_map<Dish,int,Hash>::operator[](it->first) += (it->second - m_count_delta[it->first]); + 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]); - //std::cerr << "Process " << rank << " adding " << (it->second - m_count_delta[it->first]) << " customers." << std::endl; + 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) { -// if (rank == process) { -// // broadcast deltas -// std::cerr << " -- Rank " << rank << " broadcasting -- " << std::endl; -// -// boost::mpi::broadcast(world, m_table_delta, process); -// -// std::cerr << " -- Rank " << rank << " done broadcasting -- " << std::endl; -// } -// else { -// std::cerr << " -- Rank " << rank << " receiving -- " << std::endl; -// // receive deltas -// table_delta_type recv_table_delta; -// -// boost::mpi::broadcast(world, recv_table_delta, process); -// -// std::cerr << " -- Rank " << rank << " done receiving -- " << std::endl; -// -// for (typename table_delta_type::const_iterator dish_it=recv_table_delta.begin(); -// dish_it != recv_table_delta.end(); ++dish_it) { -// typename PYP<Dish,Hash>::TableCounter &tc = PYP<Dish,Hash>::_dish_tables[dish_it->first]; -// -// for (std::map<int,int>::const_iterator it=dish_it->second.table_histogram.begin(); -// it != dish_it->second.table_histogram.end(); ++it) { -// tc.table_histogram[it->first] += it->second; -// } -// tc.tables += dish_it->second.tables; -// PYP<Dish,Hash>::_total_tables += dish_it->second.tables; -// } -// } -// } -// std::cerr << " -- Done Reducing -- " << std::endl; + 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(); +// reset_deltas(); } #endif diff --git a/gi/pyp-topics/src/mpi-train-contexts.cc b/gi/pyp-topics/src/mpi-train-contexts.cc index 0651ecac..6e1e78a5 100644 --- a/gi/pyp-topics/src/mpi-train-contexts.cc +++ b/gi/pyp-topics/src/mpi-train-contexts.cc @@ -10,6 +10,7 @@ #include <boost/scoped_ptr.hpp> #include <boost/mpi/environment.hpp> #include <boost/mpi/communicator.hpp> +#include <boost/lexical_cast.hpp> // Local #include "mpi-pyp-topics.hh" @@ -28,9 +29,10 @@ int main(int argc, char **argv) { mpi::environment env(argc, argv); mpi::communicator world; - bool am_root = (world.rank() == 0); - if (am_root) std::cout << "I am process " << world.rank() << " of " << world.size() << "." << std::endl; + int rank = world.rank(); + bool am_root = rank; if (am_root) cout << "Pitman Yor topic models: Copyright 2010 Phil Blunsom\n"; + if (am_root) std::cout << "I am process " << world.rank() << " of " << world.size() << "." << std::endl; if (am_root) cout << REVISION << '\n' <<endl; //////////////////////////////////////////////////////////////////////////////////////////// @@ -117,60 +119,73 @@ int main(int argc, char **argv) vm["freq-cutoff-interval"].as<int>(), vm["max-contexts-per-document"].as<int>()); - if (world.rank() == 0) { - if (vm.count("document-topics-out")) { - ogzstream documents_out(vm["document-topics-out"].as<string>().c_str()); - - int document_id=0; - map<int,int> all_terms; - for (Corpus::const_iterator corpusIt=contexts_corpus.begin(); - corpusIt != contexts_corpus.end(); ++corpusIt, ++document_id) { - vector<int> unique_terms; - for (Document::const_iterator docIt=corpusIt->begin(); - docIt != corpusIt->end(); ++docIt) { - if (unique_terms.empty() || *docIt != unique_terms.back()) - unique_terms.push_back(*docIt); - // increment this terms frequency - pair<map<int,int>::iterator,bool> insert_result = all_terms.insert(make_pair(*docIt,1)); - if (!insert_result.second) - all_terms[*docIt] = all_terms[*docIt] + 1; - //insert_result.first++; - } - documents_out << contexts_corpus.key(document_id) << '\t'; - documents_out << model.max(document_id) << " " << corpusIt->size() << " ||| "; - for (std::vector<int>::const_iterator termIt=unique_terms.begin(); - termIt != unique_terms.end(); ++termIt) { - if (termIt != unique_terms.begin()) - documents_out << " ||| "; - vector<std::string> strings = contexts_corpus.context2string(*termIt); - copy(strings.begin(), strings.end(),ostream_iterator<std::string>(documents_out, " ")); - documents_out << "||| C=" << model.max(document_id, *termIt); - - } - documents_out <<endl; + if (vm.count("document-topics-out")) { + std::ofstream documents_out((vm["document-topics-out"].as<string>() + ".pyp-process-" + boost::lexical_cast<std::string>(rank)).c_str()); + int documents = contexts_corpus.num_documents(); + int mpi_start = 0, mpi_end = documents; + if (world.size() != 1) { + mpi_start = (documents / world.size()) * rank; + if (rank == world.size()-1) mpi_end = documents; + else mpi_end = (documents / world.size())*(rank+1); + } + + map<int,int> all_terms; + for (int document_id=mpi_start; document_id<mpi_end; ++document_id) { + assert (document_id < contexts_corpus.num_documents()); + const Document& doc = contexts_corpus.at(document_id); + vector<int> unique_terms; + for (Document::const_iterator docIt=doc.begin(); docIt != doc.end(); ++docIt) { + if (unique_terms.empty() || *docIt != unique_terms.back()) + unique_terms.push_back(*docIt); + // increment this terms frequency + pair<map<int,int>::iterator,bool> insert_result = all_terms.insert(make_pair(*docIt,1)); + if (!insert_result.second) + all_terms[*docIt] = all_terms[*docIt] + 1; } - documents_out.close(); - - if (vm.count("default-topics-out")) { - ofstream default_topics(vm["default-topics-out"].as<string>().c_str()); - default_topics << model.max_topic() <<endl; - for (std::map<int,int>::const_iterator termIt=all_terms.begin(); termIt != all_terms.end(); ++termIt) { - vector<std::string> strings = contexts_corpus.context2string(termIt->first); - default_topics << model.max(-1, termIt->first) << " ||| " << termIt->second << " ||| "; - copy(strings.begin(), strings.end(),ostream_iterator<std::string>(default_topics, " ")); - default_topics <<endl; - } + documents_out << contexts_corpus.key(document_id) << '\t'; + documents_out << model.max(document_id) << " " << doc.size() << " ||| "; + for (std::vector<int>::const_iterator termIt=unique_terms.begin(); termIt != unique_terms.end(); ++termIt) { + if (termIt != unique_terms.begin()) + documents_out << " ||| "; + vector<std::string> strings = contexts_corpus.context2string(*termIt); + copy(strings.begin(), strings.end(),ostream_iterator<std::string>(documents_out, " ")); + documents_out << "||| C=" << model.max(document_id, *termIt); } + documents_out <<endl; + } + documents_out.close(); + + if (am_root) { + ogzstream root_documents_out(vm["document-topics-out"].as<string>().c_str()); + for (int p=0; p < world.size(); ++p) { + std::string rank_p_prefix((vm["document-topics-out"].as<string>() + ".pyp-process-" + boost::lexical_cast<std::string>(p)).c_str()); + std::ifstream rank_p_trees_istream(rank_p_prefix.c_str(), std::ios_base::binary); + root_documents_out << rank_p_trees_istream.rdbuf(); + rank_p_trees_istream.close(); + remove((rank_p_prefix).c_str()); + } + root_documents_out.close(); } - if (vm.count("topic-words-out")) { - ogzstream topics_out(vm["topic-words-out"].as<string>().c_str()); - model.print_topic_terms(topics_out); - topics_out.close(); + if (am_root && vm.count("default-topics-out")) { + ofstream default_topics(vm["default-topics-out"].as<string>().c_str()); + default_topics << model.max_topic() <<endl; + for (std::map<int,int>::const_iterator termIt=all_terms.begin(); termIt != all_terms.end(); ++termIt) { + vector<std::string> strings = contexts_corpus.context2string(termIt->first); + default_topics << model.max(-1, termIt->first) << " ||| " << termIt->second << " ||| "; + copy(strings.begin(), strings.end(),ostream_iterator<std::string>(default_topics, " ")); + default_topics <<endl; + } } + } - cout <<endl; + if (am_root && vm.count("topic-words-out")) { + ogzstream topics_out(vm["topic-words-out"].as<string>().c_str()); + model.print_topic_terms(topics_out); + topics_out.close(); } + cout <<endl; + return 0; } diff --git a/gi/pyp-topics/src/pyp-topics.cc b/gi/pyp-topics/src/pyp-topics.cc index b154f922..06499291 100644 --- a/gi/pyp-topics/src/pyp-topics.cc +++ b/gi/pyp-topics/src/pyp-topics.cc @@ -200,7 +200,7 @@ void PYPTopics::sample_corpus(const Corpus& corpus, int samples, } if (m_use_topic_pyp) { - m_topic_pyp.resample_prior(); + m_topic_pyp.resample_prior(rnd); log_p += m_topic_pyp.log_restaurant_prob(); } @@ -233,7 +233,7 @@ PYPTopics::F PYPTopics::hresample_docs(int start, int end) assert(start <= end); for (int i=start; i < end; ++i) { - m_document_pyps[i].resample_prior(); + m_document_pyps[i].resample_prior(rnd); log_p += m_document_pyps[i].log_restaurant_prob(); if (resample_counter++ % 5000 == 0) { std::cerr << "."; std::cerr.flush(); @@ -250,7 +250,7 @@ PYPTopics::F PYPTopics::hresample_topics() for (PYPs::iterator pypIt=levelIt->begin(); pypIt != levelIt->end(); ++pypIt) { - pypIt->resample_prior(); + pypIt->resample_prior(rnd); log_p += pypIt->log_restaurant_prob(); } } diff --git a/gi/pyp-topics/src/pyp.hh b/gi/pyp-topics/src/pyp.hh index 84decb0f..19cd6be8 100644 --- a/gi/pyp-topics/src/pyp.hh +++ b/gi/pyp-topics/src/pyp.hh @@ -71,9 +71,12 @@ public: static double log_prior_a(double a, double beta_a, double beta_b); static double log_prior_b(double b, double gamma_c, double gamma_s); - void resample_prior(); - void resample_prior_a(); - void resample_prior_b(); + template <typename Uniform01> + void resample_prior(Uniform01& rnd); + template <typename Uniform01> + void resample_prior_a(Uniform01& rnd); + template <typename Uniform01> + void resample_prior_b(Uniform01& rnd); protected: double _a, _b; // parameters of the Pitman-Yor distribution @@ -402,13 +405,18 @@ PYP<Dish,Hash>::debug_info(std::ostream& os) const hists += dtit->second.table_histogram.size(); tables += dtit->second.tables; +// if (dtit->second.tables <= 0) +// std::cerr << dtit->first << " " << count(dtit->first) << std::endl; assert(dtit->second.tables > 0); assert(!dtit->second.table_histogram.empty()); +// os << "Dish " << dtit->first << " has " << count(dtit->first) << " customers, and is sitting at " << dtit->second.tables << " tables.\n"; for (std::map<int,int>::const_iterator hit = dtit->second.table_histogram.begin(); - hit != dtit->second.table_histogram.end(); ++hit) + hit != dtit->second.table_histogram.end(); ++hit) { +// os << " " << hit->second << " tables with " << hit->first << " customers." << std::endl; assert(hit->second > 0); + } } os << "restaurant has " @@ -510,41 +518,46 @@ long double PYP<Dish,Hash>::lgammadist(long double x, long double alpha, long do template <typename Dish, typename Hash> + template <typename Uniform01> void -PYP<Dish,Hash>::resample_prior() { +PYP<Dish,Hash>::resample_prior(Uniform01& rnd) { for (int num_its=5; num_its >= 0; --num_its) { - resample_prior_b(); - resample_prior_a(); + resample_prior_b(rnd); + resample_prior_a(rnd); } - resample_prior_b(); + resample_prior_b(rnd); } template <typename Dish, typename Hash> + template <typename Uniform01> void -PYP<Dish,Hash>::resample_prior_b() { +PYP<Dish,Hash>::resample_prior_b(Uniform01& rnd) { if (_total_tables == 0) return; - int niterations = 10; // number of resampling iterations + //int niterations = 10; // number of resampling iterations + int niterations = 5; // number of resampling iterations //std::cerr << "\n## resample_prior_b(), initial a = " << _a << ", b = " << _b << std::endl; resample_b_type b_log_prob(_total_customers, _total_tables, _a, _b_gamma_c, _b_gamma_s); - //_b = slice_sampler1d(b_log_prob, _b, rnd, (double) 0.0, std::numeric_limits<double>::infinity(), - _b = slice_sampler1d(b_log_prob, _b, mt_genrand_res53, (double) 0.0, std::numeric_limits<double>::infinity(), + _b = slice_sampler1d(b_log_prob, _b, rnd, (double) 0.0, std::numeric_limits<double>::infinity(), + //_b = slice_sampler1d(b_log_prob, _b, mt_genrand_res53, (double) 0.0, std::numeric_limits<double>::infinity(), (double) 0.0, niterations, 100*niterations); //std::cerr << "\n## resample_prior_b(), final a = " << _a << ", b = " << _b << std::endl; } template <typename Dish, typename Hash> + template <typename Uniform01> void -PYP<Dish,Hash>::resample_prior_a() { +PYP<Dish,Hash>::resample_prior_a(Uniform01& rnd) { if (_total_tables == 0) return; - int niterations = 10; + //int niterations = 10; + int niterations = 5; //std::cerr << "\n## Initial a = " << _a << ", b = " << _b << std::endl; resample_a_type a_log_prob(_total_customers, _total_tables, _b, _a_beta_a, _a_beta_b, _dish_tables); - //_a = slice_sampler1d(a_log_prob, _a, rnd, std::numeric_limits<double>::min(), - _a = slice_sampler1d(a_log_prob, _a, mt_genrand_res53, std::numeric_limits<double>::min(), + _a = slice_sampler1d(a_log_prob, _a, rnd, std::numeric_limits<double>::min(), + //_a = slice_sampler1d(a_log_prob, _a, mt_genrand_res53, std::numeric_limits<double>::min(), (double) 1.0, (double) 0.0, niterations, 100*niterations); } |