WIP Prepare next version

Makefile

@@ -46,10 +46,10 @@ CFLAGS_nat_profile := -pg -DNDEBUG $(OMP_FLAG) $(CFLAGS_all)
 
 # Emscripten compiler information
 CXX_web := emcc
-OFLAGS_web_all := $(CXXFLAGS) -Wno-mismatched-tags -Wno-empty-body -s USE_ZLIB=1 -s USE_LIBLZMA=1 -s "EXTRA_EXPORTED_RUNTIME_METHODS=['ccall', 'cwrap']" -s TOTAL_MEMORY=671088640 --js-library $(EMP_DIR)/web/library_emp.js -s EXPORTED_FUNCTIONS="['_main', '_empCppCallback', '_empDoCppCallback']" -s DISABLE_EXCEPTION_CATCHING=1 -s NO_EXIT_RUNTIME=1 -s ABORTING_MALLOC=0 -I/usr/lib/x86_64-linux-gnu/openmpi/include/
+OFLAGS_web_all := $(CXXFLAGS) -Wno-mismatched-tags -Wno-empty-body -s USE_ZLIB=1 -s USE_LIBLZMA=1 -s "EXTRA_EXPORTED_RUNTIME_METHODS=['ccall', 'cwrap']" -s TOTAL_MEMORY=671088640 --js-library $(EMP_DIR)/web/library_emp.js -s EXPORTED_FUNCTIONS="['_main', '_empCppCallback', '_empDoCppCallback']" -s NO_EXIT_RUNTIME=1 -s ABORTING_MALLOC=0 -I/usr/lib/x86_64-linux-gnu/openmpi/include/
 OFLAGS_web_pthread := -s USE_PTHREADS=1 -s PROXY_TO_PTHREAD=1
-OFLAGS_web := -O3 -DNDEBUG
-OFLAGS_web_debug := -g4 -Wno-dollar-in-identifier-extension -s DEMANGLE_SUPPORT=1 -s ASSERTIONS=2 -s SAFE_HEAP=1 -s STACK_OVERFLOW_CHECK=2 -D_GLIBCXX_DEBUG -D_LIBCPP_DEBUG
+OFLAGS_web := -O3 -DNDEBUG -s DISABLE_EXCEPTION_CATCHING=1
+OFLAGS_web_debug := -g4 -Oz -Wno-dollar-in-identifier-extension -s DEMANGLE_SUPPORT=1 -s ASSERTIONS=2 -s SAFE_HEAP=1 -s STACK_OVERFLOW_CHECK=2 -D_GLIBCXX_DEBUG -D_LIBCPP_DEBUG -fexceptions
 
 CFLAGS_web := $(CFLAGS_all) $(OFLAGS_web) $(OFLAGS_web_all)
 CFLAGS_web_pthread := $(CFLAGS_all) $(OFLAGS_web) $(OFLAGS_web_pthread) $(OFLAGS_web_all)

include/dish2/config/dump_config_csv.hpp

@@ -25,12 +25,9 @@ void dump_config_csv() {
   auto keyname_attributes = emp::keyname::unpack_t{
     {"a", "asconfigured"},
     {"proc", emp::to_string( uitsl::get_proc_id() ) },
-    {"source", EMP_STRINGIFY(DISHTINY_HASH_)},
     {"ext", ".csv"}
   };
 
-  if ( dish2::get_repro() ) keyname_attributes[ "repro" ] = *dish2::get_repro();
-
   dish2::mkdir_exists_ok( "./outmeta" );
 
   const std::string outname = dish2::pare_keyname_filename(
@@ -39,6 +36,7 @@ void dump_config_csv() {
   const std::string outpath = emp::to_string("outmeta/", outname);
 
   emp::DataFile df( outpath );
+  df.AddVal( EMP_STRINGIFY(DISHTINY_HASH_), "source" );
   if ( dish2::get_repro() ) df.AddVal( *dish2::get_repro(), "Repro" );
   if ( dish2::get_endeavor() ) df.AddVal( *dish2::get_endeavor(), "Endeavor" );
   if ( dish2::get_slurm_job_id() ) df.AddVal(

include/dish2/genome/PhyloFingerprints.hpp

@@ -0,0 +1,145 @@
+#pragma once
+#ifndef DISH2_GENOME_PHYLOFINGERPRINTS_HPP_INCLUDE
+#define DISH2_GENOME_PHYLOFINGERPRINTS_HPP_INCLUDE
+
+#include <algorithm>
+#include <cmath>
+
+#include "../polyfill/bit_floor.hpp"
+#include "../polyfill/bit_width.hpp"
+#include "../polyfill/countr_zero.hpp"
+
+// #include "../../../third-party/Empirical/include/emp/base/vector.hpp"
+#include "../../../third-party/signalgp-lite/include/sgpl/utility/ThreadLocalRandom.hpp"
+
+namespace dish2 {
+
+class PhyloFingerprints {
+
+  uint64_t generation_counter{};
+
+  // ordered from most ancient (index 0 / fingerprints.front())
+  // to most recent (index n - 1 / fingerprints.back())
+  std::vector<uint64_t> fingerprints;
+  // absolute generation corresponding to each fingerprint
+  std::vector<uint64_t> generations;
+
+// todo remove
+public:
+
+  // msb == most significant bit
+  static uint64_t clear_msb(const uint64_t v) {
+    return v - std::bit_floor(v);
+  }
+
+  // lsb == lowest set bit
+  // aka (x & -x).set_width()
+  // not defined for x == 0
+  // == https://oeis.org/A001511 - 1
+  static uint64_t get_lsb_index(const uint64_t v) {
+    emp_assert(v);
+    return std::countr_zero(v);
+  }
+
+  // 0 == no drop
+  // should generate sequence
+  // 0, 0, 1, 0, 1, 2, 1, 0, 1, 2, 1, 3, 1, 2, 1, 0, ...
+  // non-zero interludes are from https://oeis.org/A001511
+  // zeros occur when index is an even power of two
+  static uint64_t calc_drop_idx(const uint64_t gen) {
+    const uint64_t leftover = clear_msb(gen);
+    if ( leftover ) return get_lsb_index(leftover) + 1;
+    else return 0;
+  }
+
+  void append_fingerprint() {
+    fingerprints.push_back(
+      sgpl::tlrand.Get().GetUInt64()
+    );
+    generations.push_back(
+      generation_counter
+    );
+  }
+
+  void maybe_drop_fingerprint(const size_t drop_idx) {
+    if ( drop_idx ) {
+      fingerprints.erase(
+        std::next( std::rbegin(fingerprints), drop_idx ).base()
+      );
+      generations.erase(
+        std::next( std::rbegin(generations), drop_idx ).base()
+      );
+    }
+  }
+
+  void print() {
+    for ( auto& g : generations ) std::cout << generation_counter - g << " ";
+    std::cout << '\n';
+  }
+
+public:
+
+  PhyloFingerprints() { append_fingerprint(); ++generation_counter; }
+
+  void ElapseGeneration() {
+    ++generation_counter;
+
+    maybe_drop_fingerprint( calc_drop_idx(generation_counter) );
+
+    append_fingerprint();
+  }
+
+  size_t DivergedAtLeast( const PhyloFingerprints& other ) const {
+    const auto [our_mismatch, others_mismatch] = std::mismatch(
+      std::begin( fingerprints ), std::end( fingerprints ),
+      std::begin( other.fingerprints )
+    );
+
+    const size_t num_divergent_fingerprints = std::distance(
+      our_mismatch, std::end( fingerprints )
+    );
+
+    if ( num_divergent_fingerprints ) {
+      const size_t first_divergent_generation = generations[
+        generations.size() - num_divergent_fingerprints
+      ];
+      return generation_counter - first_divergent_generation;
+    } else return 0;
+
+  }
+
+  size_t DivergedLessThan( const PhyloFingerprints& other ) const {
+    const auto [our_mismatch, others_mismatch] = std::mismatch(
+      std::begin( fingerprints ), std::end( fingerprints ),
+      std::begin( other.fingerprints )
+    );
+
+    const size_t num_common_fingerprints = std::distance(
+      std::begin( fingerprints ), our_mismatch
+    );
+
+    if ( num_common_fingerprints ) {
+      const size_t last_common_generation = generations[
+        num_common_fingerprints - 1
+      ];
+      return generation_counter - last_common_generation;
+    } else return -1;
+
+  }
+
+  [[deprecated("Temporary interface for Phylogenetic Fingerprints Demo.")]]
+  const std::vector<uint64_t>& GetGenerations() const { return generations; }
+
+  [[deprecated("Temporary interface for Phylogenetic Fingerprints Demo.")]]
+  const size_t GetGenerationCount() const { return generation_counter; }
+
+  [[deprecated("Temporary interface for Phylogenetic Fingerprints Demo.")]]
+  const size_t GetFingerprint(const size_t idx) const {
+    return fingerprints[idx];
+  }
+
+};
+
+} // namespace dish2
+
+#endif // #ifndef DISH2_GENOME_PHYLOFINGERPRINTS_HPP_INCLUDE

include/dish2/load/reconstitute_population_load.hpp

@@ -16,7 +16,6 @@
 #include "../../../third-party/Empirical/include/emp/tools/keyname_utils.hpp"
 #include "../../../third-party/Empirical/include/emp/tools/string_utils.hpp"
 
-#include "../algorithm/seed_genomes_into.hpp"
 #include "../genome/Genome.hpp"
 #include "../utility/autoload.hpp"
 

include/dish2/peripheral/readable_state/introspective_state/raw_introspective_state/Epoch.hpp

@@ -7,9 +7,9 @@
 
 namespace dish2 {
 
-struct Epoch : public uitsl::PodLeafNode<size_t> {
+struct Epoch : public uitsl::PodLeafNode<uint64_t> {
   // inherit constructors
-  using parent_t = uitsl::PodLeafNode<size_t>;
+  using parent_t = uitsl::PodLeafNode<uint64_t>;
   using parent_t::parent_t;
 };
 

include/dish2/peripheral/readable_state/introspective_state/raw_introspective_state/IncomingInterMessageCounter.hpp

@@ -7,9 +7,9 @@
 
 namespace dish2 {
 
-struct IncomingInterMessageCounter : public uitsl::PodLeafNode<size_t> {
+struct IncomingInterMessageCounter : public uitsl::PodLeafNode<uint64_t> {
   // inherit constructors
-  using parent_t = uitsl::PodLeafNode<size_t>;
+  using parent_t = uitsl::PodLeafNode<uint64_t>;
   using parent_t::parent_t;
 };
 

include/dish2/peripheral/readable_state/introspective_state/raw_introspective_state/IncomingIntraMessageCounter.hpp

@@ -7,9 +7,9 @@
 
 namespace dish2 {
 
-struct IncomingIntraMessageCounter : public uitsl::PodLeafNode<size_t> {
+struct IncomingIntraMessageCounter : public uitsl::PodLeafNode<uint64_t> {
   // inherit constructors
-  using parent_t = uitsl::PodLeafNode<size_t>;
+  using parent_t = uitsl::PodLeafNode<uint64_t>;
   using parent_t::parent_t;
 };
 

include/dish2/peripheral/readable_state/introspective_state/raw_introspective_state/KinGroupAge.hpp

@@ -10,13 +10,13 @@
 namespace dish2 {
 
 template< typename Spec >
-struct KinGroupAge : public uitsl::PodLeafNode< size_t, Spec::NLEV > {
+struct KinGroupAge : public uitsl::PodLeafNode< uint64_t, Spec::NLEV > {
   // inherit constructors
-  using parent_t = uitsl::PodLeafNode<size_t, Spec::NLEV>;
+  using parent_t = uitsl::PodLeafNode<uint64_t, Spec::NLEV>;
   using parent_t::parent_t;
 
   void Refresh(
-    const size_t epoch, const dish2::KinGroupEpochStamps< Spec > stamps
+    const uint64_t epoch, const dish2::KinGroupEpochStamps< Spec > stamps
   ) {
     std::transform(
       std::begin( stamps.GetBuffer() ),

include/dish2/peripheral/readable_state/introspective_state/raw_introspective_state/KinGroupIDAncestorView.hpp

@@ -13,9 +13,9 @@
 namespace dish2 {
 
 template< typename Spec >
-struct KinGroupIDAncestorView : public uitsl::PodLeafNode< size_t, Spec::NLEV > {
+struct KinGroupIDAncestorView : public uitsl::PodLeafNode< uint64_t, Spec::NLEV > {
   // inherit constructors
-  using parent_t = uitsl::PodLeafNode<size_t, Spec::NLEV>;
+  using parent_t = uitsl::PodLeafNode<uint64_t, Spec::NLEV>;
   using parent_t::parent_t;
 
 };

include/dish2/peripheral/readable_state/introspective_state/raw_introspective_state/NumKnownQuorumBits.hpp

@@ -13,9 +13,9 @@
 namespace dish2 {
 
 template< typename Spec >
-struct NumKnownQuorumBits : public uitsl::PodLeafNode< size_t, Spec::NLEV > {
+struct NumKnownQuorumBits : public uitsl::PodLeafNode< uint64_t, Spec::NLEV > {
   // inherit constructors
-  using parent_t = uitsl::PodLeafNode<size_t, Spec::NLEV>;
+  using parent_t = uitsl::PodLeafNode<uint64_t, Spec::NLEV>;
   using parent_t::parent_t;
 
 };

include/dish2/peripheral/readable_state/introspective_state/raw_introspective_state/PhylogeneticRootView.hpp

@@ -10,9 +10,9 @@
 
 namespace dish2 {
 
-struct PhylogeneticRootView : public uitsl::PodLeafNode< size_t > {
+struct PhylogeneticRootView : public uitsl::PodLeafNode< uint64_t > {
   // inherit constructors
-  using parent_t = uitsl::PodLeafNode<size_t>;
+  using parent_t = uitsl::PodLeafNode<uint64_t>;
   using parent_t::parent_t;
 
 };

include/dish2/peripheral/readable_state/introspective_state/raw_introspective_state/SpawnCount.hpp

@@ -7,8 +7,8 @@
 
 namespace dish2 {
 
-struct SpawnCount : public uitsl::PodLeafNode<char> {
-  using parent_t = uitsl::PodLeafNode<char>;
+struct SpawnCount : public uitsl::PodLeafNode<uint64_t> {
+  using parent_t = uitsl::PodLeafNode<uint64_t>;
   using parent_t::parent_t;
 };
 

include/dish2/polyfill/bit_floor.hpp

@@ -0,0 +1,17 @@
+#pragma once
+#ifndef DISH2_POLYFILL_BIT_FLOOR_HPP_INCLUDE
+#define DISH2_POLYFILL_BIT_FLOOR_HPP_INCLUDE
+
+#include "bit_width.hpp"
+
+namespace std {
+
+  template< typename T >
+  T bit_floor(T x) {
+    if (x != 0) return T{1} << (std::bit_width(x) - 1);
+    else return 0;
+  }
+
+} // namespace std
+
+#endif // #ifndef DISH2_POLYFILL_BIT_FLOOR_HPP_INCLUDE

include/dish2/polyfill/bit_width.hpp

@@ -0,0 +1,19 @@
+#pragma once
+#ifndef DISH2_POLYFILL_BIT_WIDTH_HPP_INCLUDE
+#define DISH2_POLYFILL_BIT_WIDTH_HPP_INCLUDE
+
+namespace std {
+
+  template< typename T >
+  size_t bit_width(T x) {
+    size_t res{};
+    while (x) {
+      x >>= 1;
+      ++res;
+    }
+    return res;
+  }
+
+} // namespace std
+
+#endif // #ifndef DISH2_POLYFILL_BIT_WIDTH_HPP_INCLUDE

include/dish2/polyfill/countr_zero.hpp

@@ -0,0 +1,18 @@
+#pragma once
+#ifndef DISH2_POLYFILL_COUNTR_ZERO_HPP_INCLUDE
+#define DISH2_POLYFILL_COUNTR_ZERO_HPP_INCLUDE
+
+namespace std {
+
+  // adapted from https://johnmcfarlane.github.io/cnl/bit_8h_source.html
+  template< typename T >
+  size_t countr_zero(T x) {
+    return (x & 1)
+      ? 0
+      : countr_zero<T>(static_cast<T>(x >> 1)) + 1
+    ;
+  }
+
+} // namespace std
+
+#endif // #ifndef DISH2_POLYFILL_COUNTR_ZERO_HPP_INCLUDE

include/dish2/record/dump_genome_statistics.hpp

@@ -56,7 +56,8 @@ void dump_genome_statistics(
       file.AddVal( v, emp::to_string("Treatment ", k) );
     }
   }
-  file.AddVal( "proc", emp::to_string( uitsl::get_proc_id() ) );
+  file.AddVal( uitsl::get_proc_id(), "proc" );
+  file.AddVal( dish2::thread_idx, "thread" );
 
   const std::string slug = dish2::make_genome_slug( genome_filename );
   file.AddVar(slug, "Genome Slug");

include/dish2/record/dump_spawn_log.hpp

@@ -5,12 +5,12 @@
 #include <algorithm>
 #include <string>
 
+#include "../../../third-party/bxzstr/include/bxzstr.hpp"
 #include "../../../third-party/conduit/include/uitsl/algorithm/for_each.hpp"
 #include "../../../third-party/conduit/include/uitsl/mpi/comm_utils.hpp"
 #include "../../../third-party/Empirical/include/emp/data/DataFile.hpp"
 #include "../../../third-party/Empirical/include/emp/tools/keyname_utils.hpp"
 #include "../../../third-party/Empirical/include/emp/tools/string_utils.hpp"
-#include "../../../third-party/header-only-gzstream/include/hogzstr/gzstream.hpp"
 #include "../../../third-party/signalgp-lite/include/sgpl/utility/CountingIterator.hpp"
 
 #include "../config/has_replicate.hpp"
@@ -30,12 +30,12 @@ void dump_spawn_log( const dish2::ThreadWorld< Spec >& world ) {
 
   const auto& population = world.population;
 
-  const thread_local std::string out_filename = dish2::pare_keyname_filename(
+  const std::string out_filename = dish2::pare_keyname_filename(
     dish2::make_spawn_log_filename(),
     dish2::make_data_path()
   );
 
-  thread_local bxz::ofstream out_stream(
+  bxz::ofstream out_stream(
     dish2::make_data_path( out_filename ), bxz::lzma, 6
   );
   emp::DataFile file( out_stream );

include/dish2/services/BirthSetupService.hpp

@@ -40,7 +40,8 @@ struct BirthSetupService {
     fresh_input_idxs.clear();
 
     for (size_t idx{}; idx < cell.cardinals.size(); ++idx) {
-      if ( cell.cardinals[idx].genome_node_input.Jump() ) {
+      const size_t num_entries = cell.cardinals[idx].genome_node_input.Jump();
+      for ( size_t ticket{}; ticket < num_entries; ++ticket ) {
         fresh_input_idxs.push_back( idx );
       }
     }