Record stint root id changeovers

include/dish2/algorithm/seed_genomes_into.hpp

@@ -5,6 +5,7 @@
 #include <algorithm>
 
 #include "../../../third-party/conduit/include/uitsl/algorithm/for_each.hpp"
+#include "../../../third-party/Empirical/include/emp/base/optional.hpp"
 #include "../../../third-party/Empirical/include/emp/base/vector.hpp"
 #include "../../../third-party/Empirical/include/emp/math/random_utils.hpp"
 #include "../../../third-party/signalgp-lite/include/sgpl/introspection/count_modules.hpp"
@@ -13,12 +14,13 @@
 #include "../cell/Cell.hpp"
 #include "../config/cfg.hpp"
 #include "../enum/CauseOfDeath.hpp"
+#include "../record/StintRootIDChangeoverRecorder.hpp"
 #include "../world/iterators/LiveCellIterator.hpp"
 #include "../world/ThreadWorld.hpp"
 
 namespace dish2 {
 
-template< typename Spec >
+template< typename Spec, bool record_stint_root_id_changeover=false >
 void seed_genomes_into(
   emp::vector< emp::vector<dish2::Genome<Spec>> > seed_buckets,
   dish2::ThreadWorld<Spec>& world
@@ -61,22 +63,34 @@ void seed_genomes_into(
     // shuffle incoming_population...
     emp::Shuffle( sgpl::tlrand.Get(), incoming_population );
 
+    emp::optional<dish2::StintRootIDChangeoverRecorder> recorder;
+    if constexpr ( record_stint_root_id_changeover ) recorder.emplace();
+
     // ... then inject into ThreadWorld's population
     uitsl::for_each(
       std::begin( incoming_population ), std::end( incoming_population ),
       std::begin( population ),
-      []( const auto& seed, auto& cell ){
+      [&recorder]( const auto& seed, auto& cell ){
         cell.genome = seed;
         cell.genome->SetupSeededGenotype();
         cell.MakeAliveRoutine();
+
+        if constexpr (
+          record_stint_root_id_changeover
+        ) recorder->record_changeover(
+          seed.root_id.GetID(),
+          seed.stint_root_id.GetID(),
+          cell.genome->stint_root_id.GetID()
+        );
+
       }
     );
 
   }
 
 }
 
-template< typename Spec >
+template< typename Spec, bool record_stint_root_id_changeover=false >
 void seed_genomes_into(
   const emp::vector< dish2::Genome<Spec> >& seeds,
   dish2::ThreadWorld<Spec>& world
@@ -90,7 +104,9 @@ void seed_genomes_into(
     []( const auto& seed ){ return emp::vector<dish2::Genome<Spec>>{ seed }; }
   );
 
-  dish2::seed_genomes_into<Spec>( seed_buckets, world );
+  dish2::seed_genomes_into<Spec, record_stint_root_id_changeover>(
+    seed_buckets, world
+  );
 
 }
 

include/dish2/load/innoculate_population.hpp

@@ -73,7 +73,7 @@ void innoculate_population( dish2::ThreadWorld<Spec>& world ) {
   }(), emp::to_string( innoculum_paths ));
 
 
-  dish2::seed_genomes_into<Spec>( innoculum_buckets, world );
+  dish2::seed_genomes_into<Spec, true>( innoculum_buckets, world );
 
   dish2::log_msg( "loaded ", innoculum_buckets.size(), " innoculum buckets" );
 

include/dish2/load/monoculture_population.hpp

@@ -40,7 +40,7 @@ void monoculture_population( dish2::ThreadWorld<Spec>& world ) {
 
   dish2::log_msg( " loaded monoculture from ", monoculture_paths.front() );
 
-  dish2::seed_genomes_into<Spec>( {monoculture}, world );
+  dish2::seed_genomes_into<Spec, true>( {monoculture}, world );
 
   dish2::log_msg( "applied monoculture" );
 

include/dish2/load/reconstitute_population.hpp

@@ -21,7 +21,7 @@ void reconstitute_population( dish2::ThreadWorld<Spec>& world ) {
 
   dish2::log_msg("reconstituted ", reconstituted.size(), " cells from ", src);
 
-  dish2::seed_genomes_into<Spec>( reconstituted, world );
+  dish2::seed_genomes_into<Spec, true>( reconstituted, world );
 
 }
 

include/dish2/record/StintRootIDChangeoverRecorder.hpp

@@ -0,0 +1,94 @@
+#pragma once
+#ifndef DISH2_RECORD_STINTROOTIDCHANGEOVERRECORDER_HPP_INCLUDE
+#define DISH2_RECORD_STINTROOTIDCHANGEOVERRECORDER_HPP_INCLUDE
+
+#include <string>
+
+#include "../../../third-party/bxzstr/include/bxzstr.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/signalgp-lite/include/sgpl/utility/CountingIterator.hpp"
+
+#include "../config/has_replicate.hpp"
+#include "../config/has_series.hpp"
+#include "../config/has_stint.hpp"
+#include "../config/thread_idx.hpp"
+#include "../debug/log_msg.hpp"
+#include "../utility/pare_keyname_filename.hpp"
+
+#include "make_filename/make_data_path.hpp"
+#include "make_filename/make_stint_root_id_changeover_filename.hpp"
+
+
+namespace dish2 {
+
+class StintRootIDChangeoverRecorder {
+
+  std::string outpath;
+  bxz::ofstream ofstream;
+  emp::DataFile file;
+
+  // thread_local so that copying/moving doesn't break DataFile refs
+  inline static thread_local uint64_t root_id_;
+  inline static thread_local uint64_t incoming_stint_root_id_;
+  inline static thread_local uint64_t outgoing_stint_root_id_;
+
+public:
+
+  StintRootIDChangeoverRecorder()
+  : outpath(
+    dish2::make_data_path(
+      dish2::pare_keyname_filename(
+        dish2::make_stint_root_id_changeover_filename(),
+        dish2::make_data_path()
+      )
+    )
+  )
+  , ofstream(
+    outpath, bxz::lzma, 6
+  )
+  , file( ofstream ) {
+
+    if ( dish2::has_stint() ) file.AddVal(cfg.STINT(), "Stint");
+    if ( dish2::has_series() ) file.AddVal(cfg.SERIES(), "Series");
+    if ( dish2::has_replicate() ) file.AddVal(cfg.REPLICATE(), "Replicate");
+    file.AddVal(cfg.TREATMENT(), "Treatment");
+    if ( cfg.TREATMENT().find('=') != std::string::npos ) {
+      for ( const auto& [k, v] : emp::keyname::unpack( cfg.TREATMENT() ) ) {
+        file.AddVal( v, emp::to_string("Treatment ", k) );
+      }
+    }
+    file.AddVal( uitsl::get_proc_id(), "proc" );
+    file.AddVal( dish2::thread_idx, "thread" );
+
+    file.AddVar(root_id_, "Root ID");
+    file.AddVar(incoming_stint_root_id_, "Incoming Stint Root ID");
+    file.AddVar(outgoing_stint_root_id_, "Outgoing Stint Root ID");
+
+    file.PrintHeaderKeys();
+
+    dish2::log_msg( "initialized stint_root_id record at ", outpath );
+
+  }
+
+  void record_changeover(
+    const uint64_t root_id,
+    const uint64_t incoming_stint_root_id,
+    const uint64_t outgoing_stint_root_id
+  ) {
+
+    root_id_ = root_id;
+    incoming_stint_root_id_ = incoming_stint_root_id;
+    outgoing_stint_root_id_ = outgoing_stint_root_id;
+
+    file.Update();
+
+  }
+
+};
+
+} // namespace dish2
+
+#endif // #ifndef DISH2_RECORD_STINTROOTIDCHANGEOVERRECORDER_HPP_INCLUDE

include/dish2/record/make_filename/make_stint_root_id_changeover_filename.hpp

@@ -0,0 +1,65 @@
+#pragma once
+#ifndef DISH2_RECORD_MAKE_FILENAME_MAKE_STINT_ROOT_ID_CHANGEOVER_FILENAME_HPP_INCLUDE
+#define DISH2_RECORD_MAKE_FILENAME_MAKE_STINT_ROOT_ID_CHANGEOVER_FILENAME_HPP_INCLUDE
+
+#include <cstdlib>
+#include <string>
+
+#include "../../../../third-party/conduit/include/uitsl/mpi/comm_utils.hpp"
+#include "../../../../third-party/Empirical/include/emp/base/macros.hpp"
+#include "../../../../third-party/Empirical/include/emp/tools/keyname_utils.hpp"
+#include "../../../../third-party/Empirical/include/emp/tools/string_utils.hpp"
+
+#include "../../config/cfg.hpp"
+#include "../../config/get_endeavor.hpp"
+#include "../../config/get_repro.hpp"
+#include "../../config/get_slurm_job_id.hpp"
+#include "../../config/has_replicate.hpp"
+#include "../../config/has_series.hpp"
+#include "../../config/has_stint.hpp"
+#include "../../config/thread_idx.hpp"
+
+namespace dish2 {
+
+std::string make_stint_root_id_changeover_filename() {
+  auto keyname_attributes = emp::keyname::unpack_t{
+    {"a", "stint_root_id_changeover"},
+    {"proc", emp::to_string( uitsl::get_proc_id() )},
+    {"_source", EMP_STRINGIFY(DISHTINY_HASH_)},
+    {"thread", emp::to_string( dish2::thread_idx )},
+    {"_treatment", emp::keyname::demote( dish2::cfg.TREATMENT() )},
+    {"ext", ".csv.xz"}
+  };
+
+  if ( dish2::get_repro() ) {
+    keyname_attributes[ "_repro" ] = *dish2::get_repro();
+  }
+
+  if ( dish2::has_series() ) {
+    keyname_attributes[ "series" ] = emp::to_string( cfg.SERIES() );
+  }
+
+  if ( dish2::has_stint() ) {
+    keyname_attributes[ "stint" ] = emp::to_string( cfg.STINT() );
+  }
+
+  if ( dish2::has_replicate() ) {
+    keyname_attributes[ "replicate" ] = cfg.REPLICATE();
+  }
+
+  if ( dish2::get_endeavor() ) {
+    keyname_attributes[ "_endeavor" ] = emp::to_string(*dish2::get_endeavor());
+  }
+
+  if ( dish2::get_slurm_job_id() ) {
+    keyname_attributes[ "_slurm_job_id" ] = emp::to_string(
+      *dish2::get_slurm_job_id()
+    );
+  }
+
+  return emp::keyname::pack( keyname_attributes );
+}
+
+} // namespace dish2
+
+#endif // #ifndef DISH2_RECORD_MAKE_FILENAME_MAKE_STINT_ROOT_ID_CHANGEOVER_FILENAME_HPP_INCLUDE

slurm/evolve/evolvejob.slurm.sh.jinja

@@ -250,6 +250,24 @@ for p in outdata/*a={demographic_phenotypic_phylogenetic_metrics,kin_conflict_st
 
 done
 
+echo "uploading any changeover files..."
+for p in outdata/*a=stint_root_id_changeover*; do
+  f="$(basename "${p}")"
+  echo "uploading ${p} -> ${f}"
+  for retry in {1..20}; do
+    aws s3 cp --quiet \
+      "${p}" \
+      "s3://{{ bucket }}/endeavor=${ENDEAVOR}/evolve/stint-root-id-changeover/stage=0+what=generated/stint={{ stint }}/series={{ series }}/${f}" \
+    && echo "  ${f} upload success" && break \
+    || (echo "retrying ${f} upload (${retry})" && sleep $((RANDOM % 10)))
+    if ((${retry}==20)); then echo "$f upload fail" && exit 123123; fi
+  done & pids+=($!)
+
+  # limit to twenty concurrent upload jobs
+  while (( $(jobs -p | wc -l) > 20 )); do sleep 1; done
+
+done
+
 echo "uploading any asconfigured files..."
 for p in outmeta/*a=asconfigured*.csv*; do
   f="$(basename "${p}")"

slurm/polycultures/polyculturejob.slurm.sh.jinja

@@ -225,6 +225,24 @@ for p in outdata/*a={demographic_phenotypic_phylogenetic_metrics,kin_conflict_st
 
 done
 
+echo "uploading any changeover files..."
+for p in outdata/*a=stint_root_id_changeover*; do
+  f="$(basename "${p}")"
+  echo "uploading ${p} -> ${f}"
+  for retry in {1..20}; do
+    aws s3 cp --quiet \
+      "${p}" \
+      "s3://{{ bucket }}/endeavor=${ENDEAVOR}/polycultures/stint-root-id-changeover/stage=0+what=generated/stint={{ stint }}/series={{ series }}/${f}" \
+    && echo "  ${f} upload success" && break \
+    || (echo "retrying ${f} upload (${retry})" && sleep $((RANDOM % 10)))
+    if ((${retry}==20)); then echo "$f upload fail" && exit 123123; fi
+  done & pids+=($!)
+
+  # limit to twenty concurrent upload jobs
+  while (( $(jobs -p | wc -l) > 20 )); do sleep 1; done
+
+done
+
 echo "uploading any running log files..."
 for p in outdata/*a={birth_log,death_log,spawn_log}*; do
   f="$(basename "${p}")"