[Avida-SVN] r3415 - development/source/main
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Tue Sep 22 12:52:43 PDT 2009
Author: brysonda
Date: 2009-09-22 15:52:43 -0400 (Tue, 22 Sep 2009)
New Revision: 3415
Modified:
development/source/main/cPopulation.cc
development/source/main/cPopulation.h
Log:
Implement execution offset compensation for structured population dumps. This attempts to compensate for the execution state of organisms at the time of the save by boosting first gestation cycle merit accordingly.
Modified: development/source/main/cPopulation.cc
===================================================================
--- development/source/main/cPopulation.cc 2009-09-21 19:33:37 UTC (rev 3414)
+++ development/source/main/cPopulation.cc 2009-09-22 19:52:43 UTC (rev 3415)
@@ -4551,27 +4551,38 @@
}
+struct sOrgInfo {
+ int cell_id;
+ int offset;
+
+ sOrgInfo() { ; }
+ sOrgInfo(int c, int o) : cell_id(c), offset(o) { ; }
+};
+
bool cPopulation::SaveStructuredPopulation(const cString& filename)
{
cDataFile& df = m_world->GetDataFile(filename);
df.WriteRawComment("#filetype genotype_data");
- df.WriteRawComment("#format id parent_id parent2_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence cells");
+ df.WriteRawComment("#format id parent_id parent2_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence cells gest_offset");
df.WriteComment("");
df.WriteComment("Structured Population Dump");
df.WriteTimeStamp();
// Build up hash table of all current genotypes and the cells in which the organisms reside
- tHashTable<int, tKVPair<cGenotype*, tArray<int> >* > genotype_map;
+ tHashTable<int, tKVPair<cGenotype*, tArray<sOrgInfo> >* > genotype_map;
for (int i = 0; i < cell_array.GetSize(); i++) {
if (cell_array[i].IsOccupied()) {
- cGenotype* genotype = cell_array[i].GetOrganism()->GetGenotype();
- tKVPair<cGenotype*, tArray<int> >* map_entry = NULL;
+ cOrganism* org = cell_array[i].GetOrganism();
+ cGenotype* genotype = org->GetGenotype();
+ int offset = org->GetPhenotype().GetCPUCyclesUsed();
+
+ tKVPair<cGenotype*, tArray<sOrgInfo> >* map_entry = NULL;
if (genotype_map.Find(genotype->GetID(), map_entry)) {
- map_entry->Value().Push(i);
+ map_entry->Value().Push(sOrgInfo(i, offset));
} else {
- map_entry = new tKVPair<cGenotype*, tArray<int> >(genotype, tArray<int>(0));
- map_entry->Value().Push(i);
+ map_entry = new tKVPair<cGenotype*, tArray<sOrgInfo> >(genotype, tArray<sOrgInfo>(0));
+ map_entry->Value().Push(sOrgInfo(i, offset));
genotype_map.Add(genotype->GetID(), map_entry);
}
}
@@ -4579,7 +4590,7 @@
// Output all current genotypes
- tArray<tKVPair<cGenotype*, tArray<int> >* > genotype_entries;
+ tArray<tKVPair<cGenotype*, tArray<sOrgInfo> >* > genotype_entries;
genotype_map.GetValues(genotype_entries);
for (int i = 0; i < genotype_entries.GetSize(); i++) {
cGenotype* genotype = genotype_entries[i]->Key();
@@ -4599,13 +4610,17 @@
df.Write(genotype->GetDepth(), "Phylogenetic Depth");
df.Write(genotype->GetGenome().AsString(), "Genome Sequence");
- tArray<int>& cells = genotype_entries[i]->Value();
+ tArray<sOrgInfo>& cells = genotype_entries[i]->Value();
cString cellstr;
- cellstr.Set("%d", cells[0]);
+ cString offsetstr;
+ cellstr.Set("%d", cells[0].cell_id);
+ offsetstr.Set("%d", cells[0].offset);
for (int cell_i = 1; cell_i < cells.GetSize(); cell_i++) {
- cellstr.Set("%s,%d", (const char*)cellstr, cells[cell_i]);
+ cellstr.Set("%s,%d", (const char*)cellstr, cells[cell_i].cell_id);
+ offsetstr.Set("%s,%d", (const char*)offsetstr, cells[cell_i].offset);
}
df.Write(cellstr, "Occupied Cell IDs");
+ df.Write(offsetstr, "Gestation (CPU) Cycle Offsets");
df.Endl();
delete genotype_entries[i];
@@ -4651,7 +4666,7 @@
tmp.total_cpus = cur_line.PopWord().AsInt();
/* length */ cur_line.PopWord();
tmp.merit = cur_line.PopWord().AsDouble();
- /* gest_time */ cur_line.PopWord();
+ tmp.gest_time = cur_line.PopWord().AsDouble();
/* fitness */ cur_line.PopWord();
tmp.update_born = cur_line.PopWord().AsInt();
tmp.update_dead = cur_line.PopWord().AsInt();
@@ -4664,6 +4679,11 @@
while (cellstr.GetSize()) tmp.cells.Push(cellstr.Pop(',').AsInt());
assert(tmp.cells.GetSize() == tmp.num_cpus);
+ // Process gestation time offsets
+ cString offsetstr(cur_line.PopWord());
+ while (offsetstr.GetSize()) tmp.offsets.Push(offsetstr.Pop(',').AsInt());
+ assert(tmp.offsets.GetSize() == tmp.num_cpus);
+
// Don't allow birth or death times larger than the current update
if (update > tmp.update_born) tmp.update_born = update;
if (update > tmp.update_dead) tmp.update_dead = update;
@@ -4723,7 +4743,20 @@
InjectGenotype(cell_id, tmp.genotype);
cPhenotype& phenotype = GetCell(cell_id).GetOrganism()->GetPhenotype();
+
+ // Set the phenotype merit from the save file
if (tmp.merit > 0) phenotype.SetMerit(cMerit(tmp.merit));
+
+ // Adjust initial merit to account for organism execution at the time the population was saved
+ // - this factors the merit by the fraction of the gestation time remaining
+ // - this will be approximate, since gestation time may vary for each organism, but it should work for many cases
+ double gest_remain = tmp.gest_time - (double)tmp.offsets[cell_i];
+ if (gest_remain > 0.0 && tmp.gest_time > 0.0) {
+ double new_merit = phenotype.GetMerit().GetDouble() * (tmp.gest_time / gest_remain);
+ phenotype.SetMerit(cMerit(new_merit));
+ }
+
+ // Schedule the organism
AdjustSchedule(GetCell(cell_id), phenotype.GetMerit());
LineageSetupOrganism(GetCell(cell_id).GetOrganism(), NULL, 0, tmp.genotype->GetParentGenotype());
Modified: development/source/main/cPopulation.h
===================================================================
--- development/source/main/cPopulation.h 2009-09-21 19:33:37 UTC (rev 3414)
+++ development/source/main/cPopulation.h 2009-09-22 19:52:43 UTC (rev 3415)
@@ -353,9 +353,11 @@
int num_cpus;
int total_cpus;
double merit;
+ double gest_time;
int update_born;
int update_dead;
tArray<int> cells;
+ tArray<int> offsets;
cGenotype *genotype;
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