[Avida-SVN] r2762 - in branches/movement/source: actions analyze cpu main platform tools
grabow38 at myxo.css.msu.edu
grabow38 at myxo.css.msu.edu
Wed Aug 27 06:22:24 PDT 2008
Author: grabow38
Date: 2008-08-27 09:22:23 -0400 (Wed, 27 Aug 2008)
New Revision: 2762
Modified:
branches/movement/source/actions/EnvironmentActions.cc
branches/movement/source/actions/PrintActions.cc
branches/movement/source/analyze/cAnalyze.cc
branches/movement/source/analyze/cAnalyzeGenotype.cc
branches/movement/source/analyze/cAnalyzeGenotype.h
branches/movement/source/cpu/cCPUTestInfo.cc
branches/movement/source/cpu/cCPUTestInfo.h
branches/movement/source/cpu/cHardwareExperimental.cc
branches/movement/source/cpu/cHardwareExperimental.h
branches/movement/source/cpu/cHardwareManager.cc
branches/movement/source/cpu/cHardwareManager.h
branches/movement/source/cpu/cTestCPU.cc
branches/movement/source/main/cDemeCellEvent.cc
branches/movement/source/main/cEnvironment.cc
branches/movement/source/main/cLandscape.cc
branches/movement/source/main/cOrganism.cc
branches/movement/source/main/cOrganism.h
branches/movement/source/main/cPhenPlastGenotype.cc
branches/movement/source/main/cPhenPlastGenotype.h
branches/movement/source/main/cPhenotype.cc
branches/movement/source/main/cPhenotype.h
branches/movement/source/main/cTaskLib.cc
branches/movement/source/platform/platform.h
branches/movement/source/tools/cDataFileManager.cc
Log:
Merged development changes r2749:2761 into branches/movement.
Modified: branches/movement/source/actions/EnvironmentActions.cc
===================================================================
--- branches/movement/source/actions/EnvironmentActions.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/actions/EnvironmentActions.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -536,6 +536,33 @@
};
/**
+ Sets resource availiblity to seasonal
+ */
+class cActionSetSeasonalResource : public cAction
+ {
+ private:
+ cString m_res_name;
+
+ public:
+ cActionSetSeasonalResource(cWorld* world, const cString& args): cAction(world, args), m_res_name("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_res_name = largs.PopWord();
+ }
+
+ static const cString GetDescription() { return "Arguments: <string reaction_name>"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ int time = m_world->GetStats().GetUpdate();
+ double m_res_count = -1*(0.4*tanh((time-182500)/50000)+0.5)*(0.5*sin(time/58.091)+0.5)+1;
+ cResource* res = m_world->GetEnvironment().GetResourceLib().GetResource(m_res_name);
+ if (res != NULL) m_world->GetPopulation().SetResource(res->GetID(), m_res_count);
+
+ }
+ };
+
+/**
Sets resource availiblity to periodic
*/
class cActionSetPeriodicResource : public cAction
@@ -850,6 +877,7 @@
action_lib->Register<cActionSetEnvironmentInputs>("SetEnvironmentInputs");
action_lib->Register<cActionSetEnvironmentRandomMask>("SetEnvironmentRandomMask");
+ action_lib->Register<cActionSetSeasonalResource>("SetSeasonalResource");
action_lib->Register<cActionSetPeriodicResource>("SetPeriodicResource");
action_lib->Register<cActionSetNumInstBefore0Energy>("SetNumInstBefore0Energy");
Modified: branches/movement/source/actions/PrintActions.cc
===================================================================
--- branches/movement/source/actions/PrintActions.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/actions/PrintActions.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -1580,6 +1580,8 @@
void Process(cAvidaContext& ctx)
{
+ cCPUTestInfo test_info;
+
if (ctx.GetAnalyzeMode()){ // Analyze mode
cString this_path = m_filename;
ofstream& fot = m_world->GetDataFileOFStream(this_path);
@@ -1587,7 +1589,7 @@
tListIterator<cAnalyzeGenotype> batch_it(m_world->GetAnalyze().GetCurrentBatch().List());
cAnalyzeGenotype* genotype = NULL;
while((genotype = batch_it.Next())){
- const cPhenPlastGenotype* ppgen = new cPhenPlastGenotype(genotype->GetGenome(), m_num_trials, m_world, ctx);
+ const cPhenPlastGenotype* ppgen = new cPhenPlastGenotype(genotype->GetGenome(), m_num_trials, test_info, m_world, ctx);
PrintPPG(fot, ppgen, genotype->GetID(), genotype->GetParentID());
delete ppgen;
}
@@ -1598,7 +1600,7 @@
PrintHeader(fot);
cGenotype* genotype = m_world->GetClassificationManager().GetBestGenotype();
for (int k = 0; k < m_world->GetClassificationManager().GetGenotypeCount(); k++){
- const cPhenPlastGenotype* ppgen = new cPhenPlastGenotype(genotype->GetGenome(), m_num_trials, m_world, ctx);
+ const cPhenPlastGenotype* ppgen = new cPhenPlastGenotype(genotype->GetGenome(), m_num_trials, test_info, m_world, ctx);
PrintPPG(fot, ppgen, genotype->GetID(), genotype->GetParentID());
delete ppgen;
genotype = genotype->GetNext();
Modified: branches/movement/source/analyze/cAnalyze.cc
===================================================================
--- branches/movement/source/analyze/cAnalyze.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/analyze/cAnalyze.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -4723,7 +4723,7 @@
fp << endl;
} else { // if (file_type == FILE_TYPE_HTML) {
- // Mark file as html
+ // Mark file as html
fp << "<html>" << endl;
// Setup any javascript macros needed...
@@ -4743,16 +4743,10 @@
fp << "</head>" << endl;
// Setup the body...
- fp << "<body bgcolor=\"#FFFFFF\"" << endl
- << " text=\"#000000\"" << endl
- << " link=\"#0000AA\"" << endl
- << " alink=\"#0000FF\"" << endl
- << " vlink=\"#000044\">" << endl
- << endl
- << "<h1 align=center>Run " << batch[cur_batch].Name()
- << ", ID " << genotype->GetID() << "</h1>" << endl
- << "<center>" << endl
- << endl;
+ fp << "<body>" << endl
+ << "<div align=\"center\">" << endl
+ << "<h1 align=\"center\">Run " << batch[cur_batch].Name() << ", ID " << genotype->GetID() << "</h1>" << endl
+ << endl;
// Links?
fp << "<table width=90%><tr><td align=left>";
@@ -4836,7 +4830,7 @@
// Print the individual columns...
output_it.Reset();
- tDataEntryCommand<cAnalyzeGenotype> * data_command = NULL;
+ tDataEntryCommand<cAnalyzeGenotype>* data_command = NULL;
int cur_col = 0;
while ((data_command = output_it.Next()) != NULL) {
data_command->SetTarget(&test_genotype);
@@ -4844,9 +4838,6 @@
const cFlexVar test_value = data_command->GetValue();
int compare = CompareFlexStat(test_value, data_command->GetValue(genotype), data_command->GetCompareType());
- // BUG! Either of the next two conditional print commands can
- // cause landscaping to be triggered in a context that causes a crash,
- // notably, if you don't provide any column parameters to MapTasks.. @JEB
if (file_type == FILE_TYPE_HTML) {
HTMLPrintStat(test_value, fp, compare, data_command->GetHtmlCellFlags(), data_command->GetNull(),
!(data_command->HasArg("blank")));
@@ -4882,14 +4873,14 @@
// And close everything up...
fp << "</table>" << endl
- << "</center>" << endl;
+ << "</div>" << endl;
}
delete [] col_pass_count;
delete [] col_fail_count;
m_world->GetDataFileManager().Remove(filename); // Close the data file object
- }
- }
+ }
+}
void cAnalyze::CommandAverageModularity(cString cur_string)
{
Modified: branches/movement/source/analyze/cAnalyzeGenotype.cc
===================================================================
--- branches/movement/source/analyze/cAnalyzeGenotype.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/analyze/cAnalyzeGenotype.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -40,13 +40,15 @@
#include "cWorld.h"
#include "cWorldDriver.h"
+#include "tAutoRelease.h"
+
#include <cmath>
using namespace std;
cAnalyzeGenotype::cAnalyzeGenotype(cWorld* world, cString symbol_string, cInstSet& in_inst_set)
: m_world(world)
, genome(symbol_string)
- , inst_set(in_inst_set)
+ , m_inst_set(in_inst_set)
, name("")
, aligned_sequence("")
, tag("")
@@ -81,11 +83,11 @@
// Make sure that the sequences jive with the inst_set
for (int i = 0; i < genome.GetSize(); i++) {
- if (genome[i].GetOp() >= inst_set.GetSize()) {
+ if (genome[i].GetOp() >= m_inst_set.GetSize()) {
cString msg("Trying to load instruction ");
msg += genome[i].GetOp();
msg += ". Max in set is";
- msg += (inst_set.GetSize() - 1);
+ msg += (m_inst_set.GetSize() - 1);
m_world->GetDriver().RaiseException(msg);
}
}
@@ -94,7 +96,7 @@
cAnalyzeGenotype::cAnalyzeGenotype(cWorld* world, const cGenome& _genome, cInstSet& in_inst_set)
: m_world(world)
, genome(_genome)
- , inst_set(in_inst_set)
+ , m_inst_set(in_inst_set)
, name("")
, aligned_sequence("")
, tag("")
@@ -131,7 +133,7 @@
cAnalyzeGenotype::cAnalyzeGenotype(const cAnalyzeGenotype& _gen)
: m_world(_gen.m_world)
, genome(_gen.genome)
- , inst_set(_gen.inst_set)
+ , m_inst_set(_gen.m_inst_set)
, name(_gen.name)
, aligned_sequence(_gen.aligned_sequence)
, tag(_gen.tag)
@@ -212,7 +214,7 @@
// Calculate the base fitness for the genotype we're working with...
// (This may not have been run already, and cost negligiably more time
// considering the number of knockouts we need to do.
- cAnalyzeGenotype base_genotype(m_world, genome, inst_set);
+ cAnalyzeGenotype base_genotype(m_world, genome, m_inst_set);
base_genotype.Recalculate(ctx);
double base_fitness = base_genotype.GetFitness();
const tArray<int> base_task_counts( base_genotype.GetTaskCounts() );
@@ -227,7 +229,7 @@
cGenome mod_genome(genome);
// Setup a NULL instruction in a special inst set.
- cInstSet ko_inst_set(inst_set);
+ cInstSet ko_inst_set(m_inst_set);
const cInstruction null_inst = ko_inst_set.ActivateNullInst();
// If we are keeping track of the specific effects on tasks from the
@@ -347,7 +349,7 @@
void cAnalyzeGenotype::CheckLand() const
{
if (m_land == NULL) {
- m_land = new cLandscape(m_world, genome, inst_set);
+ m_land = new cLandscape(m_world, genome, m_inst_set);
m_land->SetDistance(1);
m_land->Process(m_world->GetDefaultContext());
}
@@ -356,8 +358,11 @@
void cAnalyzeGenotype::CheckPhenPlast() const
{
// Implicit genotype recalculation if required
- if (m_phenplast_stats == NULL){
- cPhenPlastGenotype pp(genome, 1000, m_world, m_world->GetDefaultContext());
+ if (m_phenplast_stats == NULL) {
+ cCPUTestInfo test_info;
+ test_info.SetInstSet(&m_inst_set);
+
+ cPhenPlastGenotype pp(genome, 1000, test_info, m_world, m_world->GetDefaultContext());
SummarizePhenotypicPlasticity(pp);
}
}
@@ -381,34 +386,26 @@
void cAnalyzeGenotype::CalcLandscape(cAvidaContext& ctx)
{
- if (m_land == NULL) m_land = new cLandscape(m_world, genome, inst_set);
+ if (m_land == NULL) m_land = new cLandscape(m_world, genome, m_inst_set);
m_land->SetDistance(1);
m_land->Process(ctx);
}
void cAnalyzeGenotype::Recalculate(cAvidaContext& ctx, cCPUTestInfo* test_info, cAnalyzeGenotype* parent_genotype, int num_trials)
{
- //Allocate our own test info if it wasn't provided
- cCPUTestInfo* temp_test_info = NULL;
+ // Allocate our own test info if it wasn't provided
+ tAutoRelease<cCPUTestInfo> local_test_info;
if (!test_info)
{
- temp_test_info = new cCPUTestInfo();
- test_info = temp_test_info;
+ test_info = new cCPUTestInfo();
+ local_test_info.Set(test_info);
}
- // @DMB - This does some 'interesting' things with the instruction set
- // Use the inst lib for this genotype... and syncrhonize environment
-
- // Backup old instruction set, update with new
- cInstSet env_inst_set_backup = m_world->GetHardwareManager().GetInstSet();
- m_world->GetHardwareManager().GetInstSet() = inst_set;
+ test_info->SetInstSet(&m_inst_set);
// Handling recalculation here
cPhenPlastGenotype recalc_data(genome, num_trials, *test_info, m_world, ctx);
- // Restore the instruction set
- m_world->GetHardwareManager().GetInstSet() = env_inst_set_backup;
-
// The most likely phenotype will be assigned to the phenotype stats
const cPlasticPhenotype* likely_phenotype = recalc_data.GetMostLikelyPhenotype();
@@ -432,17 +429,12 @@
fitness_ratio = GetFitness() / parent_genotype->GetFitness();
efficiency_ratio = GetEfficiency() / parent_genotype->GetEfficiency();
comp_merit_ratio = GetCompMerit() / parent_genotype->GetCompMerit();
- parent_dist = cStringUtil::EditDistance(genome.AsString(),
- parent_genotype->GetGenome().AsString(), parent_muts);
+ parent_dist = cStringUtil::EditDistance(genome.AsString(), parent_genotype->GetGenome().AsString(), parent_muts);
ancestor_dist = parent_genotype->GetAncestorDist() + parent_dist;
}
// Summarize plasticity information if multiple recalculations performed
- if (num_trials > 1)
- SummarizePhenotypicPlasticity(recalc_data);
-
- //Deallocate if we created
- if (temp_test_info) delete temp_test_info;
+ if (num_trials > 1) SummarizePhenotypicPlasticity(recalc_data);
}
Modified: branches/movement/source/analyze/cAnalyzeGenotype.h
===================================================================
--- branches/movement/source/analyze/cAnalyzeGenotype.h 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/analyze/cAnalyzeGenotype.h 2008-08-27 13:22:23 UTC (rev 2762)
@@ -103,7 +103,7 @@
private:
cWorld* m_world;
cGenome genome; // Full Genome
- cInstSet& inst_set; // Instruction set used in this genome
+ cInstSet& m_inst_set; // Instruction set used in this genome
cString name; // Name, if one was provided in loading
cString aligned_sequence; // Sequence (in ASCII) after alignment
cString tag; // All genotypes in a batch can be tagged
Modified: branches/movement/source/cpu/cCPUTestInfo.cc
===================================================================
--- branches/movement/source/cpu/cCPUTestInfo.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/cpu/cCPUTestInfo.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -33,11 +33,11 @@
cCPUTestInfo::cCPUTestInfo(int max_tests)
: generation_tests(max_tests) // These vars not reset on Clear()
- , trace_execution(false)
, trace_task_order(false)
, use_random_inputs(false)
, use_manual_inputs(false)
, m_tracer(NULL)
+ , m_inst_set(NULL)
, org_array(max_tests)
, m_res_method(RES_INITIAL)
, m_res(NULL)
@@ -73,13 +73,6 @@
}
-void cCPUTestInfo::SetTraceExecution(cHardwareTracer *tracer)
-{
- trace_execution = (tracer)?(true):(false);
- m_tracer = tracer;
-}
-
-
double cCPUTestInfo::GetGenotypeFitness()
{
if (org_array[0] != NULL) return org_array[0]->GetPhenotype().GetFitness();
Modified: branches/movement/source/cpu/cCPUTestInfo.h
===================================================================
--- branches/movement/source/cpu/cCPUTestInfo.h 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/cpu/cCPUTestInfo.h 2008-08-27 13:22:23 UTC (rev 2762)
@@ -39,6 +39,7 @@
#endif
class cHardwareTracer;
+class cInstSet;
class cOrganism;
class cPhenotype;
class cString;
@@ -57,12 +58,12 @@
private:
// Inputs...
const int generation_tests; // Maximum depth in generations to test
- bool trace_execution; // Should we trace this CPU?
bool trace_task_order; // Should we keep track of ordering of tasks?
bool use_random_inputs; // Should we give the organism random inputs?
bool use_manual_inputs; // Do we have inputs that we must use?
tArray<int> manual_inputs; // if so, use these.
cHardwareTracer* m_tracer;
+ cInstSet* m_inst_set;
// Outputs...
bool is_viable; // Is this organism colony forming?
@@ -94,7 +95,8 @@
void UseRandomInputs(bool _rand=true) { use_random_inputs = _rand; use_manual_inputs = false; }
void UseManualInputs(tArray<int> inputs) {use_manual_inputs = true; use_random_inputs = false; manual_inputs = inputs;}
void ResetInputMode() {use_manual_inputs = false; use_random_inputs = false;}
- void SetTraceExecution(cHardwareTracer *tracer = NULL);
+ void SetTraceExecution(cHardwareTracer* tracer = NULL) { m_tracer = tracer; }
+ void SetInstSet(cInstSet* inst_set = NULL) { m_inst_set = inst_set; }
void SetResourceOptions(int res_method = RES_INITIAL, std::vector<std::pair<int, std::vector<double> > > * res = NULL, int update = 0, int cpu_cycle_offset = 0)
{ m_res_method = (eTestCPUResourceMethod)res_method; m_res = res; m_res_update = update; m_res_cpu_cycle_offset = cpu_cycle_offset; }
@@ -103,7 +105,8 @@
int GetGenerationTests() const { return generation_tests; }
bool GetTraceTaskOrder() const { return trace_task_order; }
bool GetUseRandomInputs() const { return use_random_inputs; }
- bool GetTraceExecution() const { return trace_execution; }
+ bool GetTraceExecution() const { return (m_tracer); }
+ cInstSet* GetInstSet() const { return m_inst_set; }
bool GetUseManualInputs() const { return use_manual_inputs; }
tArray<int> GetTestCPUInputs() const { return used_inputs; }
cHardwareTracer *GetTracer() { return m_tracer; }
Modified: branches/movement/source/cpu/cHardwareExperimental.cc
===================================================================
--- branches/movement/source/cpu/cHardwareExperimental.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/cpu/cHardwareExperimental.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -503,9 +503,12 @@
fp << organism->GetPhenotype().GetCPUCyclesUsed() << " ";
fp << "IP:" << IP().GetPosition() << " ";
+
for (int i = 0; i < NUM_REGISTERS; i++) {
+ sInternalValue& reg = m_threads[m_cur_thread].reg[i];
fp << static_cast<char>('A' + i) << "X:" << GetRegister(i) << " ";
- fp << setbase(16) << "[0x" << GetRegister(i) << "] " << setbase(10);
+ fp << setbase(16) << "[0x" << reg.value << "] " << setbase(10);
+ fp << "(" << reg.from_env << " " << reg.env_component << " " << reg.originated << " " << reg.oldest_component << ") ";
}
// Add some extra information if additional time costs are used for instructions,
@@ -520,6 +523,7 @@
<< "W-Head:" << GetHead(nHardware::HEAD_WRITE).GetPosition() << " "
<< "F-Head:" << GetHead(nHardware::HEAD_FLOW).GetPosition() << " "
<< "RL:" << GetReadLabel().AsString() << " "
+ << "Ex:" << m_last_output
<< endl;
int number_of_stacks = GetNumStacks();
Modified: branches/movement/source/cpu/cHardwareExperimental.h
===================================================================
--- branches/movement/source/cpu/cHardwareExperimental.h 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/cpu/cHardwareExperimental.h 2008-08-27 13:22:23 UTC (rev 2762)
@@ -530,7 +530,7 @@
dest.from_env = false;
dest.originated = m_cycle_count;
dest.oldest_component = src.oldest_component;
- dest.env_component = src.from_env;
+ dest.env_component = src.env_component;
}
Modified: branches/movement/source/cpu/cHardwareManager.cc
===================================================================
--- branches/movement/source/cpu/cHardwareManager.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/cpu/cHardwareManager.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -82,22 +82,22 @@
}
-cHardwareBase* cHardwareManager::Create(cOrganism* in_org)
+cHardwareBase* cHardwareManager::Create(cOrganism* in_org, cInstSet* inst_set)
{
assert(in_org != NULL);
switch (m_type)
{
case HARDWARE_TYPE_CPU_ORIGINAL:
- return new cHardwareCPU(m_world, in_org, m_inst_set);
+ return new cHardwareCPU(m_world, in_org, inst_set);
case HARDWARE_TYPE_CPU_SMT:
- return new cHardwareSMT(m_world, in_org, m_inst_set);
+ return new cHardwareSMT(m_world, in_org, inst_set);
case HARDWARE_TYPE_CPU_TRANSSMT:
- return new cHardwareTransSMT(m_world, in_org, m_inst_set);
+ return new cHardwareTransSMT(m_world, in_org, inst_set);
case HARDWARE_TYPE_CPU_EXPERIMENTAL:
- return new cHardwareExperimental(m_world, in_org, m_inst_set);
+ return new cHardwareExperimental(m_world, in_org, inst_set);
case HARDWARE_TYPE_CPU_GX:
- return new cHardwareGX(m_world, in_org, m_inst_set);
+ return new cHardwareGX(m_world, in_org, inst_set);
default:
return NULL;
}
Modified: branches/movement/source/cpu/cHardwareManager.h
===================================================================
--- branches/movement/source/cpu/cHardwareManager.h 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/cpu/cHardwareManager.h 2008-08-27 13:22:23 UTC (rev 2762)
@@ -61,7 +61,8 @@
cHardwareManager(cWorld* world);
~cHardwareManager() { ; }
- cHardwareBase* Create(cOrganism* in_org);
+ cHardwareBase* Create(cOrganism* in_org, cInstSet* inst_set);
+ inline cHardwareBase* Create(cOrganism* in_org) { return Create(in_org, m_inst_set); }
cTestCPU* CreateTestCPU() { return new cTestCPU(m_world); }
const cInstSet& GetInstSet() const { return *m_inst_set; }
Modified: branches/movement/source/cpu/cTestCPU.cc
===================================================================
--- branches/movement/source/cpu/cTestCPU.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/cpu/cTestCPU.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -359,10 +359,13 @@
if (test_info.org_array[cur_depth] != NULL) {
delete test_info.org_array[cur_depth];
}
- test_info.org_array[cur_depth] = new cOrganism(m_world, ctx, genome);
- cOrganism & organism = *( test_info.org_array[cur_depth] );
- organism.SetOrgInterface(new cTestCPUInterface(this));
- organism.GetPhenotype().SetupInject(genome);
+ cOrganism* organism = NULL;
+
+ if (test_info.GetInstSet()) organism = new cOrganism(m_world, ctx, genome, test_info.GetInstSet());
+ else organism = new cOrganism(m_world, ctx, genome);
+ test_info.org_array[cur_depth] = organism;
+ organism->SetOrgInterface(new cTestCPUInterface(this));
+ organism->GetPhenotype().SetupInject(genome);
// Run the current organism.
ProcessGestation(ctx, test_info, cur_depth);
@@ -377,10 +380,10 @@
// 4: It copied false => we must check the child.
// Case 1: ////////////////////////////////////
- if (organism.GetPhenotype().GetNumDivides() == 0) return false;
+ if (organism->GetPhenotype().GetNumDivides() == 0) return false;
// Case 2: ////////////////////////////////////
- if (organism.GetPhenotype().CopyTrue() == true) {
+ if (organism->GetPhenotype().CopyTrue() == true) {
test_info.depth_found = cur_depth;
test_info.is_viable = true;
return true;
@@ -389,7 +392,7 @@
// Case 3: ////////////////////////////////////
bool is_ancestor = false;
for (int anc_depth = 0; anc_depth < cur_depth; anc_depth++) {
- if (organism.ChildGenome() == test_info.org_array[anc_depth]->GetGenome()){
+ if (organism->ChildGenome() == test_info.org_array[anc_depth]->GetGenome()){
is_ancestor = true;
const int cur_cycle = cur_depth - anc_depth;
if (test_info.max_cycle < cur_cycle) test_info.max_cycle = cur_cycle;
@@ -406,7 +409,7 @@
// If we haven't reached maximum depth yet, check out the child.
if (cur_depth+1 < test_info.generation_tests) {
// Run the child's genome.
- return TestGenome_Body(ctx, test_info, organism.ChildGenome(), cur_depth+1);
+ return TestGenome_Body(ctx, test_info, organism->ChildGenome(), cur_depth+1);
}
// All options have failed; just return false.
Modified: branches/movement/source/main/cDemeCellEvent.cc
===================================================================
--- branches/movement/source/main/cDemeCellEvent.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cDemeCellEvent.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -11,11 +11,11 @@
, m_event_width(x2-x1)
, m_event_height(y2-y1)
, m_active(false)
+ , m_static_pos(static_pos)
, m_dead(false)
- , m_static_pos(static_pos)
+ , m_id_set(false)
, m_deme(deme)
, m_world(world)
- , m_id_set(false)
{
assert(x1 <= x2);
assert(y1 <= y2);
Modified: branches/movement/source/main/cEnvironment.cc
===================================================================
--- branches/movement/source/main/cEnvironment.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cEnvironment.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -1043,7 +1043,7 @@
if (cur_process->GetDemeFraction()) {
deme_bonus = cur_process->GetDemeFraction() * bonus;
bonus = (1-cur_process->GetDemeFraction()) * bonus;
- }
+ }
// Take care of the organism's bonus:
switch (cur_process->GetType()) {
Modified: branches/movement/source/main/cLandscape.cc
===================================================================
--- branches/movement/source/main/cLandscape.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cLandscape.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -38,11 +38,12 @@
#include "cWorld.h"
-cLandscape::cLandscape(cWorld* world, const cGenome & in_genome, const cInstSet & in_inst_set)
+cLandscape::cLandscape(cWorld* world, const cGenome& in_genome, const cInstSet& in_inst_set)
: m_world(world), inst_set(in_inst_set), base_genome(1), peak_genome(1), trials(1), m_min_found(0),
m_max_trials(0), site_count(NULL)
{
Reset(in_genome);
+ test_info.SetInstSet(const_cast<cInstSet*>(&inst_set));
}
cLandscape::~cLandscape()
@@ -777,7 +778,6 @@
pos_frac = GetProbPos();
// Print the information on the current best.
- cCPUTestInfo test_info;
testcpu->TestGenome(ctx, test_info, cur_genome);
cPhenotype& colony_phenotype = test_info.GetColonyOrganism()->GetPhenotype();
df.Write(gen, "Generation");
Modified: branches/movement/source/main/cOrganism.cc
===================================================================
--- branches/movement/source/main/cOrganism.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cOrganism.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -77,10 +77,47 @@
, m_msg(0)
, m_opinion(0)
{
- // Initialization of structures...
m_hardware = m_world->GetHardwareManager().Create(this);
-// m_cpu_stats.Setup();
+ initialize(ctx);
+}
+
+cOrganism::cOrganism(cWorld* world, cAvidaContext& ctx, const cGenome& in_genome, cInstSet* inst_set)
+ : m_world(world)
+ , m_genotype(NULL)
+ , m_phenotype(world)
+ , m_initial_genome(in_genome)
+ , m_mut_info(world->GetEnvironment().GetMutationLib(), in_genome.GetSize())
+ , m_interface(NULL)
+ , m_lineage_label(-1)
+ , m_lineage(NULL)
+ , m_input_pointer(0)
+ , m_input_buf(world->GetEnvironment().GetInputSize())
+ , m_output_buf(world->GetEnvironment().GetOutputSize())
+ , m_received_messages(RECEIVED_MESSAGES_SIZE)
+ , m_sent_value(0)
+ , m_sent_active(false)
+ , m_test_receive_pos(0)
+ , m_pher_drop(false)
+ , m_max_executed(-1)
+ , m_is_running(false)
+ , m_is_sleeping(false)
+ , m_is_dead(false)
+ , killed_event(false)
+ , m_net(NULL)
+ , m_msg(0)
+ , m_opinion(0)
+{
+ m_hardware = m_world->GetHardwareManager().Create(this, inst_set);
+
+ initialize(ctx);
+}
+
+
+void cOrganism::initialize(cAvidaContext& ctx)
+{
+ m_phenotype.SetInstSetSize(m_hardware->GetInstSet().GetSize());
+
if (m_world->GetConfig().DEATH_METHOD.Get() > DEATH_METHOD_OFF) {
m_max_executed = m_world->GetConfig().AGE_LIMIT.Get();
if (m_world->GetConfig().AGE_DEVIATION.Get() > 0.0) {
@@ -89,13 +126,13 @@
if (m_world->GetConfig().DEATH_METHOD.Get() == DEATH_METHOD_MULTIPLE) {
m_max_executed *= m_initial_genome.GetSize();
}
-
+
// m_max_executed must be positive or an organism will not die!
if (m_max_executed < 1) m_max_executed = 1;
}
if (m_world->GetConfig().NET_ENABLED.Get()) m_net = new cNetSupport();
- m_id = m_world->GetStats().GetTotCreatures();
+ m_id = m_world->GetStats().GetTotCreatures();
}
Modified: branches/movement/source/main/cOrganism.h
===================================================================
--- branches/movement/source/main/cOrganism.h 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cOrganism.h 2008-08-27 13:22:23 UTC (rev 2762)
@@ -80,6 +80,7 @@
class cGenotype;
class cHardwareBase;
class cInjectGenotype;
+class cInstSet;
class cLineage;
class cOrgSinkMessage;
class cSaleItem;
@@ -104,8 +105,7 @@
int cclade_id; // @MRR Coalescence clade information (set in cPopulation)
// Other stats
- cCPUMemory m_child_genome; // Child genome, while under construction.
-// sCPUStats m_cpu_stats; // Info for statistics
+ cCPUMemory m_child_genome; // Child genome, while under construction.
// Input and Output with the environment
int m_input_pointer;
@@ -146,12 +146,16 @@
};
cNetSupport* m_net;
+
+ void initialize(cAvidaContext& ctx);
+
cOrganism(); // @not_implemented
cOrganism(const cOrganism&); // @not_implemented
cOrganism& operator=(const cOrganism&); // @not_implemented
public:
cOrganism(cWorld* world, cAvidaContext& ctx, const cGenome& in_genome);
+ cOrganism(cWorld* world, cAvidaContext& ctx, const cGenome& in_genome, cInstSet* inst_set);
~cOrganism();
// -------- Accessor Methods --------
@@ -184,7 +188,6 @@
int GetMaxExecuted() const { return m_max_executed; }
cCPUMemory& ChildGenome() { return m_child_genome; }
-// sCPUStats& CPUStats() { return m_cpu_stats; }
void SetRunning(bool in_running) { m_is_running = in_running; }
bool IsRunning() { return m_is_running; }
@@ -439,16 +442,5 @@
};
-#ifdef ENABLE_UNIT_TESTS
-namespace nOrganism {
- /**
- * Run unit tests
- *
- * @param full Run full test suite; if false, just the fast tests.
- **/
- void UnitTests(bool full = false);
-}
-#endif
-
#endif
Modified: branches/movement/source/main/cPhenPlastGenotype.cc
===================================================================
--- branches/movement/source/main/cPhenPlastGenotype.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cPhenPlastGenotype.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -26,14 +26,6 @@
#include <iostream>
#include <cmath>
-cPhenPlastGenotype::cPhenPlastGenotype(const cGenome& in_genome, int num_trials, cWorld* world, cAvidaContext& ctx)
-: m_genome(in_genome), m_num_trials(num_trials), m_world(world)
-{
- cCPUTestInfo test_info;
- test_info.UseRandomInputs(true);
- Process(test_info, world, ctx);
-}
-
cPhenPlastGenotype::cPhenPlastGenotype(const cGenome& in_genome, int num_trials, cCPUTestInfo& test_info, cWorld* world, cAvidaContext& ctx)
: m_genome(in_genome), m_num_trials(num_trials), m_world(world)
{
Modified: branches/movement/source/main/cPhenPlastGenotype.h
===================================================================
--- branches/movement/source/main/cPhenPlastGenotype.h 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cPhenPlastGenotype.h 2008-08-27 13:22:23 UTC (rev 2762)
@@ -82,7 +82,6 @@
void Process(cCPUTestInfo& test_info, cWorld* world, cAvidaContext& ctx);
public:
- cPhenPlastGenotype(const cGenome& in_genome, int num_trials, cWorld* world, cAvidaContext& ctx);
cPhenPlastGenotype(const cGenome& in_genome, int num_trails, cCPUTestInfo& test_info, cWorld* world, cAvidaContext& ctx);
~cPhenPlastGenotype();
Modified: branches/movement/source/main/cPhenotype.cc
===================================================================
--- branches/movement/source/main/cPhenotype.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cPhenotype.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -28,7 +28,6 @@
#include "cEnvironment.h"
#include "cDeme.h"
#include "cHardwareManager.h"
-#include "cInstSet.h"
#include "cReactionResult.h"
#include "cTaskState.h"
#include "cTools.h"
@@ -49,7 +48,6 @@
, cur_task_value(m_world->GetEnvironment().GetNumTasks())
, cur_reaction_count(m_world->GetEnvironment().GetReactionLib().GetSize())
, cur_reaction_add_reward(m_world->GetEnvironment().GetReactionLib().GetSize())
- , cur_inst_count(world->GetHardwareManager().GetInstSet().GetSize())
, cur_sense_count(m_world->GetStats().GetSenseSize())
, sensed_resources(m_world->GetEnvironment().GetResourceLib().GetSize())
, cur_task_time(m_world->GetEnvironment().GetNumTasks()) // Added for tracking time; WRE 03-18-07
@@ -58,7 +56,6 @@
, last_task_value(m_world->GetEnvironment().GetNumTasks())
, last_reaction_count(m_world->GetEnvironment().GetReactionLib().GetSize())
, last_reaction_add_reward(m_world->GetEnvironment().GetReactionLib().GetSize())
- , last_inst_count(world->GetHardwareManager().GetInstSet().GetSize())
, last_sense_count(m_world->GetStats().GetSenseSize())
, target_best_dist(100000) // @LMG for movement tracking
{
@@ -256,7 +253,7 @@
assert(age >= 0);
assert(child_copied_size >= 0);
// assert(to_die == false);
- return true;
+ return (m_world);
}
@@ -1148,222 +1145,8 @@
}
-///// For Loading and Saving State: /////
-bool cPhenotype::SaveState(ofstream& fp)
-{
- assert(fp.good());
- fp << "cPhenotype" << endl;
-
- fp << merit.GetDouble() << " ";
- fp << genome_length << " ";
- fp << copied_size << " ";
- fp << executed_size << " ";
- fp << gestation_time << " ";
- fp << gestation_start << " ";
- fp << fitness << " ";
- fp << div_type << " ";
-
- fp << cur_bonus << " ";
- fp << cur_num_errors << " ";
- fp << cur_num_donates << " ";
- for (int i = 0; i < cur_task_count.GetSize(); i++) {
- fp << cur_task_count[i] << " ";
- }
- for (int i = 0; i < cur_reaction_count.GetSize(); i++) {
- fp << cur_reaction_count[i] << " ";
- }
- for (int i = 0; i < cur_inst_count.GetSize(); i++) {
- fp << cur_inst_count[i] << " ";
- }
-
- fp << last_merit_base << " ";
- fp << last_bonus << " ";
- fp << last_num_errors << " ";
- fp << last_num_donates << " ";
- for (int i = 0; i < last_task_count.GetSize(); i++) {
- fp << last_task_count[i] << " ";
- }
- for (int i = 0; i < last_reaction_count.GetSize(); i++) {
- fp << last_reaction_count[i] << " ";
- }
- for (int i = 0; i < last_inst_count.GetSize(); i++) {
- fp << last_inst_count[i] << " ";
- }
-
- fp << num_divides << " ";
- fp << generation << " ";
- fp << cpu_cycles_used << " ";
- fp << time_used << " ";
- fp << age << " ";
- fp << neutral_metric << " ";
- fp << life_fitness << " ";
-
- fp << is_injected << " ";
- fp << is_donor_last << " ";
- fp << is_donor_cur << " ";
- fp << is_donor_rand_last << " ";
- fp << is_donor_rand << " ";
- fp << is_donor_null_last << " ";
- fp << is_donor_null << " ";
- fp << is_donor_kin_last << " ";
- fp << is_donor_kin << " ";
- fp << is_donor_edit_last << " ";
- fp << is_donor_edit << " ";
- fp << is_donor_gbg_last << " ";
- fp << is_donor_gbg << " ";
- fp << is_donor_truegb_last << " ";
- fp << is_donor_truegb << " ";
- fp << is_donor_threshgb_last << " ";
- fp << is_donor_threshgb << " ";
- fp << is_donor_quanta_threshgb_last << " ";
- fp << is_donor_quanta_threshgb << " ";
- fp << num_thresh_gb_donations_last << " ";
- fp << num_thresh_gb_donations << " ";
- fp << num_quanta_thresh_gb_donations_last << " ";
- fp << num_quanta_thresh_gb_donations << " ";
-
- fp << is_receiver_last << " ";
- fp << is_receiver << " ";
- fp << is_receiver_rand << " ";
- fp << is_receiver_kin << " ";
- fp << is_receiver_kin_last << " ";
- fp << is_receiver_edit << " ";
- fp << is_receiver_edit_last << " ";
- fp << is_receiver_gbg << " ";
- fp << is_receiver_truegb_last << " ";
- fp << is_receiver_truegb << " ";
- fp << is_receiver_threshgb_last << " ";
- fp << is_receiver_threshgb << " ";
- fp << is_receiver_quanta_threshgb_last << " ";
- fp << is_receiver_quanta_threshgb << " ";
- fp << is_modifier << " ";
- fp << is_modified << " ";
- fp << is_fertile << " ";
- fp << is_mutated << " ";
- fp << parent_true << " ";
- fp << parent_sex << " ";
- fp << parent_cross_num << " ";
-
- fp << copy_true << " ";
- fp << divide_sex << " ";
- fp << mate_select_id << " ";
- fp << cross_num << " ";
- fp << child_fertile << " ";
- fp << last_child_fertile << " ";
-
- fp << endl;
- return true;
-}
-
-
-bool cPhenotype::LoadState(ifstream & fp)
-{
- double tmp_merit;
- assert(fp.good());
- if( !fp.good() ) return false;
-
- fp >> tmp_merit; merit = tmp_merit;
- fp >> genome_length;
- fp >> copied_size;
- fp >> executed_size;
- fp >> gestation_time;
- fp >> gestation_start;
- fp >> fitness;
- fp >> div_type;
-
- fp >> cur_bonus;
- fp >> cur_num_errors;
- fp >> cur_num_donates;
-
- for (int i = 0; i < cur_task_count.GetSize(); i++) {
- fp >> cur_task_count[i];
- }
- for (int i = 0; i < cur_reaction_count.GetSize(); i++) {
- fp >> cur_reaction_count[i];
- }
- for (int i = 0; i < cur_inst_count.GetSize(); i++) {
- fp >> cur_inst_count[i];
- }
-
- fp >> last_merit_base;
- fp >> last_bonus;
- fp >> last_num_errors;
- fp >> last_num_donates;
- for (int i = 0; i < last_task_count.GetSize(); i++) {
- fp >> last_task_count[i];
- }
- for (int i = 0; i < last_reaction_count.GetSize(); i++) {
- fp >> last_reaction_count[i];
- }
- for (int i = 0; i < last_inst_count.GetSize(); i++) {
- fp >> last_inst_count[i];
- }
-
- fp >> num_divides;
- fp >> generation;
- fp >> cpu_cycles_used;
- fp >> time_used;
- fp >> age;
- fp >> neutral_metric;
- fp >> life_fitness;
-
- fp >> is_injected;
- fp >> is_donor_last;
- fp >> is_donor_cur;
- fp >> is_donor_rand_last;
- fp >> is_donor_rand;
- fp >> is_donor_null_last;
- fp >> is_donor_null;
- fp >> is_donor_kin_last;
- fp >> is_donor_kin;
- fp >> is_donor_edit_last;
- fp >> is_donor_edit;
- fp >> is_donor_gbg_last;
- fp >> is_donor_gbg;
- fp >> is_donor_truegb_last;
- fp >> is_donor_truegb;
- fp >> is_donor_threshgb_last;
- fp >> is_donor_threshgb;
- fp >> is_donor_quanta_threshgb_last;
- fp >> is_donor_quanta_threshgb;
- fp >> num_thresh_gb_donations_last;
- fp >> num_thresh_gb_donations;
- fp >> num_quanta_thresh_gb_donations_last;
- fp >> num_quanta_thresh_gb_donations;
- fp >> is_receiver_last;
- fp >> is_receiver;
- fp >> is_receiver_rand;
- fp >> is_receiver_kin;
- fp >> is_receiver_kin_last;
- fp >> is_receiver_edit;
- fp >> is_receiver_edit_last;
- fp >> is_receiver_gbg;
- fp >> is_receiver_truegb_last;
- fp >> is_receiver_truegb;
- fp >> is_receiver_threshgb_last;
- fp >> is_receiver_threshgb;
- fp >> is_receiver_quanta_threshgb_last;
- fp >> is_receiver_quanta_threshgb;
- fp >> is_modifier;
- fp >> is_modified;
- fp >> is_fertile;
- fp >> is_mutated;
- fp >> parent_true;
- fp >> parent_sex;
- fp >> parent_cross_num;
-
- fp >> copy_true;
- fp >> divide_sex;
- fp >> mate_select_id;
- fp >> cross_num;
- fp >> child_fertile;
- fp >> last_child_fertile;
-
- return true;
-}
-
void cPhenotype::PrintStatus(ostream& fp) const
{
fp << " MeritBase:"
Modified: branches/movement/source/main/cPhenotype.h
===================================================================
--- branches/movement/source/main/cPhenotype.h 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cPhenotype.h 2008-08-27 13:22:23 UTC (rev 2762)
@@ -86,6 +86,7 @@
class cPhenotype
{
+ friend class cOrganism;
private:
cWorld* m_world;
bool initialized;
@@ -231,12 +232,20 @@
// 7. Information that is set once (when organism was born)
double permanent_germline_propensity;
+
+ inline void SetInstSetSize(int inst_set_size);
+
+
+ cPhenotype(cWorld* world);
+
+
public:
- cPhenotype() { ; } // @not_implemented
- cPhenotype(cWorld* world);
+ cPhenotype() : m_world(NULL) { ; } // Will not construct a valid cPhenotype! Only exists to support incorrect cDeme tArray usage.
+
cPhenotype(const cPhenotype&);
cPhenotype& operator=(const cPhenotype&);
~cPhenotype();
+
bool OK();
@@ -263,8 +272,6 @@
tArray<int>& insts_triggered);
// State saving and loading, and printing...
- bool SaveState(std::ofstream& fp);
- bool LoadState(std::ifstream & fp);
void PrintStatus(std::ostream& fp) const;
// Some useful methods...
@@ -520,15 +527,10 @@
};
-#ifdef ENABLE_UNIT_TESTS
-namespace nPhenotype {
- /**
- * Run unit tests
- *
- * @param full Run full test suite; if false, just the fast tests.
- **/
- void UnitTests(bool full = false);
+inline void cPhenotype::SetInstSetSize(int inst_set_size)
+{
+ cur_inst_count.Resize(inst_set_size, 0);
+ last_inst_count.Resize(inst_set_size, 0);
}
-#endif
#endif
Modified: branches/movement/source/main/cTaskLib.cc
===================================================================
--- branches/movement/source/main/cTaskLib.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/main/cTaskLib.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -49,6 +49,11 @@
# define log2(x) (log(x)/log(2.0))
#endif
+// Various workarounds for FreeBSD
+#if AVIDA_PLATFORM(FREEBSD)
+# define log2(x) (log(x)/log(2.0))
+#endif
+
static const double dCastPrecision = 100000.0;
Modified: branches/movement/source/platform/platform.h
===================================================================
--- branches/movement/source/platform/platform.h 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/platform/platform.h 2008-08-27 13:22:23 UTC (rev 2762)
@@ -39,11 +39,15 @@
# pragma warning( disable : 4355 )
#endif
-#if defined(__APPLE__) || defined(unix) || defined(__unix) || defined(__unix__) || defined (__NetBSD__) || defined(_AIX)
+#if defined(__APPLE__) || defined(unix) || defined(__unix) || defined(__unix__) || defined (__NetBSD__) || defined(_AIX) || defined(__FreeBSD__)
# define AVIDA_PLATFORM_UNIX 1
# define AVIDA_PLATFORM_THREADS 1
#endif
+#if defined(__FreeBSD__)
+# define AVIDA_PLATFORM_FREEBSD 1
+#endif
+
#if defined(__APPLE__)
# define AVIDA_PLATFORM_APPLE 1
#endif
Modified: branches/movement/source/tools/cDataFileManager.cc
===================================================================
--- branches/movement/source/tools/cDataFileManager.cc 2008-08-27 07:28:06 UTC (rev 2761)
+++ branches/movement/source/tools/cDataFileManager.cc 2008-08-27 13:22:23 UTC (rev 2762)
@@ -96,7 +96,11 @@
if (d == -1) break;
// If directory name is not null
- if (d - i > 0) cTools::MkDir(dir_prefix + target.Substring(0, d - i), false);
+ if (d - i > 0) {
+ cString dir = target.Substring(i, d - i);
+ // Create if that this directory is not a relative path component
+ if (dir.GetSize() > 2 || (dir != "." && dir != "..")) cTools::MkDir(dir_prefix + target.Substring(0, d), false);
+ }
// Adjust next directory name starting point
i = d + 1;
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