[Avida-SVN] r1861 - development/source/analyze
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Sun Jul 29 17:55:46 PDT 2007
Author: brysonda
Date: 2007-07-29 20:55:46 -0400 (Sun, 29 Jul 2007)
New Revision: 1861
Modified:
development/source/analyze/cMutationalNeighborhood.cc
development/source/analyze/cMutationalNeighborhood.h
Log:
MutationalNeighborhood: Rework Two Step point mutation calculations to use ProcessTwoStepGenome function. Move pending lists into sTwoStep structure to avoid possible race condition where two threads may attempt to write to the list simultaneously.
Modified: development/source/analyze/cMutationalNeighborhood.cc
===================================================================
--- development/source/analyze/cMutationalNeighborhood.cc 2007-07-27 20:22:35 UTC (rev 1860)
+++ development/source/analyze/cMutationalNeighborhood.cc 2007-07-30 00:55:46 UTC (rev 1861)
@@ -261,7 +261,7 @@
int cur_site, cGenome& mod_genome)
{
const int inst_size = m_inst_set.GetSize();
- sStep& tdata = m_twostep_point[cur_site];
+ sTwoStep& tdata = m_twostep_point[cur_site];
// Loop through remaining lines of genome, testing trying all combinations.
for (int line_num = cur_site + 1; line_num < m_base_genome.GetSize(); line_num++) {
@@ -272,57 +272,7 @@
if (cur_inst == inst_num) continue;
mod_genome[line_num].SetOp(inst_num);
- testcpu->TestGenome(ctx, test_info, mod_genome);
-
- double test_fitness = test_info.GetColonyFitness();
-
- tdata.total_fitness += test_fitness;
- tdata.total_sqr_fitness += test_fitness * test_fitness;
- tdata.total++;
- if (test_fitness == 0.0) {
- tdata.dead++;
- } else if (test_fitness < m_neut_min) {
- tdata.neg++;
- tdata.size_neg += test_fitness;
- } else if (test_fitness <= m_neut_max) {
- tdata.neut++;
- } else {
- tdata.pos++;
- tdata.size_pos += test_fitness;
- if (test_fitness > tdata.peak_fitness) {
- tdata.peak_fitness = test_fitness;
- tdata.peak_genome = mod_genome;
- }
- }
-
- if (test_fitness >= m_neut_min) tdata.site_count[line_num]++;
-
- if (test_fitness != 0.0) { // Only count tasks if the organism is alive
- const tArray<int>& cur_tasks = test_info.GetColonyOrganism()->GetPhenotype().GetLastTaskCount();
- bool knockout = false;
- bool anytask = false;
- for (int i = 0; i < m_base_tasks.GetSize(); i++) {
- if (m_base_tasks[i] && !cur_tasks[i]) knockout = true;
- else if (!m_base_tasks[i] && cur_tasks[i]) anytask = true;
- }
- if (knockout) {
- tdata.task_knockout++;
- tdata.task_size_knockout += test_fitness;
- }
- if (anytask) {
- tdata.task_total++;
- tdata.task_size_total += test_fitness;
- }
- if (m_base_tasks.GetSize() && !m_base_tasks[m_target] && cur_tasks[m_target]) {
- tdata.task_target++;
- tdata.task_size_target += test_fitness;
-
- // Push both instructions as possible first mutations, for post determination of first step fitness effect
- m_pending.Push(new sPendingTarget(cur_site, mod_genome[cur_site].GetOp()));
- m_pending.Push(new sPendingTarget(line_num, inst_num));
- }
- }
-
+ ProcessTwoStepGenome(ctx, testcpu, test_info, mod_genome, tdata, line_num, cur_site);
}
mod_genome[line_num].SetOp(cur_inst);
@@ -330,6 +280,65 @@
}
+double cMutationalNeighborhood::ProcessTwoStepGenome(cAvidaContext& ctx, cTestCPU* testcpu, cCPUTestInfo& test_info,
+ const cGenome& mod_genome, sTwoStep& tdata, int cur_site, int oth_site)
+{
+ // Run the modified genome through the Test CPU
+ testcpu->TestGenome(ctx, test_info, mod_genome);
+
+ // Collect the calculated fitness
+ double test_fitness = test_info.GetColonyFitness();
+
+ tdata.total_fitness += test_fitness;
+ tdata.total_sqr_fitness += test_fitness * test_fitness;
+ tdata.total++;
+ if (test_fitness == 0.0) {
+ tdata.dead++;
+ } else if (test_fitness < m_neut_min) {
+ tdata.neg++;
+ tdata.size_neg += test_fitness;
+ } else if (test_fitness <= m_neut_max) {
+ tdata.neut++;
+ } else {
+ tdata.pos++;
+ tdata.size_pos += test_fitness;
+ if (test_fitness > tdata.peak_fitness) {
+ tdata.peak_fitness = test_fitness;
+ tdata.peak_genome = mod_genome;
+ }
+ }
+
+ if (test_fitness >= m_neut_min) tdata.site_count[cur_site]++;
+
+ if (test_fitness != 0.0) { // Only count tasks if the organism is alive
+ const tArray<int>& cur_tasks = test_info.GetColonyOrganism()->GetPhenotype().GetLastTaskCount();
+ bool knockout = false;
+ bool anytask = false;
+ for (int i = 0; i < m_base_tasks.GetSize(); i++) {
+ if (m_base_tasks[i] && !cur_tasks[i]) knockout = true;
+ else if (!m_base_tasks[i] && cur_tasks[i]) anytask = true;
+ }
+ if (knockout) {
+ tdata.task_knockout++;
+ tdata.task_size_knockout += test_fitness;
+ }
+ if (anytask) {
+ tdata.task_total++;
+ tdata.task_size_total += test_fitness;
+ }
+ if (m_base_tasks.GetSize() && !m_base_tasks[m_target] && cur_tasks[m_target]) {
+ tdata.task_target++;
+ tdata.task_size_target += test_fitness;
+
+ // Push both instructions as possible first mutations, for post determination of first step fitness effect
+ tdata.pending.Push(new sPendingTarget(oth_site, mod_genome[oth_site].GetOp()));
+ tdata.pending.Push(new sPendingTarget(cur_site, mod_genome[cur_site].GetOp()));
+ }
+ }
+
+ return test_fitness;
+}
+
void cMutationalNeighborhood::ProcessComplete(cAvidaContext& ctx)
{
m_op.peak_fitness = m_base_fitness;
@@ -385,12 +394,14 @@
// Initialize values
+ sPendingTarget* pend = NULL;
+
m_tp.peak_fitness = m_base_fitness;
m_tp.peak_genome = m_base_genome;
m_tp.site_count.Resize(m_base_genome.GetSize(), 0);
for (int i = 0; i < m_twostep_point.GetSize(); i++) {
- sStep& tdata = m_twostep_point[i];
+ sTwoStep& tdata = m_twostep_point[i];
m_tp.total += tdata.total;
m_tp.total_fitness += tdata.total_fitness;
m_tp.total_sqr_fitness += tdata.total_sqr_fitness;
@@ -418,6 +429,24 @@
m_tp.task_size_target += tdata.task_size_target;
m_tp.task_size_total += tdata.task_size_total;
m_tp.task_size_knockout += tdata.task_size_knockout;
+
+ while ((pend = tdata.pending.Pop())) {
+ double fitness = m_fitness_point[pend->site][pend->inst];
+
+ if (fitness == 0.0) {
+ m_tp.task_target_dead++;
+ } else if (fitness < m_neut_min) {
+ m_tp.task_target_neg++;
+ m_tp.task_size_target_neg += fitness;
+ } else if (fitness <= m_neut_max) {
+ m_tp.task_target_neut++;
+ } else {
+ m_tp.task_target_pos++;
+ m_tp.task_size_target_pos += fitness;
+ }
+
+ delete pend;
+ }
}
const double max_ent = log(static_cast<double>(m_inst_set.GetSize()));
@@ -428,25 +457,6 @@
}
m_tp.complexity = m_base_genome.GetSize() - m_tp.total_entropy;
- sPendingTarget* pend = NULL;
- while ((pend = m_pending.Pop())) {
- double fitness = m_fitness_point[pend->site][pend->inst];
-
- if (fitness == 0.0) {
- m_tp.task_target_dead++;
- } else if (fitness < m_neut_min) {
- m_tp.task_target_neg++;
- m_tp.task_size_target_neg += fitness;
- } else if (fitness <= m_neut_max) {
- m_tp.task_target_neut++;
- } else {
- m_tp.task_target_pos++;
- m_tp.task_size_target_pos += fitness;
- }
-
- delete pend;
- }
-
m_rwlock.WriteUnlock();
}
Modified: development/source/analyze/cMutationalNeighborhood.h
===================================================================
--- development/source/analyze/cMutationalNeighborhood.h 2007-07-27 20:22:35 UTC (rev 1860)
+++ development/source/analyze/cMutationalNeighborhood.h 2007-07-30 00:55:46 UTC (rev 1861)
@@ -106,11 +106,6 @@
tArray<sStep> m_onestep_point;
tArray<sStep> m_onestep_insert;
tArray<sStep> m_onestep_delete;
- tArray<sStep> m_twostep_point;
-
- tMatrix<double> m_fitness_point;
- tMatrix<double> m_fitness_insert;
- tArray<double> m_fitness_delete;
struct sPendingTarget
{
@@ -118,8 +113,19 @@
int inst;
sPendingTarget(int in_site, int in_inst) : site(in_site), inst(in_inst) { ; }
};
- tList<sPendingTarget> m_pending;
-
+
+ struct sTwoStep : public sStep
+ {
+ tList<sPendingTarget> pending;
+ };
+ tArray<sTwoStep> m_twostep_point;
+ tArray<sTwoStep> m_twostep_insert;
+ tArray<sTwoStep> m_twostep_delete;
+
+ tMatrix<double> m_fitness_point;
+ tMatrix<double> m_fitness_insert;
+ tArray<double> m_fitness_delete;
+
const cInstSet& m_inst_set;
int m_target;
@@ -223,6 +229,8 @@
};
sTwoStepAggregate m_tp;
+ sTwoStepAggregate m_ti;
+ sTwoStepAggregate m_td;
@@ -238,7 +246,10 @@
// void ProcessTwoStepInsert(cAvidaContext& ctx, cTestCPU* testcpu, cCPUTestInfo& test_info, int cur_site, cGenome& mod_genome);
// void ProcessTwoStepDelete(cAvidaContext& ctx, cTestCPU* testcpu, cCPUTestInfo& test_info, int cur_site, cGenome& mod_genome);
// void ProcessInDelPointCombo(cAvidaContext& ctx, cTestCPU* testcpu, cCPUTestInfo& test_info, int cur_site, cGenome& mod_genome);
-
+ double ProcessTwoStepGenome(cAvidaContext& ctx, cTestCPU* testcpu, cCPUTestInfo& test_info, const cGenome& mod_genome,
+ sTwoStep& tdata, int cur_site, int oth_site);
+
+
void ProcessComplete(cAvidaContext& ctx);
void AggregateOneStep(tArray<sStep>& steps, sOneStepAggregate osa);
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