[Avida-cvs] [avida-svn] r834 - in development/source: cpu main utils/task_events
covertar@myxo.css.msu.edu
covertar at myxo.css.msu.edu
Fri Jul 14 11:10:38 PDT 2006
Author: covertar
Date: 2006-07-14 14:10:38 -0400 (Fri, 14 Jul 2006)
New Revision: 834
Modified:
development/source/cpu/cHardwareBase.cc
development/source/cpu/cHardwareBase.h
development/source/cpu/cHardwareCPU.cc
development/source/cpu/cHardwareCPU.h
development/source/main/cAvidaConfig.h
development/source/main/cOrganism.cc
development/source/main/cOrganism.h
development/source/main/cStats.cc
development/source/main/cStats.h
development/source/utils/task_events/Makefile
Log:
Added suport for
1) Specifing a NEUTRAL_MIN and NEUTRAL_MAX, which are used to set the uper and lower bounds for a "neutral" mutation as a fraction of parent fitness.
2) Implemented resampling divide instruction h-divdeRS, when this is used inplace of h-divide, a reverted organism will have it's mutations resampled instead of reverted.
Modified: development/source/cpu/cHardwareBase.cc
===================================================================
--- development/source/cpu/cHardwareBase.cc 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/cpu/cHardwareBase.cc 2006-07-14 18:10:38 UTC (rev 834)
@@ -112,8 +112,13 @@
}
-void cHardwareBase::Divide_DoMutations(cAvidaContext& ctx, double mut_multiplier)
+/*
+ Return the number of mutations that occur on divide. AWC 06/29/06
+*/
+unsigned cHardwareBase::Divide_DoMutations(cAvidaContext& ctx, double mut_multiplier)
{
+ unsigned totalMutations = 0;
+
sCPUStats& cpu_stats = organism->CPUStats();
cCPUMemory& child_genome = organism->ChildGenome();
@@ -123,21 +128,21 @@
if (organism->TestDivideMut(ctx)) {
const unsigned int mut_line = ctx.GetRandom().GetUInt(child_genome.GetSize());
child_genome[mut_line] = m_inst_set->GetRandomInst(ctx);
- cpu_stats.mut_stats.divide_mut_count++;
+ totalMutations += ++cpu_stats.mut_stats.divide_mut_count;
}
// Divide Insertions
if (organism->TestDivideIns(ctx) && child_genome.GetSize() < MAX_CREATURE_SIZE) {
const unsigned int mut_line = ctx.GetRandom().GetUInt(child_genome.GetSize() + 1);
child_genome.Insert(mut_line, m_inst_set->GetRandomInst(ctx));
- cpu_stats.mut_stats.divide_insert_mut_count++;
+ totalMutations += ++cpu_stats.mut_stats.divide_insert_mut_count;
}
// Divide Deletions
if (organism->TestDivideDel(ctx) && child_genome.GetSize() > MIN_CREATURE_SIZE) {
const unsigned int mut_line = ctx.GetRandom().GetUInt(child_genome.GetSize());
child_genome.Remove(mut_line);
- cpu_stats.mut_stats.divide_delete_mut_count++;
+ totalMutations += ++cpu_stats.mut_stats.divide_delete_mut_count;
}
// Divide Mutations (per site)
@@ -152,6 +157,7 @@
cpu_stats.mut_stats.div_mut_count++;
}
}
+ totalMutations += cpu_stats.mut_stats.div_mut_count;
}
@@ -176,6 +182,7 @@
for (int i = num_mut-1; i >= 0; i--) {
child_genome.Insert(mut_sites[i], m_inst_set->GetRandomInst(ctx));
cpu_stats.mut_stats.insert_mut_count++;
+ totalMutations++; //Unline the others we can't be sure this was done only on divide -- AWC 06/29/06
}
}
}
@@ -204,6 +211,8 @@
if (organism->TestParentMut(ctx)) {
GetMemory()[i] = m_inst_set->GetRandomInst(ctx);
cpu_stats.mut_stats.parent_mut_line_count++;
+ totalMutations++; //Unline the others we can't be sure this was done only on divide -- AWC 06/29/06
+
}
}
}
@@ -220,28 +229,34 @@
cpu_stats.mut_stats.copy_mut_line_count++;
}
}
+
+ return totalMutations;
}
// test whether the offspring creature contains an advantageous mutation.
-void cHardwareBase::Divide_TestFitnessMeasures(cAvidaContext& ctx)
+/*
+ Return true iff only a reversion is performed -- returns false is steralized regardless of weather or
+ not a reversion is performed. AWC 06/29/06
+*/
+bool cHardwareBase::Divide_TestFitnessMeasures(cAvidaContext& ctx)
{
cPhenotype & phenotype = organism->GetPhenotype();
phenotype.CopyTrue() = ( organism->ChildGenome() == organism->GetGenome() );
phenotype.ChildFertile() = true;
// Only continue if we're supposed to do a fitness test on divide...
- if (organism->GetTestOnDivide() == false) return;
+ if (organism->GetTestOnDivide() == false) return false;
// If this was a perfect copy, then we don't need to worry about any other
// tests... Theoretically, we need to worry about the parent changing,
// but as long as the child is always compared to the original genotype,
// this won't be an issue.
- if (phenotype.CopyTrue() == true) return;
+ if (phenotype.CopyTrue() == true) return false;
const double parent_fitness = organism->GetTestFitness();
- const double neut_min = parent_fitness * nHardware::FITNESS_NEUTRAL_MIN;
- const double neut_max = parent_fitness * nHardware::FITNESS_NEUTRAL_MAX;
+ const double neut_min = parent_fitness * (1.0 - organism->GetNeutralMin());//nHardware::FITNESS_NEUTRAL_MIN;
+ const double neut_max = parent_fitness * (1.0 + organism->GetNeutralMax());//nHardware::FITNESS_NEUTRAL_MAX;
cTestCPU* testcpu = m_world->GetHardwareManager().CreateTestCPU();
cCPUTestInfo test_info;
@@ -257,7 +272,7 @@
if (organism->GetFailImplicit() == true) {
if (test_info.GetMaxDepth() > 0) sterilize = true;
}
-
+
if (child_fitness == 0.0) {
// Fatal mutation... test for reversion.
if (ctx.GetRandom().P(organism->GetRevertFatal())) revert = true;
@@ -268,7 +283,7 @@
} else if (child_fitness <= neut_max) {
if (ctx.GetRandom().P(organism->GetRevertNeut())) revert = true;
if (ctx.GetRandom().P(organism->GetSterilizeNeut())) sterilize = true;
- } else {
+ } else (child_fitness > neut_max){
if (ctx.GetRandom().P(organism->GetRevertPos())) revert = true;
if (ctx.GetRandom().P(organism->GetSterilizePos())) sterilize = true;
}
@@ -282,6 +297,8 @@
if (sterilize == true) {
organism->GetPhenotype().ChildFertile() = false;
}
+
+ return (!sterilize) && revert;
}
int cHardwareBase::PointMutate(cAvidaContext& ctx, const double mut_rate)
Modified: development/source/cpu/cHardwareBase.h
===================================================================
--- development/source/cpu/cHardwareBase.h 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/cpu/cHardwareBase.h 2006-07-14 18:10:38 UTC (rev 834)
@@ -29,6 +29,7 @@
class cOrganism;
class cString;
class cWorld;
+//class cStats; //AWC 06/29/06
class cHardwareBase
{
@@ -42,8 +43,8 @@
virtual int GetCopiedSize(const int parent_size, const int child_size) = 0;
bool Divide_CheckViable(cAvidaContext& ctx, const int parent_size, const int child_size);
- void Divide_DoMutations(cAvidaContext& ctx, double mut_multiplier = 1.0);
- void Divide_TestFitnessMeasures(cAvidaContext& ctx);
+ unsigned Divide_DoMutations(cAvidaContext& ctx, double mut_multiplier = 1.0);
+ bool Divide_TestFitnessMeasures(cAvidaContext& ctx);
void TriggerMutations_Body(cAvidaContext& ctx, int type, cCPUMemory& target_memory, cHeadCPU& cur_head);
bool TriggerMutations_ScopeGenome(cAvidaContext& ctx, const cMutation* cur_mut,
Modified: development/source/cpu/cHardwareCPU.cc
===================================================================
--- development/source/cpu/cHardwareCPU.cc 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/cpu/cHardwareCPU.cc 2006-07-14 18:10:38 UTC (rev 834)
@@ -191,6 +191,7 @@
cInstEntryCPU("if-n-cpy", &cHardwareCPU::Inst_IfNCpy),
cInstEntryCPU("allocate", &cHardwareCPU::Inst_Allocate),
cInstEntryCPU("divide", &cHardwareCPU::Inst_Divide),
+ cInstEntryCPU("divideRS", &cHardwareCPU::Inst_DivideRS),
cInstEntryCPU("c-alloc", &cHardwareCPU::Inst_CAlloc),
cInstEntryCPU("c-divide", &cHardwareCPU::Inst_CDivide),
cInstEntryCPU("inject", &cHardwareCPU::Inst_Inject),
@@ -231,6 +232,8 @@
"Allocate maximum allowed space"),
cInstEntryCPU("h-divide", &cHardwareCPU::Inst_HeadDivide, true,
"Divide code between read and write heads."),
+ cInstEntryCPU("h-divideRS", &cHardwareCPU::Inst_HeadDivideRS, true,
+ "Divide code between read and write heads, resample reversions."),
cInstEntryCPU("h-read", &cHardwareCPU::Inst_HeadRead),
cInstEntryCPU("h-write", &cHardwareCPU::Inst_HeadWrite),
cInstEntryCPU("h-copy", &cHardwareCPU::Inst_HeadCopy, true,
@@ -1253,7 +1256,93 @@
return true;
}
+/*
+ Almost the same as Divide_Main, but resamples reverted offspring.
+ RESAMPLING ONLY WORKS CORRECTLY WHEN ALL MUTIONS OCCUR ON DIVIDE!!
+
+ AWC - 06/29/06
+*/
+bool cHardwareCPU::Divide_MainRS(cAvidaContext& ctx, const int div_point,
+ const int extra_lines, double mut_multiplier)
+{
+
+ //cStats stats = m_world->GetStats();
+ const int child_size = GetMemory().GetSize() - div_point - extra_lines;
+
+ // Make sure this divide will produce a viable offspring.
+ const bool viable = Divide_CheckViable(ctx, div_point, child_size);
+ if (viable == false) return false;
+
+ // Since the divide will now succeed, set up the information to be sent
+ // to the new organism
+ cGenome & child_genome = organism->ChildGenome();
+ child_genome = cGenomeUtil::Crop(memory, div_point, div_point+child_size);
+
+ // Cut off everything in this memory past the divide point.
+ GetMemory().Resize(div_point);
+
+ unsigned
+ totalMutations = 0,
+ mutations = 0,
+ RScount = 0;
+
+
+
+ // Handle Divide Mutations...
+ /*
+ Do mutations until one of these conditions are satisified:
+ we have resampled X times
+ we have an offspring with the same number of muations as the first offspring
+ that is not reverted
+ the parent is steralized (usually means an implicit mutation)
+ */
+ do{
+ if(!RScount){
+ mutations = totalMutations = Divide_DoMutations(ctx, mut_multiplier);
+ }
+ else{
+ mutations = Divide_DoMutations(ctx, mut_multiplier);
+ m_world->GetStats().IncResamplings();
+ }
+
+
+
+ }while (RScount++ < 10 && mutations >= totalMutations && Divide_TestFitnessMeasures(ctx));
+ // think about making this mutations == totalMuations - though this may be too hard...
+ /*
+ if(RScount > 2)
+ cerr << "Resampled " << RScount << endl;
+ */
+ //org could not be resampled beneath the hard cap -- it is then steraalized
+ if(RScount == 10) {
+ organism->GetPhenotype().ChildFertile() = false;
+ m_world->GetStats().IncFailedResamplings();
+ }
+
+#if INSTRUCTION_COSTS
+ // reset first time instruction costs
+ for (int i = 0; i < inst_ft_cost.GetSize(); i++) {
+ inst_ft_cost[i] = m_inst_set->GetFTCost(cInstruction(i));
+ }
+#endif
+
+ mal_active = false;
+ if (m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_SPLIT) {
+ advance_ip = false;
+ }
+
+ // Activate the child, and do more work if the parent lives through the
+ // birth.
+ bool parent_alive = organism->ActivateDivide(ctx);
+ if (parent_alive) {
+ if (m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_SPLIT) Reset();
+ }
+
+ return true;
+}
+
+
//////////////////////////
// And the instructions...
//////////////////////////
@@ -1998,6 +2087,20 @@
return Divide_Main(ctx, GetRegister(nHardwareCPU::REG_AX));
}
+/*
+ Divide with resampling -- Same as regular divide but on reversions will be
+ resampled after they are reverted.
+
+ AWC 06/29/06
+
+ */
+
+bool cHardwareCPU::Inst_DivideRS(cAvidaContext& ctx)
+{
+ return Divide_MainRS(ctx, GetRegister(nHardwareCPU::REG_AX));
+}
+
+
bool cHardwareCPU::Inst_CDivide(cAvidaContext& ctx)
{
return Divide_Main(ctx, GetMemory().GetSize() / 2);
@@ -2666,8 +2769,26 @@
bool cHardwareCPU::Inst_HeadDivide(cAvidaContext& ctx)
{
return Inst_HeadDivideMut(ctx, 1);
+
}
+/*
+ Resample Divide -- AWC 06/29/06
+*/
+
+bool cHardwareCPU::Inst_HeadDivideRS(cAvidaContext& ctx)
+{
+ AdjustHeads();
+ const int divide_pos = GetHead(nHardware::HEAD_READ).GetPosition();
+ int child_end = GetHead(nHardware::HEAD_WRITE).GetPosition();
+ if (child_end == 0) child_end = GetMemory().GetSize();
+ const int extra_lines = GetMemory().GetSize() - child_end;
+ bool ret_val = Divide_MainRS(ctx, divide_pos, extra_lines, 1);
+ // Re-adjust heads.
+ AdjustHeads();
+ return ret_val;
+}
+
bool cHardwareCPU::Inst_HeadDivideSex(cAvidaContext& ctx)
{
organism->GetPhenotype().SetDivideSex(true);
Modified: development/source/cpu/cHardwareCPU.h
===================================================================
--- development/source/cpu/cHardwareCPU.h 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/cpu/cHardwareCPU.h 2006-07-14 18:10:38 UTC (rev 834)
@@ -47,6 +47,9 @@
#ifndef tArray_h
#include "tArray.h"
#endif
+#ifndef cStats_h
+#include "cStats.h"
+#endif
/**
* Each organism may have a cHardwareCPU structure which keeps track of the
@@ -138,6 +141,8 @@
int GetCopiedSize(const int parent_size, const int child_size);
bool Divide_Main(cAvidaContext& ctx, const int divide_point, const int extra_lines=0, double mut_multiplier=1);
+ bool Divide_MainRS(cAvidaContext& ctx, const int divide_point, const int extra_lines=0, double mut_multiplier=1); //AWC 06/29/06
+
void InjectCode(const cGenome& injection, const int line_num);
@@ -324,6 +329,7 @@
bool Inst_IfNCpy(cAvidaContext& ctx);
bool Inst_Allocate(cAvidaContext& ctx);
bool Inst_Divide(cAvidaContext& ctx);
+ bool Inst_DivideRS(cAvidaContext& ctx); // AWC 06/29/06
bool Inst_CAlloc(cAvidaContext& ctx);
bool Inst_CDivide(cAvidaContext& ctx);
bool Inst_MaxAlloc(cAvidaContext& ctx);
@@ -378,6 +384,7 @@
bool Inst_IfLabel(cAvidaContext& ctx);
bool Inst_IfLabel2(cAvidaContext& ctx);
bool Inst_HeadDivide(cAvidaContext& ctx);
+ bool Inst_HeadDivideRS(cAvidaContext& ctx); //AWC 06/29/06
bool Inst_HeadRead(cAvidaContext& ctx);
bool Inst_HeadWrite(cAvidaContext& ctx);
bool Inst_HeadCopy(cAvidaContext& ctx);
Modified: development/source/main/cAvidaConfig.h
===================================================================
--- development/source/main/cAvidaConfig.h 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/main/cAvidaConfig.h 2006-07-14 18:10:38 UTC (rev 834)
@@ -229,6 +229,8 @@
CONFIG_ADD_VAR(STERILIZE_NEUTRAL, double, 0.0, "");
CONFIG_ADD_VAR(STERILIZE_BENEFICIAL, double, 0.0, "");
CONFIG_ADD_VAR(FAIL_IMPLICIT, int, 0, "Should copies that failed *not* due to mutations\nbe eliminated?");
+ CONFIG_ADD_VAR(NEUTRAL_MAX,double, 0.0, "The percent benifical change from parent fitness to be considered neutral.");
+ CONFIG_ADD_VAR(NEUTRAL_MIN,double, 0.0, "The percent deleterious change from parent fitness to be considered neutral.");
CONFIG_ADD_GROUP(TIME_GROUP, "Time Slicing");
CONFIG_ADD_VAR(AVE_TIME_SLICE, int, 30, "Ave number of insts per org per update");
Modified: development/source/main/cOrganism.cc
===================================================================
--- development/source/main/cOrganism.cc 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/main/cOrganism.cc 2006-07-14 18:10:38 UTC (rev 834)
@@ -400,6 +400,8 @@
bool cOrganism::GetSterilizeNeg() const { return m_world->GetConfig().STERILIZE_DETRIMENTAL.Get(); }
bool cOrganism::GetSterilizeNeut() const { return m_world->GetConfig().STERILIZE_NEUTRAL.Get();}
bool cOrganism::GetSterilizePos() const { return m_world->GetConfig().STERILIZE_BENEFICIAL.Get(); }
+double cOrganism::GetNeutralMin() const { return m_world->GetConfig().NEUTRAL_MIN.Get();}
+double cOrganism::GetNeutralMax() const { return m_world->GetConfig().NEUTRAL_MAX.Get();}
void cOrganism::PrintStatus(ostream& fp, const cString & next_name)
Modified: development/source/main/cOrganism.h
===================================================================
--- development/source/main/cOrganism.h 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/main/cOrganism.h 2006-07-14 18:10:38 UTC (rev 834)
@@ -217,8 +217,9 @@
bool GetSterilizeNeg() const;
bool GetSterilizeNeut() const;
bool GetSterilizePos() const;
+ double GetNeutralMin() const;
+ double GetNeutralMax() const;
-
// Access to private variables
int GetMaxExecuted() const { return max_executed; }
Modified: development/source/main/cStats.cc
===================================================================
--- development/source/main/cStats.cc 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/main/cStats.cc 2006-07-14 18:10:38 UTC (rev 834)
@@ -141,7 +141,10 @@
data_manager.Add("richness", "Number of Different Genotypes (Richness)", &cStats::GetNumGenotypes);
data_manager.Add("eveness", "Equitability of Genotype Distribution (Evenness)", &cStats::GetEvenness);
data_manager.Add("coal_depth", "Depth of Coalescent Genotype", &cStats::GetCoalescentDepth);
+ data_manager.Add("num_resamplings", "Total Number of resamplings this time step", &cStats::GetResamplings);
+ data_manager.Add("num_failedResamplings", "Total Number of divide commands that reached the resampling hard-cap this time step", &cStats::GetFailedResamplings);
+
// Dominant Genotype Stats
data_manager.Add("dom_merit", "Ave Merit of Dominant Genotype", &cStats::GetDomMerit);
data_manager.Add("dom_gest", "Ave Gestation Time of Dominant Genotype", &cStats::GetDomGestation);
@@ -382,6 +385,10 @@
dom_gestation = 0.0;
dom_fitness = 0.0;
max_fitness = 0.0;
+
+ num_resamplings = 0;
+ num_failedResamplings = 0;
+
}
void cStats::RemoveLineage(int id_num, int parent_id, int update_born, double generation_born, int total_CPUs,
@@ -551,16 +558,19 @@
df.WriteComment( "Generic Statistics Data" );
df.WriteTimeStamp();
- df.Write( GetUpdate(), "update" );
- df.Write( energy, "average inferiority (energy)");
- df.Write( 1.0 - ave_fidelity, "ave probability of any mutations in genome" );
- df.Write( 1.0 - dom_fidelity, "probability of any mutations in dom genome" );
- df.Write( log_ave_fid, "log(average fidelity)");
- df.Write( log_dom_fid, "log(dominant fidelity)");
- df.Write( genotype_change, "change in number of genotypes");
- df.Write( entropy, "genotypic entropy");
- df.Write( species_entropy, "species entropy");
- df.Write( coal_depth, "depth of most reacent coalescence");
+ df.Write( GetUpdate(), "update" );
+ df.Write( energy, "average inferiority (energy)");
+ df.Write( 1.0 - ave_fidelity, "ave probability of any mutations in genome" );
+ df.Write( 1.0 - dom_fidelity, "probability of any mutations in dom genome" );
+ df.Write( log_ave_fid, "log(average fidelity)");
+ df.Write( log_dom_fid, "log(dominant fidelity)");
+ df.Write( genotype_change, "change in number of genotypes");
+ df.Write( entropy, "genotypic entropy");
+ df.Write( species_entropy, "species entropy");
+ df.Write( coal_depth, "depth of most reacent coalescence");
+ df.Write( num_resamplings, "Total number of resamplings this generation");
+ df.Write( num_failedResamplings, "Total number of organisms that failed to resample this generation");
+
df.Endl();
}
Modified: development/source/main/cStats.h
===================================================================
--- development/source/main/cStats.h 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/main/cStats.h 2006-07-14 18:10:38 UTC (rev 834)
@@ -222,7 +222,12 @@
tArray<cString> inst_names;
tArray<cString> reaction_names;
tArray<cString> resource_names;
+
+ // Resampling Statistics AWC - 06/29/06
+ int num_resamplings;
+ int num_failedResamplings;
+
// State variables
int last_update;
@@ -383,6 +388,10 @@
const cDoubleSum& SumExeSize() const { return sum_exe_size; }
const cDoubleSum& SumMemSize() const { return sum_mem_size; }
+
+ void IncResamplings() { ++num_resamplings;} //AWC 06/29/06
+ void IncFailedResamplings() { ++num_failedResamplings;} //AWC 06/29/06
+
void CalcEnergy();
void CalcFidelity();
@@ -518,6 +527,10 @@
int GetMinGenomeLength() const { return min_genome_length; }
+ int GetResamplings() const { return num_resamplings;} //AWC 06/29/06
+ int GetFailedResamplings() const { return num_failedResamplings;} //AWC 06/29/06
+
+
// this value gets recorded when a creature with the particular
// fitness value gets born. It will never change to a smaller value,
// i.e., when the maximum fitness in the population drops, this value will
Modified: development/source/utils/task_events/Makefile
===================================================================
--- development/source/utils/task_events/Makefile 2006-07-14 17:11:11 UTC (rev 833)
+++ development/source/utils/task_events/Makefile 2006-07-14 18:10:38 UTC (rev 834)
@@ -1,24 +1,26 @@
# CMAKE generated Makefile, DO NOT EDIT!
# Generated by "Unix Makefiles" Generator, CMake Version 2.0
# Generated from the following files:
-# /Users/charles/Development/avida/trunk.sherri/CMakeCache.txt
-# /Users/charles/Development/avida/trunk.sherri/CMakeCCompiler.cmake
-# /Users/charles/Development/avida/trunk.sherri/CMakeCXXCompiler.cmake
-# /Users/charles/Development/avida/trunk.sherri/CMakeSystem.cmake
-# /Users/charles/Development/avida/trunk/CMakeLists.txt
-# /Users/charles/Development/avida/trunk/CMakeModules/FindNcurses.cmake
-# /Users/charles/Development/avida/trunk/source/CMakeLists.txt
-# /Users/charles/Development/avida/trunk/source/utils/task_events/CMakeLists.txt
+# /home/covertar/source/development_52205/CMakeCache.txt
+# /home/covertar/source/development_52205/CMakeCCompiler.cmake
+# /home/covertar/source/development_52205/CMakeCXXCompiler.cmake
+# /home/covertar/source/development_52205/CMakeLists.txt
+# /home/covertar/source/development_52205/CMakeSystem.cmake
+# /home/covertar/source/development_52205/source/CMakeLists.txt
+# /home/covertar/source/development_52205/source/utils/task_events/CMakeLists.txt
# /usr/local/share/CMake/Modules/CMakeDefaultMakeRuleVariables.cmake
# /usr/local/share/CMake/Modules/CMakeSystemSpecificInformation.cmake
-# /usr/local/share/CMake/Modules/Platform/Darwin.cmake
+# /usr/local/share/CMake/Modules/Dart.cmake
+# /usr/local/share/CMake/Modules/FindDart.cmake
+# /usr/local/share/CMake/Modules/FindTclsh.cmake
+# /usr/local/share/CMake/Modules/Platform/Linux.cmake
# /usr/local/share/CMake/Modules/Platform/gcc.cmake
# disable some common implicit rules to speed things up
.SUFFIXES:
.SUFFIXES:.hpuxmakemusthaverule
-CMAKE_MAKEFILE_SOURCES = /Users/charles/Development/avida/trunk.sherri/CMakeCCompiler.cmake /Users/charles/Development/avida/trunk.sherri/CMakeCXXCompiler.cmake /Users/charles/Development/avida/trunk.sherri/CMakeSystem.cmake /Users/charles/Development/avida/trunk/CMakeLists.txt /Users/charles/Development/avida/trunk/CMakeModules/FindNcurses.cmake /Users/charles/Development/avida/trunk/source/CMakeLists.txt /Users/charles/Development/avida/trunk/source/utils/task_events/CMakeLists.txt /usr/local/share/CMake/Modules/CMakeDefaultMakeRuleVariables.cmake /usr/local/share/CMake/Modules/CMakeSystemSpecificInformation.cmake /usr/local/share/CMake/Modules/Platform/Darwin.cmake /usr/local/share/CMake/Modules/Platform/gcc.cmake /Users/charles/Development/avida/trunk.sherri/CMakeCache.txt
+CMAKE_MAKEFILE_SOURCES = /home/covertar/source/development_52205/CMakeCCompiler.cmake /home/covertar/source/development_52205/CMakeCXXCompiler.cmake /home/covertar/source/development_52205/CMakeLists.txt /home/covertar/source/development_52205/CMakeSystem.cmake /home/covertar/source/development_52205/source/CMakeLists.txt /home/covertar/source/development_52205/source/utils/task_events/CMakeLists.txt /usr/local/share/CMake/Modules/CMakeDefaultMakeRuleVariables.cmake /usr/local/share/CMake/Modules/CMakeSystemSpecificInformation.cmake /usr/local/share/CMake/Modules/Dart.cmake /usr/local/share/CMake/Modules/FindDart.cmake /usr/local/share/CMake/Modules/FindTclsh.cmake /usr/local/share/CMake/Modules/Platform/Linux.cmake /usr/local/share/CMake/Modules/Platform/gcc.cmake /home/covertar/source/development_52205/CMakeCache.txt
# the standard shell for make
@@ -27,22 +29,25 @@
CMAKE_COMMAND = /usr/local/bin/cmake
RM = /usr/local/bin/cmake -E remove -f
CMAKE_EDIT_COMMAND = /usr/local/bin/ccmake
-CMAKE_CURRENT_SOURCE = /Users/charles/Development/avida/trunk/source/utils/task_events
-CMAKE_CURRENT_BINARY = /Users/charles/Development/avida/trunk.sherri/source/utils/task_events
-CMAKE_SOURCE_DIR = /Users/charles/Development/avida/trunk
-CMAKE_BINARY_DIR = /Users/charles/Development/avida/trunk.sherri
-INCLUDE_FLAGS = -I/Users/charles/Development/avida/trunk/source/tools -I/Users/charles/Development/avida/trunk/source/cpu -I/Users/charles/Development/avida/trunk/source/event -I/Users/charles/Development/avida/trunk.sherri/source/event -I/Users/charles/Development/avida/trunk/source/main -I/Users/charles/Development/avida/trunk/source
+CMAKE_CURRENT_SOURCE = /home/covertar/source/development_52205/source/utils/task_events
+CMAKE_CURRENT_BINARY = /home/covertar/source/development_52205/source/utils/task_events
+CMAKE_SOURCE_DIR = /home/covertar/source/development_52205
+CMAKE_BINARY_DIR = /home/covertar/source/development_52205
+INCLUDE_FLAGS = -I/home/covertar/source/development_52205/source/tools -I/home/covertar/source/development_52205/source/actions -I/home/covertar/source/development_52205/source/analyze -I/home/covertar/source/development_52205/source/archive -I/home/covertar/source/development_52205/source/third-party/boost -I/home/covertar/source/development_52205/source/classification -I/home/covertar/source/development_52205/source/cpu -I/home/covertar/source/development_52205/source/drivers -I/home/covertar/source/development_52205/source/event -I/home/covertar/source/development_52205/source/main -I/home/covertar/source/development_52205/source
#---------------------------------------------------------
# Default target executed when no arguments are given to make, first make sure cmake.depends exists, cmake.check_depends is up-to-date, check the sources, then build the all target
#
-default_target: /Users/charles/Development/avida/trunk.sherri/cmake.check_cache
+default_target: /home/covertar/source/development_52205/cmake.check_cache
$(MAKE) $(MAKESILENT) cmake.depends
$(MAKE) $(MAKESILENT) cmake.check_depends
$(MAKE) $(MAKESILENT) -f cmake.check_depends
$(MAKE) $(MAKESILENT) all
+# Suppresses display of executed commands
+$(VERBOSE).SILENT:
+
help:
@echo "The following are some of the valid targets for this Makefile:"
@echo "... all (the default if no target is provided)"
@@ -54,7 +59,7 @@
TARGETS = \
-/Users/charles/Development/avida/trunk/bin/task_event_gen
+/home/covertar/source/development_52205/bin/task_event_gen
task_event_gen_SRC_OBJS = \
task_event_gen.o
@@ -70,24 +75,30 @@
CLEAN_OBJECT_FILES = $(task_event_gen_SRC_OBJS)
-task_event_gen_DEPEND_LIBS = /Users/charles/Development/avida/trunk/lib/libtools.a
+task_event_gen_DEPEND_LIBS = /home/covertar/source/development_52205/lib/libtools.a /home/covertar/source/development_52205/lib/libarchive.a /home/covertar/source/development_52205/lib/libboost_serialization.a
-/Users/charles/Development/avida/trunk/lib/libtools.a:
- cd /Users/charles/Development/avida/trunk.sherri/source/tools; $(MAKE) $(MAKESILENT) cmake.depends; $(MAKE) $(MAKESILENT) cmake.check_depends; $(MAKE) $(MAKESILENT) -f cmake.check_depends; $(MAKE) $(MAKESILENT) libtools.a
+/home/covertar/source/development_52205/lib/libarchive.a:
+ cd /home/covertar/source/development_52205/source/archive; $(MAKE) $(MAKESILENT) cmake.depends; $(MAKE) $(MAKESILENT) cmake.check_depends; $(MAKE) $(MAKESILENT) -f cmake.check_depends; $(MAKE) $(MAKESILENT) libarchive.a
+/home/covertar/source/development_52205/lib/libboost_serialization.a:
+ cd /home/covertar/source/development_52205/source/third-party/boost/serialization; $(MAKE) $(MAKESILENT) cmake.depends; $(MAKE) $(MAKESILENT) cmake.check_depends; $(MAKE) $(MAKESILENT) -f cmake.check_depends; $(MAKE) $(MAKESILENT) libboost_serialization.a
+
+/home/covertar/source/development_52205/lib/libtools.a:
+ cd /home/covertar/source/development_52205/source/tools; $(MAKE) $(MAKESILENT) cmake.depends; $(MAKE) $(MAKESILENT) cmake.check_depends; $(MAKE) $(MAKESILENT) -f cmake.check_depends; $(MAKE) $(MAKESILENT) libtools.a
+
#---------------------------------------------------------
# executable
#
-/Users/charles/Development/avida/trunk/bin/task_event_gen: $(task_event_gen_SRC_OBJS) $(task_event_gen_EXTERNAL_OBJS) $(task_event_gen_DEPEND_LIBS)
- @echo "Building executable /Users/charles/Development/avida/trunk/bin/task_event_gen..."
- c++ -fPIC $(task_event_gen_SRC_OBJS) $(task_event_gen_EXTERNAL_OBJS) -o /Users/charles/Development/avida/trunk/bin/task_event_gen -L/Users/charles/Development/avida/trunk/lib -L/Users/charles/Development/avida/trunk.sherri/source/tools -L/Users/charles/Development/avida/trunk.sherri/source/cpu -L/Users/charles/Development/avida/trunk.sherri/source/event -L/Users/charles/Development/avida/trunk.sherri/source/main -ltools
+/home/covertar/source/development_52205/bin/task_event_gen: $(task_event_gen_SRC_OBJS) $(task_event_gen_EXTERNAL_OBJS) $(task_event_gen_DEPEND_LIBS)
+ @echo "Building executable /home/covertar/source/development_52205/bin/task_event_gen..."
+ c++ -fPIC $(task_event_gen_SRC_OBJS) $(task_event_gen_EXTERNAL_OBJS) -o /home/covertar/source/development_52205/bin/task_event_gen -rdynamic -L/home/covertar/source/development_52205/lib -L/home/covertar/source/development_52205/source/tools -L/home/covertar/source/development_52205/source/actions -L/home/covertar/source/development_52205/source/analyze -L/home/covertar/source/development_52205/source/archive -L/home/covertar/source/development_52205/source/third-party/boost/serialization -L/home/covertar/source/development_52205/source/cpu -L/home/covertar/source/development_52205/source/drivers -L/home/covertar/source/development_52205/source/event -L/home/covertar/source/development_52205/source/main -ltools -larchive -lboost_serialization
#---------------------------------------------------------
# executable
#
-task_event_gen: /Users/charles/Development/avida/trunk/bin/task_event_gen
+task_event_gen: /home/covertar/source/development_52205/bin/task_event_gen
#---------------------------------------------------------
# default build rule
@@ -114,7 +125,7 @@
# dependencies
#
-cmake.check_depends: /Users/charles/Development/avida/trunk/source/utils/task_events/task_event_gen.cc
+cmake.check_depends: /home/covertar/source/development_52205/source/utils/task_events/task_event_gen.cc
@echo "Building dependencies cmake.check_depends..."
$(CMAKE_COMMAND) -S$(CMAKE_CURRENT_SOURCE) -O$(CMAKE_CURRENT_BINARY) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
@@ -146,8 +157,8 @@
# CMakeCache.txt because out-of-date:
#
-/Users/charles/Development/avida/trunk.sherri/cmake.check_cache: $(CMAKE_MAKEFILE_SOURCES)
- @echo "Building CMakeCache.txt because out-of-date: /Users/charles/Development/avida/trunk.sherri/cmake.check_cache..."
+/home/covertar/source/development_52205/cmake.check_cache: $(CMAKE_MAKEFILE_SOURCES)
+ @echo "Building CMakeCache.txt because out-of-date: /home/covertar/source/development_52205/cmake.check_cache..."
$(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
#---------------------------------------------------------
@@ -162,8 +173,8 @@
# CMakeCache.txt
#
-/Users/charles/Development/avida/trunk.sherri/CMakeCache.txt:
- @echo "Building CMakeCache.txt /Users/charles/Development/avida/trunk.sherri/CMakeCache.txt..."
+/home/covertar/source/development_52205/CMakeCache.txt:
+ @echo "Building CMakeCache.txt /home/covertar/source/development_52205/CMakeCache.txt..."
$(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
#---------------------------------------------------------
@@ -177,11 +188,20 @@
# object file
#
-task_event_gen.o: /Users/charles/Development/avida/trunk/source/utils/task_events/task_event_gen.cc
+task_event_gen.o: /home/covertar/source/development_52205/source/utils/task_events/task_event_gen.cc
@echo "Building object file task_event_gen.o..."
- c++ -o task_event_gen.o -O3 -ffast-math -DNDEBUG $(INCLUDE_FLAGS) -c /Users/charles/Development/avida/trunk/source/utils/task_events/task_event_gen.cc
+ c++ -o task_event_gen.o -O3 $(INCLUDE_FLAGS) -c /home/covertar/source/development_52205/source/utils/task_events/task_event_gen.cc
+ARGS=
#---------------------------------------------------------
+# tests
+#
+
+test:
+ @echo "Building tests test..."
+ /usr/local/bin/ctest $(ARGS)
+
+#---------------------------------------------------------
# installation
#
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