re-enable non-neutral caching

Author: bhaller

QtSLiM/QtSLiMAppDelegate.cpp

@@ -322,7 +322,7 @@ QtSLiMAppDelegate::~QtSLiMAppDelegate(void)
 {
     //qDebug() << "QtSLiMAppDelegate::~QtSLiMAppDelegate";
 
-#if SLIM_LEAK_CHECKING
+#if SLIM_LEAK_CHECKING()
     QtSLiM_FreeGLBuffers();
 #endif
 

QtSLiM/QtSLiMGraphView_PopulationVisualization.cpp

@@ -32,12 +32,6 @@
 #include "QtSLiMWindow.h"
 #include "subpopulation.h"
 
-// This define changes the visualization a little for use making Perry's icon; should be 0 otherwise
-#define PERRY_ICON 0
-
-#if PERRY_ICON
-#warning PERRY_ICON should be 0!
-#endif
 
 QtSLiMGraphView_PopulationVisualization::QtSLiMGraphView_PopulationVisualization(QWidget *p_parent, QtSLiMWindow *controller) : QtSLiMGraphView(p_parent, controller)
 {
@@ -126,7 +120,6 @@ void QtSLiMGraphView_PopulationVisualization::drawSubpop(QPainter &painter, Subp
     painter.drawEllipse(center, subpopRadius, subpopRadius);
 
 	// label it with the subpopulation ID
-#if !PERRY_ICON
     painter.setWorldMatrixEnabled(false);
 
 	QString popString = QString("p%1").arg(subpopID);
@@ -144,7 +137,6 @@ void QtSLiMGraphView_PopulationVisualization::drawSubpop(QPainter &painter, Subp
 
     painter.drawText(drawPoint, popString);
     painter.setWorldMatrixEnabled(true);
-#endif
 }
 
 void QtSLiMGraphView_PopulationVisualization::drawArrowFromSubpopToSubpop(QPainter &painter, Subpopulation *sourceSubpop, Subpopulation *destSubpop, double migrantFraction)
@@ -182,11 +174,7 @@ void QtSLiMGraphView_PopulationVisualization::drawArrowFromSubpopToSubpop(QPaint
 	// now we figure out our line width, and we calculate a spatial translation of the bezier to shift in slightly off of
 	// the midline, based on the line width, so that incoming and outgoing vectors do not overlap at the start/end points
 	double lineWidth = 0.001 * (sqrt(migrantFraction) / 0.03);	// non-linear line width scale
-#if PERRY_ICON
-    double finalShiftMagnitude = 0.0;
-#else    
 	double finalShiftMagnitude = std::max(lineWidth * 0.75, 0.010);
-#endif
 	double finalShiftX = perpendicularFromSourceDX * finalShiftMagnitude / partVecLength;
 	double finalShiftY = perpendicularFromSourceDY * finalShiftMagnitude / partVecLength;
 	double arrowheadSize = std::max(lineWidth * 1.5, 0.008);
@@ -208,20 +196,14 @@ void QtSLiMGraphView_PopulationVisualization::drawArrowFromSubpopToSubpop(QPaint
 	double shiftedControl1X = controlPoint1X + finalShiftX, shiftedControl1Y = controlPoint1Y + finalShiftY;
 	double shiftedControl2X = controlPoint2X + finalShiftX, shiftedControl2Y = controlPoint2Y + finalShiftY;
 
-#if PERRY_ICON
-    bezierLines.moveTo(QPointF(shiftedSourceEndX, shiftedSourceEndY));
-    bezierLines.lineTo(QPointF(shiftedDestEndX, shiftedDestEndY));
-#else    
     bezierLines.moveTo(QPointF(shiftedSourceEndX, shiftedSourceEndY));
     bezierLines.cubicTo(QPointF(shiftedControl1X, shiftedControl1Y), QPointF(shiftedControl2X, shiftedControl2Y), QPointF(shiftedDestEndX, shiftedDestEndY));
-#endif
 
     painter.strokePath(bezierLines, QPen(Qt::black, lineWidth));
 
 	// restore the clipping path
     painter.restore();
 
-#if !PERRY_ICON    
 	// draw the arrowhead; this is oriented along the line from (shiftedDestEndX, shiftedDestEndY) to (shiftedControl2X, shiftedControl2Y),
 	// of length partVecLength, and is calculated using a perpendicular off of that vector
     QPainterPath bezierArrowheads;
@@ -242,7 +224,6 @@ void QtSLiMGraphView_PopulationVisualization::drawArrowFromSubpopToSubpop(QPaint
     bezierArrowheads.closeSubpath();
 
     painter.fillPath(bezierArrowheads, Qt::black);
-#endif
 }
 
 static bool is_line_intersection(double p0_x, double p0_y, double p1_x, double p1_y, double p2_x, double p2_y, double p3_x, double p3_y)

QtSLiM/QtSLiMWindow.cpp

@@ -4163,7 +4163,7 @@ void QtSLiMWindow::displayProfileResults(void)
 		}
 	}
 
-#if SLIM_USE_NONNEUTRAL_CACHES
+#if SLIM_PROFILE_NONNEUTRAL_CACHES()
 	//
 	//	MutationRun metrics, presented per Species
 	//

QtSLiM/main.cpp

@@ -15,7 +15,7 @@
 #include "eidos_globals.h"
 #include "interaction_type.h"
 
-#if SLIM_LEAK_CHECKING
+#if SLIM_LEAK_CHECKING()
 static void clean_up_leak_false_positives(void)
 {
 	// This does a little cleanup that helps Valgrind to understand that some things have not been leaked.
@@ -332,7 +332,7 @@ int main(int argc, char *argv[])
     // Run the event loop
     int appReturn = app.exec();
 
-#if SLIM_LEAK_CHECKING
+#if SLIM_LEAK_CHECKING()
     clean_up_leak_false_positives();
 #endif
 

SLiMgui/SLiMWindowController.mm

@@ -1965,7 +1965,7 @@ - (void)displayProfileResults
 		}
 	}
 
-#if SLIM_USE_NONNEUTRAL_CACHES
+#if SLIM_PROFILE_NONNEUTRAL_CACHES()
 	//
 	//	MutationRun metrics, presented per Species
 	//

TO_DO

@@ -18,7 +18,7 @@ look for exported symbols that are not tagged with "eidos" or "Eidos" somewhere
 dump demangled symbols from SLiMgui:
 	nm -g -U -j ./SLiMgui | c++filt
 
-some valgrind commands (set SLIM_LEAK_CHECKING to 1, and change the compile C/C++ flags to -O1 -g):
+some valgrind commands (set SLIM_LEAK_CHECKING() to 1, and change the compile C/C++ flags to -O1 -g):
 	valgrind --leak-check=yes --track-origins=yes --expensive-definedness-checks=yes --num-callers=20 ./slim -testEidos		(with Debug version)
 	valgrind --leak-check=yes --track-origins=yes --expensive-definedness-checks=yes --num-callers=20 ./slim -testSLiM		(with Debug version)
 	valgrind --tool=cachegrind ./slim -seed 1 /Users/bhaller/Desktop/MK_SLiMGUIsim4.txt		(with Release version)

VERSIONS

@@ -145,6 +145,7 @@ multitrait branch:
 		add trait pseudo-parameter to mutationEffect() callbacks
 		add [Niso<Trait>$ trait = NULL] parameter to registerMutationEffectCallback() to allow the trait specifier to be given (defaults to NULL for backward compatibility)
 	add a new return option for mutationEffect() callbacks: NULL now indicates neutrality for the focal trait, meaning either 1.0 (multiplicative) or 0.0 (additive)
+	re-enable non-neutral caching (but without independent dominance optimizations, so far)
 
 
 version 5.1 (Eidos version 4.1):
@@ -340,7 +341,7 @@ version 5.0 (Eidos version 4.0):
 		add a "page guide at column" pref to SLiMgui, for those trying to lay out code to a maximum width
 		fix a SLiMgui bug where an error panel would not be visible because it was obscured by a floating window above it, appearing to lock up the whole app
 		fixed a long-standing SLiMgui bug involving mutation frequencies and mutation run reuse when a subset of the subpopulations are selected in the GUI
-			as part of this, (1) cleaned up and improved the SLIM_CLEAR_HAPLOSOMES debugging code, (2) separated SLiMgui's refcounting more completely from
+			as part of this, (1) cleaned up and improved the SLIM_CLEAR_HAPLOSOMES() debugging code, (2) separated SLiMgui's refcounting more completely from
 			SLiM's, and (3) fixed unreleased bugs in mutationFrequencies()/mutationCounts()/mutationFrequenciesInHaplosomes()/mutationCountsInHaplosomes()
 		cleaned up the confusion around Dictionary vs. DictionaryBase; methods/functions can now use Dictionary in their signature without problems
 		fix a bug in treeSeqMetadata(); if no metadata was found, it would return object<Dictionary>(0), not an empty Dictionary object (and it leaked)

core/chromosome.cpp

@@ -1074,10 +1074,7 @@ Mutation *Chromosome::ApplyMutationCallbacks(Mutation *p_mut, Haplosome *p_haplo
 
 			if ((callback_mutation_type_id == -1) || (callback_mutation_type_id == mutation_type_id))
 			{
-#ifndef DEBUG_POINTS_ENABLED
-#error "DEBUG_POINTS_ENABLED is not defined; include eidos_globals.h"
-#endif
-#if DEBUG_POINTS_ENABLED
+#if DEBUG_POINTS_ENABLED()
 				// SLiMgui debugging point
 				EidosDebugPointIndent indenter;
 

core/chromosome.h

@@ -283,14 +283,14 @@ class Chromosome : public EidosDictionaryRetained
 
 	// PROFILING : Chromosome keeps track of some additional profile information that is per-chromosome
 #if (SLIMPROFILING == 1)
-#if SLIM_USE_NONNEUTRAL_CACHES
+#if SLIM_PROFILE_NONNEUTRAL_CACHES()
 	std::vector<int32_t> profile_mutcount_history_;									// a record of the mutation run count used in each cycle
 	int64_t profile_mutation_total_usage_ = 0;										// how many (non-unique) mutations were used by mutation runs, summed across cycles
 	int64_t profile_nonneutral_mutation_total_ = 0;									// of profile_mutation_total_usage_, how many were deemed to be nonneutral
 	int64_t profile_mutrun_total_usage_ = 0;										// how many (non-unique) mutruns were used by haplosomes, summed across cycles
 	int64_t profile_unique_mutrun_total_ = 0;										// of profile_mutrun_total_usage_, how many unique mutruns existed, summed across cycles
 	int64_t profile_mutrun_nonneutral_recache_total_ = 0;							// of profile_unique_mutrun_total_, how many mutruns regenerated their nonneutral cache
-#endif	// SLIM_USE_NONNEUTRAL_CACHES
+#endif	// SLIM_PROFILE_NONNEUTRAL_CACHES()
 #endif	// (SLIMPROFILING == 1)
 
 	Chromosome(const Chromosome&) = delete;									// no copying
@@ -744,13 +744,13 @@ inline __attribute__((always_inline)) Haplosome *Chromosome::NewHaplosome_NONNUL
 			if (mutrun_count_ <= SLIM_HAPLOSOME_MUTRUN_BUFSIZE)
 			{
 				back->mutruns_ = back->run_buffer_;
-#if SLIM_CLEAR_HAPLOSOMES
+#if SLIM_CLEAR_HAPLOSOMES()
 				EIDOS_BZERO(back->run_buffer_, SLIM_HAPLOSOME_MUTRUN_BUFSIZE * sizeof(const MutationRun *));
 #endif
 			}
 			else
 			{
-#if SLIM_CLEAR_HAPLOSOMES
+#if SLIM_CLEAR_HAPLOSOMES()
 				back->mutruns_ = (const MutationRun **)calloc(mutrun_count_, sizeof(const MutationRun *));
 #else
 				back->mutruns_ = (const MutationRun **)malloc(mutrun_count_ * sizeof(const MutationRun *));
@@ -759,7 +759,7 @@ inline __attribute__((always_inline)) Haplosome *Chromosome::NewHaplosome_NONNUL
 		}
 		else
 		{
-#if SLIM_CLEAR_HAPLOSOMES
+#if SLIM_CLEAR_HAPLOSOMES()
 			// the number of mutruns is unchanged, but we need to zero out the reused buffer here
 			EIDOS_BZERO(back->mutruns_, mutrun_count_ * sizeof(const MutationRun *));
 #endif
@@ -782,7 +782,7 @@ inline __attribute__((always_inline)) void Chromosome::FreeHaplosome(Haplosome *
 #if DEBUG
 	p_haplosome->individual_ = nullptr;		// crash if anybody tries to use this pointer after the free
 #endif
-#if SLIM_CLEAR_HAPLOSOMES
+#if SLIM_CLEAR_HAPLOSOMES()
 	p_haplosome->clear_to_nullptr();
 #endif
 

core/community.cpp

@@ -52,7 +52,7 @@
 #include <ctime>
 
 #include "eidos_globals.h"
-#if EIDOS_ROBIN_HOOD_HASHING
+#if EIDOS_ROBIN_HOOD_HASHING()
 #include "robin_hood.h"
 #endif
 
@@ -2421,10 +2421,7 @@ void Community::ExecuteEidosEvent(SLiMEidosBlock *p_script_block)
 	if (!p_script_block->block_active_)
 		return;
 
-#ifndef DEBUG_POINTS_ENABLED
-#error "DEBUG_POINTS_ENABLED is not defined; include eidos_globals.h"
-#endif
-#if DEBUG_POINTS_ENABLED
+#if DEBUG_POINTS_ENABLED()
 	// SLiMgui debugging point
 	EidosDebugPointIndent indenter;
 
@@ -2645,7 +2642,7 @@ bool Community::_RunOneTickWF(void)
 {
 #if (SLIMPROFILING == 1)
 	// PROFILING
-#if SLIM_USE_NONNEUTRAL_CACHES
+#if SLIM_PROFILE_NONNEUTRAL_CACHES()
 	if (gEidosProfilingClientCount)
 		for (Species *species : all_species_)
 			species->CollectMutationProfileInfo();
@@ -3008,7 +3005,7 @@ bool Community::_RunOneTickNonWF(void)
 {
 #if (SLIMPROFILING == 1)
 	// PROFILING
-#if SLIM_USE_NONNEUTRAL_CACHES
+#if SLIM_PROFILE_NONNEUTRAL_CACHES()
 	if (gEidosProfilingClientCount)
 		for (Species *species : all_species_)
 			species->CollectMutationProfileInfo();
@@ -3548,7 +3545,7 @@ void Community::StartProfiling(void)
 			signature->body_script_->AST()->ZeroProfileTotals();
 	}
 
-#if SLIM_USE_NONNEUTRAL_CACHES
+#if SLIM_PROFILE_NONNEUTRAL_CACHES()
 	// zero out mutation run metrics that are collected by CollectMutationProfileInfo()
 	for (Species *focal_species : all_species_)
 	{