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Use "SIMD Everywhere" to enable wider portability #16

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3 changes: 3 additions & 0 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
[submodule "simde"]
path = simde
url = https://github.com/nemequ/simde-no-tests.git
6 changes: 3 additions & 3 deletions examl/Makefile.AVX.gcc
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Expand Up @@ -3,7 +3,7 @@

CC = mpicc

COMMON_FLAGS = -D__SIM_SSE3 -D__AVX -D_OPTIMIZED_FUNCTIONS -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE #-Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter
COMMON_FLAGS = -I.. -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE #-Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter

OPT_FLAG_1 = -O1
OPT_FLAG_2 = -O2
Expand All @@ -21,10 +21,10 @@ all : clean examl-AVX
GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h

examl-AVX : $(objs)
$(CC) -o examl-AVX $(objs) $(LIBRARIES) $(LDFLAGS)
$(CC) $(CFLAGS) -o $@ $(objs) $(LIBRARIES) $(LDFLAGS)

avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) $(CPPFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
$(CC) $(CFLAGS) $(CPPFLAGS) -mavx -c -o $@ avxLikelihood.c

models.o : models.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) $(COMMON_FLAGS) $(OPT_FLAG_1) $(CPPFLAGS) -c -o models.o models.c
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4 changes: 2 additions & 2 deletions examl/Makefile.KNL.icc
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Expand Up @@ -7,7 +7,7 @@ CC = mpicc

KNLFLAGS=-xMIC-AVX512 -fma -align -finline-functions -D__MIC_NATIVE -qopenmp -D_USE_OMP

COMMON_FLAGS = -std=c99 -D__SIM_SSE3 -D_OPTIMIZED_FUNCTIONS -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE $(KNLFLAGS) # -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter
COMMON_FLAGS = -I.. -std=c99 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE $(KNLFLAGS) # -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter

OPT_FLAG_1 = -O1
OPT_FLAG_2 = -O2
Expand All @@ -25,7 +25,7 @@ all : clean examl-KNL
GLOBAL_DEPS = axml.h globalVariables.h

examl-KNL : $(objs)
$(CC) -o examl-KNL $(objs) $(LIBRARIES)
$(CC) $(CFLAGS) -o examl-KNL $(objs) $(LIBRARIES)

models.o : models.c $(GLOBAL_DEPS)
$(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c
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4 changes: 2 additions & 2 deletions examl/Makefile.MIC.icc
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Expand Up @@ -4,7 +4,7 @@
CC = mpicc

MICFLAGS = -D__MIC_NATIVE -mmic -qopt-streaming-cache-evict=0 -qopenmp -D_USE_OMP #-D_PROFILE_MPI
COMMON_FLAGS = -std=c99 -D__SIM_SSE3 -D_OPTIMIZED_FUNCTIONS -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE $(MICFLAGS) # -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter
COMMON_FLAGS = -I.. -std=c99 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE $(MICFLAGS) # -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter

OPT_FLAG_1 = -O1
OPT_FLAG_2 = -O2
Expand All @@ -22,7 +22,7 @@ all : clean examl-MIC
GLOBAL_DEPS = axml.h globalVariables.h

examl-MIC : $(objs)
$(CC) -o examl-MIC $(objs) $(LIBRARIES)
$(CC) $(CFLAGS) -o examl-MIC $(objs) $(LIBRARIES)

models.o : models.c $(GLOBAL_DEPS)
$(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c
Expand Down
6 changes: 3 additions & 3 deletions examl/Makefile.OMP.AVX.gcc
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Expand Up @@ -3,7 +3,7 @@

CC = mpicc

COMMON_FLAGS = -D__SIM_SSE3 -D__AVX -D_USE_OMP -fopenmp -D_OPTIMIZED_FUNCTIONS -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE -Wall # -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter
COMMON_FLAGS = -I.. -D_USE_OMP -fopenmp -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE -Wall # -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter

OPT_FLAG_1 = -O1
OPT_FLAG_2 = -O2
Expand All @@ -21,10 +21,10 @@ all : clean examl-OMP-AVX
GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h

examl-OMP-AVX : $(objs)
$(CC) -o examl-OMP-AVX $(objs) $(LIBRARIES) $(LDFLAGS)
$(CC) $(CFLAGS) -o $@ $(objs) $(LIBRARIES) $(LDFLAGS)

avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
$(CC) $(CFLAGS) -mavx -c -o $@ avxLikelihood.c

models.o : models.c $(GLOBAL_DEPS)
$(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c
Expand Down
14 changes: 9 additions & 5 deletions examl/Makefile.OMP.SSE3.gcc
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Expand Up @@ -3,9 +3,9 @@

CC = mpicc

COMMON_FLAGS = -D_USE_OMP -fopenmp -D_GNU_SOURCE -D__SIM_SSE3 -msse3 -fomit-frame-pointer -funroll-loops -D_OPTIMIZED_FUNCTIONS -D_USE_ALLREDUCE -Wall #-Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter
COMMON_FLAGS = -I.. -D_USE_OMP -fopenmp -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE -Wall #-Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter

OPT_FLAG_1 = -O1
OPT_FLAG_1 = -O1
OPT_FLAG_2 = -O2

CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
Expand All @@ -14,14 +14,17 @@ LIBRARIES = -lm -fopenmp

RM = rm -f

objs = axml.o optimizeModel.o trash.o searchAlgo.o topologies.o treeIO.o models.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o bipartitionList.o restartHashTable.o byteFile.o partitionAssignment.o communication.o quartets.o
objs = axml.o optimizeModel.o trash.o searchAlgo.o topologies.o treeIO.o models.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o bipartitionList.o restartHashTable.o avxLikelihood.o byteFile.o partitionAssignment.o communication.o quartets.o

all : clean examl-OMP

GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h

examl-OMP : $(objs)
$(CC) -o examl-OMP $(objs) $(LIBRARIES) $(LDFLAGS)
$(CC) $(CFLAGS) -o $@ $(objs) $(LIBRARIES) $(LDFLAGS)

avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -c -o $@ avxLikelihood.c

models.o : models.c $(GLOBAL_DEPS)
$(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c
Expand All @@ -34,6 +37,7 @@ axml.o : axml.c $(GLOBAL_DEPS)
searchAlgo.o : searchAlgo.c $(GLOBAL_DEPS)
topologies.o : topologies.c $(GLOBAL_DEPS)
treeIO.o : treeIO.c $(GLOBAL_DEPS)
quartets.o : quartets.c $(GLOBAL_DEPS)
models.o : models.c $(GLOBAL_DEPS)
evaluatePartialGenericSpecial.o : evaluatePartialGenericSpecial.c $(GLOBAL_DEPS)
evaluateGenericSpecial.o : evaluateGenericSpecial.c $(GLOBAL_DEPS)
Expand All @@ -43,7 +47,7 @@ restartHashTable.o : restartHashTable.c $(GLOBAL_DEPS)
byteFile.o : byteFile.c
partitionAssignment.o : partitionAssignment.c $(GLOBAL_DEPS)
communication.o : communication.c $(GLOBAL_DEPS)
quartets.o : quartets.c $(GLOBAL_DEPS)


clean :
$(RM) *.o examl-OMP
Expand Down
17 changes: 10 additions & 7 deletions examl/Makefile.SSE3.gcc
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Expand Up @@ -3,10 +3,9 @@

CC = mpicc

COMMON_FLAGS = -I.. -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter

COMMON_FLAGS = -D_GNU_SOURCE -D__SIM_SSE3 -msse3 -fomit-frame-pointer -funroll-loops -D_OPTIMIZED_FUNCTIONS -D_USE_ALLREDUCE #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -Wno-unused-parameter

OPT_FLAG_1 = -O1
OPT_FLAG_1 = -O1
OPT_FLAG_2 = -O2

CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
Expand All @@ -15,17 +14,20 @@ LIBRARIES = -lm

RM = rm -f

objs = axml.o optimizeModel.o trash.o searchAlgo.o topologies.o treeIO.o models.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o bipartitionList.o restartHashTable.o byteFile.o partitionAssignment.o communication.o quartets.o
objs = axml.o optimizeModel.o trash.o searchAlgo.o topologies.o treeIO.o models.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o bipartitionList.o restartHashTable.o avxLikelihood.o byteFile.o partitionAssignment.o communication.o quartets.o

all : clean examl

GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h

examl : $(objs)
$(CC) -o examl $(objs) $(LIBRARIES) $(LDFLAGS)
$(CC) $(CFLAGS) -o $@ $(objs) $(LIBRARIES) $(LDFLAGS)

avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ avxLikelihood.c

models.o : models.c $(GLOBAL_DEPS)
$(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c
$(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) $(CPPFLAGS) -c -o models.o models.c

bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
Expand All @@ -35,6 +37,7 @@ axml.o : axml.c $(GLOBAL_DEPS)
searchAlgo.o : searchAlgo.c $(GLOBAL_DEPS)
topologies.o : topologies.c $(GLOBAL_DEPS)
treeIO.o : treeIO.c $(GLOBAL_DEPS)
quartets.o : quartets.c $(GLOBAL_DEPS)
models.o : models.c $(GLOBAL_DEPS)
evaluatePartialGenericSpecial.o : evaluatePartialGenericSpecial.c $(GLOBAL_DEPS)
evaluateGenericSpecial.o : evaluateGenericSpecial.c $(GLOBAL_DEPS)
Expand All @@ -44,7 +47,7 @@ restartHashTable.o : restartHashTable.c $(GLOBAL_DEPS)
byteFile.o : byteFile.c
partitionAssignment.o : partitionAssignment.c $(GLOBAL_DEPS)
communication.o : communication.c $(GLOBAL_DEPS)
quartets.o : quartets.c $(GLOBAL_DEPS)


clean :
$(RM) *.o examl
Expand Down
5 changes: 2 additions & 3 deletions examl/avxLikelihood.c
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Expand Up @@ -10,9 +10,8 @@
#include <limits.h>
#include "axml.h"
#include <stdint.h>
#include <xmmintrin.h>
#include <pmmintrin.h>
#include <immintrin.h>
#define SIMDE_ENABLE_NATIVE_ALIASES
#include "simde/x86/avx2.h"

#ifdef _FMA
#include <x86intrin.h>
Expand Down
7 changes: 5 additions & 2 deletions examl/axml.c
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Expand Up @@ -52,7 +52,9 @@

#include <mpi.h>

#if ! (defined(__ppc) || defined(__powerpc__) || defined(PPC))
#define SIMDE_ENABLE_NATIVE_ALIASES
#include "simde/x86/sse.h"
#if defined(SIMDE_SSE_NATIVE)
#include <xmmintrin.h>
/*
special bug fix, enforces denormalized numbers to be flushed to zero,
Expand Down Expand Up @@ -2591,7 +2593,8 @@ int main (int argc, char *argv[])
substantial run-time differences for vectors of equal length.
*/

#if ! (defined(__ppc) || defined(__powerpc__) || defined(PPC))
#if defined(SIMDE_SSE_NATIVE)
# include <xmmintrin.h>
_mm_setcsr( _mm_getcsr() | _MM_FLUSH_ZERO_ON);
#endif

Expand Down
8 changes: 1 addition & 7 deletions examl/axml.h
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Expand Up @@ -42,11 +42,8 @@
#ifdef __MIC_NATIVE
#define BYTE_ALIGNMENT 64
#define VECTOR_PADDING 8
#elif defined __AVX
#define BYTE_ALIGNMENT 32
#define VECTOR_PADDING 1
#else
#define BYTE_ALIGNMENT 16
#define BYTE_ALIGNMENT 32
#define VECTOR_PADDING 1
#endif

Expand Down Expand Up @@ -1337,8 +1334,6 @@ extern void scaleLG4X_EIGN(tree *tr, int model);
extern void myBinFwrite(void *ptr, size_t size, size_t nmemb, FILE *byteFile);
extern void myBinFread(void *ptr, size_t size, size_t nmemb, FILE *byteFile);

#ifdef __AVX

extern void newviewGTRGAMMAPROT_AVX_LG4(int tipCase,
double *x1, double *x2, double *x3, double *extEV[4], double *tipVector[4],
int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n,
Expand Down Expand Up @@ -1401,7 +1396,6 @@ void newviewGTRGAMMAPROT_AVX_GAPPED_SAVE(int tipCase,
double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling,
unsigned int *x1_gap, unsigned int *x2_gap, unsigned int *x3_gap,
double *x1_gapColumn, double *x2_gapColumn, double *x3_gapColumn);
#endif



Expand Down
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