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integrated david dao's faster implementation of the plausibility chec…
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…ker algorithm (-f R option)
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@stamatak
stamatak committed Nov 22, 2013
1 parent 198ca23 commit cbe6887
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Showing 34 changed files with 1,295 additions and 61 deletions.
5 changes: 3 additions & 2 deletions Makefile.AVX.HYBRID.gcc
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Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,11 @@ LIBRARIES = -lm -pthread

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC-HYBRID-AVX

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h

raxmlHPC-HYBRID-AVX : $(objs)
$(CC) -o raxmlHPC-HYBRID-AVX $(objs) $(LIBRARIES)
Expand All @@ -23,6 +23,7 @@ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX.MPI.gcc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,11 @@ LIBRARIES = -lm

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC-MPI-AVX

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h

raxmlHPC-MPI-AVX : $(objs)
$(CC) -o raxmlHPC-MPI-AVX $(objs) $(LIBRARIES)
Expand All @@ -23,6 +23,7 @@ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX.PTHREADS.gcc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ LIBRARIES = -lm -pthread

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h

raxmlHPC : $(objs)
$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES)
Expand All @@ -26,6 +26,7 @@ fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

#rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX.PTHREADS.mac
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ LIBRARIES = -lm -pthread

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h

raxmlHPC : $(objs)
$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES)
Expand All @@ -26,6 +26,7 @@ fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

#rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
7 changes: 4 additions & 3 deletions Makefile.AVX.gcc
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Original file line number Diff line number Diff line change
Expand Up @@ -3,17 +3,17 @@

CC = gcc

CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-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
CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-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

LIBRARIES = -lm

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC

GLOBAL_DEPS = axml.h globalVariables.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h

raxmlHPC : $(objs)
$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES)
Expand All @@ -24,6 +24,7 @@ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX.mac
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,11 @@ LIBRARIES = -lm

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h

raxmlHPC : $(objs)
$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES)
Expand All @@ -26,6 +26,7 @@ fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)



rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX2.HYBRID.gcc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,11 @@ LIBRARIES = -lm -pthread

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC-HYBRID-AVX2

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h

raxmlHPC-HYBRID-AVX2 : $(objs)
$(CC) -o raxmlHPC-HYBRID-AVX2 $(objs) $(LIBRARIES)
Expand All @@ -23,6 +23,7 @@ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX2.MPI.gcc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,11 @@ LIBRARIES = -lm

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC-MPI-AVX2

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h

raxmlHPC-MPI-AVX2 : $(objs)
$(CC) -o raxmlHPC-MPI-AVX2 $(objs) $(LIBRARIES)
Expand All @@ -23,6 +23,7 @@ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX2.PTHREADS.gcc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ LIBRARIES = -lm -pthread

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h

raxmlHPC : $(objs)
$(CC) -o raxmlHPC-PTHREADS-AVX2 $(objs) $(LIBRARIES)
Expand All @@ -26,6 +26,7 @@ fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

#rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX2.PTHREADS.mac
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ LIBRARIES = -lm -pthread

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h

raxmlHPC : $(objs)
$(CC) -o raxmlHPC-PTHREADS-AVX2 $(objs) $(LIBRARIES)
Expand All @@ -26,6 +26,7 @@ fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

#rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX2.gcc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,11 @@ LIBRARIES = -lm

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC

GLOBAL_DEPS = axml.h globalVariables.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h

raxmlHPC : $(objs)
$(CC) -o raxmlHPC-AVX2 $(objs) $(LIBRARIES)
Expand All @@ -24,6 +24,7 @@ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
$(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.AVX2.mac
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,11 @@ LIBRARIES = -lm

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o

all : raxmlHPC

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h

raxmlHPC : $(objs)
$(CC) -o raxmlHPC-AVX2 $(objs) $(LIBRARIES)
Expand All @@ -26,6 +26,7 @@ fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)



rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
5 changes: 3 additions & 2 deletions Makefile.HYBRID.gcc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,15 +10,16 @@ LIBRARIES = -lm -pthread

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o ancestralStates.o mem_alloc.o
objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o mem_alloc.o

all : raxmlHPC-HYBRID

GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h
GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h

raxmlHPC-HYBRID : $(objs)
$(CC) -o raxmlHPC-HYBRID $(objs) $(LIBRARIES)

rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
Expand Down
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