Permalink
Browse files

added some .mac Makefiles for MACs, compilation with llaloc for bette…

…r performance

with the -U memory saving option for gappy datasets did not work
  • Loading branch information...
1 parent 126d3a4 commit e5de6b36570ce3789795a8df2b9f8558fff911f2 @stamatak committed May 7, 2013
Showing with 95 additions and 3 deletions.
  1. +2 −3 Makefile.AVX.PTHREADS.mac
  2. +47 −0 Makefile.PTHREADS.mac
  3. +46 −0 Makefile.SSE3.PTHREADS.mac
View
5 Makefile.AVX.PTHREADS.mac
@@ -3,14 +3,14 @@
CC = clang
-CFLAGS = -D_USE_PTHREADS -D_RAXML_USE_LLALLOC -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -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 -Wdeclaration-after-statement -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_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -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 -Wdeclaration-after-statement -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 -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 ll_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 rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o
all : raxmlHPC
@@ -46,7 +46,6 @@ fastSearch.o : fastSearch.c $(GLOBAL_DEPS)
leaveDropping.o : leaveDropping.c $(GLOBAL_DEPS)
ancestralStates.o : ancestralStates.c $(GLOBAL_DEPS)
mem_alloc.o : mem_alloc.c $(GLOBAL_DEPS)
-ll_alloc.o : ll_alloc.c $(GLOBAL_DEPS)
clean :
$(RM) *.o raxmlHPC-PTHREADS-AVX
View
47 Makefile.PTHREADS.mac
@@ -0,0 +1,47 @@
+# Makefile August 2006 by Alexandros Stamatakis
+# Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+
+CC = gcc
+
+
+CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse #-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 -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
+
+all : raxmlHPC-PTHREADS
+
+GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h
+
+raxmlHPC-PTHREADS : $(objs)
+ $(CC) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES)
+
+classify.o : classify.c $(GLOBAL_DEPS)
+evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
+optimizeModel.o : optimizeModel.c $(GLOBAL_DEPS)
+multiple.o : multiple.c $(GLOBAL_DEPS)
+axml.o : axml.c $(GLOBAL_DEPS)
+searchAlgo.o : searchAlgo.c $(GLOBAL_DEPS)
+topologies.o : topologies.c $(GLOBAL_DEPS)
+parsePartitions.o : parsePartitions.c $(GLOBAL_DEPS)
+treeIO.o : treeIO.c $(GLOBAL_DEPS)
+models.o : models.c $(GLOBAL_DEPS)
+rapidBootstrap.o : rapidBootstrap.c $(GLOBAL_DEPS)
+evaluatePartialGenericSpecial.o : evaluatePartialGenericSpecial.c $(GLOBAL_DEPS)
+evaluateGenericSpecial.o : evaluateGenericSpecial.c $(GLOBAL_DEPS)
+newviewGenericSpecial.o : newviewGenericSpecial.c $(GLOBAL_DEPS)
+makenewzGenericSpecial.o : makenewzGenericSpecial.c $(GLOBAL_DEPS)
+fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
+fastSearch.o : fastSearch.c $(GLOBAL_DEPS)
+leaveDropping.o : leaveDropping.c $(GLOBAL_DEPS)
+rogueEPA.o : rogueEPA.c $(GLOBAL_DEPS)
+ancestralStates.o : ancestralStates.c $(GLOBAL_DEPS)
+mem_alloc.o : mem_alloc.c $(GLOBAL_DEPS)
+
+clean :
+ $(RM) *.o raxmlHPC-PTHREADS
View
46 Makefile.SSE3.PTHREADS.mac
@@ -0,0 +1,46 @@
+# Makefile August 2006 by Alexandros Stamatakis
+# Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+
+CC = gcc
+
+CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops #-Wall -pedantic -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 -Wdeclaration-after-statement -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 -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
+
+all : raxmlHPC
+
+GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h
+
+raxmlHPC : $(objs)
+ $(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES)
+
+#rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
+classify.o : classify.c $(GLOBAL_DEPS)
+evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
+optimizeModel.o : optimizeModel.c $(GLOBAL_DEPS)
+multiple.o : multiple.c $(GLOBAL_DEPS)
+axml.o : axml.c $(GLOBAL_DEPS)
+searchAlgo.o : searchAlgo.c $(GLOBAL_DEPS)
+topologies.o : topologies.c $(GLOBAL_DEPS)
+parsePartitions.o : parsePartitions.c $(GLOBAL_DEPS)
+treeIO.o : treeIO.c $(GLOBAL_DEPS)
+models.o : models.c $(GLOBAL_DEPS)
+rapidBootstrap.o : rapidBootstrap.c $(GLOBAL_DEPS)
+evaluatePartialGenericSpecial.o : evaluatePartialGenericSpecial.c $(GLOBAL_DEPS)
+evaluateGenericSpecial.o : evaluateGenericSpecial.c $(GLOBAL_DEPS)
+newviewGenericSpecial.o : newviewGenericSpecial.c $(GLOBAL_DEPS)
+makenewzGenericSpecial.o : makenewzGenericSpecial.c $(GLOBAL_DEPS)
+fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
+fastSearch.o : fastSearch.c $(GLOBAL_DEPS)
+leaveDropping.o : leaveDropping.c $(GLOBAL_DEPS)
+ancestralStates.o : ancestralStates.c $(GLOBAL_DEPS)
+mem_alloc.o : mem_alloc.c $(GLOBAL_DEPS)
+
+clean :
+ $(RM) *.o raxmlHPC-PTHREADS-SSE3

0 comments on commit e5de6b3

Please sign in to comment.