diff -rNu spack-src/axml.c spack-src.new/axml.c --- spack-src/axml.c 2017-06-28 17:39:42.000000000 +0900 +++ spack-src.new/axml.c 2019-07-31 09:56:14.337741033 +0900 @@ -66,7 +66,7 @@ #endif -#if ! (defined(__ppc) || defined(__powerpc__) || defined(PPC)) +#if defined(__x86_64) #include /* special bug fix, enforces denormalized numbers to be flushed to zero, @@ -13702,7 +13702,7 @@ -#if ! (defined(__ppc) || defined(__powerpc__) || defined(PPC)) +#if defined(__x86_64) /* David Defour's command diff -rNu spack-src/Makefile.HYBRID.nox86.gcc spack-src.new/Makefile.HYBRID.nox86.gcc --- spack-src/Makefile.HYBRID.nox86.gcc 1970-01-01 09:00:00.000000000 +0900 +++ spack-src.new/Makefile.HYBRID.nox86.gcc 2019-07-31 09:58:59.087746805 +0900 @@ -0,0 +1,51 @@ +# Makefile November 2009 by Alexandros Stamatakis + +CC = mpicc + + +CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS + + +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 rmqs.o rogueEPA.o ancestralStates.o mem_alloc.o eigen.o + +all : clean raxmlHPC-HYBRID + +GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h /fefs/home/r0001/work/spack/lib/spack/env/gcc/gcc.h ll_asm.h ll_list.h + +raxmlHPC-HYBRID : $(objs) + $(CC) -o raxmlHPC-HYBRID $(objs) $(LIBRARIES) $(LDFLAGS) + +rmqs.o : rmqs.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) +rogueEPA.o : rogueEPA.c $(GLOBAL_DEPS) +ancestralStates.o : ancestralStates.c $(GLOBAL_DEPS) + mem_alloc.o eigen.o : mem_alloc.c $(GLOBAL_DEPS) + +eigen.o : eigen.c $(GLOBAL_DEPS) + $(CC) -c -o eigen.o eigen.c +clean : + $(RM) *.o raxmlHPC-HYBRID + +dev : raxmlHPC-HYBRID diff -rNu spack-src/Makefile.MPI.nox86.gcc spack-src.new/Makefile.MPI.nox86.gcc --- spack-src/Makefile.MPI.nox86.gcc 1970-01-01 09:00:00.000000000 +0900 +++ spack-src.new/Makefile.MPI.nox86.gcc 2019-07-31 09:59:25.937748520 +0900 @@ -0,0 +1,51 @@ +# Makefile November 2009 by Alexandros Stamatakis + +CC = mpicc + + +CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 + + +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 rmqs.o rogueEPA.o ancestralStates.o mem_alloc.o eigen.o + +all : clean raxmlHPC-MPI + +GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h + +raxmlHPC-MPI : $(objs) + $(CC) -o raxmlHPC-MPI $(objs) $(LIBRARIES) $(LDFLAGS) + +rmqs.o : rmqs.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) +rogueEPA.o : rogueEPA.c $(GLOBAL_DEPS) +ancestralStates.o : ancestralStates.c $(GLOBAL_DEPS) + mem_alloc.o eigen.o : mem_alloc.c $(GLOBAL_DEPS) + +eigen.o : eigen.c $(GLOBAL_DEPS) + $(CC) -c -o eigen.o eigen.c +clean : + $(RM) *.o raxmlHPC-MPI + +dev : raxmlHPC-MPI diff -rNu spack-src/Makefile.nox86.gcc spack-src.new/Makefile.nox86.gcc --- spack-src/Makefile.nox86.gcc 1970-01-01 09:00:00.000000000 +0900 +++ spack-src.new/Makefile.nox86.gcc 2019-07-31 09:59:47.987749919 +0900 @@ -0,0 +1,53 @@ +# Makefile August 2006 by Alexandros Stamatakis +# Makefile cleanup October 2006, Courtesy of Peter Cordes + +CC = gcc + + +CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 #-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 rmqs.o rogueEPA.o ancestralStates.o mem_alloc.o eigen.o + +all : clean raxmlHPC + +GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h + +raxmlHPC : $(objs) + $(CC) -o raxmlHPC $(objs) $(LIBRARIES) $(LDFLAGS) + +rmqs.o : rmqs.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) +rogueEPA.o : rogueEPA.c $(GLOBAL_DEPS) +ancestralStates.o : ancestralStates.c $(GLOBAL_DEPS) +mem_alloc.o eigen.o : mem_alloc.c $(GLOBAL_DEPS) + + + +eigen.o : eigen.c $(GLOBAL_DEPS) + $(CC) -c -o eigen.o eigen.c +clean : + $(RM) *.o raxmlHPC + +dev : raxmlHPC diff -rNu spack-src/Makefile.PTHREADS.nox86.gcc spack-src.new/Makefile.PTHREADS.nox86.gcc --- spack-src/Makefile.PTHREADS.nox86.gcc 1970-01-01 09:00:00.000000000 +0900 +++ spack-src.new/Makefile.PTHREADS.nox86.gcc 2019-07-31 10:00:07.397751144 +0900 @@ -0,0 +1,52 @@ +# Makefile August 2006 by Alexandros Stamatakis +# Makefile cleanup October 2006, Courtesy of Peter Cordes + +CC = gcc + + +CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS #-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 rmqs.o rogueEPA.o ancestralStates.o mem_alloc.o eigen.o + +all : clean raxmlHPC-PTHREADS + +GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h /fefs/home/r0001/work/spack/lib/spack/env/gcc/gcc.h ll_asm.h ll_list.h + +raxmlHPC-PTHREADS : $(objs) + $(CC) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES) $(LDFLAGS) + +rmqs.o : rmqs.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) +rogueEPA.o : rogueEPA.c $(GLOBAL_DEPS) +ancestralStates.o : ancestralStates.c $(GLOBAL_DEPS) +mem_alloc.o eigen.o : mem_alloc.c $(GLOBAL_DEPS) + +eigen.o : eigen.c $(GLOBAL_DEPS) + $(CC) -c -o eigen.o eigen.c +clean : + $(RM) *.o raxmlHPC-PTHREADS + +dev : raxmlHPC-PTHREADS