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spack/var/spack/repos/builtin/packages/raxml/nox86.patch
Toyohisa Kameyama 93f6833990 raxml: compile n non-x86 hosts. (#12208) 
1. xmmintrrin.h is included x86 only.
2. Add makefiles for non-x86 hosts.
3. mpicc in Makefiles is replaced spacks mpi compile command.
4. variant check is rewite with satisfies.
2019-08-02 19:04:25 -05:00

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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 <xmmintrin.h>
/*
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 <peter@cordes.ca>
+
+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 <peter@cordes.ca>
+
+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
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