diff options
Diffstat (limited to 'var')
| -rwxr-xr-x | var/spack/repos/builtin/packages/raxml/nox86.patch | 244 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/raxml/package.py | 147 |
2 files changed, 343 insertions, 48 deletions
diff --git a/var/spack/repos/builtin/packages/raxml/nox86.patch b/var/spack/repos/builtin/packages/raxml/nox86.patch new file mode 100755 index 0000000000..16ad6fa67a --- /dev/null +++ b/var/spack/repos/builtin/packages/raxml/nox86.patch @@ -0,0 +1,244 @@ +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 diff --git a/var/spack/repos/builtin/packages/raxml/package.py b/var/spack/repos/builtin/packages/raxml/package.py index 43751fea90..4a41030648 100644 --- a/var/spack/repos/builtin/packages/raxml/package.py +++ b/var/spack/repos/builtin/packages/raxml/package.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +from spack.spec import ConflictsInSpecError import glob @@ -19,11 +20,13 @@ class Raxml(Package): variant('mpi', default=True, description='Enable MPI parallel support') variant('pthreads', default=False, description='Enable pthreads version') - variant('sse', default=True, description='Enable SSE in order to substantially speed up execution') + variant('sse', default=False, description='Enable SSE in order to substantially speed up execution') variant('avx', default=False, description='Enable AVX in order to substantially speed up execution') depends_on('mpi', when='+mpi') + patch('nox86.patch') + # Compiles with either GCC or ICC. conflicts('%cce') conflicts('%clang') @@ -35,56 +38,104 @@ class Raxml(Package): # can't build multiple binaries in parallel without things breaking parallel = False + def flag_handler(self, name, flags): + arch = '' + spec = self.spec + if spec.satisfies("platform=cray"): + # FIXME; It is assumed that cray is x86_64. + # If you support arm on cray, you need to fix it. + arch = 'x86_64' + if (arch != 'x86_64' and not spec.satisfies("target=x86_64")): + if spec.satisfies("+sse"): + raise ConflictsInSpecError( + spec, + [( + spec, + spec.architecture.target, + spec.variants['sse'], + '+sse is valid only on x86_64' + )] + ) + if spec.satisfies("+avx"): + raise ConflictsInSpecError( + spec, + [( + spec, + spec.architecture.target, + spec.variants['avx'], + '+avx is valid only on x86_64' + )] + ) + return (flags, None, None) + def install(self, spec, prefix): mkdirp(prefix.bin) files = glob.iglob("Makefile.*") for file in files: makefile = FileFilter(file) makefile.filter('gcc', spack_cc) - - if '+mpi' and '+avx' and '+pthreads' in spec: - make('-f', 'Makefile.AVX.HYBRID.gcc') - install('raxmlHPC-HYBRID-AVX', prefix.bin) - - if '+mpi' and '+sse' and '+pthreads' in spec: - make('-f', 'Makefile.SSE3.HYBRID.gcc') - install('raxmlHPC-HYBRID-SSE3', prefix.bin) - - if '+mpi' and '+pthreads' in spec: - make('-f', 'Makefile.HYBRID.gcc') - install('raxmlHPC-HYBRID', prefix.bin) - - if '+mpi' and '+avx' in spec: - make('-f', 'Makefile.AVX.MPI.gcc') - install('raxmlHPC-MPI-AVX', prefix.bin) - - if '+mpi' and '+sse' in spec: - make('-f', 'Makefile.SSE3.MPI.gcc') - install('raxmlHPC-MPI-SSE3', prefix.bin) - - if '+mpi' in spec: - make('-f', 'Makefile.MPI.gcc') - install('raxmlHPC-MPI', prefix.bin) - - if '+pthreads' and '+avx' in spec: - make('-f', 'Makefile.AVX.PTHREADS.gcc') - install('raxmlHPC-PTHREADS-AVX', prefix.bin) - - if '+pthreads' and '+sse' in spec: - make('-f', 'Makefile.SSE3.PTHREADS.gcc') - install('raxmlHPC-PTHREADS-SSE3', prefix.bin) - - if '+pthreads' in spec: - make('-f', 'Makefile.PTHREADS.gcc') - install('raxmlHPC-PTHREADS', prefix.bin) - - if '+sse' in spec: - make('-f', 'Makefile.SSE3.gcc') - install('raxmlHPC-SSE3', prefix.bin) - - if '+avx' in spec: - make('-f', 'Makefile.AVX.gcc') - install('raxmlHPC-AVX', prefix.bin) - - make('-f', 'Makefile.gcc') - install('raxmlHPC', prefix.bin) + if spec.satisfies('+mpi'): + makefile.filter('mpicc', self.spec['mpi'].mpicc) + + if spec.satisfies('target=x86_64'): + if spec.satisfies('+mpi +avx +pthreads'): + make('-f', 'Makefile.AVX.HYBRID.gcc') + install('raxmlHPC-HYBRID-AVX', prefix.bin) + + if spec.satisfies('+mpi +sse +pthreads'): + make('-f', 'Makefile.SSE3.HYBRID.gcc') + install('raxmlHPC-HYBRID-SSE3', prefix.bin) + + if spec.satisfies('+mpi +pthreads'): + make('-f', 'Makefile.HYBRID.gcc') + install('raxmlHPC-HYBRID', prefix.bin) + + if spec.satisfies('+mpi +avx'): + make('-f', 'Makefile.AVX.MPI.gcc') + install('raxmlHPC-MPI-AVX', prefix.bin) + + if spec.satisfies('+mpi +sse'): + make('-f', 'Makefile.SSE3.MPI.gcc') + install('raxmlHPC-MPI-SSE3', prefix.bin) + + if spec.satisfies('+mpi'): + make('-f', 'Makefile.MPI.gcc') + install('raxmlHPC-MPI', prefix.bin) + + if spec.satisfies('+pthreads +avx'): + make('-f', 'Makefile.AVX.PTHREADS.gcc') + install('raxmlHPC-PTHREADS-AVX', prefix.bin) + + if spec.satisfies('+pthreads +sse'): + make('-f', 'Makefile.SSE3.PTHREADS.gcc') + install('raxmlHPC-PTHREADS-SSE3', prefix.bin) + + if spec.satisfies('+pthreads'): + make('-f', 'Makefile.PTHREADS.gcc') + install('raxmlHPC-PTHREADS', prefix.bin) + + if spec.satisfies('+sse'): + make('-f', 'Makefile.SSE3.gcc') + install('raxmlHPC-SSE3', prefix.bin) + + if spec.satisfies('+avx'): + make('-f', 'Makefile.AVX.gcc') + install('raxmlHPC-AVX', prefix.bin) + + make('-f', 'Makefile.gcc') + install('raxmlHPC', prefix.bin) + else: + if spec.satisfies('+mpi +pthreads'): + make('-f', 'Makefile.HYBRID.nox86.gcc') + install('raxmlHPC-HYBRID', prefix.bin) + + if spec.satisfies('+mpi'): + make('-f', 'Makefile.MPI.nox86.gcc') + install('raxmlHPC-MPI', prefix.bin) + + if spec.satisfies('+pthreads'): + make('-f', 'Makefile.PTHREADS.nox86.gcc') + install('raxmlHPC-PTHREADS', prefix.bin) + + make('-f', 'Makefile.nox86.gcc') + install('raxmlHPC', prefix.bin) |