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cdd2c0e9b9
Remove previously upstreamed patches New Makefile patch that preserves default behavior and should be palatable to upstream
144 lines
5.5 KiB
Text
144 lines
5.5 KiB
Text
--- src/Makefile.orig 2019-08-11 03:05:04 UTC
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+++ src/Makefile
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@@ -1,31 +1,35 @@
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+
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### modify these paths to local Boost and NLopt install directories
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-BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
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-NLOPT_INSTALL_DIR = /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
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+### by setting them in the environment or make command line args
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+### which will override variables set with ?=
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-INTELROOT = /n/groups/price/poru/external_software/intel_mkl_2019u4
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-MKLROOT = ${INTELROOT}/mkl
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-ZLIB_STATIC_DIR = /n/groups/price/poru/external_software/zlib/zlib-1.2.11 # probably unnecessary on most systems
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-LIBSTDCXX_STATIC_DIR = /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
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-GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
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+BOOST_INSTALL_DIR ?= /home/pl88/boost_1_58_0/install
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+NLOPT_INSTALL_DIR ?= /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
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+INTELROOT ?= /n/groups/price/poru/external_software/intel_mkl_2019u4
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+MKLROOT ?= ${INTELROOT}/mkl
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+ZLIB_STATIC_DIR ?= /n/groups/price/poru/external_software/zlib/zlib-1.2.11 # probably unnecessary on most systems
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+LIBSTDCXX_STATIC_DIR ?= /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
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+GLIBC_STATIC_DIR ?= /home/pl88/glibc-static/usr/lib64
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+
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ifeq ($(strip ${linking}),)
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linking = dynamic
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endif
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-# CC = g++
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-CC = icpc
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+# CXX = g++
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+CXX ?= icpc
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ifeq (${debug},true)
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- CFLAGS += -g
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+ CXXFLAGS += -g
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else
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- CFLAGS += -O2
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+ CXXFLAGS += -O2
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endif
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-CFLAGS += -msse -msse2
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-CFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
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-CFLAGS += -Wall
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+# Set SSEFLAGS to empty string in the env or make command line if building on
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+# systems with no SSE such as PowerPC
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+SSEFLAGS ?= -msse -msse2 -DUSE_SSE
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+CXXFLAGS += ${SSEFLAGS} -DMEASURE_DGEMM -DVERBOSE -Wall
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-
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# add Boost include and lib paths
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ifneq ($(strip ${BOOST_INSTALL_DIR}),)
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CPATHS += -I${BOOST_INSTALL_DIR}/include
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@@ -52,7 +56,7 @@ ifneq ($(strip ${ZLIB_STATIC_DIR}),)
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endif
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# add MKL paths (if not compiling with g++, i.e., compiling with icpc)
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-ifneq (${CC},g++)
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+ifeq (${CXX},icpc)
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CPATHS += -I${MKLROOT}/include
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ifeq (${linking},static)
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LPATHS += -L${INTELROOT}/lib/intel64 '-Wl,-rpath,$$ORIGIN/lib' # for libiomp5.so (now packaged with binary)
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@@ -65,34 +69,34 @@ ifneq (${CC},g++)
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endif
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# add flags for static linking; build LAPACK/MKL component of link line
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-ifeq (${CC},g++)
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- CFLAGS += -fopenmp
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- LFLAGS += -fopenmp
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- LLAPACK = -llapack -lgfortran
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+ifneq (${CXX},icpc)
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+ CXXFLAGS += -fopenmp
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+ LDFLAGS += -fopenmp
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+ LLAPACK ?= -llapack -lgfortran
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ifeq (${linking},static)
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- LFLAGS += -static
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+ LDFLAGS += -static
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LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
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else ifeq (${linking},static-except-glibc)
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- LFLAGS += -static-libgcc -static-libstdc++
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+ LDFLAGS += -static-libgcc -static-libstdc++
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LPATHS += -L${ZLIB_STATIC_DIR}
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endif
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else
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- CFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
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- CFLAGS += -qopenmp
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- LFLAGS += -qopenmp
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- CFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
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+ CXXFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
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+ CXXFLAGS += -qopenmp
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+ LDFLAGS += -qopenmp
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+ CXXFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
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LIOMP5 = -liomp5
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LDL = -ldl
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ifeq (${linking},static)
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- LFLAGS += -static
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+ LDFLAGS += -static
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LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
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LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group
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else ifeq (${linking},static-except-glibc)
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- LFLAGS += -static-intel -static-libstdc++ -static-libgcc
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+ LDFLAGS += -static-intel -static-libstdc++ -static-libgcc
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LPATHS += -L${ZLIB_STATIC_DIR}
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LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group
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else ifeq (${linking},static-except-glibc-intel)
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- LFLAGS += -static-libstdc++ -static-libgcc
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+ LDFLAGS += -static-libstdc++ -static-libgcc
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LPATHS += -L${ZLIB_STATIC_DIR}
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LLAPACK = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
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else
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@@ -105,7 +109,7 @@ else
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endif
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# build link line (minus flags)
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-LLIBS = -lboost_program_options -lboost_iostreams -lz -lnlopt
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+LLIBS = -lnlopt -lboost_program_options -lboost_iostreams -lz
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ifeq (${linking},static-except-glibc)
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L = -L${LIBSTDCXX_STATIC_DIR} ${LPATHS} -Wl,--wrap=memcpy -Wl,-Bstatic ${LLIBS} ${LLAPACK} -Wl,-Bdynamic ${LIOMP5} -lpthread -lm ${LDL}
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else ifeq (${linking},static-except-glibc-intel)
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@@ -117,16 +121,20 @@ endif
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T = bolt
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-O = Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o memcpy.o
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+# Set to empty string in env or make command line to use system memcpy
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+MEMCPY ?= memcpy.o
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+O = Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o ${MEMCPY}
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OMAIN = BoltMain.o $O
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-.PHONY: clean
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+.PHONY: clean all
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+all: ${T}
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+
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%.o: %.cpp
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- ${CC} ${CFLAGS} ${CPATHS} -o $@ -c $<
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+ ${CXX} ${CXXFLAGS} ${CPATHS} -o $@ -c $<
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$T: ${OMAIN}
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- ${CC} ${LFLAGS} -o $T ${OMAIN} $L
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+ ${CXX} ${LDFLAGS} -o $T ${OMAIN} $L
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clean:
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rm -f *.o
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