--- src/Makefile.orig	2025-06-21 19:47:39 UTC
+++ src/Makefile
@@ -1,33 +1,38 @@
 ### modify these paths to local Boost and NLopt install directories
-BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
-NLOPT_INSTALL_DIR = /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
+### or set them as make arguments or environment variables.
+BOOST_INSTALL_DIR ?= /home/pl88/boost_1_58_0/install
+NLOPT_INSTALL_DIR ?= /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
 
-INTELROOT = /n/groups/price/poru/external_software/intel_mkl_2019u4
-MKLROOT = ${INTELROOT}/mkl
-ZLIB_STATIC_DIR = /n/groups/price/poru/external_software/zlib/zlib-1.2.11 # probably unnecessary on most systems
-LIBSTDCXX_STATIC_DIR = /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
-GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
+INTELROOT ?= /n/groups/price/poru/external_software/intel_mkl_2019u4
+MKLROOT ?= ${INTELROOT}/mkl
+ZLIB_STATIC_DIR ?= /n/groups/price/poru/external_software/zlib/zlib-1.2.11 # probably unnecessary on most systems
+LIBSTDCXX_STATIC_DIR ?= /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
+GLIBC_STATIC_DIR ?= /home/pl88/glibc-static/usr/lib64
 
-ZSTD_DIR = /n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib
+ZSTD_DIR ?= /n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib
 
 ifeq ($(strip ${linking}),)
 	linking = dynamic
 endif
 
 # CC = g++
-CC = icpc
+CXX ?= icpc
 
 ifeq (${debug},true)
-	CFLAGS += -g
+	CXXFLAGS += -g
 else
-	CFLAGS += -O2
+	CXXFLAGS += -O2
 endif
 
-CFLAGS += -msse2 -mavx
-CFLAGS += -std=c++11
-CFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
-CFLAGS += -Wall
+# CXXFLAGS += -msse2 -mavx
+CXXFLAGS += -std=c++14
+# CXXFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
+# CXXFLAGS += -Wall
 
+# Set SSEFLAGS to empty string in the env or make command line if building on
+# systems with no SSE such as PowerPC
+SSEFLAGS ?= -msse -msse2 -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
+CXXFLAGS += ${SSEFLAGS} -DMEASURE_DGEMM -DVERBOSE -Wall
 
 # add Boost include and lib paths
 ifneq ($(strip ${BOOST_INSTALL_DIR}),)
@@ -59,7 +64,7 @@ LPATHS += -L${ZSTD_DIR}
 LPATHS += -L${ZSTD_DIR}
 
 # add MKL paths (if not compiling with g++, i.e., compiling with icpc)
-ifneq (${CC},g++)
+ifneq (${CXX},g++)
 	CPATHS += -I${MKLROOT}/include
 	ifeq (${linking},static)
 		LPATHS += -L${INTELROOT}/lib/intel64 '-Wl,-rpath,$$ORIGIN/lib' # for libiomp5.so (now packaged with binary)
@@ -72,34 +77,33 @@ endif
 endif
 
 # add flags for static linking; build LAPACK/MKL component of link line
-ifeq (${CC},g++)
-	CFLAGS += -fopenmp
-	LFLAGS += -fopenmp
+ifeq (${CXX},c++)
+	CXXFLAGS += -fopenmp
+	LDFLAGS += -fopenmp
 	LLAPACK = -llapack -lgfortran
 	ifeq (${linking},static)
-		LFLAGS += -static
+		LDFLAGS += -static
 		LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
 	else ifeq (${linking},static-except-glibc)
-		LFLAGS += -static-libgcc -static-libstdc++
+		LDFLAGS += -static-libgcc -static-libstdc++
 		LPATHS += -L${ZLIB_STATIC_DIR}
 	endif
 else
-	CFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
-	CFLAGS += -qopenmp
-	LFLAGS += -qopenmp
-	CFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
+	CXXFLAGS += -fopenmp
+	LDFLAGS += -fopenmp
+	CXXFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
 	LIOMP5 = -liomp5
 	LDL = -ldl
 	ifeq (${linking},static)
-		LFLAGS += -static
+		LDFLAGS += -static
 		LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
-		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
+		LLAPACK ?= -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group
 	else ifeq (${linking},static-except-glibc)
-		LFLAGS += -static-intel -static-libstdc++ -static-libgcc
+		LDFLAGS += -static-intel -static-libstdc++ -static-libgcc
 		LPATHS += -L${ZLIB_STATIC_DIR}
-		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
+		LLAPACK ?= -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group
 	else ifeq (${linking},static-except-glibc-intel)
-		LFLAGS += -static-libstdc++ -static-libgcc
+		LDFLAGS += -static-libstdc++ -static-libgcc
 		LPATHS += -L${ZLIB_STATIC_DIR}
 		LLAPACK = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
 	else
@@ -112,7 +116,7 @@ endif
 endif
 
 # build link line (minus flags)
-LLIBS = -lboost_program_options -lboost_iostreams -lzstd -lz -lnlopt
+LLIBS = -lnlopt -lboost_program_options -lboost_iostreams -lzstd -lz
 ifeq (${linking},static-except-glibc)
 	L = -L${LIBSTDCXX_STATIC_DIR} ${LPATHS} -Wl,--wrap=memcpy -Wl,-Bstatic ${LLIBS} ${LLAPACK} -Wl,-Bdynamic ${LIOMP5} -lpthread -lm ${LDL}
 else ifeq (${linking},static-except-glibc-intel)
@@ -124,16 +128,19 @@ T = bolt
 
 
 T = bolt
-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
+MEMCPY ?= memcpy.o
+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}
 OMAIN = BoltMain.o $O
 
-.PHONY: clean
+.PHONY: clean all
 
+all: ${T}
+
 %.o: %.cpp
-	${CC} ${CFLAGS} ${CPATHS} -o $@ -c $<
+	${CXX} ${CXXFLAGS} ${CPATHS} -o $@ -c $<
 
 $T: ${OMAIN}
-	${CC} ${LFLAGS} -o $T ${OMAIN} $L
+	${CXX} ${LDFLAGS} -o $T ${OMAIN} $L
 
 clean:
 	rm -f *.o