update makefile for linux

Author: Zilong-Li

Makefile

@@ -16,23 +16,22 @@ ONEAPI_OMP5       := $(ONEAPI_COMPILER)/lib/libiomp5.a
 
 # for MacOS use accelerate framework in default
 # install openblas lapack on mac with brew install openblas lapack
-OPENBLAS_ROOT  =
-LAPACK_ROOT   := ${OPENBLAS_ROOT}
+OPENBLAS  =
 
 
 STATIC        = 0  # by default dynamical linking
 IOMP5         = 1  # use libiomp5 for mkl
-AVX           = 1  # enable avx2 fma
 DEBUG         = 0  # debug
+AVX           =    # 1: enable avx2 fma, 0: do nothing
 
 ########################### end ###########################
 
 
 ####### INC, LPATHS, LIBS, MYFLAGS
 program       = PCAone
 CXX           ?= g++    # use default g++ only if not set in env
-CXXSTD         = c++17  # default c++17 if not set by the user
-CXXFLAGS	  += -O3 -Wall -std=$(CXXSTD) -m64 -fPIC
+CXXSTD         = c++17
+CXXFLAGS	  += -O3 -Wall -std=$(CXXSTD) -m64
 MYFLAGS        = -DVERSION=\"$(VERSION)\"
 # CURRENT_DIR   = $(shell pwd)
 INC           = -I./external -I./external/zstd/lib
@@ -41,15 +40,15 @@ PCALIB = libpcaone.a
 ifeq ($(Platform), Darwin)
 	CXXFLAGS += -march=native
 else
-	ifeq ($(strip $(AVX)),1)
-		$(info "use -mavx2 for PCAone")
+	ifeq ($(strip $(AVX)),)
+		CXXFLAGS += -march=native
+	else ifeq ($(strip $(AVX)),1)
 		CXXFLAGS += -mavx2 -mfma
 	endif
 endif
 
 ifeq ($(strip $(DEBUG)),1)
-  $(info "use -mavx2 for PCAone")
-  MYFLAGS += -DDEBUG
+	MYFLAGS += -DDEBUG
 endif
 
 
@@ -69,10 +68,8 @@ ifeq ($(Platform),Linux)
 			DLIBS += -Wl,--no-as-needed -Wl,-rpath,${ONEAPI_COMPILER}/lib,-rpath,${MKLROOT}/lib/intel64 -L${ONEAPI_COMPILER}/lib -L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
 		endif
 
-	else ifneq ($(strip $(OPENBLAS_ROOT)),)
+	else ifneq ($(strip $(OPENBLAS)),)
 		MYFLAGS += -DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE
-		INC     += -I${OPENBLAS_ROOT}/include -I${LAPACK_ROOT}/include
-		LPATHS  += -L${OPENBLAS_ROOT}/lib -L${LAPACK_ROOT}/lib
 		DLIBS   += -llapack -llapacke -lopenblas -lgfortran -lgomp
 
 	else
@@ -83,7 +80,7 @@ else ifeq ($(Platform),Darwin)
 ###### for mac
 	MYFLAGS  += -Xpreprocessor -fopenmp
 
-	ifneq ($(strip $(OPENBLAS_ROOT)),)
+	ifneq ($(strip $(OPENBLAS)),)
 		MYFLAGS += -DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE
 		ifeq ($(strip $(STATIC)),1)
 			# SLIBS += /usr/local/opt/gcc/lib/gcc/11/libgomp.a  # gcc need libgomp.a	
@@ -110,7 +107,7 @@ ifeq ($(strip $(STATIC)),1)
 		SLIBS += /opt/homebrew/opt/zlib/lib/libz.a
 		# CXXFLAGS += -stdlib=libc++
 	else
-		SLIBS    += /usr/lib64/libz.a # /usr/lib/x86_64-linux-gnu/libz.a
+		SLIBS    += /usr/lib/x86_64-linux-gnu/libz.a # /usr/lib64/libz.a # 
 		CXXFLAGS += -static
 		# CXXFLAGS += -static-libgcc -static-libstdc++
 	endif

README.org

@@ -208,8 +208,6 @@ make -j4
 ./PCAone -h
 #+end_src
 
-If this doesn't work because the server is too outdated, run =make clean && make -j4 AVX=0= instead.
-
 *** For MacOS users, check out the [[https://github.com/Zilong-Li/PCAone/blob/dev/.github/workflows/mac.yml#L21][mac workflow]].
 
 #+begin_src shell

publish.sh

@@ -11,25 +11,16 @@ mkdir -p $dir
 platform=$(uname -s)
 
 if [ $platform == "Darwin" ];then
-    echo "Publishing releases on MacOS avx2";
-    echo "Publishing PCAone without libiomp5 threading";
-    export CC="gcc"
-    export CXX="g++"
-    make clean && make -j6 MKLROOT=/opt/intel/oneapi/mkl/latest STATIC=1 && zip PCAone-avx2-Mac.zip PCAone PCAone.pdf && mv PCAone-avx2-Mac.zip $dir && echo "Publishing PCAone-avx2-Mac.zip done";
-
-    # echo "Publishing PCAone with libiomp5 threading";
-    # export CC=$(find $(brew --prefix)/bin/ -name "gcc-[0-9]*" | tail -1)
-    # export CXX=$(find $(brew --prefix)/bin/ -name "g++-[0-9]*" | tail -1)
-    # export LDFLAGS="-L/usr/local/lib/"
-
-    # awk ' NR==7 {$0="#"$0}; NR==6 {sub("# ", "")}; NR==16 || NR==18 {sub("0", "1")}; 1' Makefile >mac2.makefile
+    
+    echo "Publishing releases on MacOS Silicon";
+    export LDFLAGS="-L"$(brew --prefix libomp)/lib
+    export CPPFLAGS="-I"$(brew --prefix libomp)/include
+    make clean && make -j6 STATIC=1 && zip PCAone-Mac.zip PCAone PCAone.pdf && mv PCAone-Mac.zip $dir && echo "Publishing PCAone-Mac.zip done";
 
 elif [ $platform == "Linux" ];then
-    echo "Publishing releases on Linux x86_x64";
-    make clean && make -j6 MKLROOT=$HOME/intel/oneapi/mkl/latest STATIC=1 AVX=0 && zip PCAone-x64-Linux.zip PCAone PCAone.pdf && mv PCAone-x64-Linux.zip $dir && echo "Publishing PCAone_Linux.zip PCAone-x64-Linux.zip done";
-    make clean && make -j6 MKLROOT=$HOME/intel/oneapi/mkl/latest STATIC=1 AVX=1  && zip PCAone-avx2-Linux.zip PCAone PCAone.pdf && mv PCAone-avx2-Linux.zip $dir && echo "Publishing PCAone_Linux.zip PCAone-avx2-Linux.zip done";
-    # awk ' NR==7 {$0="#"$0}; NR==5 {sub("# ", "")}; NR==16 {sub("0", "1")}; 1' Makefile >linux.makefile
-    # awk 'NR==7 {$0="#"$0}; NR==5 {sub("# ", "")}; NR==16 || NR==18 {sub("0", "1")}; 1' Makefile >linux2.makefile
+
+    echo "Publishing releases on Linux ";
+    make clean && make -j6 MKLROOT=/opt/intel/oneapi/mkl/latest ONEAPI_COMPILER=/opt/intel/oneapi/compiler/latest STATIC=1 && zip PCAone-Linux.zip PCAone PCAone.pdf && mv PCAone-Linux.zip $dir && echo "Publishing PCAone-Linux.zip done";
 
 fi