diff options
| -rw-r--r-- | .gitignore | 2 | ||||
| -rw-r--r-- | Makefile.float.linux | 125 | ||||
| -rw-r--r-- | Makefile.linux | 2 | ||||
| -rw-r--r-- | Makefile.macosx (renamed from Makefile.osx) | 0 | ||||
| -rwxr-xr-x[-rw-r--r--] | src/d2f.sh | 30 |
5 files changed, 143 insertions, 16 deletions
diff --git a/.gitignore b/.gitignore index 4fcf8a3..1b3dc47 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,7 @@ *.o *.tar.gz +src/*_float.h +src/*_float.cpp example/output doc/manual.aux doc/manual.bbl diff --git a/Makefile.float.linux b/Makefile.float.linux new file mode 100644 index 0000000..5c82ede --- /dev/null +++ b/Makefile.float.linux @@ -0,0 +1,125 @@ +#Makefile + +# Supported platforms +# Unix / Linux LNX +# Mac MAC +# Compilation options +# link to LAPACK WITH_LAPACK +# 32-bit binary FORCE_32BIT +# dynamic compilation FORCE_DYNAMIC +# float precision FORCE_FLOAT + +# Set this variable to either LNX or MAC +SYS = LNX +# Leave blank after "=" to disable; put "= 1" to enable +# Disable WITH_LAPACK option can slow computation speed significantly and is not recommended +# Disable WITH_ARPACK option only disable -apprx option in the software +WITH_LAPACK = 1 +FORCE_32BIT = +FORCE_DYNAMIC = +FORCE_FLOAT = 1 +DIST_NAME = gemma-0.95.2alpha + +# -------------------------------------------------------------------- +# Edit below this line with caution +# -------------------------------------------------------------------- + + +BIN_DIR = ./bin + +SRC_DIR = ./src + +CPP = g++ + +CPPFLAGS = -Wall -Weffc++ -O3 -std=gnu++11 + +LIBS = /software/gsl-2.2.1-el7-x86_64/lib/libgslcblas.a \ + /software/gsl-2.2.1-el7-x86_64/lib/libgsl.a \ + -pthread -lz + +# ifdef FORCE_DYNAMIC +# LIBS = -lgsl -lgslcblas -lblas -pthread -lz +# else +# LIBS = -lgsl -lgslcblas -pthread -lz +# endif + +OUTPUT = $(BIN_DIR)/gemma + +ifdef FORCE_FLOAT +OUTPUT = $(BIN_DIR)/gemmaf +endif + +SOURCES = $(SRC_DIR)/main.cpp + +HDR = + +# Detailed libary paths, D for dynamic and S for static +LIBS_LNX_D_LAPACK = -llapack +LIBS_MAC_D_LAPACK = -framework Veclib +LIBS_LNX_S_LAPACK = /software/atlas-3.10.3-el7-x86_64/lib/liblapack.a \ + /software/atlas-3.10.3-el7-x86_64/lib/libcblas.a \ + /software/atlas-3.10.3-el7-x86_64/lib/libf77blas.a \ + /software/atlas-3.10.3-el7-x86_64/lib/libatlas.a -lgfortran \ + -Wl,--allow-multiple-definition + +# Options + +ifdef FORCE_FLOAT + CPPFLAGS += -DFORCE_FLOAT + SOURCES += $(SRC_DIR)/param_float.cpp $(SRC_DIR)/gemma_float.cpp $(SRC_DIR)/io_float.cpp $(SRC_DIR)/lm_float.cpp $(SRC_DIR)/vc_float.cpp $(SRC_DIR)/lmm_float.cpp $(SRC_DIR)/mvlmm_float.cpp $(SRC_DIR)/bslmm_float.cpp $(SRC_DIR)/prdt_float.cpp $(SRC_DIR)/mathfunc_float.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp + HDR += $(SRC_DIR)/param_float.h $(SRC_DIR)/gemma_float.h $(SRC_DIR)/io_float.h $(SRC_DIR)/lm_float.h $(SRC_DIR)/lmm_float.h $(SRC_DIR)/vc_float.h $(SRC_DIR)/mvlmm_float.h $(SRC_DIR)/bslmm_float.h $(SRC_DIR)/prdt_float.h $(SRC_DIR)/mathfunc_float.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h +else + SOURCES += $(SRC_DIR)/param.cpp $(SRC_DIR)/gemma.cpp $(SRC_DIR)/io.cpp $(SRC_DIR)/lm.cpp $(SRC_DIR)/lmm.cpp $(SRC_DIR)/vc.cpp $(SRC_DIR)/mvlmm.cpp $(SRC_DIR)/bslmm.cpp $(SRC_DIR)/prdt.cpp $(SRC_DIR)/mathfunc.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp $(SRC_DIR)/ldr.cpp $(SRC_DIR)/bslmmdap.cpp $(SRC_DIR)/logistic.cpp $(SRC_DIR)/varcov.cpp + HDR += $(SRC_DIR)/param.h $(SRC_DIR)/gemma.h $(SRC_DIR)/io.h $(SRC_DIR)/lm.h $(SRC_DIR)/lmm.h $(SRC_DIR)/vc.h $(SRC_DIR)/mvlmm.h $(SRC_DIR)/bslmm.h $(SRC_DIR)/prdt.h $(SRC_DIR)/mathfunc.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h +endif + +ifdef WITH_LAPACK + OBJS += $(SRC_DIR)/lapack.o + CPPFLAGS += -DWITH_LAPACK +ifeq ($(SYS), MAC) + LIBS += $(LIBS_MAC_D_LAPACK) +else +ifdef FORCE_DYNAMIC + LIBS += $(LIBS_LNX_D_LAPACK) +else + LIBS += $(LIBS_LNX_S_LAPACK) +endif +endif + SOURCES += $(SRC_DIR)/lapack.cpp + HDR += $(SRC_DIR)/lapack.h +endif + +ifdef FORCE_32BIT + CPPFLAGS += -m32 +else + CPPFLAGS += -m64 +endif + +# all +OBJS = $(SOURCES:.cpp=.o) + +all: $(OUTPUT) + +$(OUTPUT): $(OBJS) + $(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT) + +$(OBJS) : $(HDR) + +.cpp.o: + $(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o +.SUFFIXES : .cpp .c .o $(SUFFIXES) + + +clean: + rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ ${SRC_DIR}/*_float.* $(OUTPUT) + +DIST_COMMON = COPYING.txt README.txt Makefile +DIST_SUBDIRS = src doc example bin + +tar: + mkdir -p ./$(DIST_NAME) + cp $(DIST_COMMON) ./$(DIST_NAME)/ + cp -r $(DIST_SUBDIRS) ./$(DIST_NAME)/ + tar cvzf $(DIST_NAME).tar.gz ./$(DIST_NAME)/ + rm -r ./$(DIST_NAME) + diff --git a/Makefile.linux b/Makefile.linux index 322f1e6..25a2e1b 100644 --- a/Makefile.linux +++ b/Makefile.linux @@ -18,7 +18,7 @@ WITH_LAPACK = 1 FORCE_32BIT = FORCE_DYNAMIC = FORCE_FLOAT = -DIST_NAME = gemma-0.95.2alpha +DIST_NAME = gemma-0.96alpha # -------------------------------------------------------------------- # Edit below this line with caution diff --git a/Makefile.osx b/Makefile.macosx index 798f09c..798f09c 100644 --- a/Makefile.osx +++ b/Makefile.macosx diff --git a/src/d2f.sh b/src/d2f.sh index 8267ee3..d3252e0 100644..100755 --- a/src/d2f.sh +++ b/src/d2f.sh @@ -5,21 +5,21 @@ do for extension in cpp h do cp ${prefix}.${extension} ${prefix}_float.${extension} -sed -i .bak 's/_vector_/_vector_float_/g' ${prefix}_float.${extension} -sed -i .bak 's/_vector /_vector_float /g' ${prefix}_float.${extension} -sed -i .bak 's/_matrix_/_matrix_float_/g' ${prefix}_float.${extension} -sed -i .bak 's/_matrix /_matrix_float /g' ${prefix}_float.${extension} -sed -i .bak 's/ddot/dsdot/g' ${prefix}_float.${extension} -sed -i .bak 's/dtrsv/strsv/g' ${prefix}_float.${extension} -sed -i .bak 's/dtrsy/strsy/g' ${prefix}_float.${extension} -sed -i .bak 's/dgemm/sgemm/g' ${prefix}_float.${extension} -sed -i .bak 's/dgemv/sgemv/g' ${prefix}_float.${extension} -sed -i .bak 's/dsyr/ssyr/g' ${prefix}_float.${extension} -sed -i .bak 's/dsyr2/ssyr2/g' ${prefix}_float.${extension} -sed -i .bak 's/ddot/sdot/g' ${prefix}_float.${extension} -sed -i .bak 's/dger/sger/g' ${prefix}_float.${extension} -sed -i .bak 's/dsyrk/ssyrk/g' ${prefix}_float.${extension} -sed -i .bak 's/daxpy/saxpy/g' ${prefix}_float.${extension} +sed -i.bak 's/_vector_/_vector_float_/g' ${prefix}_float.${extension} +sed -i.bak 's/_vector /_vector_float /g' ${prefix}_float.${extension} +sed -i.bak 's/_matrix_/_matrix_float_/g' ${prefix}_float.${extension} +sed -i.bak 's/_matrix /_matrix_float /g' ${prefix}_float.${extension} +sed -i.bak 's/ddot/dsdot/g' ${prefix}_float.${extension} +sed -i.bak 's/dtrsv/strsv/g' ${prefix}_float.${extension} +sed -i.bak 's/dtrsy/strsy/g' ${prefix}_float.${extension} +sed -i.bak 's/dgemm/sgemm/g' ${prefix}_float.${extension} +sed -i.bak 's/dgemv/sgemv/g' ${prefix}_float.${extension} +sed -i.bak 's/dsyr/ssyr/g' ${prefix}_float.${extension} +sed -i.bak 's/dsyr2/ssyr2/g' ${prefix}_float.${extension} +sed -i.bak 's/ddot/sdot/g' ${prefix}_float.${extension} +sed -i.bak 's/dger/sger/g' ${prefix}_float.${extension} +sed -i.bak 's/dsyrk/ssyrk/g' ${prefix}_float.${extension} +sed -i.bak 's/daxpy/saxpy/g' ${prefix}_float.${extension} rm ${prefix}_float.${extension}.bak done done |