Add personalised makefile

README.md

@@ -334,6 +334,7 @@ You can set an environment variable `SKETCHLIB_INSTALL` to affect `python setup.
 - Empty: uses cmake
 - `conda`: sets library location to the conda environment, and uses `src/Makefile` (used to be used in conda-forge recipe)
 - `azure`: Uses `src/Makefile`
+- `jlees`: Uses `src/Makefile_fedora38`
 
 ### cmake
 Now requires v3.19. If nvcc version is 11.0 or higher, sm8.6 with device link time optimisation will be used.

setup.py

@@ -88,6 +88,9 @@ def build_extension(self, ext):
         elif target == 'azure':
             subprocess.check_call(['make', 'python'], cwd=ext.sourcedir + '/src', env=env)
             subprocess.check_call(['make', 'install_python', 'PYTHON_LIB_PATH=' + extdir], cwd=ext.sourcedir + '/src', env=env)
+        elif target == 'jlees':
+            subprocess.check_call(['make', '-f', 'Makefile_fedora38', 'python'], cwd=ext.sourcedir + '/src', env=env)
+            subprocess.check_call(['make', 'install_python', 'PYTHON_LIB_PATH=' + extdir], cwd=ext.sourcedir + '/src', env=env)
         else:
             subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
             subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp)

src/Makefile_fedora38

@@ -0,0 +1,141 @@
+CXX=gcc-11
+CC=gcc-11
+CFLAGS+=-Wall -Wextra -fPIC
+CXXFLAGS+=-Wall -Wextra -std=c++14 -fopenmp -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -fPIC
+ifdef DEBUG
+  CXXFLAGS+= -O0 -g
+  CUDAFLAGS = -g -G
+else ifdef PROFILE
+  CXXFLAGS+= -O2 -g -flto -fno-fat-lto-objects -fvisibility=hidden
+  CUDAFLAGS = -O2 -pg -lineinfo
+else
+  CXXFLAGS+= -march=native -O3 -flto -fno-fat-lto-objects -fvisibility=hidden
+  CFLAGS+= -march=native -O3 -flto -fno-fat-lto-objects -fvisibility=hidden
+endif
+
+UNAME_S := $(shell uname -s)
+LIBLOC = ${CONDA_PREFIX}
+LDLIBS = -lz -lhdf5_cpp -lhdf5 -lopenblas -lgomp
+ifeq ($(UNAME_S),Linux)
+	CXXFLAGS+= -m64
+	ifdef PROFILE
+		CXXFLAGS+= -Wl,--compress-debug-sections=none
+	endif
+	LDLIBS+= -lpthread -lgfortran -lm -ldl -lrt
+	LDFLAGS=-Wl,-as-needed
+endif
+ifeq ($(UNAME_S),Darwin)
+	LDLIBS+= -pthread
+endif
+
+CPPFLAGS+=-I"/home/linuxbrew/.linuxbrew/include" -I"." -I"../vendor/highfive/include" -I$(LIBLOC)/include -I$(LIBLOC)/include/eigen3
+LDFLAGS+= -L$(LIBLOC)/lib -L"/home/linuxbrew/.linuxbrew/lib" -L/usr/local/cuda-12.3/lib64
+CUDA_LDLIBS=-lcudadevrt -lcudart_static $(LDLIBS)
+
+CUDA_LDFLAGS =-L$(LIBLOC)/lib -L${CUDA_HOME}/targets/x86_64-linux/lib/stubs -L${CUDA_HOME}/targets/x86_64-linux/lib
+CUDAFLAGS +=-ccbin /home/linuxbrew/.linuxbrew/bin/g++-11 -Xcompiler -fPIC --cudart static --relocatable-device-code=true --expt-relaxed-constexpr -gencode arch=compute_70,code=sm_70 -gencode arch=compute_75,code=sm_75
+ifdef GPU
+	CXXFLAGS += -DGPU_AVAILABLE
+	CUDAFLAGS += -gencode arch=compute_86,code=sm_86
+	CUDA_LDFLAGS += -L/usr/local/cuda-12.3/lib64
+endif
+
+PYTHON_LIB = pp_sketchlib$(shell python3-config --extension-suffix)
+
+# python specific options
+python: CPPFLAGS += -DGPU_AVAILABLE -DPYTHON_EXT -DNDEBUG -Dpp_sketchlib_EXPORTS $(shell python3 -m pybind11 --includes)
+
+PROGRAMS=sketch_test matrix_test read_test gpu_dist_test
+
+SKETCH_OBJS=dist/dist.o dist/matrix_ops.o reference.o sketch/seqio.o sketch/sketch.o database/database.o sketch/countmin.o api.o dist/linear_regression.o random/rng.o random/random_match.o random/kmeans/KMeansRexCore.o random/kmeans/mersenneTwister2002.o
+GPU_SKETCH_OBJS=gpu/gpu_api.o
+CUDA_OBJS=gpu/dist.cu.o gpu/sketch.cu.o gpu/device_reads.cu.o gpu/gpu_countmin.cu.o gpu/device_memory.cu.o
+
+# web specific options
+web: CXX = em++
+# optimised compile options
+# NB turn exceptions back on for testing
+# NB `--closure 1` can be used to reduce size of js file (this minifies variable names!)
+web: CXXFLAGS = -O3 -s ASSERTIONS=1  \
+				-DNOEXCEPT \
+				-DJSON_NOEXCEPTION \
+				-s DISABLE_EXCEPTION_CATCHING=1 \
+				-fno-exceptions \
+				-flto --bind -s STRICT=1 \
+				-s ALLOW_MEMORY_GROWTH=1 \
+				-s USE_ZLIB=1 \
+				-s MODULARIZE=1 \
+				-s "EXPORTED_FUNCTIONS=['_malloc']" \
+				-s 'EXPORTED_RUNTIME_METHODS=["FS"]' \
+				-s EXPORT_NAME=WebSketch \
+				-Wall -Wextra -std=c++14
+web: CPPFLAGS += -DWEB_SKETCH
+web: LDFLAGS = -lnodefs.js -lworkerfs.js
+
+WEB_OUT=web/web_sketch
+WEB_OBJS=${WEB_OUT}.js ${WEB_OUT}.html ${WEB_OUT}.wasm
+
+web: web/web_sketch.o sketch/seqio.o sketch/sketch.o sketch/countmin.o
+	$(LINK.cpp) $^ -o ${WEB_OUT}.js
+	sed -i.old '1s;^;\/* eslint-disable *\/;' ${WEB_OUT}.js
+
+all: $(PROGRAMS)
+
+clean:
+	$(RM) $(SKETCH_OBJS) $(GPU_SKETCH_OBJS) $(CUDA_OBJS) $(WEB_OBJS) *.o *.so version.h ~* $(PROGRAMS)
+
+install: all
+	install -d $(BINDIR)
+	install $(PROGRAMS) $(BINDIR)
+
+sketch_test: $(SKETCH_OBJS) test/main.o
+	$(LINK.cpp) $(CUDA_LDFLAGS) $(LDFLAGS) $^ -o $@ $(LDLIBS)
+
+matrix_test: $(SKETCH_OBJS) test/matrix_test.o
+	$(LINK.cpp) $^ -o $@ $(LDLIBS)
+
+read_test: $(SKETCH_OBJS) $(GPU_SKETCH_OBJS) $(CUDA_OBJS) test/read_test.o
+	nvcc $(CUDAFLAGS) $(CUDA_LDFLAGS) -Wno-deprecated-gpu-targets -shared -dlink $^ -o device_link.o -Xnvlink $(CUDA_LDLIBS)
+	$(LINK.cpp) $(CUDA_LDFLAGS) $(LDFLAGS) $^ device_link.o -o $@ $(CUDA_LDLIBS)
+
+gpu_dist_test: $(SKETCH_OBJS) $(GPU_SKETCH_OBJS) $(CUDA_OBJS) test/gpu_dist_test.o
+	nvcc $(CUDAFLAGS) $(CUDA_LDFLAGS) -Wno-deprecated-gpu-targets -shared -dlink $^ -o device_link.o -Xnvlink $(CUDA_LDLIBS)
+	$(LINK.cpp) $(CUDA_LDFLAGS) $(LDFLAGS) $^ device_link.o -o $@ $(CUDA_LDLIBS)
+
+version.h:
+	cat sketch/*.cpp sketch/*.hpp gpu/sketch.cu | openssl sha1 | awk '{print "#define SKETCH_VERSION \"" $$2 "\""}' > version.h
+
+database/database.o: version.h
+
+web/web_sketch.o: version.h
+
+python: $(PYTHON_LIB)
+
+$(PYTHON_LIB): $(SKETCH_OBJS) $(GPU_SKETCH_OBJS) $(CUDA_OBJS) sketchlib_bindings.o
+	nvcc $(CUDAFLAGS) $(CUDA_LDFLAGS) -Wno-deprecated-gpu-targets -shared -dlink $^ -o device_link.o -Xnvlink $(CUDA_LDLIBS)
+	$(LINK.cpp) $(CUDA_LDFLAGS) $(LDFLAGS) -shared $^ device_link.o -o $(PYTHON_LIB) $(CUDA_LDLIBS)
+
+install_python: python
+	install -d $(PYTHON_LIB_PATH)
+	install $(PYTHON_LIB) $(PYTHON_LIB_PATH)
+
+gpu/dist.cu.o:
+	echo ${CUDAFLAGS}
+	echo ${CPPFLAGS}
+	echo ${CXXFLAGS}
+	echo ${CFLAGS}
+	nvcc $(CUDAFLAGS) $(CPPFLAGS) -DGPU_AVAILABLE -x cu -c gpu/dist.cu -o $@
+
+gpu/sketch.cu.o:
+	nvcc $(CUDAFLAGS) $(CPPFLAGS) -DGPU_AVAILABLE -x cu -c gpu/sketch.cu -o $@
+
+gpu/device_memory.cu.o:
+	nvcc $(CUDAFLAGS) $(CPPFLAGS) -DGPU_AVAILABLE -x cu -c gpu/device_memory.cu -o $@
+
+gpu/device_reads.cu.o:
+	nvcc $(CUDAFLAGS) $(CPPFLAGS) -DGPU_AVAILABLE -x cu -c gpu/device_reads.cu -o $@
+
+gpu/gpu_countmin.cu.o:
+	nvcc $(CUDAFLAGS) $(CPPFLAGS) -DGPU_AVAILABLE -x cu -c gpu/gpu_countmin.cu -o $@
+
+.PHONY: all clean install python install_python web