[nsd/11arraydesign] Update data prep to use SimpleArray

yungyuc · Jan 23, 2023 · c55eb58 · c55eb58
1 parent 9250507
commit c55eb58
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Showing 4 changed files with 154 additions and 67 deletions.
diff --git a/.github/workflows/nsd.yml b/.github/workflows/nsd.yml
@@ -201,11 +201,9 @@ jobs:
 
     - name: 11arraydesign_solve_cpp
       run: |
-        make -C ${{ env.ARRAYDESIGNROOT }} solve_cpp.so
+        make -j -C ${{ env.ARRAYDESIGNROOT }} solve_cpp.so
         make -C ${{ env.ARRAYDESIGNROOT }} solve_cpp_xarray.so
 
     - name: 11arraydesign_data_prep
-      # macos does not have MKL.
-      if: startsWith(matrix.os, 'ubuntu')
       run: |
         make -C ${{ env.ARRAYDESIGNROOT }} data_prep.so
diff --git a/nsd/11arraydesign/code/04_fit_poly.py b/nsd/11arraydesign/code/04_fit_poly.py
@@ -12,6 +12,7 @@ def __exit__(self, *args, **kw):
         self._t1 = time.time()
         print("Wall time: {:g} s".format(self._t1 - self._t0))
 
+print("prep")
 # [begin prep pycon]
 with Timer():
     # np.unique returns a sorted array.
@@ -44,6 +45,7 @@ def plot_poly_fitted(i):
 print('write to {}'.format(imagepath))
 plt.savefig(imagepath, dpi=150)
 
+print("lumped")
 # [begin lumped pycon]
 with Timer():
     # Do the calculation for the 1000 groups of points.
@@ -56,6 +58,7 @@ def plot_poly_fitted(i):
         polygroup[i,:] = data_prep.fit_poly(sub_x, sub_y, 2)
 # [end lumped pycon]
 
+print("point build")
 # [begin point build pycon]
 with Timer():
     # Using numpy to build the point groups takes a lot of time.
@@ -65,6 +68,7 @@ def plot_poly_fitted(i):
         data_groups.append((xdata[slct], ydata[slct]))
 # [end point build pycon]
 
+print("fitting")
 # [begin fitting pycon]
 with Timer():
     # Fitting helper runtime is much less than building the point groups.
@@ -73,13 +77,16 @@ def plot_poly_fitted(i):
         polygroup[it,:] = data_prep.fit_poly(sub_x, sub_y, 2)
 # [end fitting pycon]
 
+print("batch")
 # [begin batch pycon]
 with Timer():
     rbatch = data_prep.fit_polys(xdata, ydata, 2)
 # [end batch pycon]
 
 print(rbatch.shape)
 # Verify batch.
-assert (rbatch[i] == polygroup[i]).all()
+assert len(rbatch) == len(polygroup)
+for i in range(1000):
+    assert (rbatch[i] == polygroup[i]).all()
 
 # vim: set ff=unix fenc=utf8 et sw=4 ts=4 sts=4 tw=79:
diff --git a/nsd/11arraydesign/code/Makefile b/nsd/11arraydesign/code/Makefile
@@ -3,22 +3,26 @@ export PYTHONPATH=modmesh-master
 UNAME_S := $(shell uname -s)
 
 ifeq ($(UNAME_S),Darwin)
-MKLROOT ?= /opt/intel/mkl
-MKLINC ?= ${MKLROOT}/include
-MKLLIB ?= ${MKLROOT}/lib
-MKLEXT ?= a
+# Do not define "HASMKL" macro.
+INC += -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/Headers
+LINKFLAGS := -framework Accelerate
 else ifeq ($(UNAME_S),Linux)
-MKLINC ?= /usr/include/mkl
+CXXFLAGS += -DHASMKL -Wl,--no-as-needed
+ifeq (${MKLROOT},)
+INC += -I/usr/include/mkl
 MKLLIB ?= /usr/lib/x86_64-linux-gnu
-MKLEXT ?= so
-CXXFLAGS += -Wl,--no-as-needed
+else
+INC += -I${MKLROOT}/include
+MKLLIB ?= ${MKLROOT}/lib/intel64
 endif
+MKLEXT ?= so
 
-MKLLINKLINE := \
+LINKFLAGS := \
 	${MKLLIB}/libmkl_intel_lp64.${MKLEXT} \
 	${MKLLIB}/libmkl_sequential.${MKLEXT} \
 	${MKLLIB}/libmkl_core.${MKLEXT} \
 	-lpthread -lm -ldl
+endif
 
 PYTHON ?= $(shell which python3)
 PYTHON_VERSION ?= $(shell $(PYTHON) -c 'import sys; print("%d.%d" % (sys.version_info.major, sys.version_info.minor))')
@@ -28,16 +32,12 @@ NUMPY_INC := $(shell python3 -c 'import numpy ; print(numpy.get_include())')
 MODMESH_ROOT=modmesh_copy
 MODMESH_PYMOD=$(MODMESH_ROOT)/modmesh/buffer/pymod
 
-INC := -I$(shell python3-config --prefix)/include -I$(MODMESH_ROOT)
+INC += -I$(shell python3-config --prefix)/include -I$(MODMESH_ROOT)
 
 PYTHON_LIB := $(shell python3-config --prefix)/lib
 
 CPATH := $(PYTHON_INC):$(NUMPY_INC)
 
-ifdef YHROOT
-CPATH := $(CPATH):$(YHROOT)/usr/$(YHFLAVOR)/include
-endif
-
 export CPATH
 
 BASES := 01_grid 01_solve_python_loop 01_solve_analytical
@@ -64,8 +64,11 @@ testimport: libst
 
 #cpp -v /dev/null -o /dev/null
 
-data_prep.so: data_prep.cpp Makefile
-	g++ $< -o $@ -O3 -fPIC -shared -std=c++17 -lpython$(PYTHON_VERSION) -L$(PYTHON_LIB) ${INC} -I${MKLINC} ${MKLLINKLINE}
+data_prep.o: data_prep.cpp Makefile
+	g++ -c $< -o $@ -O3 -fPIC -std=c++17 ${INC}
+
+data_prep.so: data_prep.o wrap_SimpleArray.o wrap_ConcreteBuffer.o buffer_pymod.o Makefile
+	g++ $< wrap_ConcreteBuffer.o wrap_SimpleArray.o buffer_pymod.o -o $@ -shared -std=c++17 -lpython$(PYTHON_VERSION) -L$(PYTHON_LIB) ${LINKFLAGS}
 
 solve_cpp_xarray.so: solve_cpp_xarray.cpp Makefile
 	g++ $< -o $@ -O3 -fPIC -shared -std=c++17 -lpython$(PYTHON_VERSION) -L$(PYTHON_LIB) ${INC}
@@ -80,7 +83,7 @@ solve_cpp.o: solve_cpp.cpp Makefile
 	g++ -c $< -o $@ -O3 -fPIC -std=c++17 ${INC}
 
 solve_cpp.so: solve_cpp.o wrap_SimpleArray.o wrap_ConcreteBuffer.o buffer_pymod.o Makefile
-	g++ solve_cpp.o wrap_ConcreteBuffer.o wrap_SimpleArray.o buffer_pymod.o -o $@ -shared -std=c++17 -lpython$(PYTHON_VERSION) -L$(PYTHON_LIB)
+	g++ $< wrap_ConcreteBuffer.o wrap_SimpleArray.o buffer_pymod.o -o $@ -shared -std=c++17 -lpython$(PYTHON_VERSION) -L$(PYTHON_LIB)
 
 ../image/03_solve_cpp.png: 03_solve_cpp.py solve_cpp.so
 	./$<