Fixed lblas issue with null pointers

MakefileHPC

@@ -0,0 +1,251 @@
+# to find path to openmpi, type mpiexec --test , the error messege reveals path
+MKL_HOME = /apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl
+BROWN_MPI_HOME = /apps/brown/openmpi/2.1.0/gcc-5.2.0
+SNYDER_MPI_HOME = /apps/snyder7/openmpi/2.1.0_gcc-5.2.0
+MPI_HOME = $(SNYDER_MPI_HOME)
+
+BLAS_LIB = -L$(MKL_HOME)/lib/intel64 -Wl,-rpath=$(MKL_HOME)/lib/intel64 -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp
+LAPACK_LIB = -L$(MKL_HOME)/lib/intel64 -Wl,-rpath=$(MKL_HOME)/lib/intel64 -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core
+
+EXTRA_FLAGS = '-Wl,-rpath=$(MKL_HOME)/lib/intel64' ,  '-Wl,-rpath=$(MPI_HOME)/lib'
+
+EXTRA_DIRS = '$(MKL_HOME)/lib/intel64' , '$(MPI_HOME)/lib'
+
+#BLAS_LIB = -lblas
+#LAPACK_LIB = -llapack
+
+# OPTIONAL
+# Typically if installed,
+#  FFTW3_INC can be left empty
+#  FFTW3_LIB = -lfftw3 
+#  or, if Fedora and/or fftw is version 3 but named fftw rather than fftw3
+#  FTW3_LIB = -lfftw 
+#  May need to link libraries properly as with blas and lapack above
+FFTW3_INC = -I$(MLK_HOME)/include/fftw/
+FFTW3_LIB = $(BLAS_LIB)
+
+# Typically,
+#  PTHREAD_INC = -DHAVE_UNISTD_H
+#  PTHREAD_LIB = -lpthread
+PTHREAD_INC = -DHAVE_UNISTD_H
+PTHREAD_LIB = -lpthread
+
+# OPTIONAL
+# If not installed:
+# Fedora: dnf install libsuitsparse-devel
+# Typically, if installed:
+#CHOLMOD_INC = -I/usr/include/suitesparse
+#CHOLMOD_LIB = -lcholmod -lamd -lcolamd -lcamd -lccolamd
+#CHOLMOD_INC = -I/usr/include/suitesparse
+#CHOLMOD_LIB = -lcholmod -lamd -lcolamd -lcamd -lccolamd
+
+# Specify the MPI library
+# For example, on Fedora: dnf  install openmpi-devel
+#MPI_INC = -I/usr/include/openmpi-x86_64/openmpi/ompi
+#MPI_LIB = -lmpi
+# or, explicitly link to the library with -L, example below
+MPI_LIB = -L$(MPI_HOME)/lib -Wl,-rpath=$(MPI_HOME)/lib -lmpi
+MPI_INC = -I$(MPI_HOME)/include
+#MPI_LIB = -L/usr/lib64/openmpi/lib/libmpi.so
+
+# Specify custom compilers if needed
+CXX = $(MPI_HOME)/bin/mpic++
+CC  = $(MPI_HOME)/bin/mpicc
+
+#CFLAGS += -O3 -fPIC
+CFLAGS = -O3 -msse3 -msse2 -msse -fPIC
+
+# options for Sampler module
+OPTFLAGS = -O3
+
+OBJDIR = ./build
+S4_BINNAME = $(OBJDIR)/S4
+S4_LIBNAME = $(OBJDIR)/libS4.a
+S4r_LIBNAME = $(OBJDIR)/libS4r.a
+
+##################### DO NOT EDIT BELOW THIS LINE #####################
+
+#### Set the compilation flags
+
+CPPFLAGS = -I. -IS4 -IS4/RNP -IS4/kiss_fft
+
+ifdef BLAS_LIB
+CPPFLAGS += -DHAVE_BLAS
+endif
+
+ifdef LAPACK_LIB
+CPPFLAGS += -DHAVE_LAPACK
+endif
+
+ifdef FFTW3_LIB
+CPPFLAGS += -DHAVE_FFTW3 $(FFTW3_INC)
+endif
+
+ifdef PTHREAD_LIB
+CPPFLAGS += -DHAVE_LIBPTHREAD $(PTHREAD_INC)
+endif
+
+ifdef CHOLMOD_LIB
+CPPFLAGS += -DHAVE_LIBCHOLMOD $(CHOLMOD_INC)
+endif
+
+ifdef MPI_LIB
+CPPFLAGS += -DHAVE_MPI $(MPI_INC)
+endif
+
+LIBS = $(BLAS_LIB) $(LAPACK_LIB) $(FFTW3_LIB) $(PTHREAD_LIB) $(CHOLMOD_LIB) $(MPI_LIB)
+
+#### Compilation targets
+
+all: $(S4_LIBNAME)
+
+objdir:
+	mkdir -p $(OBJDIR)
+	mkdir -p $(OBJDIR)/S4k
+	mkdir -p $(OBJDIR)/S4r
+	mkdir -p $(OBJDIR)/modules
+
+S4_LIBOBJS = \
+	$(OBJDIR)/S4k/S4.o \
+	$(OBJDIR)/S4k/rcwa.o \
+	$(OBJDIR)/S4k/fmm_common.o \
+	$(OBJDIR)/S4k/fmm_FFT.o \
+	$(OBJDIR)/S4k/fmm_kottke.o \
+	$(OBJDIR)/S4k/fmm_closed.o \
+	$(OBJDIR)/S4k/fmm_PolBasisNV.o \
+	$(OBJDIR)/S4k/fmm_PolBasisVL.o \
+	$(OBJDIR)/S4k/fmm_PolBasisJones.o \
+	$(OBJDIR)/S4k/fmm_experimental.o \
+	$(OBJDIR)/S4k/fft_iface.o \
+	$(OBJDIR)/S4k/pattern.o \
+	$(OBJDIR)/S4k/intersection.o \
+	$(OBJDIR)/S4k/predicates.o \
+	$(OBJDIR)/S4k/numalloc.o \
+	$(OBJDIR)/S4k/gsel.o \
+	$(OBJDIR)/S4k/sort.o \
+	$(OBJDIR)/S4k/kiss_fft.o \
+	$(OBJDIR)/S4k/kiss_fftnd.o \
+	$(OBJDIR)/S4k/SpectrumSampler.o \
+	$(OBJDIR)/S4k/cubature.o \
+	$(OBJDIR)/S4k/Interpolator.o \
+	$(OBJDIR)/S4k/convert.o
+
+S4r_LIBOBJS = \
+	$(OBJDIR)/S4r/Material.o \
+	$(OBJDIR)/S4r/LatticeGridRect.o \
+	$(OBJDIR)/S4r/LatticeGridArb.o \
+	$(OBJDIR)/S4r/POFF2Mesh.o \
+	$(OBJDIR)/S4r/PeriodicMesh.o \
+	$(OBJDIR)/S4r/Shape.o \
+	$(OBJDIR)/S4r/Simulation.o \
+	$(OBJDIR)/S4r/Layer.o \
+	$(OBJDIR)/S4r/Pseudoinverse.o \
+	$(OBJDIR)/S4r/Eigensystems.o \
+	$(OBJDIR)/S4r/IRA.o \
+	$(OBJDIR)/S4r/intersection.o \
+	$(OBJDIR)/S4r/predicates.o \
+	$(OBJDIR)/S4r/periodic_off2.o
+
+ifndef LAPACK_LIB
+  S4_LIBOBJS += $(OBJDIR)/S4k/Eigensystems.o
+endif
+
+$(S4_LIBNAME): objdir $(S4_LIBOBJS)
+	$(AR) crvs $@ $(S4_LIBOBJS)
+$(S4r_LIBNAME): objdir $(S4r_LIBOBJS)
+	$(AR) crvs $@ $(S4r_LIBOBJS)
+
+$(OBJDIR)/S4k/S4.o: S4/S4.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/rcwa.o: S4/rcwa.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/fmm_common.o: S4/fmm/fmm_common.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/fmm_FFT.o: S4/fmm/fmm_FFT.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/fmm_kottke.o: S4/fmm/fmm_kottke.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/fmm_closed.o: S4/fmm/fmm_closed.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/fmm_PolBasisNV.o: S4/fmm/fmm_PolBasisNV.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/fmm_PolBasisVL.o: S4/fmm/fmm_PolBasisVL.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/fmm_PolBasisJones.o: S4/fmm/fmm_PolBasisJones.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/fmm_experimental.o: S4/fmm/fmm_experimental.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/fft_iface.o: S4/fmm/fft_iface.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/pattern.o: S4/pattern/pattern.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/intersection.o: S4/pattern/intersection.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/predicates.o: S4/pattern/predicates.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/numalloc.o: S4/numalloc.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/gsel.o: S4/gsel.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/sort.o: S4/sort.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/kiss_fft.o: S4/kiss_fft/kiss_fft.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/kiss_fftnd.o: S4/kiss_fft/tools/kiss_fftnd.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/SpectrumSampler.o: S4/SpectrumSampler.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/cubature.o: S4/cubature.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/Interpolator.o: S4/Interpolator.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/convert.o: S4/convert.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4k/Eigensystems.o: S4/RNP/Eigensystems.cpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+
+
+$(OBJDIR)/S4r/Material.o: S4r/Material.cpp S4r/Material.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/LatticeGridRect.o: S4r/LatticeGridRect.cpp S4r/PeriodicMesh.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/LatticeGridArb.o: S4r/LatticeGridArb.cpp S4r/PeriodicMesh.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/POFF2Mesh.o: S4r/POFF2Mesh.cpp S4r/PeriodicMesh.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/PeriodicMesh.o: S4r/PeriodicMesh.cpp S4r/PeriodicMesh.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/Shape.o: S4r/Shape.cpp S4r/Shape.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/Simulation.o: S4r/Simulation.cpp S4r/Simulation.hpp S4r/StarProduct.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/Layer.o: S4r/Layer.cpp S4r/Layer.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/Pseudoinverse.o: S4r/Pseudoinverse.cpp S4r/Pseudoinverse.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/Eigensystems.o: S4r/Eigensystems.cpp S4r/Eigensystems.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/IRA.o: S4r/IRA.cpp S4r/IRA.hpp S4r/Types.hpp
+	$(CXX) -c $(CFLAGS) $(CPPFLAGS) -I. $< -o $@
+$(OBJDIR)/S4r/intersection.o: S4r/intersection.c S4r/intersection.h
+	$(CC) -c -O3 $< -o $@
+$(OBJDIR)/S4r/periodic_off2.o: S4r/periodic_off2.c S4r/periodic_off2.h 
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@
+$(OBJDIR)/S4r/predicates.o: S4r/predicates.c
+	$(CC) -c -O3 $< -o $@
+
+#### Python extension
+
+check:
+	@echo $(LIBS)
+
+S4_pyext: objdir $(S4_LIBNAME)
+	echo "Linking...."
+	echo $(EXTRA_FLAGS) $(EXTRA_DIRS)
+	sh gensetupHPC.py.sh $(OBJDIR) $(S4_LIBNAME) "$(LIBS)" "$(EXTRA_FLAGS)" "$(EXTRA_DIRS)"
+	python setup.py build
+	#pip3 install --upgrade ./
+
+clean:
+	rm S4.so
+	rm -rf $(OBJDIR)

PythonTest.py

@@ -0,0 +1,122 @@
+
+# all lengths normalized in terms of a 
+# frequency normalized in terms of 2*pi*c/a
+
+# this test file plots a frequency spectrum and field plot for the python extension
+
+import S4
+import numpy as np
+import matplotlib.pyplot as plt
+
+a = 1e-6; #1nm
+c_const = 3e8;
+print('Bontempi, Kivshar et al. \"Highly sensitive biosensors based on all-dielectric nanoresonator\"')
+p = 0.96
+d = 0.73
+h = 0.22
+period = [p,p]
+S = S4.New(Lattice=((period[0],0),(0,period[1])),NumBasis=20)
+S.SetMaterial(Name = 'SiO2',Epsilon = (1.45 + 0.0j)**2)
+S.SetMaterial(Name = 'Si',Epsilon = (3.487+0.0j)**2)
+S.SetMaterial(Name = 'Vacuum',Epsilon = (1 + 0j)**2)
+
+S.AddLayer(Name = 'AirAbove',Thickness = 0, Material = 'Vacuum')
+S.AddLayer(Name = 'AirDisp',Thickness = 1, Material = 'Vacuum')
+S.AddLayer(Name = 'Si_disks',Thickness = h,Material = 'Vacuum')
+
+S.SetRegionCircle(
+    Layer = 'Si_disks',
+    Material = 'Si',
+    Center = (0,0),
+    Radius = d/2
+)
+
+S.AddLayer(Name = 'Glass_Below',Thickness = 2, Material = 'SiO2')
+#S.AddLayerCopy(Name = 'AirBelow',Thickness = 0, Layer = 'AirAbove')
+S.AddLayer(Name = 'AirBelow',Thickness = 0,Material = 'Vacuum')
+
+S.SetExcitationPlanewave(
+    IncidenceAngles=(
+        0,# polar angle in [0,180)
+        0 # azimuthal angle in [0,360)
+    ),
+    sAmplitude = 0,
+    pAmplitude = 1,
+    Order = 0
+)
+
+S.SetOptions(
+    PolarizationDecomposition = True
+)
+
+wavelength_um = float(wavelength_p_nm)/1000; # [8.0,14.0]
+freq = 1 / float(wavelength_um);  
+S.SetFrequency(freq)  #unit 2*pi*c_const / a
+forward,backward = S.GetPowerFlux(Layer = 'AirAbove', zOffset = 0) # reflected power
+forward = S.GetPowerFlux(Layer = 'AirBelow',zOffset = 0)
+print('f='+str(1/freq)+', Power_forward= '+str(forward[0].real)+', Power_backward='+str(backward.real))
+
+# get fields at points
+
+
+
+
+# frequency sweep
+wavelength_space = np.linspace(1.3, 1.7, 200)
+
+R = wavelength_space * 0
+T=R
+i=0
+for lam in wavelength_space:
+    f = 1 / float(lam)
+    S.SetFrequency(f)
+    (forw,back) = S.GetPowerFlux(Layer = 'AirAbove', zOffset = 0)
+    forw = S.GetPowerFlux(Layer = 'AirBelow', zOffset = 0)
+    R[i] = np.abs(forw[0])
+    #T[i] = np.abs(back)
+    i +=1
+
+plt.plot(wavelength_space, R)
+#plt.hold
+#plt.plot(wavelength_space, T)
+plt.xlabel('Wavelength (um)')
+plt.ylabel('T')
+plt.title('Figure 3(a)')
+
+#field map
+
+wavelength_p_nm = 1400;
+wavelength_um = float(wavelength_p_nm)/1000; # [8.0,14.0]
+freq = 1 / float(wavelength_um);  
+S.SetFrequency(freq)  #unit 2*pi*c_const / a
+x_space = np.linspace(-p/2,p/2,300)
+z_space = np.linspace(0.8,1.4,300)
+
+X,Z = np.meshgrid(x_space,z_space)
+Ey = np.zeros((X.shape[0], X.shape[1]))
+xc = 0
+zc = 0
+
+for x in x_space:
+    zc=0
+    #print('x='+str(x)+'\n')
+    for z in z_space:
+        #print('z='+str(z)+'\tzc='+str(zc)+'\n')
+        E,H = S.GetFields(x,0,z)
+        Ey[zc,xc] = np.abs(H[1]) ** 2 + np.abs(H[2]) ** 2 + np.abs(H[0]) ** 2
+        #print(str(x)+'\t'+str(z)+'\t'+str(abs(E[1])))
+        zc += 1
+    xc += 1
+
+fig = plt.figure()
+cm = np.linspace(np.min(Ey),np.max(Ey), 100)
+plt.contourf(x_space, z_space, Ey, cm)
+plt.plot([-p/2, p/2], [1, 1], color='w', linestyle='-', linewidth=2)
+plt.plot([-d/2, d/2], [1+h, 1+h], color='w', linestyle='-', linewidth=2)
+plt.plot([-d/2, -d/2], [1, 1+h], color='w', linestyle='-', linewidth=2)
+plt.plot([d/2, d/2], [1, 1+h], color='w', linestyle='-', linewidth=2)
+plt.title('Figure 3(c) - |H|^2 - lam = ' + str(wavelength_p_nm))
+plt.show(block=True)
+
+
+print('If you can read this, the configuration work is finished!')

README

@@ -8,3 +8,14 @@ See the S4 manual, in doc/index.html, for a complete
 description of the package and its user interface, as well as
 installation instructions, the license and copyright, contact
 addresses, and other important information.
+
+Sajidmc:
+This fork focuses on HPC compilation, especially on Purdue University clusters.
+We are only using the python extension. 
+
+Note: you must edit the MakefileHPC and manually check/add the paths to each of the libraries
+
+Usage: 
+
+make -f MakefileHPC clean
+make -f MakefileHPC S4_pyext