Speeding up BigClam implementation

contrib/ICL-bigclam_speedup/.gitignore

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+# Temp files
+*~
+
+# C++ object files
+*.o
+
+# R command cache
+*.Rhistory
+
+# iPython notebook checkpoints
+*.ipynb_checkpoint
+
+# Data files
+data/*.txt
+
+# Plots
+*.pdf

contrib/ICL-bigclam_speedup/Makefile

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+include ./Makefile.config
+
+.SECONDARY:
+
+all: bigclam bigclam_old cmtycompare
+
+bigclam_old: src/bigclam.cpp $(BIGCLAM_OLD_DEP_O) $(SNAPLIB)
+	$(CC) $(CXXFLAGS) $(CXXOPENMP) $(LDFLAGS) $(LIBS) \
+	$(BIGCLAM_HEADERFLAGS) \
+	$(BIGCLAM_OLD_DEP_O) $(SNAPLIB) \
+	$< \
+	-o $@
+
+bigclam: src/bigclam.cpp $(BIGCLAM_DEP_O) $(SNAPLIB)
+	$(CC) $(CXXFLAGS) $(CXXOPENMP) $(LDFLAGS) $(LIBS) \
+	$(BIGCLAM_HEADERFLAGS) \
+	$(BIGCLAM_DEP_O) $(SNAPLIB) \
+	$< \
+	-o $@
+
+cmtycompare: src/cmtycompare.cpp $(SNAPLIB)
+	$(CC) $(CXXFLAGS) $(CXXOPENMP) $(LDFLAGS) $(LIBS) \
+	$(BIGCLAM_HEADERFLAGS) \
+	$(SNAPLIB) \
+	$< \
+	-o $@
+
+$(SNAPLIB):
+	$(MAKE) -C $(SNAPDIR)
+
+$(BINDIR)/agmfast_old.o: src/agmfast_old.cpp
+	$(CC) $(CXXFLAGS) $(CXXOPENMP) $(LDFLAGS) $(LIBS) \
+	$(BIGCLAM_HEADERFLAGS) \
+	-c $< -o $@
+
+$(BINDIR)/ag%.o: $(AGMDIR)/ag%.cpp
+	$(CC) $(CXXFLAGS) $(CXXOPENMP) $(LDFLAGS) $(LIBS) \
+	$(BIGCLAM_HEADERFLAGS) \
+	-c $< -o $@
+
+$(BINDIR)/%.o: %.cpp
+	$(CC) $(CXXFLAGS) $(CXXOPENMP) $(LDFLAGS) $(LIBS) \
+	$(BIGCLAM_HEADERFLAGS) \
+	-c $< -o $@
+
+clean:
+	rm -rf bin/*.*
+	rm bigclam
+	rm bigclam_old
+	rm cmtycompare
+
+deepclean: clean
+	$(MAKE) clean -C $(SNAPDIR)
+
+.PHONY: all clean deepclean
+

contrib/ICL-bigclam_speedup/Makefile.config

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+
+# Compiler settings
+
+UNAME := $(shell uname)
+
+ifeq ($(UNAME), Linux)
+  # Linux flags
+  CC = g++
+  CXXFLAGS += -std=c++98 -Wall
+  CXXFLAGS += -O3 -DNDEBUG -fopenmp
+  # turn on for crash debugging, get symbols with <prog> 2>&1 | c++filt
+  #CXXFLAGS += -g -rdynamic
+  #CXXFLAGS += -ggdb
+  # turn on for OpenMP
+  CXXOPENMP = 
+  LDFLAGS +=
+  LIBS += -lrt
+
+else ifeq ($(UNAME), Darwin)
+  # OS X flags
+  CC = g++
+  CXXFLAGS += -std=c++98 -Wall -Wno-unknown-pragmas
+  CXXFLAGS += -O3 -DNDEBUG
+  CLANG := $(shell g++ -v 2>&1 | grep clang | cut -d " " -f 2)
+  ifeq ($(CLANG), LLVM)
+    CXXFLAGS += -DNOMP
+    CXXOPENMP =
+  else ifeq ($(CLANG), clang)
+    CXXFLAGS += -DNOMP
+    CXXOPENMP =
+  else
+    CXXFLAGS += -fopenmp
+    #CXXOPENMP += -fopenmp
+  endif
+  LDFLAGS +=
+  LIBS +=
+
+  # If a dynamic library, i.e. gtest, is installed in some local directory,
+  # for example by Anaconda, the program might fail with 'image not found'.
+  # Use one of the solutions below.
+  # 1. set the path to the lib directory in the executable at linking time
+  #LDFLAGS += -Wl,-rpath,$(HOME)/miniconda3/lib
+  # 2. set one of the following environment variables from your shell at run time
+  #export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/miniconda3/lib
+  #export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$HOME/miniconda3/lib
+  #export DYLD_FALLBACK_LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH:$HOME/miniconda3/lib
+
+else ifeq ($(shell uname -o), Cygwin)
+  # Cygwin flags
+  CC = g++
+  CXXFLAGS += -Wall -D__STDC_LIMIT_MACROS
+  CXXFLAGS += -O3 -DNDEBUG
+  CXXOPENMP = -fopenmp
+  LDFLAGS += -fopenmp
+  LIBS +=
+
+endif
+
+
+# Directories ---
+
+SNAPDIR = ../../snap-core
+GLIBDIR = ../../glib-core
+AGMDIR = ../../snap-adv
+
+BINDIR = bin
+
+# Compiled Libraries ---
+
+SNAPLIB = $(SNAPDIR)/Snap.o
+
+
+# BigClam-related ---
+
+BIGCLAM_CORE_O = $(BINDIR)/agm.o \
+                 $(BINDIR)/agmfit.o 
+
+BIGCLAM_DEP_O = $(BIGCLAM_CORE_O) \
+                $(BINDIR)/agmfast.o 
+BIGCLAM_OLD_DEP_O = $(BIGCLAM_CORE_O) \
+                    $(BINDIR)/agmfast_old.o 
+
+BIGCLAM_HEADERFLAGS = -I. \
+                      -I$(SNAPDIR) \
+                      -I$(GLIBDIR) \
+                      -I$(AGMDIR) 

contrib/ICL-bigclam_speedup/Pipfile

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+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+
+[packages]
+numpy = "*"
+pandas = "*"
+matplotlib = "*"
+scipy = "*"
+jupyter = "*"
+
+[requires]
+python_version = "3.7"