Initial commit

Author: govertb

.gitignore

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+.DS_Store
+demo_data/*
+results/*
+
+*.swp
+
+*.trace
+*.o
+*.out
+# Xcode
+#
+# gitignore contributors: remember to update Global/Xcode.gitignore, Objective-C.gitignore & Swift.gitignore
+
+## Build generated
+build/
+DerivedData/
+
+## Various settings
+*.pbxuser
+!default.pbxuser
+*.mode1v3
+!default.mode1v3
+*.mode2v3
+!default.mode2v3
+*.perspectivev3
+!default.perspectivev3
+xcuserdata/
+
+## Other
+*.moved-aside
+*.xccheckout
+*.xcscmblueprint

.gitmodules

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+[submodule "lib/pngwriter"]
+	path = lib/pngwriter
+	url = https://github.com/pngwriter/pngwriter.git

LICENSE

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+CC:=gcc
+
+# Directories
+L_SRC_DIR         := ../../lib
+SRC_DIR           := ../../src
+OBJ_DIR           := obj
+
+# C/C++ compiler flags
+COMMON_FLAGS:=-O3
+CFLAGS   :=$(COMMON_FLAGS) -D NO_FREETYPE
+CXXFLAGS :=$(COMMON_FLAGS) -std=c++11 #-g
+NVCCFLAGS:=#-G
+
+# C preprocessor flags
+CPPFLAGS :=-D NO_FREETYPE
+ifeq ($(CUDA_SUPPORT), 1)
+	CPPFLAGS:=$(CPPFLAGS) -D __CUDA__ -isystem /usr/local/cuda/include/
+endif
+ifeq ($(DEBUG_PRINTING), 1)
+	CPPFLAGS:=$(CPPFLAGS) -D DEBUGPRINT
+endif
+
+# Linker flags
+LDFLAGS  :=-lc -lm -lstdc++ -fopenmp -lpng
+ifeq ($(CUDA_SUPPORT), 1)
+	LDFLAGS:=$(LDFLAGS) -L/usr/local/cuda/lib64 -lcudart
+endif
+
+# src./obj. files
+
+
+GRAPH_VIEWER_SRCS := $(wildcard $(SRC_DIR)/*.cpp)
+GRAPH_VIEWER_OBJS := $(GRAPH_VIEWER_SRCS:$(SRC_DIR)/%.cpp=$(OBJ_DIR)/%.o)
+
+PNGWRITER_SRCS    := $(L_SRC_DIR)/pngwriter/src/pngwriter.cc
+PNGWRITER_OBJS    := $(PNGWRITER_SRCS:$(L_SRC_DIR)/%.cc=$(OBJ_DIR)/%.o)
+
+CUDA_SRCS         := $(wildcard $(SRC_DIR)/*.cu)
+CUDA_OBJS         := $(CUDA_SRCS:$(SRC_DIR)/%.cu=$(OBJ_DIR)/%.o)
+CUDA_DEPS         := $(wildcard $(SRC_DIR)/*.cuh)
+
+# Don't compile with CUDA support by default
+CUDA_SUPPORT      ?= 0
+
+CPP_SRC           := $(GRAPH_VIEWER_SRCS) $(PNGWRITER_SRCS)
+CUDA_SRC          := $(CUDA_SRCS)
+SOURCES           := $(C_SRC) $(CPP_SRC)
+OBJECTS           := $(GRAPH_VIEWER_OBJS) $(PNGWRITER_OBJS)
+
+ifeq ($(CUDA_SUPPORT), 1)
+OBJECTS           := $(OBJECTS) $(CUDA_OBJS)
+SOURCES           := $(SOURCES) $(CUDA_SRCS)
+endif
+
+# Generate dependency (.h, .hpp)
+# ala http://stackoverflow.com/questions/2394609/makefile-header-dependencies
+depend: .depend
+.depend: $(SRCS)
+	rm -f ./.depend
+	$(CC) $(CXXFLAGS) $(CPPFLAGS) -MM $(CPP_SRC) >> ./.depend
+
+include ./.depend
+
+graph_viewer: $(OBJECTS)
+	$(CC) $(OBJECTS) $(LDFLAGS) -o graph_viewer
+
+$(GRAPH_VIEWER_OBJS): $(GRAPH_VIEWER_SRCS)
+	mkdir -p $(@D)
+	$(CC) -c $(CPPFLAGS) $(CXXFLAGS) --std=c++11 -o $@ $(@:$(OBJ_DIR)/%.o=$(SRC_DIR)/%.cpp)
+
+$(CUDA_OBJS): $(CUDA_SRCS) $(CUDA_DEPS)
+	mkdir -p $(@D)
+	nvcc -c $(CXXFLAGS) $(NVCCFLAGS) $(CPPFLAGS) -o $@ $(@:$(OBJ_DIR)/%.o=$(SRC_DIR)/%.cu)
+
+$(PNGWRITER_OBJS): $(PNGWRITER_SRCS)
+	mkdir -p $(@D)
+	$(CC) -c $(CPPFLAGS) $(CXXFLAGS) -o $@ $(@:$(OBJ_DIR)/%.o=$(L_SRC_DIR)/%.cc)
+
+clear: clean
+
+clean:
+	rm -r graph_viewer $(OBJ_DIR)/* ./.depend
+
+.PHONY: all clear clean depend

builds/linux/Makefile

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+`graph_viewer` | GPU accelerated graph layout
+=============================================
+
+This repository contains experimental code for large scale graph layout using the GPU. Currently we only implement the basics of ForceAtlas2, a graph layout algorithm  designed for social network visualization in Gephi<sup>[1](#jacomy14),[2](#bastian09)</sup>. Our implementation of ForceAtlas2 is based on [the open source implementation](https://github.com/gephi/gephi/tree/6efb108718fa67d1055160f3a18b63edb4ca7be2/modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/forceAtlas2) used in Gephi itself. For force approximation, we use a CUDA implementation of the Barnes-Hut approximation algorithm<sup>[3](#barnes86)</sup> by Martin Burtscher and Keshav Pingali<sup>[4](#burtscher11)</sup>. This implementation is available as part of [Galois](http://iss.ices.utexas.edu/?p=projects/galois). The average speedup, compared to a *de facto* CPU implementation of ForceAtlas2, is over 40x. This makes it feasible to compute layouts for networks with millions of nodes and edges. More details and results can be found in:
+
+* G.G. Brinkmann, K.F.D. Rietveld and F.W. Takes, Exploiting GPUs for fast force-directed visualization of large-scale networks, in Proceedings of the 46th International Conference on Parallel Processing (ICPP), pp. 382-391, 2017. doi: https://dx.doi.org/10.1109/ICPP.2017.47
+
+
+#### System Requirements
+
+A CUDA capable GPU. Currently only Linux is supported.
+
+#### Obtaining all code
+This repository contains a submodule (`lib/pngwriter`). Be sure to run
+```
+git submodule init && git submodule update
+```
+from the root of this Git repository before compiling. The code also depends on the `libpng` library (including its development headers). It should be possible to obtain this using the package manager for your Linux distribution.
+
+#### Compiling
+A `Makefile` is located in `builds/linux`. Running
+```
+make graph_viewer CUDA_SUPPORT=1
+```
+from this directory compiles `graph_viewer` with CUDA support.
+
+#### Usage
+`graph_viewer cuda|seq max_iterations num_snaps sg|wg scale gravity exact|approximate edgelist_path out_path test|image`
+
+`cuda|seq`           : choose between a CUDA parallel implementation or a sequential implementation.
+
+`max_iterations`     : how many iterations of the layout algorithm to run
+
+`num_snaps`          : choose how many times during the layout process a visualization should be rendered
+
+`wg|sg`              : choose between weak gravity (inversely proportional to distance) or
+                     strong gravity
+
+`scale`              : scale repulsive force
+
+`gravity`            : scale gravitational force
+
+`exact|approximate`  : choose between the exact/pairwise O(|V|^2) repulsive force calculation or the O(|V|lg(|V|))
+                     approximation using Barnes-Hut (CUDA implementation only supports Barnes-Hut)
+
+`edgelist_path`      : ASCII file containing node IDs for each edge on a separate line (whitespace separated)
+
+`out_path`           : path to write rendered .png files to
+
+`test|image`         : measure runningtimes or produce image of layout
+
+#### References
+<a name="jacomy14"><sup>1</sup></a> M. Jacomy, T. Venturini, S. Heymann, and M. Bastian, ["Forceatlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software"](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098679), PLoS ONE, vol. 9, no. 6, pp. 1–12, 2014.
+
+<a name="bastian09"><sup>2</sup></a> M. Bastian, S. Heymann, and M. Jacomy, ["Gephi: an open source software for exploring and manipulating networks."](https://aaai.org/ocs/index.php/ICWSM/09/paper/view/154) in Proceedings of International Conference on Web and Social Media (ICWSM), 2009, pp. 361–362.
+
+<a name="barnes86"><sup>3</sup></a>J. Barnes and P. Hut, ["A hierarchical O(N log N) force-calculation algorithm"](https://www.nature.com/nature/journal/v324/n6096/abs/324446a0.html), Nature, vol. 324, pp. 446–449, 1986.
+
+<a name="burtscher11"><sup>4</sup></a> M. Burtscher and K. Pingali, "An efficient CUDA implementation of the tree-based Barnes Hut n-body algorithm", in GPU Computing Gems Emerald Edition, W. mei W. Hwu, Ed., 2011, ch. 6, pp. 75–92.
+
+#### Disclaimer
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.