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pgd's Issues

command was killed by system

hi, today I run this command (./pgd -f europe-airports.mtx --macro sample_graph.macro)in Ubuntu system, but soon the shell was killed, I think that I have enough memory. If you know why, please let me know, thinks.
there is some information about dataset:
europe-airports: nodes:399, edges:5995, mean_degree:30.050125, mean_path:2.323611 , mean_clustering:0.539272, degree_assortativity: -0.22479390366

number of nodes

Hi there! I tried to apply the method to the CiteSeer dataset with edgelist.txt as input. The input has 3312 nodes, but the --macro returned 3264 nodes. There's no isolated node in the dataset. The number of edges didn't match either. Has anyone met this problem?

Error in compilation

Hello,

Thanks for sharing your implementation

However, I cannot compile the program on my computer, I am on Ubuntu 20.04

Here is the error message :

graphlet_utils.cpp: In function ‘bool fexists(const char*)’:
graphlet_utils.cpp:42:12: error: cannot convert ‘std::ifstream’ {aka ‘std::basic_ifstream<char>’} to ‘bool’ in return
   42 |     return ifile;
      |            ^~~~~
make: *** [Makefile:47: pgd] Error 1

Thank you for your help

input file format csv or mtx

Thank you for making your code public. I want to use this for comparing two networks. If I take a small, well studied graph: karate club; changing the edge-list to .mtx and then giving that as input to pgd isn't working. Here is what I do:

  1. I changed the KC edge-list file to mtx as so:
%% Karate Club Graph (graph is undirected, each edge is saved twice)
%% Nodes: 34 Edges:78*2=156
34 34 78
0 1
0 2
<snip>

Then I tried to do: /pgd -f kc.mtx

On the other hand, if I change the original edgelist file by removing the comments and replace them with a header line: src,dst it seems to work, so the whole thing on MatrixMarket input file format is confusing, but I'm sure I'm missing part of the big-picture.

can we get other modify?

Hi, can we get other modify except the follow:
triangle,2-star,4-clique,4-chordal-cycle,4-tailed-triangle,4-cycle,3-star,4-path

Fixing Compile Issue on macOS 10.13 High Sierra and GCC 7.2.0

When compiling using gcc 7.2.0 on macOS 10.13 High Sierra, I encountered the following error:

graphlet_utils.cpp: In function 'bool fexists(const char*)':
graphlet_utils.cpp:42:12: error: cannot convert 'std::ifstream {aka std::basic_ifstream<char>}' to 'bool' in return
     return ifile;
            ^~~~~
make: *** [pgd] Error 1

I changed 'return ifile;' to be 'return (bool)ifile;' and was able to compile successfully.

Reference: https://stackoverflow.com/questions/38659115/make-fails-with-error-cannot-convert-stdistream-aka-stdbasic-istreamchar

Invalid Micro Counts

Running PGD with the --micro flag yields incorrect micro counts.
For example, on a graph with two tailed triangles, PGD is counting zero tailed triangles for each edge.

Graph tested

Edgelist:

1,2
1,3
2,3
2,4
3,5

image

PGD output

[reading generic edge list: read_edge_list func]  filename: ./double_tailed_triangle.edgelist
|V|: 5
|E|: 5
p: 0.5
d_max: 3
d_avg: 2
r = -0.5625
K = 2
************************************************************
total_2_1edge = 5
total_2_indep = 5
----------------------------------------
total_3_tris = 1
total_2_star = 4
total_3_1edge = 4
total_3_indep = 1
----------------------------------------
total_4_clique = 0
total_4_chordcycle = 0
total_4_tailed_tris = 2
total_4_cycle = 0
total_3_star = 0
total_4_path = 1
----------------------------------------
total_4_1edge = 0
total_4_2edge = 0
total_4_2star = 2
total_4_tri = 0
total_4_indep = 0
************************************************************
--------------------------------------------------------------------------------


Micro graphlet statistics
--------------------------------------------------------------------------------
src,dst,triangle,2-star,4-clique,4-chordal-cycle,4-tailed-triangle,4-cycle,3-star,4-path
3,2,1,2,0,0,0,0,0,1
1,2,1,1,0,0,0,0,0,0
1,3,1,1,0,0,0,0,0,0
5,3,0,2,0,0,0,0,1,0
4,2,0,2,0,0,0,0,1,0

graphlet decomposition time: 2.40803e-05 sec
--------------------------------------------------------------------------------
Graphlet Frequency Distribution (GFD)
--------------------------------------------------------------------------------
4-clique     	0
4-chordal-cycle	0
4-tailed-tri	0.4
4-cycle       	0
3-star       	0
4-path       	0.2
4-node-1-tri   	0
4-node-2-star  	0.4
4-node-2-edge	0
4-node-1-edge  	0
4-node-indep  	0


--------------------------------------------------------------------------------
Connected Motif Graphlet Frequency Distribution (GFD)
--------------------------------------------------------------------------------
4-clique     	0
4-chordal-cycle	0
4-tailed-tri	0.666667
4-cycle       	0
3-star       	0
4-path       	0.333333


--------------------------------------------------------------------------------
Disconnected Motif Graphlet Frequency Distribution (GFD)
--------------------------------------------------------------------------------
4-node-1-tri   	0
4-node-2-star	1
4-node-2-edge  	0
4-node-1-edge  	0
4-node-indep  	0


mean	= 0
median	= 0
max	= 0
min	= 0
range	= 0
std	= 0
var	= 0
iqr	= 0
q1	= 0
q3	= 0

The vertex ids are different between input and output

Thank you very much for your open code! But these is something wrong when I try to use these code.

I use the edge list as the input of PGD as follow:

1 2
1 6
1 4
4 5
4 3
3 5

The output of the PGD is :

% src,dst,triangle,2-star,4-clique,4-chordal-cycle,4-tailed-triangle,4-cycle,3-star,4-path
6,5,1,0,0,0,0,0,0,0
5,4,1,1,0,0,0,0,0,0
6,4,1,1,0,0,0,0,0,0
2,1,0,2,0,0,0,0,1,0
3,1,0,2,0,0,0,0,1,0
4,1,0,4,0,0,0,0,2,4

It's easy to see that the vertex ids are different between input and output
So do you have any method to solve it ?

Best Regards

Compilation Issue

When running make, I get the following output

g++ -O3 -fopenmp -ffast-math -funroll-loops -fno-strict-aliasing -fomit-frame-pointer -fexpensive-optimizations -funroll-loops -fmove-loop-invariants -fprefetch-loop-arrays -ftree-loop-optimize -ftree-vect-loop-version -ftree-vectorize -o pgd graphlet_driver.o graphlet_utils.cpp graphlet_core.cpp graphlet_rand.cpp
graphlet_driver.o: file not recognized: File format not recognized
collect2: error: ld returned 1 exit status
make: *** [pgd] Error 1

Is this an issue with my environment's setup or with the build process? I got the same error on two machines.
Thanks

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