First commit on github -- NetBunch 1.0

5 files changed, 1145 insertions, 0 deletions

diff --git a/src/betweenness/Makefile.am b/src/betweenness/Makefile.am
new file mode 100644
index 0000000..6adf93f
--- /dev/null
+++ b/src/betweenness/Makefile.am
@@ -0,0 +1,7 @@
+include ../common.mk 
+bin_PROGRAMS = betweenness bet_dependency
+betweenness_SOURCES = betweenness.c ../utils/utils.c ../include/utils.h
+betweenness_LDADD = -lm
+bet_dependency_SOURCES = bet_dependency.c ../utils/utils.c ../include/utils.h
+bet_dependency_LDADD = -lm
+
diff --git a/src/betweenness/Makefile.in b/src/betweenness/Makefile.in
new file mode 100644
index 0000000..776f7a1
--- /dev/null
+++ b/src/betweenness/Makefile.in
@@ -0,0 +1,590 @@
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+	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+	fi
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+	-rm -f ../utils/$(DEPDIR)/$(am__dirstamp)
+	-rm -f ../utils/$(am__dirstamp)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+	clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+	distclean distclean-compile distclean-generic distclean-tags \
+	distdir dvi dvi-am html html-am info info-am install \
+	install-am install-binPROGRAMS install-data install-data-am \
+	install-dvi install-dvi-am install-exec install-exec-am \
+	install-html install-html-am install-info install-info-am \
+	install-man install-pdf install-pdf-am install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installdirs maintainer-clean maintainer-clean-generic \
+	mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+	ps ps-am tags tags-am uninstall uninstall-am \
+	uninstall-binPROGRAMS
+
+.PRECIOUS: Makefile
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/betweenness/README b/src/betweenness/README
new file mode 100644
index 0000000..c41e3d1
--- /dev/null
+++ b/src/betweenness/README
@@ -0,0 +1,8 @@
+- bet_dependency computes the contribution to betweenness of each node in the graph
+  restricted to shortest paths originating from a range of nodes
+
+ --- TODO ---
+
+- make a multi-threaded version
+- make an MPI implementation
+- make a version which considers only X% of the nodes, sampled at random
diff --git a/src/betweenness/bet_dependency.c b/src/betweenness/bet_dependency.c
new file mode 100644
index 0000000..2b55543
--- /dev/null
+++ b/src/betweenness/bet_dependency.c
@@ -0,0 +1,224 @@
+/**
+ *  This program is free software: you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or (at your option) any later version.
+ *
+ *  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.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see
+ *  <http://www.gnu.org/licenses/>.
+ *
+ *  (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk>
+ * 
+ *  This file is part of NetBunch, a package for complex network
+ *  analysis and modelling. For more information please visit:
+ *
+ *             http://www.complex-networks.net/
+ *
+ *  If you use this software, please add a reference to 
+ *
+ *               V. Latora, V. Nicosia, G. Russo             
+ *   "Complex Networks: Principles, Methods and Applications"
+ *              Cambridge University Press (2017) 
+ *                ISBN: 9781107103184
+ *
+ ***********************************************************************
+ *
+ *  This program computes the betweenness dependency of all the nodes
+ *  of a graph, using Brandes' algorithm, and counting all the
+ *  shortest paths originating from a set of nodes (potentially the
+ *  whole set of vertices).
+ *
+ *  References: 
+ *     U. Brandes. "A Faster Algorithm for Betweenness 
+ *     Centrality". J. Math. Sociol. 25 (2001), 163-177.  
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "utils.h"
+
+
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                  -*-  bet_dependency  -*-                      **\n"
+         "**                                                                **\n"
+         "**  Compute the betweenness dependency of all the nodes of a      **\n"
+         "**  network due to the shortest paths originating from a set      **\n"
+         "**  of initial nodes. If no start node is specified, compute      **\n"
+         "**  the dependency due to all the nodes of the graph. If no end   **\n"
+         "**  node is specified, compute the dependency due to the nodes    **\n"
+         "**  between node_start and the last node of the graph.            **\n"
+         "**                                                                **\n"
+         "**  The dependency of each node is printed on standard output.    **\n"
+         "**                                                                **\n"
+         "**                                                                **\n"
+         "********************************************************************\n"
+         "\n\n"
+         " This is Free Software - You can use and distribute it under \n"
+         " the terms of the GNU General Public License, version 3 or later\n\n"
+         " (c) Vincenzo Nicosia 2009-2017 (katolaz@yahoo.it)\n\n");
+  printf("Usage: %s <graph_in> [<node_start> [<node_end>]]\n\n" , argv[0]);
+}
+
+void add_predecessor(unsigned int **pred, unsigned int k){
+  
+  (*pred)[0] += 1;
+  *pred = realloc(*pred, ((*pred)[0] + 1)  * sizeof(unsigned int));
+  (*pred)[ (*pred)[0] ] = k;
+}
+
+
+
+/*
+ * Returns a list of dependencies
+ */
+double* compute_bet_dependency(unsigned int N, unsigned int *J_slap, unsigned int *r_slap, 
+                                      unsigned int n_start, unsigned int n_end){
+  
+  int i, j, k, w, idx, cur_node;
+  unsigned int  *marked, **preds, *dist, *nj;
+  double  *delta, *cB;
+  unsigned int d;
+  unsigned int n, nd, ndp;
+  
+  dist = malloc(N * sizeof(unsigned int));
+  marked = malloc(N * sizeof(unsigned int));
+  preds = malloc(N * sizeof(unsigned int *));
+  
+  nj = malloc(N * sizeof(unsigned int));
+  delta = malloc(N * sizeof(double));
+  cB = malloc(N * sizeof(double));
+  
+  for (i=0; i<N; i++){
+    cB[i] = 0;
+    preds[i] = NULL;
+  }
+
+  for (j=n_start; j<=n_end && j<N; j++){
+    for(i=0; i<N; i ++){
+      dist[i] = N;
+      if (! preds[i]){
+        preds[i] = malloc(sizeof(unsigned int));
+      }
+      preds[i][0] = 0; /* The list of predecessors is now empty! */
+      
+      nj[i] = 0;
+      delta[i]= 0;
+    }
+    dist[j] = 0;
+    nj[j] = 1;
+    marked[0] = j;
+    d = 0;
+    n = 0;
+    nd = 1;
+    ndp = 0;
+    while (d<N && nd > 0){
+      for(i = n; i< n+nd; i ++){
+        cur_node = marked[i];
+        for (k=r_slap[cur_node]; k<r_slap[cur_node +1] ; k++){
+          w = J_slap[k];
+          if ( dist[w] == d+1){
+            add_predecessor((unsigned int **)(preds + w), cur_node);
+            nj[w] += nj[cur_node];
+          }
+          if ( dist[w] == N){
+            dist[w] = d+1;
+            marked[n + nd + ndp] = w;
+            add_predecessor(preds + w, cur_node);
+            ndp +=1;
+            nj[w] += nj[cur_node];
+          }
+        }
+      }
+      n = n + nd;
+      nd = ndp;
+      ndp = 0;
+      d += 1; 
+    }
+    for (k= n-1; k>=1; k--){
+      w = marked[k];
+      for (idx=1; idx <= preds[w][0]; idx ++ ){
+        i = preds[w][idx];
+        delta[i] += 1.0 * nj[i] / nj[w] * (1 + delta[w]);
+      }
+      cB[w] += delta[w];
+    }
+  }
+  free(dist);
+  free(marked);
+  for (i=0; i<N; i++){
+    free(preds[i]);
+  }
+  free(preds);
+  free(nj);
+  free(delta);
+  
+  return cB;
+}
+
+
+
+void dump_cB(double *cB, unsigned int N){
+
+  unsigned int i;
+  for (i=0; i<N; i++){
+    printf("%g\n", cB[i]);
+  }
+}
+
+
+int main(int argc, char *argv[]){
+  
+  unsigned int *J_slap=NULL, *r_slap=NULL;
+  unsigned int K, N;
+  unsigned int n_start, n_end;
+  double *cB;
+  FILE *filein;
+  
+  n_start = 0;
+  n_end = -1;
+
+  switch (argc){
+
+  case 4:
+    n_end = atoi(argv[3]);
+  case 3:
+    n_start = atoi(argv[2]);
+  case 2:
+    break;
+  default:     
+    usage(argv);
+    exit(1);
+    break;
+  }
+  
+  if (!strcmp(argv[1], "-")){
+    /* take the input from STDIN */
+    filein = stdin;
+  }
+  else {
+    filein = openfile_or_exit(argv[1], "r", 2);
+  }
+
+  read_slap(filein, &K, &N, &J_slap, &r_slap);
+  if (n_end == -1)
+    n_end = N-1;
+  cB = compute_bet_dependency(N, J_slap, r_slap, n_start, n_end);
+  dump_cB(cB, N);
+
+  free(cB);
+  free(J_slap);
+  free(r_slap);
+  
+}
diff --git a/src/betweenness/betweenness.c b/src/betweenness/betweenness.c
new file mode 100644
index 0000000..5e37747
--- /dev/null
+++ b/src/betweenness/betweenness.c
@@ -0,0 +1,316 @@
+/**
+ *  This program is free software: you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or (at your option) any later version.
+ *
+ *  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.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see
+ *  <http://www.gnu.org/licenses/>.
+ *
+ *  (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk>
+ * 
+ *  This file is part of NetBunch, a package for complex network
+ *  analysis and modelling. For more information please visit:
+ *
+ *             http://www.complex-networks.net/
+ *
+ *  If you use this software, please add a reference to 
+ *
+ *               V. Latora, V. Nicosia, G. Russo             
+ *   "Complex Networks: Principles, Methods and Applications"
+ *              Cambridge University Press (2017) 
+ *                ISBN: 9781107103184
+ *
+ ***********************************************************************
+ *
+ *  This program computes the betweenness of all the nodes of a graph,
+ *  using Brandes' algorithm, and counting all the shortest paths
+ *  originating from a set of nodes (potentially the whole set of
+ *  vertices).
+ *
+ *  References: 
+ *     U. Brandes. "A Faster Algorithm for Betweenness 
+ *     Centrality". J. Math. Sociol. 25 (2001), 163-177.  
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <time.h>
+
+#include "utils.h"
+
+
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                      -*-  betweenness  -*-                     **\n"
+         "**                                                                **\n"
+         "**  Compute the betweenness of all the nodes and edges of a       **\n"
+         "**  network due to the shortest paths originating from a set      **\n"
+         "**  of initial nodes.  The set can be either a sequence of        **\n"
+         "**  nodes (if the second argument is 'SEQ') or a random sample    **\n"
+         "**  from the set of all the nodes (if it is 'RND').               **\n"
+         "**                                                                **\n"
+         "**  The input file is an edge-list (use '-' to read from STDIN).  **\n"
+         "**                                                                **\n"
+         "**  With 'SEQ':                                                   **\n"
+         "**  If <node_start> is not specified, computes the betweenness    **\n"
+         "**  using shortest paths from *all* the nodes (WARNING: This can  **\n"
+         "**  be slow for large graphs!). If <node_end> is not specified,   **\n"
+         "**  use shortest paths from all the nodes between <node_start>    **\n"
+         "**  and the node with the largest label.                          **\n"
+         "**                                                                **\n"
+         "**  With 'RND':                                                   **\n"
+         "**  Compute the betweenness based on the shortest paths from      **\n"
+         "**  <num> nodes sampled uniformly at random.                      **\n"
+         "**                                                                **\n"
+         "**  When called with just <graph_in>, use all the nodes.          **\n"
+         "**                                                                **\n"
+         "**  The betweenness of all the nodes is printed on standard       **\n"
+         "**  output (STDOUT), while the edge betweenness is printed on     **\n"
+         "**  standard error (STDERR)                                       **\n"
+         "**                                                                **\n"
+         "********************************************************************\n"
+         "\n\n"
+         " This is Free Software - You can use and distribute it under \n"
+         " the terms of the GNU General Public License, version 3 or later\n\n"
+         " (c) Vincenzo Nicosia 2009-2017 (v.nicosia@qmul.ac.uk)\n\n");
+  printf("Usage: %s <graph_in> [SEQ <node_start> [<node_end>]]\n" , argv[0]);
+  printf("Usage: %s <graph_in> [RND <num>]\n" , argv[0]);
+
+}
+
+/*
+ * Add a node the a list of predecessors
+ */
+
+void add_predecessor(unsigned int **pred, unsigned int k){
+  
+  (*pred)[0] += 1;
+  *pred = realloc(*pred, ((*pred)[0] + 1)  * sizeof(unsigned int));
+  (*pred)[ (*pred)[0] ] = k;
+}
+
+
+
+/*
+ *
+ * Compute node and edge betweenness, based on shortest paths
+ * originating on the "num" nodes specified in "nlist".  "edge_bet"
+ * should be an appropriately allocated (and initialised to zero!!!!)
+ * vector of length equal to J_slap, and will contain the values of
+ * edge betweenness.
+ *
+ */
+double* compute_bet_dependency(unsigned int N, unsigned int *J_slap, unsigned int *r_slap, 
+                               unsigned int *nlist, unsigned int num, double *edge_bet){
+  
+  int i, j, k, w, idx, cur_node, m;
+  unsigned int  *marked, **preds, *dist, *nj;
+  double  *delta, *cB, val;
+  unsigned int d;
+  unsigned int n, nd, ndp;
+  unsigned int edge_pos;
+  
+  dist = malloc(N * sizeof(unsigned int));
+  marked = malloc(N * sizeof(unsigned int));
+  preds = malloc(N * sizeof(unsigned int *));
+  
+  nj = malloc(N * sizeof(unsigned int));
+  delta = malloc(N * sizeof(double));
+  cB = malloc(N * sizeof(double));
+  
+  for (i=0; i<N; i++){
+    cB[i] = 0;
+    preds[i] = NULL;
+  }
+
+  for (m=0; m<num; m++){
+    /* We start from the m-th node in nlist*/
+    j = nlist[m];
+
+    for(i=0; i<N; i ++){
+      dist[i] = N;
+      if (! preds[i]){
+        preds[i] = malloc(sizeof(unsigned int));
+      }
+      preds[i][0] = 0; /* The list of predecessors is now empty! */
+      
+      nj[i] = 0;
+      delta[i]= 0;
+    }
+    dist[j] = 0;
+    nj[j] = 1;
+    marked[0] = j;
+    d = 0;
+    n = 0;
+    nd = 1;
+    ndp = 0;
+    while (d<N && nd > 0){
+      for(i = n; i< n+nd; i ++){
+        cur_node = marked[i];
+        for (k=r_slap[cur_node]; k<r_slap[cur_node +1] ; k++){
+          w = J_slap[k];
+          if ( dist[w] == d+1){
+            add_predecessor((unsigned int **)(preds + w), cur_node);
+            nj[w] += nj[cur_node];
+          }
+          if ( dist[w] == N){
+            dist[w] = d+1;
+            marked[n + nd + ndp] = w;
+            add_predecessor(preds + w, cur_node);
+            ndp +=1;
+            nj[w] += nj[cur_node];
+          }
+        }
+      }
+      n = n + nd;
+      nd = ndp;
+      ndp = 0;
+      d += 1; 
+    }
+    for (k= n-1; k>=1; k--){
+      w = marked[k];
+      for (idx=1; idx <= preds[w][0]; idx ++ ){
+        i = preds[w][idx];
+        val = 1.0 * nj[i] / nj[w] * (1 + delta[w]);
+        delta[i] += val;
+        /* Now we should update the betweenness of the edge (i,w) in
+           the appropriate position of the vector  edge_bet*/
+        find_neigh_in_Jslap(J_slap, r_slap, N, i, w, &edge_pos);
+        edge_bet[edge_pos] += val;
+        find_neigh_in_Jslap(J_slap, r_slap, N, w, i, &edge_pos);
+        edge_bet[edge_pos] += val;
+      }
+      cB[w] += delta[w];
+    }
+  }
+  free(dist);
+  free(marked);
+  for (i=0; i<N; i++){
+    free(preds[i]);
+  }
+  free(preds);
+  free(nj);
+  free(delta);
+  return cB;
+}
+
+
+
+/*
+ * print of STDOUT the betweenness of each node
+ */
+void dump_cB(double *cB, unsigned int N){
+
+  unsigned int i;
+  for (i=0; i<N; i++){
+    printf("%g\n", cB[i]);
+  }
+}
+
+/*
+ * print on STDERR the betweenness of each edge
+ */
+
+void dump_edge_bet(unsigned int *J_slap, unsigned int *r_slap, unsigned int N,
+                   double *v,  FILE *fout){
+
+  unsigned int i, j;
+
+  for(i=0; i<N; i++){
+    for (j=r_slap[i]; j<r_slap[i+1]; j++)
+      fprintf(fout, "%d %d %g\n", i, J_slap[j], v[j]);
+  }
+}
+
+
+
+int main(int argc, char *argv[]){
+  
+  unsigned int *J_slap=NULL, *r_slap=NULL;
+  unsigned int K, N, i;
+  unsigned int n_start, n_end;
+  unsigned int *nlist=NULL;
+  unsigned int num;
+  double *edge_bet = NULL;
+  double *cB;
+  FILE *filein;
+  
+
+  if(argc < 2){
+    usage(argv);
+    exit(1);
+  }
+
+  srand(time(NULL));
+
+  if (!strcmp(argv[1], "-")){
+    /* take the input from STDIN */
+    filein = stdin;
+  }
+  else {
+    filein = openfile_or_exit(argv[1], "r", 2);
+  }
+
+  read_slap(filein, &K, &N, &J_slap, &r_slap);
+
+  nlist = malloc(N * sizeof(unsigned int));
+
+  for(i=0; i<N; i++){
+    nlist[i] = i;
+  }
+
+  n_start = 0;
+  n_end = N-1;
+  num = N;
+
+
+  if (argc > 3){
+    if(!my_strcasecmp(argv[2], "SEQ")){
+      n_start = atoi(argv[3]);
+      if (n_start > N-1)
+        n_start = 0;
+      if (argc > 4){
+        n_end = atoi(argv[4]);
+      }
+      else{
+        n_end = N-1;
+      }
+      num = n_end - n_start + 1;
+    }
+    else if (!my_strcasecmp(argv[2], "RND")){
+      num = atoi(argv[3]);
+      n_start = 0;
+      n_end = num-1;
+      if (num > N || num < 1)
+        num = N;
+      shuffle_vector(nlist, N);
+    }
+  }
+  
+  sort_neighbours(J_slap, r_slap, N);
+  edge_bet = malloc(K * sizeof(double));
+  memset(edge_bet, 0, K * sizeof(double));
+  cB = compute_bet_dependency(N, J_slap, r_slap, nlist+n_start, num, edge_bet);
+
+  dump_cB(cB, N);
+  dump_edge_bet(J_slap, r_slap, N, edge_bet, stderr);
+
+  free(cB);
+  free(J_slap);
+  free(r_slap);
+  free(edge_bet);
+  free(nlist);
+  
+}