path: root/sci-libs/bliss/files/bliss-0.72-fedora.patch

Pulled on 28-04-13 from
http://pkgs.fedoraproject.org/cgit/bliss.git/tree/

- Man page written by Jerry James using text borrowed from the sources.
  The man page therefore has the same copyright and license as the sources.
- Don't call exit() in library code.
- Patch from Thomas Rehn, also sent upstream.  Fix one bug and add one
   performance enhancement.

diff -Naur bliss-0.72.orig/bliss.1 bliss-0.72/bliss.1
--- bliss-0.72.orig/bliss.1	1969-12-31 17:00:00.000000000 -0700
+++ bliss-0.72/bliss.1	2013-04-28 14:35:37.000000000 -0600
@@ -0,0 +1,55 @@
+.TH "BLISS" "1" "@VERSION@" "Tommi Junttila & Petteri Kaski" "User Commands"
+.SH "NAME"
+bliss \- Compute automorphism groups and canonical labelings of graphs
+.SH "SYNOPSIS"
+.B bliss
+[\fIOPTIONS\fR] [<\fIGRAPH FILE\fR>]
+.SH "DESCRIPTION"
+.PP
+Bliss is an open source tool for computing automorphism groups and
+canonical forms of graphs.  The graphs are specified in DIMACS format.
+.TP
+\fB\-directed\fR
+the input graph is directed
+.TP
+\fB\-can\fR
+compute canonical form
+.TP
+\fB\-ocan\fR=\fIf\fR
+compute canonical form and output it in file \fIf\fR
+.TP
+\fB\-v\fR=\fIN\fR
+set verbosity level to N [N >= 0, default: 1]
+.TP
+\fB\-sh\fR=\fIX\fR
+select splitting heuristics, where X is:
+.TS
+tab(;);
+R L.
+f;first non-singleton cell
+fl;first largest non-singleton cell
+fs;first smallest non-singleton cell
+fm;first maximally non-trivially connected non-singleton cell
+flm;first largest maximally non-trivially connected
+;non-singleton cell
+fsm;first smallest maximally non-trivially connected
+;non-singleton cell (default)
+.TE
+.TP
+\fB\-fr\fR=\fIX\fR
+use failure recording? [X=y/n, default: y]
+.TP
+\fB\-cr\fR=\fIX\fR
+use component recursion? [X=y/n, default: y]
+.TP
+\fB\-version\fR
+print the version number and exit
+.TP
+\fB\-help\fR
+print this help and exit
+.SH "AUTHORS"
+Bliss was written by Tommi Junttila <Tommi.Junttila@tkk.fi> and
+Petteri Kaski <petteri.kaski@aalto.fi>.
+.PP
+This man page was written by Jerry James <loganjerry@gmail.com>.
+It is distributed under the same terms as bliss.
diff -Naur bliss-0.72.orig/bliss.cc bliss-0.72/bliss.cc
--- bliss-0.72.orig/bliss.cc	2013-04-28 14:35:20.582085167 -0600
+++ bliss-0.72/bliss.cc	2013-04-28 14:36:28.792330603 -0600
@@ -276,13 +276,16 @@
   if(opt_canonize == false)
     {
       /* No canonical labeling, only automorphism group */
-      g->find_automorphisms(stats, &report_aut, stdout);
+      if (!g->find_automorphisms(stats, &report_aut, stdout))
+	exit(1);
     }
   else
     {
       /* Canonical labeling and automorphism group */
       const unsigned int* cl = g->canonical_form(stats, &report_aut, stdout);
 
+      if (!cl)
+	exit(1);
       fprintf(stdout, "Canonical labeling: ");
       bliss::print_permutation(stdout, g->get_nof_vertices(), cl, 1);
       fprintf(stdout, "\n");
@@ -290,6 +293,8 @@
       if(opt_output_can_file)
 	{
 	  bliss::AbstractGraph* cf = g->permute(cl);
+	  if (!cf)
+	    exit(1);
 	  FILE* const fp = fopen(opt_output_can_file, "w");
 	  if(!fp)
 	    _fatal("Cannot open '%s' for outputting the canonical form, aborting", opt_output_can_file);
diff -Naur bliss-0.72.orig/bliss_C.cc bliss-0.72/bliss_C.cc
--- bliss-0.72.orig/bliss_C.cc	2013-04-28 14:35:20.582085167 -0600
+++ bliss-0.72/bliss_C.cc	2013-04-28 14:36:28.792330603 -0600
@@ -131,7 +131,7 @@
 }
 
 extern "C"
-void
+int
 bliss_find_automorphisms(BlissGraph *graph,
 			 void (*hook)(void *user_param,
 				      unsigned int n,
@@ -142,7 +142,8 @@
   bliss::Stats s;
   assert(graph);
   assert(graph->g);
-  graph->g->find_automorphisms(s, hook, hook_user_param);
+  if (!graph->g->find_automorphisms(s, hook, hook_user_param))
+    return 0;
 
   if(stats)
     {
@@ -154,6 +155,7 @@
       stats->nof_generators = s.get_nof_generators();
       stats->max_level = s.get_max_level();
     }
+  return 1;
 }
 
 
@@ -173,7 +175,7 @@
   
   canonical_labeling = graph->g->canonical_form(s, hook, hook_user_param);
 
-  if(stats)
+  if(canonical_labeling && stats)
     {
       stats->group_size_approx = s.get_group_size_approx();
       stats->nof_nodes = s.get_nof_nodes();
diff -Naur bliss-0.72.orig/bliss_C.h bliss-0.72/bliss_C.h
--- bliss-0.72.orig/bliss_C.h	2013-04-28 14:35:20.582085167 -0600
+++ bliss-0.72/bliss_C.h	2013-04-28 14:36:28.792330603 -0600
@@ -156,6 +156,7 @@
  * The argument \a perm should be an array of
  * N=bliss::bliss_get_nof_vertices(\a graph) elements describing
  * a bijection on {0,...,N-1}.
+ * Returns NULL if insufficient memory or internal error.
  */
 BlissGraph *bliss_permute(BlissGraph *graph, const unsigned int *perm);
 
@@ -174,8 +175,9 @@
  * if you want to use the automorphism later, you have to take a copy of it.
  * Do not call bliss_* functions in the hook.
  * If \a stats is non-null, then some search statistics are copied there.
+ * \return nonzero if successful, zero if insufficient memory or internal error
  */
-void
+int
 bliss_find_automorphisms(BlissGraph *graph,
 			 void (*hook)(void *user_param,
 				      unsigned int N,
@@ -194,6 +196,7 @@
  * then bliss_permute() with the returned canonical labeling.
  * Note that the computed canonical version may depend on the applied version
  * of bliss.
+ * Returns NULL if insufficient memory or internal error.
  */
 const unsigned int *
 bliss_find_canonical_labeling(BlissGraph *graph,
diff -Naur bliss-0.72.orig/defs.cc bliss-0.72/defs.cc
--- bliss-0.72.orig/defs.cc	2013-04-28 14:35:20.582085167 -0600
+++ bliss-0.72/defs.cc	2013-04-28 14:36:28.792330603 -0600
@@ -33,7 +33,6 @@
   vfprintf(stderr, fmt, ap);
   fprintf(stderr, "\nAborting!\n");
   va_end(ap);
-  exit(1);
 }
 
 }
diff -Naur bliss-0.72.orig/graph.cc bliss-0.72/graph.cc
--- bliss-0.72.orig/graph.cc	2013-04-28 14:35:20.582085167 -0600
+++ bliss-0.72/graph.cc	2013-04-28 14:37:16.162501050 -0600
@@ -34,7 +34,10 @@
 namespace bliss {
 
 #define _INTERNAL_ERROR() fatal_error("%s:%d: internal error",__FILE__,__LINE__)
-#define _OUT_OF_MEMORY() fatal_error("%s:%d: out of memory",__FILE__,__LINE__)
+#define _OUT_OF_MEMORY(label) do {				\
+    fatal_error("%s:%d: out of memory",__FILE__,__LINE__);	\
+    goto label;							\
+  } while (0)
 
 /*-------------------------------------------------------------------------
  *
@@ -279,20 +282,6 @@
     *perm = i;
 }
 
-bool
-AbstractGraph::is_automorphism(unsigned int* const perm)
-{
-  _INTERNAL_ERROR();
-  return false;
-}
-
-bool
-AbstractGraph::is_automorphism(const std::vector<unsigned int>& perm) const
-{
-  _INTERNAL_ERROR();
-  return false;
-}
-
 
 
 
@@ -608,17 +597,7 @@
 };
 
 
-
-
-typedef struct {
-  unsigned int splitting_element;
-  unsigned int certificate_index;
-  unsigned int subcertificate_length;
-  UintSeqHash eqref_hash;
-} PathInfo;
-
-
-void
+bool
 AbstractGraph::search(const bool canonical, Stats& stats)
 {
   const unsigned int N = get_nof_vertices();
@@ -658,7 +637,7 @@
   if(N == 0)
     {
       /* Nothing to do, return... */
-      return;
+      return true;
     }
 
   /* Initialize the partition ... */
@@ -696,10 +675,10 @@
    */
   if(first_path_labeling) free(first_path_labeling);
   first_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int));
-  if(!first_path_labeling) _OUT_OF_MEMORY();
+  if(!first_path_labeling) _OUT_OF_MEMORY(oom1);
   if(best_path_labeling) free(best_path_labeling);
   best_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int));
-  if(!best_path_labeling) _OUT_OF_MEMORY();
+  if(!best_path_labeling) _OUT_OF_MEMORY(oom2);
 
   /*
    * Is the initial partition discrete?
@@ -710,7 +689,7 @@
       update_labeling(best_path_labeling);
       /* Update statistics */
       stats.nof_leaf_nodes = 1;
-      return;
+      return true;
     }
 
   /*
@@ -718,20 +697,39 @@
    */
   if(first_path_labeling_inv) free(first_path_labeling_inv);
   first_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int));
-  if(!first_path_labeling_inv) _OUT_OF_MEMORY();
+  if(!first_path_labeling_inv) _OUT_OF_MEMORY(oom3);
   if(best_path_labeling_inv) free(best_path_labeling_inv);
   best_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int));
-  if(!best_path_labeling_inv) _OUT_OF_MEMORY();
+  if(!best_path_labeling_inv) _OUT_OF_MEMORY(oom4);
 
   /*
    * Allocate space for the automorphisms
    */
   if(first_path_automorphism) free(first_path_automorphism);
   first_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int));
-  if(!first_path_automorphism) _OUT_OF_MEMORY();
+  if(!first_path_automorphism) _OUT_OF_MEMORY(oom5);
   if(best_path_automorphism) free(best_path_automorphism);
   best_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int));
-  if(!best_path_automorphism) _OUT_OF_MEMORY();
+  if(!best_path_automorphism) {
+    _OUT_OF_MEMORY(oom6);
+  oom6:
+    free(first_path_automorphism);
+    first_path_automorphism = NULL;
+  oom5:
+    free(best_path_labeling_inv);
+    best_path_labeling_inv = NULL;
+  oom4:
+    free(first_path_labeling_inv);
+    first_path_labeling_inv = NULL;
+  oom3:
+    free(best_path_labeling);
+    best_path_labeling = NULL;
+  oom2:
+    free(first_path_labeling);
+    first_path_labeling = NULL;
+  oom1:
+    return false;
+  }
 
   /*
    * Initialize orbit information so that all vertices are in their own orbits
@@ -745,7 +743,6 @@
   initialize_certificate();
 
   std::vector<TreeNode> search_stack;
-  std::vector<PathInfo> first_path_info;
   std::vector<PathInfo> best_path_info;
 
   search_stack.clear();
@@ -974,7 +971,6 @@
        */
       {
 	unsigned int  next_split_element = UINT_MAX;
-	unsigned int* next_split_element_pos = 0;
 	unsigned int* ep = p.elements + cell->first;
 	if(current_node.fp_on)
 	  {
@@ -985,7 +981,6 @@
 		 *ep < next_split_element and
 		 first_path_orbits.is_minimal_representative(*ep)) {
 		next_split_element = *ep;
-		next_split_element_pos = ep;
 	      }
 	    }
 	  }
@@ -1001,7 +996,6 @@
 		  current_node.long_prune_redundant.find(*ep) ==
 		  current_node.long_prune_redundant.end())) {
 		next_split_element = *ep;
-		next_split_element_pos = ep;
 	      }
 	    }
 	  }
@@ -1015,7 +1009,6 @@
 		  current_node.long_prune_redundant.find(*ep) ==
 		  current_node.long_prune_redundant.end())) {
 		next_split_element = *ep;
-		next_split_element_pos = ep;
 	      }
 	    }
 	  }
@@ -1203,8 +1196,10 @@
 
 #if defined(BLISS_VERIFY_EQUITABLEDNESS)
       /* The new partition should be equitable */
-      if(!is_equitable())
+      if(!is_equitable()) {
 	fatal_error("consistency check failed - partition after refinement is not equitable");
+	return false;
+      }
 #endif
 
       /*
@@ -1366,6 +1361,7 @@
 			  goto handle_first_path_automorphism;
 			/* Should never get here because of CR:FP */
 			_INTERNAL_ERROR();
+			return false;
 		      }
 		  }
 
@@ -1598,8 +1594,10 @@
 	
 #if defined(BLISS_VERIFY_AUTOMORPHISMS)
 	/* Verify that it really is an automorphism */
-	if(!is_automorphism(best_path_automorphism))
+	if(!is_automorphism(best_path_automorphism)) {
 	  fatal_error("Best path automorhism validation check failed");
+	  return false;
+	}
 #endif
 	
 	unsigned int gca_level_with_first = 0;
@@ -1666,6 +1664,7 @@
 
 
       _INTERNAL_ERROR();
+      return false;
 
       
     handle_first_path_automorphism:
@@ -1701,8 +1700,10 @@
 
 #if defined(BLISS_VERIFY_AUTOMORPHISMS)
       /* Verify that it really is an automorphism */
-      if(!is_automorphism(first_path_automorphism))
+      if(!is_automorphism(first_path_automorphism)) {
 	fatal_error("First path automorphism validation check failed");
+	return false;
+      }
 #endif
       
       if(opt_use_long_prune)
@@ -1749,12 +1750,13 @@
   /* Release component recursion data in partition */
   if(opt_use_comprec)
     p.cr_free();
+  return true;
 }
 
 
 
 
-void
+bool
 AbstractGraph::find_automorphisms(Stats& stats,
 				  void (*hook)(void *user_param,
 					       unsigned int n,
@@ -1764,7 +1766,8 @@
   report_hook = hook;
   report_user_param = user_param;
 
-  search(false, stats);
+  if (!search(false, stats))
+    return false;
 
   if(first_path_labeling)
     {
@@ -1776,6 +1779,7 @@
       free(best_path_labeling);
       best_path_labeling = 0;
     }
+  return true;
 }
 
 
@@ -1790,7 +1794,8 @@
   report_hook = hook;
   report_user_param = user_param;
 
-  search(true, stats);
+  if (!search(true, stats))
+    return NULL;
 
   return best_path_labeling;
 }
@@ -3480,15 +3485,17 @@
  * Check whether perm is an automorphism.
  * Slow, mainly for debugging and validation purposes.
  */
-bool
+int
 Digraph::is_automorphism(unsigned int* const perm)
 {
   std::set<unsigned int, std::less<unsigned int> > edges1;
   std::set<unsigned int, std::less<unsigned int> > edges2;
 
 #if defined(BLISS_CONSISTENCY_CHECKS)
-  if(!is_permutation(get_nof_vertices(), perm))
+  if(!is_permutation(get_nof_vertices(), perm)) {
     _INTERNAL_ERROR();
+    return -1;
+  }
 #endif
 
   for(unsigned int i = 0; i < get_nof_vertices(); i++)
@@ -3507,7 +3514,7 @@
 	  ei++)
 	edges2.insert(*ei);
       if(!(edges1 == edges2))
-	return false;
+	return 0;
 
       edges1.clear();
       for(std::vector<unsigned int>::iterator ei = v1.edges_out.begin();
@@ -3520,10 +3527,10 @@
 	  ei++)
 	edges2.insert(*ei);
       if(!(edges1 == edges2))
-	return false;
+	return 0;
     }
 
-  return true;
+  return 1;
 }
 
 bool
@@ -4330,8 +4337,10 @@
 Graph::permute(const unsigned int* perm) const
 {
 #if defined(BLISS_CONSISTENCY_CHECKS)
-  if(!is_permutation(get_nof_vertices(), perm))
+  if(!is_permutation(get_nof_vertices(), perm)) {
     _INTERNAL_ERROR();
+    return NULL;
+  }
 #endif
 
   Graph* const g = new Graph(get_nof_vertices());
@@ -5270,15 +5279,17 @@
  *
  *-------------------------------------------------------------------------*/
 
-bool
+int
 Graph::is_automorphism(unsigned int* const perm)
 {
   std::set<unsigned int, std::less<unsigned int> > edges1;
   std::set<unsigned int, std::less<unsigned int> > edges2;
 
 #if defined(BLISS_CONSISTENCY_CHECKS)
-  if(!is_permutation(get_nof_vertices(), perm))
+  if(!is_permutation(get_nof_vertices(), perm)) {
     _INTERNAL_ERROR();
+    return -1;
+  }
 #endif
 
   for(unsigned int i = 0; i < get_nof_vertices(); i++)
@@ -5298,10 +5309,10 @@
 	edges2.insert(*ei);
 
       if(!(edges1 == edges2))
-	return false;
+	return 0;
     }
 
-  return true;
+  return 1;
 }
 
 
@@ -5444,7 +5455,7 @@
   component.clear();
   component_elements = 0;
   sh_return = 0;
-  unsigned int sh_first  = 0;
+  unsigned int sh_first  = 1 << 31;
   unsigned int sh_size   = 0;
   unsigned int sh_nuconn = 0;
 
diff -Naur bliss-0.72.orig/graph.hh bliss-0.72/graph.hh
--- bliss-0.72.orig/graph.hh	2013-04-28 14:35:20.582085167 -0600
+++ bliss-0.72/graph.hh	2013-04-28 14:37:16.162501050 -0600
@@ -109,9 +109,12 @@
   unsigned long int get_max_level() const {return max_level;}
 };
 
-
-
-
+typedef struct {
+  unsigned int splitting_element;
+  unsigned int certificate_index;
+  unsigned int subcertificate_length;
+  UintSeqHash eqref_hash;
+} PathInfo;
 
 
 /**
@@ -270,7 +273,7 @@
   void reset_permutation(unsigned int *perm);
 
   /* Mainly for debugging purposes */
-  virtual bool is_automorphism(unsigned int* const perm);
+  virtual int is_automorphism(unsigned int* const perm) = 0;
 
   std::vector<unsigned int> certificate_current_path;
   std::vector<unsigned int> certificate_first_path;
@@ -284,7 +287,11 @@
   virtual Partition::Cell* find_next_cell_to_be_splitted(Partition::Cell *cell) = 0;
 
 
-  void search(const bool canonical, Stats &stats);
+  /**
+   * \return true if successful, false if insufficient memory to complete or
+   * other internal error
+   */
+  bool search(const bool canonical, Stats &stats);
 
 
   void (*report_hook)(void *user_param,
@@ -351,7 +358,7 @@
    */
   unsigned int cr_component_elements;
 
-
+  std::vector<PathInfo> first_path_info;
 
 
 public:
@@ -362,7 +369,7 @@
    * Check whether \a perm is an automorphism of this graph.
    * Unoptimized, mainly for debugging purposes.
    */
-  virtual bool is_automorphism(const std::vector<unsigned int>& perm) const;
+  virtual bool is_automorphism(const std::vector<unsigned int>& perm) const = 0;
 
 
 
@@ -427,8 +434,10 @@
    * if you want to use the automorphism later, you have to take a copy of it.
    * Do not call any member functions in the hook.
    * The search statistics are copied in \a stats.
+   * \return true if successful, false if insufficient memory to search or
+   * other internal error.
    */
-  void find_automorphisms(Stats& stats,
+  bool find_automorphisms(Stats& stats,
 			  void (*hook)(void* user_param,
 				       unsigned int n,
 				       const unsigned int* aut),
@@ -448,6 +457,8 @@
    * Note that the computed canonical version may depend on the applied version
    * of bliss as well as on some other options (for instance, the splitting
    * heuristic selected with bliss::Graph::set_splitting_heuristic()).
+   * This function returns NULL if there is insufficient memory, or another
+   * internal error occurs.
    */
   const unsigned int* canonical_form(Stats& stats,
 				     void (*hook)(void* user_param,
@@ -500,6 +511,10 @@
     opt_use_long_prune = active;
   }
 
+  /**
+   * Get an information vector about the first path.
+   */
+  std::vector<PathInfo> get_first_path_info() { return first_path_info; }
 };
 
 
@@ -615,7 +630,7 @@
 
   void initialize_certificate();
   
-  bool is_automorphism(unsigned int* const perm);
+  int is_automorphism(unsigned int* const perm);
 
 
   bool nucr_find_first_component(const unsigned int level);
@@ -856,7 +871,7 @@
 
   void initialize_certificate();
 
-  bool is_automorphism(unsigned int* const perm);
+  int is_automorphism(unsigned int* const perm);
 
   void sort_edges();