Possibility to dump/retrieve tree on disk. Dump voids particle positions correctly

mytools/buildObservedVoids_conf.c

@@ -1,5 +1,5 @@
 /*
-  File autogenerated by gengetopt version 2.22
+  File autogenerated by gengetopt version 2.22.2
   generated with the following command:
   gengetopt -i buildObservedVoids.ggo -f buildObservedVoids_conf -a buildObservedVoids_info -F buildObservedVoids_conf -C 
 
@@ -17,6 +17,10 @@
 #include <stdlib.h>
 #include <string.h>
 
+#ifndef FIX_UNUSED
+#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
+#endif
+
 #include "getopt.h"
 
 #include "buildObservedVoids_conf.h"
@@ -40,8 +44,11 @@ const char *buildObservedVoids_info_help[] = {
   "  -g, --gridOutput=STRING       3d grid output of voids  \n                                  (default=`all_voids.nc')",
   "  -q, --quiet                   Quiet output  (default=off)",
   "      --dumpVoids=STRING        Dump the particles in void in a file",
+  "      --dumpIds                 Dump particle ids  (default=off)",
   "      --ramsesBase=STRING       Base directory for ramses",
   "      --ramsesId=INT            Ramses snapshot id",
+  "      --dumpTree                Dump the void tree  (default=off)",
+  "      --getTree                 Restore tree from file  (default=off)",
     0
 };
 
@@ -106,13 +113,17 @@ void clear_given (struct buildObservedVoids_info *args_info)
   args_info->gridOutput_given = 0 ;
   args_info->quiet_given = 0 ;
   args_info->dumpVoids_given = 0 ;
+  args_info->dumpIds_given = 0 ;
   args_info->ramsesBase_given = 0 ;
   args_info->ramsesId_given = 0 ;
+  args_info->dumpTree_given = 0 ;
+  args_info->getTree_given = 0 ;
 }
 
 static
 void clear_args (struct buildObservedVoids_info *args_info)
 {
+  FIX_UNUSED (args_info);
   args_info->desc_arg = NULL;
   args_info->desc_orig = NULL;
   args_info->partzone_arg = NULL;
@@ -132,9 +143,12 @@ void clear_args (struct buildObservedVoids_info *args_info)
   args_info->quiet_flag = 0;
   args_info->dumpVoids_arg = NULL;
   args_info->dumpVoids_orig = NULL;
+  args_info->dumpIds_flag = 0;
   args_info->ramsesBase_arg = NULL;
   args_info->ramsesBase_orig = NULL;
   args_info->ramsesId_orig = NULL;
+  args_info->dumpTree_flag = 0;
+  args_info->getTree_flag = 0;
   
 }
 
@@ -155,15 +169,20 @@ void init_args_info(struct buildObservedVoids_info *args_info)
   args_info->gridOutput_help = buildObservedVoids_info_help[9] ;
   args_info->quiet_help = buildObservedVoids_info_help[10] ;
   args_info->dumpVoids_help = buildObservedVoids_info_help[11] ;
-  args_info->ramsesBase_help = buildObservedVoids_info_help[12] ;
+  args_info->dumpIds_help = buildObservedVoids_info_help[12] ;
-  args_info->ramsesId_help = buildObservedVoids_info_help[13] ;
+  args_info->ramsesBase_help = buildObservedVoids_info_help[13] ;
+  args_info->ramsesId_help = buildObservedVoids_info_help[14] ;
+  args_info->dumpTree_help = buildObservedVoids_info_help[15] ;
+  args_info->getTree_help = buildObservedVoids_info_help[16] ;
   
 }
 
 void
 buildObservedVoids_conf_print_version (void)
 {
-  printf ("%s %s\n", BUILDOBSERVEDVOIDS_CONF_PACKAGE, BUILDOBSERVEDVOIDS_CONF_VERSION);
+  printf ("%s %s\n",
+     (strlen(BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME) ? BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME : BUILDOBSERVEDVOIDS_CONF_PACKAGE),
+     BUILDOBSERVEDVOIDS_CONF_VERSION);
 }
 
 static void print_help_common(void) {
@@ -178,7 +197,7 @@ static void print_help_common(void) {
   printf("\n");
 
   if (strlen(buildObservedVoids_info_description) > 0)
-    printf("%s\n", buildObservedVoids_info_description);
+    printf("%s\n\n", buildObservedVoids_info_description);
 }
 
 void
@@ -262,8 +281,9 @@ buildObservedVoids_conf_release (struct buildObservedVoids_info *args_info)
 
 
 static void
-write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
 {
+  FIX_UNUSED (values);
   if (arg) {
     fprintf(outfile, "%s=\"%s\"\n", opt, arg);
   } else {
@@ -307,10 +327,16 @@ buildObservedVoids_conf_dump(FILE *outfile, struct buildObservedVoids_info *args
     write_into_file(outfile, "quiet", 0, 0 );
   if (args_info->dumpVoids_given)
     write_into_file(outfile, "dumpVoids", args_info->dumpVoids_orig, 0);
+  if (args_info->dumpIds_given)
+    write_into_file(outfile, "dumpIds", 0, 0 );
   if (args_info->ramsesBase_given)
     write_into_file(outfile, "ramsesBase", args_info->ramsesBase_orig, 0);
   if (args_info->ramsesId_given)
     write_into_file(outfile, "ramsesId", args_info->ramsesId_orig, 0);
+  if (args_info->dumpTree_given)
+    write_into_file(outfile, "dumpTree", 0, 0 );
+  if (args_info->getTree_given)
+    write_into_file(outfile, "getTree", 0, 0 );
   
 
   i = EXIT_SUCCESS;
@@ -347,7 +373,7 @@ buildObservedVoids_conf_free (struct buildObservedVoids_info *args_info)
 char *
 gengetopt_strdup (const char *s)
 {
-  char *result = NULL;
+  char *result = 0;
   if (!s)
     return result;
 
@@ -369,7 +395,7 @@ buildObservedVoids_conf_ext (int argc, char * const *argv, struct buildObservedV
                    struct buildObservedVoids_conf_params *params)
 {
   int result;
-  result = buildObservedVoids_conf_internal (argc, argv, args_info, params, NULL);
+  result = buildObservedVoids_conf_internal (argc, argv, args_info, params, 0);
 
   if (result == EXIT_FAILURE)
     {
@@ -392,7 +418,7 @@ buildObservedVoids_conf2 (int argc, char * const *argv, struct buildObservedVoid
   params.check_ambiguity = 0;
   params.print_errors = 1;
 
-  result = buildObservedVoids_conf_internal (argc, argv, args_info, &params, NULL);
+  result = buildObservedVoids_conf_internal (argc, argv, args_info, &params, 0);
 
   if (result == EXIT_FAILURE)
     {
@@ -408,7 +434,7 @@ buildObservedVoids_conf_required (struct buildObservedVoids_info *args_info, con
 {
   int result = EXIT_SUCCESS;
 
-  if (buildObservedVoids_conf_required2(args_info, prog_name, NULL) > 0)
+  if (buildObservedVoids_conf_required2(args_info, prog_name, 0) > 0)
     result = EXIT_FAILURE;
 
   if (result == EXIT_FAILURE)
@@ -423,6 +449,7 @@ buildObservedVoids_conf_required (struct buildObservedVoids_info *args_info, con
 int
 buildObservedVoids_conf_required2 (struct buildObservedVoids_info *args_info, const char *prog_name, const char *additional_error)
 {
+  FIX_UNUSED (additional_error);
   int error = 0;
 
   /* checks for required options */
@@ -474,13 +501,15 @@ static char *package_name = 0;
 static
 int update_arg(void *field, char **orig_field,
                unsigned int *field_given, unsigned int *prev_given, 
-               char *value, char *possible_values[], const char *default_value,
+               char *value, const char *possible_values[],
+               const char *default_value,
                buildObservedVoids_conf_arg_type arg_type,
                int check_ambiguity, int override,
                int no_free, int multiple_option,
                const char *long_opt, char short_opt,
                const char *additional_error)
 {
+  FIX_UNUSED (field);
   char *stop_char = 0;
   const char *val = value;
   int found;
@@ -502,6 +531,7 @@ int update_arg(void *field, char **orig_field,
       return 1; /* failure */
     }
 
+  FIX_UNUSED (default_value);
     
   if (field_given && *field_given && ! override)
     return 0;
@@ -569,7 +599,8 @@ int update_arg(void *field, char **orig_field,
 
 
 int
-buildObservedVoids_conf_internal (int argc, char * const *argv, struct buildObservedVoids_info *args_info,
+buildObservedVoids_conf_internal (
+  int argc, char * const *argv, struct buildObservedVoids_info *args_info,
                         struct buildObservedVoids_conf_params *params, const char *additional_error)
 {
   int c;	/* Character of the parsed option.  */
@@ -616,9 +647,12 @@ buildObservedVoids_conf_internal (int argc, char * const *argv, struct buildObse
         { "gridOutput",	1, NULL, 'g' },
         { "quiet",	0, NULL, 'q' },
         { "dumpVoids",	1, NULL, 0 },
+        { "dumpIds",	0, NULL, 0 },
         { "ramsesBase",	1, NULL, 0 },
         { "ramsesId",	1, NULL, 0 },
-        { NULL,	0, NULL, 0 }
+        { "dumpTree",	0, NULL, 0 },
+        { "getTree",	0, NULL, 0 },
+        { 0,  0, 0, 0 }
       };
 
       c = getopt_long (argc, argv, "hVd:p:v:m:f:o:g:q", long_options, &option_index);
@@ -760,6 +794,18 @@ buildObservedVoids_conf_internal (int argc, char * const *argv, struct buildObse
                 additional_error))
               goto failure;
           
+          }
+          /* Dump particle ids.  */
+          else if (strcmp (long_options[option_index].name, "dumpIds") == 0)
+          {
+          
+          
+            if (update_arg((void *)&(args_info->dumpIds_flag), 0, &(args_info->dumpIds_given),
+                &(local_args_info.dumpIds_given), optarg, 0, 0, ARG_FLAG,
+                check_ambiguity, override, 1, 0, "dumpIds", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* Base directory for ramses.  */
           else if (strcmp (long_options[option_index].name, "ramsesBase") == 0)
@@ -788,6 +834,30 @@ buildObservedVoids_conf_internal (int argc, char * const *argv, struct buildObse
                 additional_error))
               goto failure;
           
+          }
+          /* Dump the void tree.  */
+          else if (strcmp (long_options[option_index].name, "dumpTree") == 0)
+          {
+          
+          
+            if (update_arg((void *)&(args_info->dumpTree_flag), 0, &(args_info->dumpTree_given),
+                &(local_args_info.dumpTree_given), optarg, 0, 0, ARG_FLAG,
+                check_ambiguity, override, 1, 0, "dumpTree", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          /* Restore tree from file.  */
+          else if (strcmp (long_options[option_index].name, "getTree") == 0)
+          {
+          
+          
+            if (update_arg((void *)&(args_info->getTree_flag), 0, &(args_info->getTree_given),
+                &(local_args_info.getTree_given), optarg, 0, 0, ARG_FLAG,
+                check_ambiguity, override, 1, 0, "getTree", '-',
+                additional_error))
+              goto failure;
+          
           }
           
           break;
@@ -830,7 +900,7 @@ failure:
 /* 3 is for "--" and "=" */
 
 static int
-_buildObservedVoids_conf_configfile (char * const filename, int *my_argc)
+_buildObservedVoids_conf_configfile (const char *filename, int *my_argc)
 {
   FILE* file;
   char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
@@ -842,14 +912,14 @@ _buildObservedVoids_conf_configfile (char * const filename, int *my_argc)
   size_t len, next_token;
   char delimiter;
 
-  if ((file = fopen(filename, "r")) == NULL)
+  if ((file = fopen(filename, "r")) == 0)
     {
       fprintf (stderr, "%s: Error opening configuration file '%s'\n",
                BUILDOBSERVEDVOIDS_CONF_PACKAGE, filename);
       return EXIT_FAILURE;
     }
 
-  while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+  while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != 0)
     {
       ++line_num;
       my_argv[0] = '\0';
@@ -876,7 +946,7 @@ _buildObservedVoids_conf_configfile (char * const filename, int *my_argc)
 
       if (fopt[next_token] == '\0') /* the line is over */
         {
-          farg  = NULL;
+          farg  = 0;
           equal = 0;
           goto noarg;
         }
@@ -967,7 +1037,8 @@ _buildObservedVoids_conf_configfile (char * const filename, int *my_argc)
 }
 
 int
-buildObservedVoids_conf_configfile (char * const filename,
+buildObservedVoids_conf_configfile (
+  const char *filename,
                            struct buildObservedVoids_info *args_info,
                            int override, int initialize, int check_required)
 {
@@ -983,7 +1054,7 @@ buildObservedVoids_conf_configfile (char * const filename,
 }
 
 int
-buildObservedVoids_conf_config_file (char * const filename,
+buildObservedVoids_conf_config_file (const char *filename,
                            struct buildObservedVoids_info *args_info,
                            struct buildObservedVoids_conf_params *params)
 {

mytools/buildObservedVoids_conf.h

@@ -1,6 +1,6 @@
 /** @file buildObservedVoids_conf.h
  *  @brief The header file for the command line option parser
- *  generated by GNU Gengetopt version 2.22
+ *  generated by GNU Gengetopt version 2.22.2
  *  http://www.gnu.org/software/gengetopt.
  *  DO NOT modify this file, since it can be overwritten
  *  @author GNU Gengetopt by Lorenzo Bettini */
@@ -20,10 +20,15 @@ extern "C" {
 #endif /* __cplusplus */
 
 #ifndef BUILDOBSERVEDVOIDS_CONF_PACKAGE
-/** @brief the program name */
+/** @brief the program name (used for printing errors) */
 #define BUILDOBSERVEDVOIDS_CONF_PACKAGE "buildObservedVoids"
 #endif
 
+#ifndef BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME
+/** @brief the complete program name (used for help and version) */
+#define BUILDOBSERVEDVOIDS_CONF_PACKAGE_NAME "buildObservedVoids"
+#endif
+
 #ifndef BUILDOBSERVEDVOIDS_CONF_VERSION
 /** @brief the program version */
 #define BUILDOBSERVEDVOIDS_CONF_VERSION "0"
@@ -63,12 +68,18 @@ struct buildObservedVoids_info
   char * dumpVoids_arg;	/**< @brief Dump the particles in void in a file.  */
   char * dumpVoids_orig;	/**< @brief Dump the particles in void in a file original value given at command line.  */
   const char *dumpVoids_help; /**< @brief Dump the particles in void in a file help description.  */
+  int dumpIds_flag;	/**< @brief Dump particle ids (default=off).  */
+  const char *dumpIds_help; /**< @brief Dump particle ids help description.  */
   char * ramsesBase_arg;	/**< @brief Base directory for ramses.  */
   char * ramsesBase_orig;	/**< @brief Base directory for ramses original value given at command line.  */
   const char *ramsesBase_help; /**< @brief Base directory for ramses help description.  */
   int ramsesId_arg;	/**< @brief Ramses snapshot id.  */
   char * ramsesId_orig;	/**< @brief Ramses snapshot id original value given at command line.  */
   const char *ramsesId_help; /**< @brief Ramses snapshot id help description.  */
+  int dumpTree_flag;	/**< @brief Dump the void tree (default=off).  */
+  const char *dumpTree_help; /**< @brief Dump the void tree help description.  */
+  int getTree_flag;	/**< @brief Restore tree from file (default=off).  */
+  const char *getTree_help; /**< @brief Restore tree from file help description.  */
   
   unsigned int help_given ;	/**< @brief Whether help was given.  */
   unsigned int version_given ;	/**< @brief Whether version was given.  */
@@ -82,8 +93,11 @@ struct buildObservedVoids_info
   unsigned int gridOutput_given ;	/**< @brief Whether gridOutput was given.  */
   unsigned int quiet_given ;	/**< @brief Whether quiet was given.  */
   unsigned int dumpVoids_given ;	/**< @brief Whether dumpVoids was given.  */
+  unsigned int dumpIds_given ;	/**< @brief Whether dumpIds was given.  */
   unsigned int ramsesBase_given ;	/**< @brief Whether ramsesBase was given.  */
   unsigned int ramsesId_given ;	/**< @brief Whether ramsesId was given.  */
+  unsigned int dumpTree_given ;	/**< @brief Whether dumpTree was given.  */
+  unsigned int getTree_given ;	/**< @brief Whether getTree was given.  */
 
 } ;
 
@@ -206,7 +220,7 @@ void buildObservedVoids_conf_free (struct buildObservedVoids_info *args_info);
  * @return 0 if everything went fine, NON 0 if an error took place
  * @deprecated use buildObservedVoids_conf_config_file() instead
  */
-int buildObservedVoids_conf_configfile (char * const filename,
+int buildObservedVoids_conf_configfile (const char *filename,
   struct buildObservedVoids_info *args_info,
   int override, int initialize, int check_required);
 
@@ -217,7 +231,7 @@ int buildObservedVoids_conf_configfile (char * const filename,
  * @param params additional parameters for the parser
  * @return 0 if everything went fine, NON 0 if an error took place
  */
-int buildObservedVoids_conf_config_file (char * const filename,
+int buildObservedVoids_conf_config_file (const char *filename,
   struct buildObservedVoids_info *args_info,
   struct buildObservedVoids_conf_params *params);
 

mytools/config.mk

@@ -2,5 +2,5 @@ CC= gcc
 CXX= g++
 CPPFLAGS=  
 LDFLAGS= -L/usr/local/lib -lCosmoTool -lgsl -lgslcblas
-CXXFLAGS= $(CPPFLAGS) -ggdb -O3 -ffast-math
+CXXFLAGS= $(CPPFLAGS) -ggdb -O0 -ftree-vectorize -ftree-vectorizer-verbose=2 -ffast-math
-CFLAGS= $(CPPFLAGS) -ggdb -O3 -ffast-math
+CFLAGS= $(CPPFLAGS) -ggdb -O0 -ftree-vectorize -ftree-vectorizer-verbose=2 -ffast-math

mytools/voidTree.hpp

@@ -15,16 +15,39 @@ struct VoidNode
   std::list<VoidNode *> children;
 };
 
+struct VoidNodeOnDisk
+{
+  int vid;
+  int parent;
+};
+
 class VoidTree
 {
 protected:
-  uint32_t totalNumNodes;
+  uint32_t totalNumNodes, activeNodes;
   VoidNode *nodes;
   VoidNode *rootNode;  
   ZobovRep& zobov;
 public:
   typedef std::list<VoidNode *> VoidList;
 
+  void dumpTree(std::ostream& o)
+  {
+    VoidNodeOnDisk data;
+
+    o.write((char*)&activeNodes, sizeof(uint32_t));
+    for (uint32_t i = 0; i < activeNodes; i++)
+      {
+	data.vid = nodes[i].vid;
+	if (nodes[i].parent == 0)
+	  data.parent = -1;
+	else
+	  data.parent = nodes[i].parent - nodes;
+	o.write((char *)&data, sizeof(VoidNodeOnDisk));
+      }
+    
+  }  
+
   int lookupParent(int voidId, const std::vector<std::list<int> >& voids_for_zones)
   {
     int lastSize = 0x7fffffff;
@@ -33,7 +56,7 @@ public:
     const std::list<int>& candidateList = voids_for_zones[ref_void.zId.front()];
     std::list<int>::const_iterator iter_candidate = candidateList.begin();
 
-    //std::cout << "candidate list size is " << candidateList.size() << std::endl;
+//    std::cout << "candidate list size is " << candidateList.size() << std::endl;
 
     while (iter_candidate != candidateList.end())
       {
@@ -91,6 +114,38 @@ public:
     std::cout << "Failure to lookup parent (2)" << std::endl;
     return -1;
   }
+
+  VoidTree(ZobovRep& rep, std::istream& disk)
+    : zobov(rep)
+  {
+    totalNumNodes = rep.allVoids.size();
+
+    disk.read((char *)&activeNodes, sizeof(uint32_t));
+    nodes = new VoidNode[activeNodes];
+    rootNode = 0;
+    for (uint32_t i = 0; i < activeNodes; i++)
+      {
+	VoidNodeOnDisk data;
+
+	disk.read((char *)&data, sizeof(data));	
+	nodes[i].vid = data.vid;
+	if (data.parent < 0)
+	  {
+	    if (rootNode != 0)
+	      {
+		std::cerr << "Multiple root to the tree !!!" << std::endl;
+		abort();
+	      }
+	    nodes[i].parent = 0;
+	    rootNode = &nodes[i];
+	  }
+	else
+	  {
+	    nodes[i].parent = nodes + data.parent;
+	    nodes[i].parent->children.push_back(&nodes[i]);
+	  }
+      }
+  }
   
   VoidTree(ZobovRep& rep)
     : zobov(rep)
@@ -113,7 +168,6 @@ public:
       {
 	nodes[i].vid = i;
 	nodes[i].parent = 0;
-	nodes[i].children.clear();
       }
 
     std::cout << "Linking voids together..." << std::endl;
@@ -149,6 +203,7 @@ public:
 	    }
 	  rootNode = &nodes[i];
 	}
+    activeNodes = inserted;
   }
 
   ~VoidTree()