Merge branch 'mpi-exp'

eo/src/CMakeLists.txt

@@ -47,6 +47,7 @@ install(DIRECTORY do es ga gp other utils
 add_subdirectory(es)
 add_subdirectory(ga)
 add_subdirectory(utils)
+add_subdirectory(serial)
 
 if(ENABLE_PYEO)
   add_subdirectory(pyeo)

eo/src/serial/Parser.cpp

@@ -118,12 +118,14 @@ Entity* Parser::parseRight(const std::string & str, size_t & pos)
 {
     Entity* value = 0;
 
+    ignoreChars( str, pos );
     if ( str[ pos ] == '{' )
     {
         // next one is an object
         DEBUG("We read an object.")
         Object* obj = new Object;
         pos += 1;
+        ignoreChars( str, pos );
         while( pos < str.size() && str[ pos ] != '}' )
         {
             parseLeft( str, pos, obj );
@@ -145,11 +147,13 @@ Entity* Parser::parseRight(const std::string & str, size_t & pos)
         DEBUG("We read an array")
         Array* array = new Array;
         pos += 1;
+        ignoreChars( str, pos );
         while( pos < str.size() && str[ pos ] != ']' )
         {
             Entity* child = parseRight( str, pos );
             if ( child )
                 array->push_back( child );
+            ignoreChars( str, pos );
         }
         DEBUG("We've finished to read our array.")
         pos += 1; // we're on the ], go to the next char

eo/src/utils/eoRNG.h

@@ -245,6 +245,18 @@ public :
     double normal(double mean, double stdev)
         { return mean + normal(stdev); }
 
+    /**
+     * @brief Forgets the last cached value of normal(), so as to be able to perform some repeatable calls to normal().
+     *
+     * As normal() stores a cached value for performance purposes, sequences of pseudo random numbers can't be repeated
+     * when reseeding, since the cached value can be yield before a number is generated. To avoid that, this method
+     * allows one to clean the cache and force to regenerate a new pseudo random number.
+     */
+    void clearCache()
+    {
+        cached = false;
+    }
+
     /** Random numbers using a negative exponential distribution
 
     @param mean Mean value of distribution

eo/src/utils/eoTimer.h

@@ -22,7 +22,7 @@ Authors:
 # ifndef __EO_TIMER_H__
 # define __EO_TIMER_H__
 
-# include <sys/time.h> // time()
+# include <sys/time.h> // gettimeofday()
 # include <sys/resource.h> // rusage()
 
 # include <vector> // std::vector
@@ -61,7 +61,7 @@ class eoTimer
          */
         void restart()
         {
-            wc_start = time(NULL);
+            gettimeofday( &wc_start, NULL );
             getrusage( RUSAGE_SELF, &_start );
         }
 
@@ -138,7 +138,9 @@ class eoTimer
          */
         double wallclock()
         {
-            return std::difftime( std::time(NULL) , wc_start );
+            struct timeval wc_end;
+            gettimeofday( &wc_end, NULL );
+            return ( wc_end.tv_sec - wc_start.tv_sec ) + ( wc_end.tv_usec - wc_start.tv_usec ) / 1000000.;
         }
 
     protected:
@@ -149,7 +151,7 @@ class eoTimer
         // Remainder (in milliseconds) for system time.
         long int usremainder;
         // Structure used to measure wallclock time.
-        time_t wc_start;
+        struct timeval wc_start;
 };
 
 /**
@@ -196,13 +198,18 @@ class eoTimer
  *
  * @ingroup Utilities
  */
-class eoTimerStat
-# ifdef WITH_MPI
-    : public eoserial::Persistent
-# endif
+class eoTimerStat : public eoserial::Persistent
 {
     public:
 
+        /**
+         * @brief Initializes a timer stat object.
+         */
+        eoTimerStat() : _forceDoMeasure(false)
+        {
+            // empty
+        }
+
         /**
          * @brief Statistic related to a key (name).
          *
@@ -212,15 +219,12 @@ class eoTimerStat
          *
          * It can readily be serialized with boost when compiling with mpi.
          */
-        struct Stat
-# ifdef WITH_MPI
-            : public eoserial::Persistent
-# endif
+        struct Stat : public eoserial::Persistent
         {
             std::vector<long int> utime;
             std::vector<long int> stime;
             std::vector<double> wtime;
-#ifdef WITH_MPI
+
             void unpack( const eoserial::Object* obj )
             {
                 utime.clear();
@@ -244,10 +248,8 @@ class eoTimerStat
                 obj->add("wtime", eoserial::makeArray< std::vector<double>, eoserial::MakeAlgorithm >( wtime ) );
                 return obj;
             }
-# endif
         };
 
-#ifdef WITH_MPI
         void unpack( const eoserial::Object* obj )
         {
             _stats.clear();
@@ -270,7 +272,14 @@ class eoTimerStat
             }
             return obj;
         }
-# endif
+
+        /**
+         * @brief Forces the measures to be retrieved.
+         */
+        void forceDoMeasure()
+        {
+            _forceDoMeasure = true;
+        }
 
         /**
          * @brief Starts a new measure for the given key.
@@ -282,7 +291,7 @@ class eoTimerStat
          */
         void start( const std::string & key )
         {
-            if( eo::parallel.doMeasure() )
+            if( eo::parallel.doMeasure() or _forceDoMeasure )
             {
                 _timers[ key ].restart();
             }
@@ -300,7 +309,7 @@ class eoTimerStat
          */
         void stop( const std::string& key )
         {
-            if( eo::parallel.doMeasure() )
+            if( eo::parallel.doMeasure() or _forceDoMeasure )
             {
                 Stat & s = _stats[ key ];
                 eoTimer & t = _timers[ key ];
@@ -318,11 +327,21 @@ class eoTimerStat
             return _stats;
         }
 
+        /**
+         * @brief Empties the statistics map.
+         */
+        void clear()
+        {
+            _stats.clear();
+        }
+
     protected:
         // Statistics map: links a key (string) to a statistic.
         std::map< std::string, Stat > _stats;
         // Timers map: links a key to its timer.
         std::map< std::string, eoTimer > _timers;
+        // boolean to force the retrieval of statistics
+        bool _forceDoMeasure;
 };
 
 # endif // __TIMER_H__