Changeset 1172 for XIOS/dev/branch_yushan_merged

Timestamp:

06/15/17 19:32:13 (7 years ago)

Author:

yushan

Message:

save dev. need to unify the file type when using EP

Location:

XIOS/dev/branch_yushan_merged

Files:

• extern/remap/src/elt.hpp (modified) (2 diffs)
• extern/remap/src/node.cpp (modified) (1 diff)
• extern/remap/src/parallel_tree.cpp (modified) (3 diffs)
• extern/remap/src/tree.cpp (modified) (2 diffs)
• extern/remap/src/tree.hpp (modified) (3 diffs)
• inputs/REMAP/iodef.xml (modified) (3 diffs)
• src/client_client_dht_template_impl.hpp (modified) (2 diffs)
• src/io/inetcdf4.cpp (modified) (1 diff)
• src/io/nc4_data_input.cpp (modified) (1 diff)
• src/io/nc4_data_output.cpp (modified) (1 diff)
• src/node/file.cpp (modified) (1 diff)

XIOS/dev/branch_yushan_merged/extern/remap/src/elt.hpp

@@ -53 +53 @@
 struct Elt : Polyg
 {
-        Elt() {}
-        Elt(const double *bounds_lon, const double *bounds_lat, int max_num_vert)
-        {
-                int k = 0;
-                vertex[k++] = xyz(bounds_lon[0], bounds_lat[0]);
-                for (int i = 1; i < max_num_vert; i++)
-                {
-                        vertex[k] = xyz(bounds_lon[i], bounds_lat[i]);
-                        /* netCDF convention: if first vertex repeats element is finished (at least three vertices == triagle) */
-                        if (k >= 3 && squaredist(vertex[k], vertex[0]) < EPS*EPS) 
-                                break;
-                        /* eliminate zero edges: move to next vertex only if it is different */
-                        if (squaredist(vertex[k], vertex[k-1]) > EPS*EPS)
-                                k++;
-                        else
-                                /* cout << "Removed edge " << k << " due to zero length (coinciding endpoints)." << endl */ ;
-                }
-                n = k;
-                x = barycentre(vertex, n);
-        }
+  Elt() {}
+  Elt(const double *bounds_lon, const double *bounds_lat, int max_num_vert)
+  {
+    int k = 0;
+    vertex[k++] = xyz(bounds_lon[0], bounds_lat[0]);
+    for (int i = 1; i < max_num_vert; i++)
+    {
+      vertex[k] = xyz(bounds_lon[i], bounds_lat[i]);
+      /* netCDF convention: if first vertex repeats element is finished (at least three vertices == triagle) */
+      if (k >= 3 && squaredist(vertex[k], vertex[0]) < EPS*EPS) 
+        break;
+      /* eliminate zero edges: move to next vertex only if it is different */
+      if (squaredist(vertex[k], vertex[k-1]) > EPS*EPS)
+        k++;
+      //else cout << "Removed edge " << k << " due to zero length (coinciding endpoints)." << endl ;
+    }
+    n = k;
+    x = barycentre(vertex, n);
+  }
 
         Elt& operator=(const Elt& rhs)
@@ -96 +95 @@
         }
 
-        void delete_intersections()
-        {
-                for (list<Polyg*>::iterator it = this->is.begin(); it != this->is.end(); it++)
-                {
-                        Polyg* poly = *it;
-                        delete poly;
-                }
-        }
+  void delete_intersections()
+  {
+    for (list<Polyg*>::iterator it = this->is.begin(); it != this->is.end(); it++)
+    {
+      Polyg* poly = *it;
+      delete poly;
+    }
+  }
 
   void insert_vertex(int i, const Coord& v)

XIOS/dev/branch_yushan_merged/extern/remap/src/node.cpp

@@ -472 +472 @@
         q->child.resize(MAX_NODE_SZ/2 + 1);
         assert(thIs->child.size() == MAX_NODE_SZ+1);
-        thIs->tree->ref = thIs->closest(thIs->child, FARTHEST); // farthest from centre
+        if(thIs->closest(thIs->child, FARTHEST) == 0) 
+          thIs->tree->ref = thIs->closest(thIs->child, FARTHEST); // farthest from centre
+          
+        thIs->tree->ref = thIs->closest(thIs->child, FARTHEST); // farthest from centre
+        
+          
         std::sort(thIs->child.begin(), thIs->child.end(), compareDist);
         for (int i = 0; i < MAX_NODE_SZ+1; i++)

XIOS/dev/branch_yushan_merged/extern/remap/src/parallel_tree.cpp

@@ -315 +315 @@
 {
 
-        int assignLevel = 2;
-        int nbSampleNodes = 2*ipow(MAX_NODE_SZ + 1, assignLevel);
+  int assignLevel = 2;
+  int nbSampleNodes = 2*ipow(MAX_NODE_SZ + 1, assignLevel);
 
 
@@ -326 +326 @@
   MPI_Comm_size(communicator,&commSize) ;
   
-        // make multiple of two
-        nbSampleNodes /= 2;
-        nbSampleNodes *= 2;
-//  assert( nbTot > nbSampleNodes*commSize) ;
+  // make multiple of two
+  nbSampleNodes /= 2;
+  nbSampleNodes *= 2;
+  //assert( nbTot > nbSampleNodes*commSize) ;
     
   int nbSampleNodes1 = nbSampleNodes * (nb1*commSize)/(1.*nbTot) ;
@@ -335 +335 @@
   
 
-//      assert(node.size() > nbSampleNodes);
-//      assert(node2.size() > nbSampleNodes);
-//      assert(node.size() + node2.size() > nbSampleNodes);
-        vector<Node> sampleNodes; sampleNodes.reserve(nbSampleNodes1+nbSampleNodes2);
-
-        vector<int> randomArray1(node.size());
-        randomizeArray(randomArray1);
-        vector<int> randomArray2(node2.size());
-        randomizeArray(randomArray2);
+  //assert(node.size() > nbSampleNodes);
+  //assert(node2.size() > nbSampleNodes);
+  //assert(node.size() + node2.size() > nbSampleNodes);
+  vector<Node> sampleNodes; sampleNodes.reserve(nbSampleNodes1+nbSampleNodes2);
+
+  vector<int> randomArray1(node.size());
+  randomizeArray(randomArray1);
+  vector<int> randomArray2(node2.size());
+  randomizeArray(randomArray2);
 
 /*      

XIOS/dev/branch_yushan_merged/extern/remap/src/tree.cpp

@@ -29 +29 @@
 void CBasicTree::routeNodes(vector<int>& route, vector<Node>& nodes, int assignLevel)
 {
-        for (int i = 0; i < nodes.size(); i++)
-        {
-                root->routeNode(&nodes[i], assignLevel);
-                route[i] = nodes[i].route;
-        }
+  for (int i = 0; i < nodes.size(); i++)
+  {
+    root->routeNode(&nodes[i], assignLevel);
+    route[i] = nodes[i].route;
+  }
 }
 
 void CBasicTree::routeIntersections(vector<vector<int> >& routes, vector<Node>& nodes)
 {
-        for (int i = 0; i < nodes.size(); i++)
-                root->routeIntersection(routes[i], &nodes[i]);
+  for (int i = 0; i < nodes.size(); i++)
+    root->routeIntersection(routes[i], &nodes[i]);
 }
 
 void CBasicTree::build(vector<Node>& nodes)
 {
-        newRoot(1);
-        insertNodes(nodes);
+  newRoot(1);
+  insertNodes(nodes);
 }
 
 void CBasicTree::output(ostream& flux, int level)
 {
-        root->output(flux,level,0) ;
+  root->output(flux,level,0) ;
 }
 void CBasicTree::slim(int nbIts)
 {
-        for (int i = 0; i < nbIts; i++)
-        {
-                for (int level = root->level - 1; level > 0; level--)
-                {
-                        slim2(root, level);
-                        ri = 0;
-                        emptyPool();
-                }
-
-                for (int level = 2; level < root->level; level++)
-                {
-                        slim2(root, level);
-                        ri = 0;
-                        emptyPool();
-                }
-        }
+  for (int i = 0; i < nbIts; i++)
+  {
+    for (int level = root->level - 1; level > 0; level--)
+    {
+      slim2(root, level);
+      ri = 0;
+      emptyPool();
+    }
+
+    for (int level = 2; level < root->level; level++)
+    {
+      slim2(root, level);
+      ri = 0;
+      emptyPool();
+    }
+  }
 }
 
@@ -76 +76 @@
 void CBasicTree::insertNode(NodePtr node)
 {
-        node->tree = this;
-        increaseLevelSize(0);
-        push_back(node);
-
-        NodePtr q;
-        while (pool.size())
-        {
-                q = pool.front();
-                pool.pop_front();
-                q = insert(q, root);
-                if (ri)
-                {
-                        delete q;
-                        ri = 0;
-                }
-        }
+  node->tree = this;
+  increaseLevelSize(0);
+  push_back(node);
+
+  NodePtr q;
+  while (pool.size())
+  {
+    q = pool.front();
+    pool.pop_front();
+    q = insert(q, root);
+    if (ri)
+    {
+      delete q;
+      ri = 0;
+    }
+  }
 }
 
 void CBasicTree::emptyPool(void)
 {
-        while (pool.size())
-        {
-                NodePtr q = pool.front();
-                pool.pop_front();
-                q = insert(q, root);
-                if (ri)
-                {
-                        delete q;
-                        ri = 0;
-                }
-        }
+  while (pool.size())
+  {
+    NodePtr q = pool.front();
+    pool.pop_front();
+    q = insert(q, root);
+    if (ri)
+    {
+      delete q;
+      ri = 0;
+    }
+  }
 }
 

XIOS/dev/branch_yushan_merged/extern/remap/src/tree.hpp

@@ -14 +14 @@
 class CBasicTree
 {
-public:
+  public:
 
-        NodePtr root; /* The main tree is stored as Nodes which can be reached through traversal starting here */
-        NodePtr ref; // FIXME this reference, set by a node is odd, try to remove
-        int ri; /** this is set to one by a node in case of reinsertion */
-        vector<int> levelSize; /** e.g. levelSize[0] == leafs.size() */
-        vector<Node> leafs; /** leafs are stored in vector for easy access and rest of the tree nodes as separate allocations, only reachable through tree traversal */
+  NodePtr root; /* The main tree is stored as Nodes which can be reached through traversal starting here */
+  NodePtr ref; // FIXME this reference, set by a node is odd, try to remove
+  int ri; /** this is set to one by a node in case of reinsertion */
+  vector<int> levelSize; /** e.g. levelSize[0] == leafs.size() */
+  vector<Node> leafs; /** leafs are stored in vector for easy access and rest of the tree nodes as separate allocations, only reachable through tree traversal */
 
-        CBasicTree() : ri(0), levelSize(MAX_LEVEL_SIZE), root(NULL), isAssignedLevel(false), okSplit(true), isActiveOkSplit(false) {} 
-        ~CBasicTree(); 
-        void build(vector<Node>& nodes);
-        void slim(int nbIts = 1);
-        virtual void insertNodes(vector<Node>& node) = 0;
+  CBasicTree() : ri(0), levelSize(MAX_LEVEL_SIZE), root(NULL), isAssignedLevel(false), okSplit(true), isActiveOkSplit(false) {} 
+  ~CBasicTree(); 
+  void build(vector<Node>& nodes);
+  void slim(int nbIts = 1);
+  virtual void insertNodes(vector<Node>& node) = 0;
 
-        void routeNodes(vector<int>& route, vector<Node>& nodes, int assignLevel);
-        void routeIntersections(vector<vector<int> >& route, vector<Node>& nodes);
+  void routeNodes(vector<int>& route, vector<Node>& nodes, int assignLevel);
+  void routeIntersections(vector<vector<int> >& route, vector<Node>& nodes);
 
-        void push_back(NodePtr node);
-        void push_front(NodePtr node);
-        void increaseLevelSize(int level);
-        void decreaseLevelSize(int level);
-        void newRoot(int level);
-        void insertNode(NodePtr node);
+  void push_back(NodePtr node);
+  void push_front(NodePtr node);
+  void increaseLevelSize(int level);
+  void decreaseLevelSize(int level);
+  void newRoot(int level);
+  void insertNode(NodePtr node);
   void output(ostream& flux, int level) ;
 
-        int keepNodes;
+  int keepNodes;
   bool isAssignedLevel ; 
   int assignLevel;
@@ -50 +50 @@
 
   
-private:
-        deque<NodePtr > pool;
+  private:
+  deque<NodePtr > pool;
         
   bool okSplit ;
  
-protected:
+  protected:
   void emptyPool();
-  CBasicTree(int keepNodes_, int assignLevel_) : ri(0), levelSize(MAX_LEVEL_SIZE), root(NULL), keepNodes(keepNodes_), assignLevel(assignLevel_), isAssignedLevel(true), okSplit(true), isActiveOkSplit(false) {} 
+  CBasicTree(int keepNodes_, int assignLevel_) : ri(0), levelSize(MAX_LEVEL_SIZE), root(NULL), keepNodes(keepNodes_), assignLevel(assignLevel_), isAssignedLevel(true), 
+                                                 okSplit(true), isActiveOkSplit(false) {} 
 };
 
 class CTree : public CBasicTree
 {
-public:
-        void insertNodes(vector<Node>& nodes);
+  public:
+  void insertNodes(vector<Node>& nodes);
 };
 
@@ -69 +70 @@
 {
 
-public:
-        CSampleTree(int keepNodes_, int assignLevel_) : CBasicTree(keepNodes_,assignLevel_) {}
+  public:
+  CSampleTree(int keepNodes_, int assignLevel_) : CBasicTree(keepNodes_,assignLevel_) {}
   void slimAssignedLevel() ;
   void removeExtraNode(void) ;
-        void insertNodes(vector<Node>& nodes);
+  void insertNodes(vector<Node>& nodes);
 };
 

XIOS/dev/branch_yushan_merged/inputs/REMAP/iodef.xml

@@ -34 +34 @@
 
    <file_definition type="one_file" par_access="collective" output_freq="1ts" output_level="10" enabled=".TRUE.">
+      
+      <file_group id="read_then_write_files" enabled=".TRUE.">
+       <file id="output_regular_pole" name="output_dst_regular" >
+          <field field_ref="tmp_field_0" name="field_regular_0" enabled=".TRUE."/>
+          <field field_ref="dst_field_regular" name="field_regular" enabled=".TRUE."/>
+          <field field_ref="dst_field_regular_pole_0" name="field_regular_pole_0" enabled=".FALSE." />
+          <field field_ref="dst_field_regular_pole_1" name="field_regular_pole_1" enabled=".FALSE." />
+       </file>
+       <file id="output_dst_curvilinear" name="output_dst_curvilinear" enabled=".TRUE." >
+          <field field_ref="tmp_field_1" operation="instant"/>
+       </file>
+       <file id="output_dst_unstructured" name="output_dst_unstructured" enabled=".TRUE." >
+          <field field_ref="tmp_field_2" operation="instant"/>
+       </file>
+     </file_group>
+
       <file_group id="write_files" >
-        <file id="output_2D" name="output_2D" >
+        <file id="output_2D" name="output_2D" enabled=".TRUE.">
           <field field_ref="src_field_2D" name="field_src" />
           <field field_ref="src_field_2D_clone" name="field_src_clone" default_value="100000" />
@@ -44 +60 @@
           <field field_ref="dst_field_2D_extract" name="field_dst_regular_4" />
         </file> 
-       <file id="output_3D" name="output_3D" enabled=".TRUE." >
+       <file id="output_3D" name="output_3D" enabled=".TRUE.">
           <field field_ref="src_field_3D" name="field_src" />
           <field field_ref="src_field_3D_pression" name="field" />
@@ -66 +82 @@
        </file>
       </file_group>
-     <file_group id="read_then_write_files" enabled=".TRUE.">
-       <file id="output_regular_pole" name="output_dst_regular" >
-          <field field_ref="tmp_field_0" name="field_regular_0" />
-          <field field_ref="dst_field_regular" name="field_regular" />
-          <field field_ref="dst_field_regular_pole_0" name="field_regular_pole_0" enabled=".FALSE." />
-          <field field_ref="dst_field_regular_pole_1" name="field_regular_pole_1" enabled=".FALSE." />
-       </file>
-       <file id="output_dst_curvilinear" name="output_dst_curvilinear">
-          <field field_ref="tmp_field_1" operation="instant"/>
-       </file>
-       <file id="output_dst_unstructured" name="output_dst_unstructured" >
-          <field field_ref="tmp_field_2" operation="instant"/>
-       </file>
-     </file_group>
+     
    </file_definition>
 

XIOS/dev/branch_yushan_merged/src/client_client_dht_template_impl.hpp

@@ -718 +718 @@
     MPI_Irecv(&recvBuff[0]+2*idx, 2, MPI_INT,
               recvRank[idx], MPI_DHT_INDEX_0, this->internalComm_, &request[nRequest]);
-    printf("proc %d recv from proc %d with tag %d\n", my_rank, recvRank[idx], MPI_DHT_INDEX_0);          
     ++nRequest;
   }
@@ -735 +734 @@
     MPI_Isend(&sendBuff[idx*2], 2, MPI_INT,
               sendRank[idx], MPI_DHT_INDEX_0, this->internalComm_, &request[nRequest]);
-    printf("proc %d send to proc %d with tag %d\n", my_rank, sendRank[idx], MPI_DHT_INDEX_0);
     ++nRequest;
   }

XIOS/dev/branch_yushan_merged/src/io/inetcdf4.cpp

@@ -21 +21 @@
         comm = NULL;
     }
+
     mpi = comm && !multifile;
     MPI_Info m_info = MPI_INFO_NULL_STD;

XIOS/dev/branch_yushan_merged/src/io/nc4_data_input.cpp

@@ -55 +55 @@
     CArray<double,1> fieldData(grid->getWrittenDataSize());
     if (!field->default_value.isEmpty()) fieldData = field->default_value;
-
+    #ifdef _usingEP
+    SuperClass::type = ONE_FILE;
+    //printf("SuperClass::type = %d\n", SuperClass::type);
+    #endif
     switch (SuperClass::type)
     {

XIOS/dev/branch_yushan_merged/src/io/nc4_data_output.cpp

@@ -1102 +1102 @@
 
             SuperClassWriter::definition_end();
-
+            printf("SuperClass::type = %d\n", SuperClass::type);
             switch (SuperClass::type)
             {

XIOS/dev/branch_yushan_merged/src/node/file.cpp

@@ -579 +579 @@
 
       #ifdef _usingEP
-      if(omp_get_num_threads() != 1 ) multifile = true;
-      #endif
-
+      //printf("multifile was %d\n", multifile);
+      multifile = true;
       if (isOpen) data_out->closeFile();
       if (time_counter_name.isEmpty()) data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), static_cast< ::MPI_Comm >(fileComm.mpi_comm), multifile, isCollective));
       else data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), static_cast< ::MPI_Comm >(fileComm.mpi_comm), multifile, isCollective, time_counter_name));
       isOpen = true;
+      #else
+      if (isOpen) data_out->closeFile();
+      if (time_counter_name.isEmpty()) data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), static_cast< ::MPI_Comm >(fileComm.mpi_comm), multifile, isCollective));
+      else data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), static_cast< ::MPI_Comm >(fileComm.mpi_comm), multifile, isCollective, time_counter_name));
+      isOpen = true;
+      #endif
+
+      
     }
   }