Changeset 2409

Timestamp:

10/04/22 14:04:11 (19 months ago)

Author:

jderouillat

Message:

Backport commits [2181,2200-2202,2250,2252] related to UGRID in XIOS3

Location:

XIOS3/trunk

Files:

• bld.cfg (modified) (1 diff)
• inputs/ugrid_test (added)
• inputs/ugrid_test/iodef.xml (added)
• src/io/nc4_data_output.cpp (modified) (5 diffs)
• src/node/file.cpp (modified) (2 diffs)
• src/node/mesh.cpp (modified) (6 diffs)
• src/test/test_ugrid.f90 (added)

XIOS3/trunk/bld.cfg

@@ -53 +53 @@
 bld::target xios_server.exe 
 bld::target generic_testcase.exe 
+bld::target test_ugrid.exe 
 #bld::target test_regular.exe
 #bld::target test_xios2_cmip6.exe

XIOS3/trunk/src/io/nc4_data_output.cpp

@@ -492 +492 @@
       std::vector<StdString> dim0;
       StdString domainName = domain->name;
-      domain->assignMesh(domainName, domain->nvertex);
-      domain->mesh->createMeshEpsilon(context->intraComm_, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
 
       StdString node_x = domainName + "_node_x";
@@ -609 +607 @@
                 SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
                 SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
+                SuperClassWriter::addAttribute("face_edge_connectivity", face_edges, &domainName);
+                SuperClassWriter::addAttribute("edge_face_connectivity", edge_faces, &domainName);
                 SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
                 dim0.clear();
@@ -628 +628 @@
                 SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
               }
+              SuperClassWriter::addAttribute("face_face_connectivity", face_faces, &domainName);
               SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
               SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
@@ -729 +730 @@
                  startNodes[0] = domain->mesh->node_start;
                  countNodes[0] = domain->mesh->node_count;
+                 if (countNodes[0]==0) startNodes[0]=0 ; // for netcdf error
                  startEdgeNodes[0] = domain->ibegin;
                  startEdgeNodes[1] = 0;
@@ -765 +767 @@
                  startNodes[0] = domain->mesh->node_start;
                  countNodes[0] = domain->mesh->node_count;
+                 if (countNodes[0]==0) startNodes[0]=0;
+
                  startEdges[0] = domain->mesh->edge_start;
                  countEdges[0] = domain->mesh->edge_count;
+                 if (countEdges[0]==0) startEdges[0]=0 ; // for netcdf error
+
                  startEdgeNodes[0] = domain->mesh->edge_start;
+                 countEdgeNodes[0] = domain->mesh->edge_count;
+                 if (countEdgeNodes[0]==0) startEdgeNodes[0]=0; // for netcdf error
                  startEdgeNodes[1] = 0;
-                 countEdgeNodes[0] = domain->mesh->edge_count;
                  countEdgeNodes[1]= 2;
+                 
                  startEdgeFaces[0] = domain->mesh->edge_start;
+                 countEdgeFaces[0] = domain->mesh->edge_count;
+                 if (countEdgeFaces[0]==0) startEdgeFaces[0]=0 ; // for netcdf error
                  startEdgeFaces[1]= 0;
-                 countEdgeFaces[0] = domain->mesh->edge_count;
                  countEdgeFaces[1]= 2;
+                 
                  startFaceConctv[0] = domain->ibegin;
+                 countFaceConctv[0] = domain->ni;
                  startFaceConctv[1] = 0;
-                 countFaceConctv[0] = domain->ni;
                  countFaceConctv[1] = domain->nvertex;
                }

XIOS3/trunk/src/node/file.cpp

@@ -863 +863 @@
      std::vector<int> domainNvertices;
      std::vector<StdString> domainNames;
+     std::map<string, tuple<set<CDomain*>,set<CDomain*>,set<CDomain*>>> registeredDomains ;
 
      for (int i = 0; i < size; ++i)
@@ -905 +906 @@
          domainNvertices.push_back(nvertex);
        }
+
+       if (nvertex==1)  std::get<0>(registeredDomains[domainName]).insert(domain[0]) ;
+       else if (nvertex==2) std::get<1>(registeredDomains[domainName]).insert(domain[0]) ;
+       else  std::get<2>(registeredDomains[domainName]).insert(domain[0]) ;
+     }
+
+     for(auto& it:registeredDomains)
+     {
+       list<CDomain*> domains ;
+       string domainName=it.first ;
+
+       for(auto& domain : std::get<0>(it.second) ) domains.push_back(domain) ;
+       for(auto& domain : std::get<1>(it.second) ) domains.push_back(domain) ;
+       for(auto& domain : std::get<2>(it.second) ) domains.push_back(domain) ;
+       
+       // for each component of a given mesh (i.e. domains with same name but different number of vertices)
+       // associate the UGRID mesh in increasing order
+       for(auto& domain : domains )
+       {
+         //domain-> computeWrittenIndex();
+         //CArray<int, 1>& indexToWrite = domain->localIndexToWriteOnServer;
+         CArray<int, 1> indexToWrite = domain->getLocalView(CElementView::WORKFLOW)->getIndex();
+         int nbWritten = indexToWrite.numElements();
+
+         CArray<double,1> writtenLat, writtenLon;
+         CArray<double,2> writtenBndsLat, writtenBndsLon;
+
+         writtenLat.resize(nbWritten);
+         writtenLon.resize(nbWritten);
+         for (int idx = 0; idx < nbWritten; ++idx)
+         {
+           writtenLat(idx) = domain->latvalue(indexToWrite(idx));
+           writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
+         }
+    
+         int nvertex = domain->nvertex, idx;
+        if (nvertex>1)
+         {
+           writtenBndsLat.resize(nvertex, nbWritten);
+           writtenBndsLon.resize(nvertex, nbWritten);
+           CArray<double,2>& boundslat = domain->bounds_latvalue;
+           CArray<double,2>& boundslon = domain->bounds_lonvalue;
+           for (idx = 0; idx < nbWritten; ++idx)
+             for (int nv = 0; nv < nvertex; ++nv)
+             {
+                writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
+                writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
+             }
+         }
+         domain->assignMesh(domainName, domain->nvertex);
+         //CContextServer* server=CContext::getCurrent()->server ;
+         //domain->mesh->createMeshEpsilon(server->intraComm, writtenLon, writtenLat, writtenBndsLon, writtenBndsLat);
+         MPI_Comm intraComm =CContext::getCurrent()->getIntraComm() ;
+         domain->mesh->createMeshEpsilon(intraComm, writtenLon, writtenLat, writtenBndsLon, writtenBndsLat);
+       }
+
      }
    }

XIOS3/trunk/src/node/mesh.cpp

@@ -430 +430 @@
     if (nvertex == 1)
     {
+      if (nodesAreWritten) return ;
+
       nbNodes_ = lonvalue.numElements();
       node_lon.resize(nbNodes_);
@@ -435 +437 @@
       node_lon = lonvalue;
       node_lat = latvalue;
+
+      unsigned long nodeCount = nbNodes_;
+      unsigned long nodeStart, nbNodes;
+      MPI_Scan(&nodeCount, &nodeStart, 1, MPI_UNSIGNED_LONG, MPI_SUM, comm);
+      int nNodes = nodeStart;
+      MPI_Bcast(&nNodes, 1, MPI_UNSIGNED_LONG, mpiSize-1, comm);
+      nbNodesGlo = nNodes;
+
+      nodeStart -= nodeCount;
+      node_start = nodeStart;
+      node_count = nodeCount;
 
       // Global node indexes
@@ -444 +457 @@
         for (size_t nh = 0; nh < 4; ++nh)
         {
-          nodeHash2IdxGlo[hashValues[nh]].push_back(mpiRank*nbNodes_ + nn);
+          nodeHash2IdxGlo[hashValues[nh]].push_back(nodeStart + nn);
         }
       }
@@ -453 +466 @@
     else if (nvertex == 2)
     {
+      if (edgesAreWritten) return ;
+
       nbEdges_ = bounds_lon.shape()[1];
       edge_lon.resize(nbEdges_);
@@ -463 +478 @@
       unsigned long nbEdgesOnProc = nbEdges_;
       unsigned long nbEdgesAccum;
+      unsigned long nbEdgesGlo;
       MPI_Scan(&nbEdgesOnProc, &nbEdgesAccum, 1, MPI_UNSIGNED_LONG, MPI_SUM, comm);
+      nbEdgesGlo = nbEdgesAccum ;
+      MPI_Bcast(&nbEdgesGlo, 1, MPI_UNSIGNED_LONG, mpiSize-1, comm);
       nbEdgesAccum -= nbEdges_;
+      edge_start = nbEdgesAccum ;
+      edge_count = nbEdgesOnProc ;
 
       CClientClientDHTSizet::Index2VectorInfoTypeMap edgeHash2IdxGlo;
@@ -674 +694 @@
     } //nvertex = 2
 
-    else
-    {
+    else // nvertex > 2
+    {
+      if (facesAreWritten) return ;
+
       nbFaces_ = bounds_lon.shape()[1];
       face_lon.resize(nbFaces_);