Changeset 1642 for XIOS/dev/branch_openmp/src/io

Timestamp:

01/23/19 10:31:44 (5 years ago)

Author:

yushan

Message:

dev on ADA. add flag switch _usingEP/_usingMPI

Location:

XIOS/dev/branch_openmp/src/io

Files:

• inetcdf4.cpp (modified) (2 diffs)
• inetcdf4.hpp (modified) (1 diff)
• nc4_data_input.cpp (modified) (20 diffs)
• nc4_data_input.hpp (modified) (1 diff)
• nc4_data_output.cpp (modified) (45 diffs)
• nc4_data_output.hpp (modified) (1 diff)
• netCdfInterface.cpp (modified) (55 diffs)
• netCdfInterface.hpp (modified) (4 diffs)
• netcdf.hpp (modified) (4 diffs)
• onetcdf4.cpp (modified) (3 diffs)
• onetcdf4.hpp (modified) (1 diff)
• onetcdf4_impl.hpp (modified) (1 diff)

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

@@ -2 +2 @@
 #include "netCdfInterface.hpp"
 #include "netCdf_cf_constant.hpp"
-#include "ep_mpi.hpp"
+
 #include <boost/algorithm/string.hpp>
 
@@ -23 +23 @@
     // even if Parallel NetCDF ends up being used.
     if (mpi)
-      CNetCdfInterface::openPar(filename, NC_NOWRITE | NC_MPIIO, to_mpi_comm((*comm)->mpi_comm), to_mpi_info(MPI_INFO_NULL), this->ncidp);
+      CNetCdfInterface::openPar(filename, NC_NOWRITE | NC_MPIIO, *comm, EP_INFO_NULL, this->ncidp);
     else
       CNetCdfInterface::open(filename, NC_NOWRITE, this->ncidp);

XIOS/dev/branch_openmp/src/io/inetcdf4.hpp

@@ -7 +7 @@
 #include "array_new.hpp"
 
-#include "mpi_std.hpp"
+#include "mpi.hpp"
 #include "netcdf.hpp"
 

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

@@ -29 +29 @@
 
   StdSize CNc4DataInput::getFieldNbRecords_(CField* field)
+  TRY
   {
     StdString fieldId = field->getFieldOutputName();
@@ -40 +41 @@
     return 1;
   }
+  CATCH
 
   void CNc4DataInput::readFieldData_(CField* field)
+  TRY
   {
     CContext* context = CContext::getCurrent();
@@ -55 +58 @@
     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)
     {
@@ -67 +66 @@
       case ONE_FILE:
       {
-/*
-        std::vector<int> nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
-        std::vector<int> nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
-        std::vector<int> nZoomSizeServer  = grid->getDistributionServer()->getZoomSizeServer();
-
-        int ssize = nZoomBeginGlobal.size();
-
-        std::vector<StdSize> start(ssize);
-        std::vector<StdSize> count(ssize);
-
-        for (int i = 0; i < ssize; ++i)
-        {
-          start[i] = nZoomBeginServer[ssize - i - 1] - nZoomBeginGlobal[ssize - i - 1];
-          count[i] = nZoomSizeServer[ssize - i - 1];
-        }
-*/
-
-        std::vector<int> nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
-        std::vector<int> nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
-        std::vector<int> nZoomSizeServer  = grid->getDistributionServer()->getZoomSizeServer();
-
         std::vector<StdSize> start, count;
 
@@ -95 +73 @@
         int numElement = axisDomainOrder.numElements();
         int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
-        int idx = nZoomBeginGlobal.size() - 1;
-
-        start.reserve(nZoomBeginGlobal.size());
-        count.reserve(nZoomBeginGlobal.size());
+        int idx = domainList.size() * 2 + axisList.size() - 1;
+
+        start.reserve(idx+1);
+        count.reserve(idx+1);
 
         for (int i = numElement - 1; i >= 0; --i)
@@ -107 +85 @@
             if ((domain->type) != CDomain::type_attr::unstructured)
             {
-              start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
-              count.push_back(nZoomSizeServer[idx]);
+              start.push_back(domain->jbegin);
+              count.push_back(domain->nj);
             }
-            --idx ;
-            start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
-            count.push_back(nZoomSizeServer[idx]);
-            --idx ;
+            start.push_back(domain->ibegin);
+            count.push_back(domain->ni);
             --idxDomain;
           }
           else if (1 == axisDomainOrder(i))
           {
-            start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
-            count.push_back(nZoomSizeServer[idx]);
-            --idx;
+            CAxis* axis = CAxis::get(axisList[idxAxis]);
+            start.push_back(axis->begin);
+            count.push_back(axis->n);
+            --idxAxis ;
           }
           else
@@ -129 +106 @@
               count.push_back(1);
             }
-            --idx;
           }
         }
@@ -148 +124 @@
     }
   }
+  CATCH
 
   void CNc4DataInput::readFieldAttributes_(CField* field, bool readAttributeValues)
+  TRY
   {
     StdString fieldId = field->getFieldOutputName();
@@ -166 +144 @@
     // Verify the compatibility of dimension of declared grid and real grid in file
     int realGridDim = 1;
-    bool isUnstructuredGrid = SuperClassWriter::isUnstructured(fieldId);
+    bool isUnstructuredGrid = ((gridDim < 2) ? false :  SuperClassWriter::isUnstructured(fieldId));
     std::map<StdString, StdSize> dimSizeMap = SuperClassWriter::getDimensions(&fieldId);
     std::list<StdString> dimList = SuperClassWriter::getDimensionsList(&fieldId);
@@ -191 +169 @@
 */
 
-    for (std::list<StdString>::const_iterator it = dimList.begin(); it != dimList.end(); ++it)
+//    if (!SuperClassWriter::isRectilinear(fieldId))
+    if (true)
+    {
+      for (std::list<StdString>::const_iterator it = dimList.begin(); it != dimList.end(); ++it)
         listDimSize.push_front(*dimSizeMap.find(*it));
+    }
+    else
+    {
+       std::list<StdString> coords = SuperClassWriter::getCoordinatesIdList(fieldId);
+       std::list<StdString>::const_iterator itCoord = coords.begin();
+       for (; itCoord != coords.end(); itCoord++)
+       {
+         const StdString& coord = *itCoord;
+         if (SuperClassWriter::hasVariable(coord) && !SuperClassWriter::isTemporal(coord))
+         {
+           std::map<StdString, StdSize> dimsTmp = SuperClassWriter::getDimensions(&coord);
+           StdString dimNameTmp = dimsTmp.begin()->first;
+           StdSize dimSizeTmp = dimsTmp.begin()->second;
+           listDimSize.push_front(make_pair(coord, dimSizeTmp));
+           dimSizeMap.erase(dimNameTmp);
+           dimList.remove(dimNameTmp);
+         }
+       }
+       for (std::list<StdString>::const_iterator it = dimList.begin(); it != dimList.end(); ++it)
+        listDimSize.push_front(*dimSizeMap.find(*it));
+    }
 
     // Now process domain and axis
@@ -251 +253 @@
     }
   }
+  CATCH
 
   /*!
@@ -261 +264 @@
   void CNc4DataInput::readDomainAttributeValueFromFile(CDomain* domain, std::list<std::pair<StdString, StdSize> >& dimSizeMap,
                                                        int elementPosition, const StdString& fieldId)
+  TRY
   {
     // There are some optional attributes of a domain to retrieve from file    // + lon lat?
@@ -439 +443 @@
     domain->fillInLonLat();
   }
+  CATCH
 
   /*!
@@ -449 +454 @@
   void CNc4DataInput::readDomainAttributesFromFile(CDomain* domain, std::list<std::pair<StdString, StdSize> >& dimSizeMap,
                                                    int elementPosition, const StdString& fieldId)
+  TRY
   {
     // There are some mandatory attributes of a domain to retrieve from file
@@ -497 +503 @@
       domain->ni_glo.setValue(itMapNi->second);
     }
-  }
+
+// determine if coordinates values are present in file
+    if ((CDomain::type_attr::rectilinear == domain->type))
+    {
+      // Ok, try to read some attributes such as longitude and latitude
+      domain->hasLatInReadFile_ = SuperClassWriter::hasVariable(itMapNj->first);
+      domain->hasLonInReadFile_  = SuperClassWriter::hasVariable(itMapNi->first);
+    }
+    else if ((CDomain::type_attr::curvilinear == domain->type) || (CDomain::type_attr::unstructured == domain->type) )
+    {
+      StdString latName = this->getLatCoordName(fieldId);
+      domain->hasLatInReadFile_ = SuperClassWriter::hasVariable(latName) ;
+      StdString lonName = this->getLonCoordName(fieldId);        
+      domain->hasLonInReadFile_ = SuperClassWriter::hasVariable(lonName) ; 
+      StdString boundsLatName = this->getBoundsId(latName);
+      domain->hasBoundsLatInReadFile_ = SuperClassWriter::hasVariable(boundsLatName) ; 
+      StdString boundsLonName = this->getBoundsId(lonName);
+      domain->hasBoundsLonInReadFile_ = SuperClassWriter::hasVariable(boundsLonName) ;
+    }
+  }
+  CATCH
 
   /*!
@@ -508 +534 @@
   void CNc4DataInput::readAxisAttributesFromFile(CAxis* axis, std::list<std::pair<StdString, StdSize> >& dimSizeMap,
                                                  int elementPosition, const StdString& fieldId)
+  TRY
   {
     std::list<std::pair<StdString, StdSize> >::const_iterator itMapN = dimSizeMap.begin(),
@@ -524 +551 @@
     axis->n_glo.setValue(itMapN->second);
   }
+  CATCH
 
   /*!
@@ -534 +562 @@
   void CNc4DataInput::readAxisAttributeValueFromFile(CAxis* axis, std::list<std::pair<StdString, StdSize> >& dimSizeMap,
                                                     int elementPosition, const StdString& fieldId)
+  TRY
   {
     std::list<std::pair<StdString, StdSize> >::const_iterator itMapN = dimSizeMap.begin(),
@@ -554 +583 @@
     }
   }
+  CATCH
 
   /*!
@@ -582 +612 @@
 
   void CNc4DataInput::closeFile_(void)
+  TRY
   {
     SuperClassWriter::close();
   }
+  CATCH
 } // namespace xios

XIOS/dev/branch_openmp/src/io/nc4_data_input.hpp

@@ -3 +3 @@
 
 /// XIOS headers ///
-#include "mpi_std.hpp"
 #include "xios_spl.hpp"
 #include "data_input.hpp"

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

@@ -54 +54 @@
 
       void CNc4DataOutput::writeDomain_(CDomain* domain)
+      TRY
       {
         StdString lonName,latName ;
@@ -154 +155 @@
 */
 
-         CArray<size_t, 1>& indexToWrite = domain->localIndexToWriteOnServer;
+         CArray<int, 1>& indexToWrite = domain->localIndexToWriteOnServer;
          int nbWritten = indexToWrite.numElements();
          CArray<double,1> writtenLat, writtenLon;
@@ -166 +167 @@
            for (int idx = 0; idx < nbWritten; ++idx)
            {
-                  if (idx < domain->latvalue.numElements())
-                  {
-                writtenLat(idx) = domain->latvalue(indexToWrite(idx));
-                writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
-                  }
-                  else
-                  {
-                writtenLat(idx) = 0.;
-                writtenLon(idx) = 0.;
-                  }
+             if (indexToWrite(idx) < 0)
+             {
+               writtenLat(idx) = -1.;   // hole
+               writtenLon(idx) = -1.;
+             }
+             else
+             {
+               writtenLat(idx) = domain->latvalue(indexToWrite(idx));
+               writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
+             }
            }
-         
 
            if (domain->hasBounds)
@@ -189 +189 @@
                for (int nv = 0; nv < nvertex; ++nv)
                {
-                 if (idx < boundslat.columns())
-                 {
+                 if (indexToWrite(idx) < 0)
+                 {
+                   writtenBndsLat(nv, idx) = -1.;  // hole
+                   writtenBndsLon(nv, idx) = -1.;
+                 }
+                 else
+                 {
                    writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
                    writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
-                 }
-                 else
-                 {
-                   writtenBndsLat(nv, idx) = 0.;
-                   writtenBndsLon(nv, idx) = 0.;
-                 }
+                 }
                }
            }
@@ -208 +208 @@
            for (int idx = 0; idx < nbWritten; ++idx)
            {
-                  if (idx < domain->areavalue.numElements())
-                writtenArea(idx) = domain->areavalue(indexToWrite(idx));
+                  if (indexToWrite(idx) < 0)
+              writtenArea(idx) = -1.;
                   else
-                writtenArea(idx) = 0.;
+              writtenArea(idx) = domain->areavalue(indexToWrite(idx));
            }
          }
@@ -221 +221 @@
               case (MULTI_FILE) :
               {
-  //               if (domain->isEmpty()) return;
-
-                 if (server->intraCommSize > 1)
-                 {
-  //                 SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
-  //                 SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
-                 }
-
                  switch (domain->type)
                  {
@@ -248 +240 @@
                  else bounds_latid = "bounds_"+latName+appendDomid;
 
-                 SuperClassWriter::addDimension(dimXid, domain->zoom_ni);
-                 SuperClassWriter::addDimension(dimYid, domain->zoom_nj);
+                 SuperClassWriter::addDimension(dimXid, domain->ni);
+                 SuperClassWriter::addDimension(dimYid, domain->nj);
 
                  if (domain->hasBounds)
@@ -256 +248 @@
                  if (server->intraCommSize > 1)
                  {
-                   this->writeLocalAttributes(domain->zoom_ibegin,
-                                              domain->zoom_ni,
-                                              domain->zoom_jbegin,
-                                              domain->zoom_nj,
+                   this->writeLocalAttributes(domain->ibegin,
+                                              domain->ni,
+                                              domain->jbegin,
+                                              domain->nj,
                                               appendDomid);
 
                    if (singleDomain)
                     this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
-                                                      domain->zoom_ibegin,
-                                                      domain->zoom_ni,
-                                                      domain->zoom_jbegin,
-                                                      domain->zoom_nj,
+                                                      domain->ibegin,
+                                                      domain->ni,
+                                                      domain->jbegin,
+                                                      domain->nj,
                                                       domain->ni_glo,domain->nj_glo,
                                                       server->intraCommRank,server->intraCommSize);
@@ -340 +332 @@
                        break;
                      case CDomain::type_attr::rectilinear :
-                       CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->zoom_ni)) ;
+                       CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->ni)) ;
                        SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
-                       CArray<double,1> lon = writtenLon(Range(0,domain->zoom_ni-1)) ;
+                       CArray<double,1> lon = writtenLon(Range(0,domain->ni-1)) ;
                        SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
                        break;
@@ -365 +357 @@
               case (ONE_FILE) :
               {
-                 SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
-                 SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
+                SuperClassWriter::addDimension(dimXid, domain->ni_glo);
+                SuperClassWriter::addDimension(dimYid, domain->nj_glo);
 
                  if (domain->hasBounds)
@@ -434 +426 @@
                      std::vector<StdSize> start(2) ;
                      std::vector<StdSize> count(2) ;
-                     if (domain->isEmpty())
+// Comment out: it is not working for a hole
+//                     if (domain->isEmpty())
+//                     {
+//                       start[0]=0 ; start[1]=0 ;
+//                       count[0]=0 ; count[1]=0 ;
+//                     }
+//                     else
                      {
-                       start[0]=0 ; start[1]=0 ;
-                       count[0]=0 ; count[1]=0 ;
-                     }
-                     else
-                     {
-                       start[1]=domain->zoom_ibegin-domain->global_zoom_ibegin;
-                       start[0]=domain->zoom_jbegin-domain->global_zoom_jbegin;
-                       count[1]=domain->zoom_ni ; count[0]=domain->zoom_nj ;
+                       start[1]=domain->ibegin;
+                       start[0]=domain->jbegin;
+                       count[1]=domain->ni ; count[0]=domain->nj ;
                      }
 
@@ -468 +461 @@
                        else
                        { 
-                         start[0]=domain->zoom_jbegin-domain->global_zoom_jbegin;
-                         count[0]=domain->zoom_nj;                         
-                         CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->zoom_ni));
+                         start[0]=domain->jbegin;
+                         count[0]=domain->nj;
+                         CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->ni));
                          SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
 
-                         start[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
-                         count[0]=domain->zoom_ni;                         
-                         CArray<double,1> lon = writtenLon(Range(0,domain->zoom_ni-1));
+                         start[0]=domain->ibegin;
+                         count[0]=domain->ni;
+                         CArray<double,1> lon = writtenLon(Range(0,domain->ni-1));
                          SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
                        }
@@ -495 +488 @@
                    {
                      start[2] = 0;
-                     start[1] = domain->zoom_ibegin - domain->global_zoom_ibegin;
-                     start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
+                     start[1] = domain->ibegin;
+                     start[0] = domain->jbegin;
                      count[2] = domain->nvertex;
-                     count[1] = domain->zoom_ni;
-                     count[0] = domain->zoom_nj;
+                     count[1] = domain->ni;
+                     count[0] = domain->nj;
                    }
                  
@@ -518 +511 @@
                    else
                    {
-                     start[1] = domain->zoom_ibegin - domain->global_zoom_ibegin;
-                     start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
-                     count[1] = domain->zoom_ni;
-                     count[0] = domain->zoom_nj;
+                     start[1] = domain->ibegin;
+                     start[0] = domain->jbegin;
+                     count[1] = domain->ni;
+                     count[0] = domain->nj;
                    }
                    
@@ -548 +541 @@
          domain->addRelFile(this->filename);
       }
+      CATCH
 
     //--------------------------------------------------------------
@@ -786 +780 @@
                else
                {
-                 startNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
-                 countNodes[0] = domain->zoom_ni ;
+                 startNodes[0] = domain->ibegin;
+                 countNodes[0] = domain->ni ;
                }
 
@@ -809 +803 @@
                else
                {
-                 startEdges[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
-                 countEdges[0] = domain->zoom_ni;
+                 startEdges[0] = domain->ibegin;
+                 countEdges[0] = domain->ni;
                  startNodes[0] = domain->mesh->node_start;
                  countNodes[0] = domain->mesh->node_count;
-                 startEdgeNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
+                 startEdgeNodes[0] = domain->ibegin;
                  startEdgeNodes[1] = 0;
-                 countEdgeNodes[0] = domain->zoom_ni;
+                 countEdgeNodes[0] = domain->ni;
                  countEdgeNodes[1] = 2;
                }
@@ -845 +839 @@
                else
                {
-                 startFaces[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
-                 countFaces[0] = domain->zoom_ni ;
+                 startFaces[0] = domain->ibegin;
+                 countFaces[0] = domain->ni ;
                  startNodes[0] = domain->mesh->node_start;
                  countNodes[0] = domain->mesh->node_count;
@@ -859 +853 @@
                  countEdgeFaces[0] = domain->mesh->edge_count;
                  countEdgeFaces[1]= 2;
-                 startFaceConctv[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
+                 startFaceConctv[0] = domain->ibegin;
                  startFaceConctv[1] = 0;
-                 countFaceConctv[0] = domain->zoom_ni;
+                 countFaceConctv[0] = domain->ni;
                  countFaceConctv[1] = domain->nvertex;
                }
@@ -883 +877 @@
           case (MULTI_FILE) :
           {
+            ERROR("CNc4DataOutput::writeDomain(domain)",
+            << "[ type = multiple_file ]"
+            << " is not yet implemented for UGRID files !");
             break;
           }
@@ -948 +945 @@
          int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
 
-         CArray<size_t, 1>& indexToWrite = domain->localIndexToWriteOnServer;
+         CArray<int, 1>& indexToWrite = domain->localIndexToWriteOnServer;
          int nbWritten = indexToWrite.numElements();
          CArray<double,1> writtenLat, writtenLon;
@@ -960 +957 @@
            for (int idx = 0; idx < nbWritten; ++idx)
            {
-             if (idx < domain->latvalue.numElements())
-             {
-               writtenLat(idx) = domain->latvalue(indexToWrite(idx));
-               writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
-             }
-             else
-             {
-               writtenLat(idx) = 0.;
-               writtenLon(idx) = 0.;
-             }
+             if (indexToWrite(idx) < 0)
+             {
+               writtenLat(idx) = -1.;
+               writtenLon(idx) = -1.;
+             }
+             else
+             {
+               writtenLat(idx) = domain->latvalue(indexToWrite(idx));
+               writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
+             }
            }
          }
@@ -984 +981 @@
              for (int nv = 0; nv < nvertex; ++nv)
              {
-               if (idx < boundslat.columns())
+               if (indexToWrite(idx) < 0)
+               {
+                 writtenBndsLat(nv, idx) = -1.;
+                 writtenBndsLon(nv, idx) = -1.;
+               }
+               else
                {
                  writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
                  writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
-               }
-               else
-               {
-                 writtenBndsLat(nv, idx) = 0.;
-                 writtenBndsLon(nv, idx) = 0.;
                 }
              }
@@ -1003 +1000 @@
            for (int idx = 0; idx < nbWritten; ++idx)
            {
-                  if (idx < domain->areavalue.numElements())
-                writtenArea(idx) = domain->areavalue(indexToWrite(idx));
-                  else
-                writtenArea(idx) = 0.;
+             if (indexToWrite(idx) < 0)
+               writtenArea(idx) = -1.;
+             else
+               writtenArea(idx) = domain->areavalue(indexToWrite(idx));
            }
          }
@@ -1017 +1014 @@
               {
                  dim0.push_back(dimXid);
-                 SuperClassWriter::addDimension(dimXid, domain->zoom_ni);
+                 SuperClassWriter::addDimension(dimXid, domain->ni);
 
                  lonid = lonName+appendDomid;
@@ -1130 +1127 @@
                  else
                  {
-                   start[0]=domain->zoom_ibegin - domain->global_zoom_ibegin;
-                   count[0]=domain->zoom_ni;
-                   startBounds[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
+                   start[0]=domain->ibegin;
+                   count[0]=domain->ni;
+                   startBounds[0]=domain->ibegin;
                    startBounds[1]=0 ;
-                   countBounds[0]=domain->zoom_ni;
+                   countBounds[0]=domain->ni;
                    countBounds[1]=nvertex ;
                  }
@@ -1183 +1180 @@
         axis->computeWrittenCompressedIndex(comm_file);
        
-        int zoom_size  = (MULTI_FILE == SuperClass::type) ? axis->zoom_n.getValue()
-                                                          : axis->global_zoom_n.getValue();
-
-        int zoom_count = axis->zoom_n;                                                 
-        int zoom_begin = axis->zoom_begin;
-        // int zoom_begin = (MULTI_FILE == SuperClass::type) ? axis->global_zoom_begin 
-        //                                                   : axis->zoom_begin;
-
-        if ((0 == axis->zoom_n) && (MULTI_FILE == SuperClass::type)) return;
+        int size  = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
+                                                          : axis->n_glo.getValue();
+
+        if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
 
         std::vector<StdString> dims;
@@ -1210 +1202 @@
           if (axis->dim_name.isEmpty()) axisDim = axisid;
           else axisDim=axis->dim_name.getValue();
-          SuperClassWriter::addDimension(axisDim, zoom_size);
+          SuperClassWriter::addDimension(axisDim, size);
           dims.push_back(axisDim);
 
@@ -1288 +1280 @@
           SuperClassWriter::definition_end();
 
-          CArray<size_t, 1>& indexToWrite = axis->localIndexToWriteOnServer;
+          CArray<int, 1>& indexToWrite = axis->localIndexToWriteOnServer;
           int nbWritten = indexToWrite.numElements();
           CArray<double,1> axis_value(indexToWrite.numElements());
@@ -1295 +1287 @@
             for (int i = 0; i < nbWritten; i++)
             {
-              if (i < axis->value.numElements())
+              if (indexToWrite(i) < 0)
+                axis_value(i) = -1;   // Some value in case of a hole
+              else
                 axis_value(i) = axis->value(indexToWrite(i));
-              else
-                axis_value(i) = 0.;
             }
           }
@@ -1308 +1300 @@
             for (int i = 0; i < nbWritten; i++)
             {
-              if (i < axis->label.numElements())
+              if (indexToWrite(i) < 0)
+                axis_label(i) = boost::lexical_cast<string>(-1);  // Some value in case of a hole
+              else
                 axis_label(i) = axis->label(indexToWrite(i));
-              else
-                axis_label(i) = boost::lexical_cast<string>(0);  // Write 0 as a label
             }
           }
@@ -1329 +1321 @@
                   for (int i = 0; i < nbWritten; ++i)
                   {
-                    if (i < axis->bounds.columns())
+                    if (indexToWrite(i) < 0)
+                    {
+                      axis_bounds(0, i) = -1.; // Some value in case of a hole
+                      axis_bounds(1, i) = -1.;
+                    }
+                    else
                     {
                       axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
                       axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
-                    }
-                    else
-                    {
-                      axis_bounds(0, i) = 0.;
-                      axis_bounds(1, i) = 0.;
-
                     }
                   }
@@ -1354 +1345 @@
               std::vector<StdSize> start(1), startBounds(2) ;
               std::vector<StdSize> count(1), countBounds(2) ;
-              start[0] = startBounds[0] = zoom_begin - axis->global_zoom_begin;
-              count[0] = countBounds[0] = zoom_count; // zoom_size
+              start[0] = startBounds[0] = axis->begin;
+              count[0] = countBounds[0] = axis->n;
               startBounds[1] = 0;
               countBounds[1] = 2;
@@ -1369 +1360 @@
                   for (int i = 0; i < nbWritten; ++i)
                   {
-                    if (i < axis->bounds.columns())
+                    if (indexToWrite(i) < 0)
+                    {
+                      axis_bounds(0, i) = -1.;
+                      axis_bounds(1, i) = -1.;
+                    }
+                    else
                     {
                       axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
                       axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
-                    }
-                    else
-                    {
-                      axis_bounds(0, i) = 0.;
-                      axis_bounds(1, i) = 0.;
                     }
                   }
@@ -2512 +2503 @@
                    if ( wtimeData)
                    {
-//                     SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
-//                     SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
                        SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
                        SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
@@ -2519 +2508 @@
                    if (wtimeCounter)
                    {
-//                     SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
-//                     if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
                      SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
                      if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
@@ -2530 +2517 @@
               case (ONE_FILE) :
               {
-                const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
-                const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
-                const std::vector<int>& nZoomSizeServer  = grid->getDistributionServer()->getZoomSizeServer();
 
                 std::vector<StdSize> start, count;
@@ -2550 +2534 @@
                     int numElement = axisDomainOrder.numElements();
                     int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
-                    int idx = nZoomBeginGlobal.size() - 1;
-
-                    start.reserve(nZoomBeginGlobal.size());
-                    count.reserve(nZoomBeginGlobal.size());
-
+                    int idx = domainList.size() * 2 + axisList.size() - 1;
+
+                    start.reserve(idx+1);
+                    count.reserve(idx+1);
 
                     for (int i = numElement - 1; i >= 0; --i)
@@ -2572 +2555 @@
                           if ((domain->type) != CDomain::type_attr::unstructured)
                           {
-                            start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
-                            count.push_back(nZoomSizeServer[idx]);
+                            start.push_back(domain->jbegin);
+                            count.push_back(domain->nj);
                           }
                           --idx;
-                          start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
-                          count.push_back(nZoomSizeServer[idx]);
+                          start.push_back(domain->ibegin);
+                          count.push_back(domain->ni);
                           --idx;
                         }
@@ -2593 +2576 @@
                         else
                         {
-                          start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
-                          count.push_back(nZoomSizeServer[idx]);
+                          start.push_back(axis->begin);
+                          count.push_back(axis->n);
                         }
-
                         --idxAxis;
                         --idx;
@@ -2610 +2592 @@
                   int numElement = axisDomainOrder.numElements();
                   int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
-                  int idx = domainList.size() * 2 + axisList.size() - 1;// nZoomBeginGlobal.size() - 1;
-
-                  start.reserve(nZoomBeginGlobal.size());
-                  count.reserve(nZoomBeginGlobal.size());
+                  int idx = domainList.size() * 2 + axisList.size() - 1;
+
+                  start.reserve(idx+1);
+                  count.reserve(idx+1);
 
                   for (int i = numElement - 1; i >= 0; --i)
@@ -2622 +2604 @@
                       if ((domain->type) != CDomain::type_attr::unstructured)
                       {
-                        start.push_back(domain->zoom_jbegin - domain->global_zoom_jbegin);
-                        count.push_back(domain->zoom_nj);
+                        start.push_back(domain->jbegin);
+                        count.push_back(domain->nj);
                       }
                       --idx ;
 
-                        start.push_back(domain->zoom_ibegin - domain->global_zoom_ibegin);
-                        count.push_back(domain->zoom_ni);
+                        start.push_back(domain->ibegin);
+                        count.push_back(domain->ni);
                       --idx ;
                       --idxDomain;
@@ -2635 +2617 @@
                     {
                         CAxis* axis = CAxis::get(axisList[idxAxis]);
-                        start.push_back(axis->zoom_begin - axis->global_zoom_begin);
-                        count.push_back(axis->zoom_n);
+                        start.push_back(axis->begin);
+                        count.push_back(axis->n);
                       --idx;
                       --idxAxis;
@@ -2662 +2644 @@
                    if ( wtimeData)
                    {
-//                     SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
-//                     SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
                      SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
                      SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
@@ -2669 +2649 @@
                    if (wtimeCounter)
                    {
-//                     SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
-//                     if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
                      SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
                      if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);

XIOS/dev/branch_openmp/src/io/nc4_data_output.hpp

@@ -4 +4 @@
 /// XIOS headers ///
 #include "xios_spl.hpp"
-#include "mpi_std.hpp"
 #include "onetcdf4.hpp"
 #include "data_output.hpp"

XIOS/dev/branch_openmp/src/io/netCdfInterface.cpp

@@ -22 +22 @@
 int CNetCdfInterface::create(const StdString& fileName, int cMode, int& ncId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_create"<<std::endl;
-    status = nc_create(fileName.c_str(), cMode, &ncId);
-    info(100)<<"end nc_create"<<std::endl;
-  }
+  int status = nc_create(fileName.c_str(), cMode, &ncId);
   if (NC_NOERR != status)
   {
@@ -53 +47 @@
 \return Status code
 */
-int CNetCdfInterface::createPar(const StdString& fileName, int cMode, MPI_Comm comm, MPI_Info info, int& ncId)
-{
-  int status = xios::nc_create_par(fileName.c_str(), cMode, comm, to_mpi_info(MPI_INFO_NULL), &ncId);
-
+int CNetCdfInterface::createPar(const StdString& fileName, int cMode, ep_lib::MPI_Comm comm, ep_lib::MPI_Info info, int& ncId)
+{
+  #ifdef _usingMPI
+  int status = xios::nc_create_par(fileName.c_str(), cMode, comm, info, &ncId);
+  #elif _usingEP
+  int status = xios::nc_create_par(fileName.c_str(), cMode, to_mpi_comm(comm->mpi_comm), to_mpi_info(info), &ncId);
+  #endif
   if (NC_NOERR != status)
   {
@@ -81 +78 @@
 int CNetCdfInterface::open(const StdString& fileName, int oMode, int& ncId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_open"<<std::endl;
-    status = nc_open(fileName.c_str(), oMode, &ncId);
-    info(100)<<"end nc_open"<<std::endl;
-  }
+  int status = nc_open(fileName.c_str(), oMode, &ncId);
   if (NC_NOERR != status)
   {
@@ -113 +104 @@
 \return Status code
 */
-int CNetCdfInterface::openPar(const StdString& fileName, int oMode, MPI_Comm comm, MPI_Info info, int& ncId)
-{
-  int status = xios::nc_open_par(fileName.c_str(), oMode, comm, to_mpi_info(MPI_INFO_NULL), &ncId);
-  
+int CNetCdfInterface::openPar(const StdString& fileName, int oMode, ep_lib::MPI_Comm comm, ep_lib::MPI_Info info, int& ncId)
+{
+  #ifdef _usingMPI
+  int status = xios::nc_open_par(fileName.c_str(), oMode, comm, info, &ncId);
+  #elif _usingEP
+  int status = xios::nc_open_par(fileName.c_str(), oMode, to_mpi_comm(comm->mpi_comm), to_mpi_info(info), &ncId);
+  #endif
   if (NC_NOERR != status)
   {
@@ -139 +133 @@
 int CNetCdfInterface::close(int ncId)
 {
-  int status = NC_NOERR;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_close"<<std::endl;
-    status = nc_close(ncId);
-    info(100)<<"end nc_close"<<std::endl;
-  }
-      
+  int status = nc_close(ncId);
   if (NC_NOERR != status)
   {
@@ -168 +155 @@
 int CNetCdfInterface::reDef(int ncId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_reDef"<<std::endl;
-    status = nc_redef(ncId);
-    info(100)<<"end nc_reDef"<<std::endl;
-  }
-  
+  int status = nc_redef(ncId);
   if (NC_NOERR != status)
   {
@@ -197 +177 @@
 int CNetCdfInterface::endDef(int ncId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_enddef"<<std::endl;
-    status = nc_enddef(ncId);
-    info(100)<<"end nc_enddef"<<std::endl;
-  }
+  int status = nc_enddef(ncId);
   if (NC_NOERR != status)
   {
@@ -228 +202 @@
 int CNetCdfInterface::inqNcId(int ncid, const StdString& grpName, int& grpId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_ncid"<<std::endl;
-    status = nc_inq_ncid(ncid, grpName.c_str(), &grpId);
-    info(100)<<"end nc_inq_ncid"<<std::endl;
-  }
-  
+  int status = nc_inq_ncid(ncid, grpName.c_str(), &grpId);
   if (NC_NOERR != status)
   {
@@ -261 +228 @@
 int CNetCdfInterface::inqVarId(int ncid, const StdString& varName, int& varId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_varid"<<std::endl;
-    status = nc_inq_varid(ncid, varName.c_str(), &varId);
-    info(100)<<"end nc_inq_varid"<<std::endl;
-  }
+  int status = nc_inq_varid(ncid, varName.c_str(), &varId);
   if (NC_NOERR != status)
   {
@@ -292 +253 @@
 int CNetCdfInterface::inqDimId(int ncid, const StdString& dimName, int& dimId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_dimid"<<std::endl;
-    status = nc_inq_dimid(ncid, dimName.c_str(), &dimId);
-    info(100)<<"end nc_inq_dimid"<<std::endl;
-  }
-  
+  int status = nc_inq_dimid(ncid, dimName.c_str(), &dimId);
   if (NC_NOERR != status)
   {
@@ -325 +279 @@
 {
   char varNameBuff[NC_MAX_NAME + 1];
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_varname"<<std::endl;
-    status = nc_inq_varname(ncid, varId, varNameBuff);
-    info(100)<<"end nc_inq_varname"<<std::endl;
-  }
+  int status = nc_inq_varname(ncid, varId, varNameBuff);
   if (NC_NOERR != status)
   {
@@ -355 +303 @@
 int CNetCdfInterface::inqUnLimDim(int ncid, int& dimId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_unlimdim"<<std::endl;
-    status = nc_inq_unlimdim(ncid, &dimId);
-    info(100)<<"end nc_inq_unlimdim"<<std::endl;
-  }
+  int status = nc_inq_unlimdim(ncid, &dimId);
   if (NC_NOERR != status)
   {
@@ -387 +329 @@
 {
   char fullNameIn[NC_MAX_NAME + 1];
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_dimname"<<std::endl;
-    status = nc_inq_dimname(ncid, dimId, fullNameIn);
-    info(100)<<"end nc_inq_dimname"<<std::endl;
-  }
+  int status = nc_inq_dimname(ncid, dimId, fullNameIn);
   if (NC_NOERR != status)
   {
@@ -418 +354 @@
 int CNetCdfInterface::inqDimLen(int ncid, int dimId, StdSize& dimLen)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_dimlen"<<std::endl;
-    status = nc_inq_dimlen(ncid, dimId, &dimLen);
-    info(100)<<"end nc_inq_dimlen"<<std::endl;
-  }
+  int status = nc_inq_dimlen(ncid, dimId, &dimLen);
   if (NC_NOERR != status)
   {
@@ -449 +379 @@
 int CNetCdfInterface::inqVarNDims(int ncid, int varId, int& nDims)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_varndims"<<std::endl;
-    status = nc_inq_varndims(ncid, varId, &nDims);
-    info(100)<<"end nc_inq_varndims"<<std::endl;
-  }
+  int status = nc_inq_varndims(ncid, varId, &nDims);
   if (NC_NOERR != status)
   {
@@ -480 +404 @@
 int CNetCdfInterface::inqVarDimId(int ncid, int varId, int* dimIds)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_vardimid"<<std::endl;
-    status = nc_inq_vardimid(ncid, varId, dimIds);
-    info(100)<<"end nc_inq_vardimid"<<std::endl;
-  }
+  int status = nc_inq_vardimid(ncid, varId, dimIds);
   if (NC_NOERR != status)
   {
@@ -512 +430 @@
 int CNetCdfInterface::inqDimIds(int ncid, int& nDims, int* dimIds, int includeParents)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_dimids"<<std::endl;
-    status = nc_inq_dimids(ncid, &nDims, dimIds, includeParents);
-    info(100)<<"end nc_inq_dimids"<<std::endl;
-  }
+  int status = nc_inq_dimids(ncid, &nDims, dimIds, includeParents);
   if (NC_NOERR != status)
   {
@@ -545 +457 @@
   StdSize strlen = 0;
   std::vector<char> buff;
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_grpname_full"<<std::endl;
-    status = nc_inq_grpname_full(ncid, &strlen, NULL);
-    info(100)<<"end nc_inq_grpname_full"<<std::endl;
-  
-    if (NC_NOERR == status)
-    {
-      buff.resize(strlen + 1);
-      status = nc_inq_grpname_full(ncid, NULL, &buff[0]);
-    }
-    info(100)<<"start nc_inq_grpname_full"<<std::endl;
-  }
+  int status = nc_inq_grpname_full(ncid, &strlen, NULL);
+  if (NC_NOERR == status)
+  {
+    buff.resize(strlen + 1);
+    status = nc_inq_grpname_full(ncid, NULL, &buff[0]);
+  }
+
   if (NC_NOERR != status)
   {
@@ -585 +490 @@
 int CNetCdfInterface::inqGrpIds(int ncid, int& numgrps, int* ncids)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_grps"<<std::endl;
-    status = nc_inq_grps(ncid, &numgrps, ncids);
-    info(100)<<"end nc_inq_grps"<<std::endl;
-  }
+  int status = nc_inq_grps(ncid, &numgrps, ncids);
   if (NC_NOERR != status)
   {
@@ -616 +515 @@
 int CNetCdfInterface::inqVarIds(int ncid, int& nvars, int* varids)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_varids"<<std::endl;
-    status = nc_inq_varids(ncid, &nvars, varids);
-    info(100)<<"end nc_inq_varids"<<std::endl;
-  }
+  int status = nc_inq_varids(ncid, &nvars, varids);
   if (NC_NOERR != status)
   {
@@ -649 +542 @@
 int CNetCdfInterface::inqAtt(int ncid, int varid, const StdString& name, nc_type& type, size_t& len)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_att"<<std::endl;
-    status = nc_inq_att(ncid, varid, name.c_str(), &type, &len);
-    info(100)<<"end nc_inq_att"<<std::endl;
-  }
-  
+  int status = nc_inq_att(ncid, varid, name.c_str(), &type, &len);
   if (NC_NOERR != status)
   {
@@ -680 +566 @@
 int CNetCdfInterface::inqNAtts(int ncid, int& ngatts)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_natts"<<std::endl;
-    status = nc_inq_natts(ncid, &ngatts);
-    info(100)<<"end nc_inq_natts"<<std::endl;
-  }
+  int status = nc_inq_natts(ncid, &ngatts);
   if (NC_NOERR != status)
   {
@@ -711 +591 @@
 int CNetCdfInterface::inqVarNAtts(int ncid, int varid, int& natts)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_varnatts"<<std::endl;
-    status = nc_inq_varnatts(ncid, varid, &natts);
-    info(100)<<"end nc_inq_varnatts"<<std::endl;
-  }
+  int status = nc_inq_varnatts(ncid, varid, &natts);
   if (NC_NOERR != status)
   {
@@ -738 +612 @@
 {
   std::vector<char> attName(NC_MAX_NAME + 1,' ');
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_inq_attname"<<std::endl;
-    status = nc_inq_attname(ncid, varid, attnum, &attName[0]);
-    info(100)<<"end nc_inq_attname"<<std::endl;
-  }
+  int status = nc_inq_attname(ncid, varid, attnum, &attName[0]);
   if (NC_NOERR != status)
   {
@@ -775 +643 @@
 int CNetCdfInterface::defGrp(int parentNcid, const StdString& grpName, int& grpId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_def_grp"<<std::endl;
-    status = nc_def_grp(parentNcid, grpName.c_str(), &grpId);
-    info(100)<<"end nc_def_grp"<<std::endl;
-  }
+  int status = nc_def_grp(parentNcid, grpName.c_str(), &grpId);
   if (NC_NOERR != status)
   {
@@ -806 +668 @@
 int CNetCdfInterface::defDim(int ncid, const StdString& dimName, StdSize dimLen, int& dimId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_def_dim"<<std::endl;
-    status = nc_def_dim(ncid, dimName.c_str(), dimLen, &dimId);
-    info(100)<<"end nc_def_dim"<<std::endl;
-  }
+  int status = nc_def_dim(ncid, dimName.c_str(), dimLen, &dimId);
   if (NC_NOERR != status)
   {
@@ -843 +699 @@
                              int nDims, const int dimIds[], int& varId)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_def_var"<<std::endl;
-    status = nc_def_var(ncid, varName.c_str(), xtype, nDims, dimIds, &varId);
-    info(100)<<"end nc_def_var"<<std::endl;
-  }
+  int status = nc_def_var(ncid, varName.c_str(), xtype, nDims, dimIds, &varId);
   if (NC_NOERR != status)
   {
@@ -878 +728 @@
 int CNetCdfInterface::defVarChunking(int ncid, int varId, int storage, StdSize chunkSize[])
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_def_var_chunking"<<std::endl;
-    status = nc_def_var_chunking(ncid, varId, storage, chunkSize);
-    info(100)<<"end nc_def_var_chunking"<<std::endl;
-  }
+  int status = nc_def_var_chunking(ncid, varId, storage, chunkSize);
   if (NC_NOERR != status)
   {
@@ -912 +756 @@
   
   if (compressionLevel == 0) return NC_NOERR ;
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_def_var_deflate"<<std::endl;
-    status = nc_def_var_deflate(ncid, varId, (compressionLevel > 0), (compressionLevel > 0), compressionLevel);
-    info(100)<<"end nc_def_var_deflate"<<std::endl;
-  }
+  int status = nc_def_var_deflate(ncid, varId, (compressionLevel > 0), (compressionLevel > 0), compressionLevel);
   if (NC_NOERR != status)
   {
@@ -944 +782 @@
 {
   int old_fill_mode;
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_set_fill"<<std::endl;
-    status = nc_set_fill(ncid, fill ? NC_FILL: NC_NOFILL, &old_fill_mode);
-    info(100)<<"end nc_set_fill"<<std::endl;
-  }
+  int status = nc_set_fill(ncid, fill ? NC_FILL: NC_NOFILL, &old_fill_mode);
   if (NC_NOERR != status)
   {
@@ -977 +809 @@
 int CNetCdfInterface::defVarFill(int ncid, int varId, int noFill, void* fillValue)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_def_var_fill"<<std::endl;
-    status = nc_def_var_fill(ncid, varId, noFill, fillValue);
-    info(100)<<"end nc_def_var_fill"<<std::endl;
-  }
+  int status = nc_def_var_fill(ncid, varId, noFill, fillValue);
   if (NC_NOERR != status)
   {
@@ -1011 +837 @@
 int CNetCdfInterface::varParAccess(int ncid, int varId, int access)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_var_par_access"<<std::endl;
-    status = nc_var_par_access(ncid, varId, access);
-    info(100)<<"end nc_var_par_access"<<std::endl;
-  }
+  int status = nc_var_par_access(ncid, varId, access);
   if (NC_NOERR != status)
   {
@@ -1040 +860 @@
 int CNetCdfInterface::sync(int ncid)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_sync"<<std::endl;
-    status = nc_sync(ncid);
-    info(100)<<"end nc_sync"<<std::endl;
-  }
+  int status = nc_sync(ncid);
   if (NC_NOERR != status)
   {
@@ -1066 +880 @@
 int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, double* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_att_double"<<std::endl;
-    status = nc_get_att_double(ncid, varid, attrName, data);
-    info(100)<<"end nc_get_att_double"<<std::endl;
-  }
-  return status;
+  return nc_get_att_double(ncid, varid, attrName, data);
 }
 
@@ -1079 +886 @@
 int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, float* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_att_float"<<std::endl;
-    status = nc_get_att_float(ncid, varid, attrName, data);
-    info(100)<<"end nc_get_att_float"<<std::endl;
-  }
-  return status;
+  return nc_get_att_float(ncid, varid, attrName, data);
 }
 
@@ -1092 +892 @@
 int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, int* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_att_int"<<std::endl;
-    status = nc_get_att_int(ncid, varid, attrName, data);
-    info(100)<<"end nc_get_att_int"<<std::endl;
-  }
-  return status; 
+  return nc_get_att_int(ncid, varid, attrName, data);
 }
 
@@ -1105 +898 @@
 int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, long* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_att_long"<<std::endl;
-    status = nc_get_att_long(ncid, varid, attrName, data);
-    info(100)<<"end nc_get_att_long"<<std::endl;
-  }
-  return status;
+  return nc_get_att_long(ncid, varid, attrName, data);
 }
 
@@ -1118 +904 @@
 int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, short* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_att_short"<<std::endl;
-    status = nc_get_att_short(ncid, varid, attrName, data);
-    info(100)<<"end nc_get_att_short"<<std::endl;
-  }
-  return status;
+  return nc_get_att_short(ncid, varid, attrName, data);
 }
 
@@ -1131 +910 @@
 int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, char* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_att_text"<<std::endl;
-    status = nc_get_att_text(ncid, varid, attrName, data);
-    info(100)<<"end nc_get_att_text"<<std::endl;
-  }
-  return status;
+  return nc_get_att_text(ncid, varid, attrName, data);
 }
 
@@ -1146 +918 @@
                                    StdSize numVal, const double* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_att_double"<<std::endl;
-    status = nc_put_att_double(ncid, varid, attrName, NC_DOUBLE, numVal, data);
-    info(100)<<"end nc_put_att_double"<<std::endl;
-  }
-  return status;
+  return nc_put_att_double(ncid, varid, attrName, NC_DOUBLE, numVal, data);
 }
 
@@ -1160 +925 @@
                                    StdSize numVal, const float* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_att_float"<<std::endl;
-    status = nc_put_att_float(ncid, varid, attrName, NC_FLOAT, numVal, data);
-    info(100)<<"end nc_put_att_float"<<std::endl;
-  }
-  return status;
+  return nc_put_att_float(ncid, varid, attrName, NC_FLOAT, numVal, data);
 }
 
@@ -1174 +932 @@
                                    StdSize numVal, const int* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_att_int"<<std::endl;
-    status = nc_put_att_int(ncid, varid, attrName, NC_INT, numVal, data);
-    info(100)<<"end nc_put_att_int"<<std::endl;
-  }
-  return status;
+  return nc_put_att_int(ncid, varid, attrName, NC_INT, numVal, data);
 }
 
@@ -1188 +939 @@
                                    StdSize numVal, const long* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_att_long"<<std::endl;
-    status = nc_put_att_long(ncid, varid, attrName, NC_LONG, numVal, data);
-    info(100)<<"end nc_put_att_long"<<std::endl;
-  }
-  return status;
+  return nc_put_att_long(ncid, varid, attrName, NC_LONG, numVal, data);
 }
 
@@ -1202 +946 @@
                                    StdSize numVal, const short* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_att_short"<<std::endl;
-    status = nc_put_att_short(ncid, varid, attrName, NC_SHORT, numVal, data);
-    info(100)<<"end nc_put_att_short"<<std::endl;
-  }
-  return status;
+  return nc_put_att_short(ncid, varid, attrName, NC_SHORT, numVal, data);
 }
 
@@ -1216 +953 @@
                                    StdSize numVal, const char* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_att_text"<<std::endl;
-    status = nc_put_att_text(ncid, varid, attrName, numVal, data);
-    info(100)<<"end nc_put_att_text"<<std::endl;
-  }
-  return status;
+  return nc_put_att_text(ncid, varid, attrName, numVal, data);
 }
 
@@ -1230 +960 @@
 int CNetCdfInterface::ncGetVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, double* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_vara_double"<<std::endl;
-    status = nc_get_vara_double(ncid, varid, start, count, data);
-    info(100)<<"end nc_get_vara_double"<<std::endl;
-  }
-  return status;
+  return nc_get_vara_double(ncid, varid, start, count, data);
 }
 
@@ -1243 +966 @@
 int CNetCdfInterface::ncGetVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, float* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_vara_float"<<std::endl;
-    status = nc_get_vara_float(ncid, varid, start, count, data);
-    info(100)<<"end nc_get_vara_float"<<std::endl;
-  }
-  return status; 
+  return nc_get_vara_float(ncid, varid, start, count, data);
 }
 
@@ -1256 +972 @@
 int CNetCdfInterface::ncGetVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, int* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_vara_int"<<std::endl;
-    status = nc_get_vara_int(ncid, varid, start, count, data);
-    info(100)<<"end nc_get_vara_int"<<std::endl;
-  }
-  return status; 
+  return nc_get_vara_int(ncid, varid, start, count, data);
 }
 
@@ -1269 +978 @@
 int CNetCdfInterface::ncGetVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, char* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_get_vara_text"<<std::endl;
-    status = nc_get_vara_text(ncid, varid, start, count, data);
-    info(100)<<"end nc_get_vara_text"<<std::endl;
-  }
-  return status;
+  return nc_get_vara_text(ncid, varid, start, count, data);
 }
 
@@ -1283 +985 @@
 int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const double* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_vara_double"<<std::endl;
-    status = nc_put_vara_double(ncid, varid, start, count, data);
-    info(100)<<"end nc_put_vara_double"<<std::endl;
-  }
-  return status;
+  return nc_put_vara_double(ncid, varid, start, count, data);
 }
 
@@ -1296 +991 @@
 int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const float* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_vara_float"<<std::endl;
-    status = nc_put_vara_float(ncid, varid, start, count, data);
-    info(100)<<"end nc_put_vara_float"<<std::endl;
-  }
-  return status;
+  return nc_put_vara_float(ncid, varid, start, count, data);
 }
 
@@ -1309 +997 @@
 int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const int* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_vara_int"<<std::endl;
-    status = nc_put_vara_int(ncid, varid, start, count, data);
-    info(100)<<"end nc_put_vara_int"<<std::endl;
-  }
-  return status;
+  return nc_put_vara_int(ncid, varid, start, count, data);
 }
 
@@ -1322 +1003 @@
 int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const char* data)
 {
-  int status;
-  #pragma omp critical (_netcdf)
-  {
-    info(100)<<"start nc_put_vara_text"<<std::endl;
-    status = nc_put_vara_text(ncid, varid, start, count, data);
-    info(100)<<"end nc_put_vara_text"<<std::endl;
-  }
-  return status;
+  return nc_put_vara_text(ncid, varid, start, count, data);
 }
 
@@ -1342 +1016 @@
 {
    int varId = 0;
-   int status;
-   #pragma omp critical (_netcdf)
-   {
-     info(100)<<"start isVarExisted"<<std::endl;
-     status = nc_inq_varid(ncId, varName.c_str(), &varId);
-     info(100)<<"end isVarExisted"<<std::endl;
-   }
-   return (NC_NOERR == status);
+   return (NC_NOERR == (nc_inq_varid(ncId, varName.c_str(), &varId)));
 }
 
@@ -1355 +1022 @@
 {
    int dimId = 0;
-   int status;
-   #pragma omp critical (_netcdf)
-   {
-     info(100)<<"start isDimExisted"<<std::endl;
-     status = nc_inq_dimid(ncId, dimName.c_str(), &dimId);
-     info(100)<<"end isDimExisted"<<std::endl;
-   }
-   return (NC_NOERR == status);
+   return (NC_NOERR == (nc_inq_dimid(ncId, dimName.c_str(), &dimId)));
 }
 

XIOS/dev/branch_openmp/src/io/netCdfInterface.hpp

@@ -10 +10 @@
 #define __NETCDF_INTERFACE_HPP_
 
-#include "mpi_std.hpp"
 #include "xios_spl.hpp"
 
@@ -17 +16 @@
 #endif
 
-
+#include "mpi.hpp"
 #include "netcdf.hpp"
 
@@ -33 +32 @@
 
     //! Create a netcdf file on a parallel file system
-    static int createPar(const StdString& path, int cmode, MPI_Comm comm, MPI_Info info, int& ncId);
+    static int createPar(const StdString& path, int cmode, ep_lib::MPI_Comm comm, ep_lib::MPI_Info info, int& ncId);
 
     //! Open a netcdf file
@@ -39 +38 @@
 
     //! Open a netcdf file
-    static int openPar(const StdString& path, int cmode, MPI_Comm comm, MPI_Info info, int& ncId);
+    static int openPar(const StdString& path, int cmode, ep_lib::MPI_Comm comm, ep_lib::MPI_Info info, int& ncId);
 
     //! Close a netcdf file

XIOS/dev/branch_openmp/src/io/netcdf.hpp

@@ -1 +1 @@
 #ifndef __XIOS_NETCDF_HPP__
 #define __XIOS_NETCDF_HPP__
-#include "mpi_std.hpp"
+#include "mpi.hpp"
 #define MPI_INCLUDED
 #include <netcdf.h>
@@ -33 +33 @@
   {
 #if defined(USING_NETCDF_PAR)
-    int status;
-    #pragma omp critical (_netcdf)
-    {
-      status = ::nc_create_par(path, cmode, comm, info, ncidp) ;
-    }
-    return status;
+    return ::nc_create_par(path, cmode, comm, info, ncidp) ;
 #else
     ERROR("int nc_create_par(const char *path, int cmode, MPI_Comm comm, MPI_Info info,int *ncidp)",
@@ -49 +44 @@
   {
 #if defined(USING_NETCDF_PAR)
-    int status;
-    #pragma omp critical (_netcdf)
-    {
-      status = ::nc_open_par(path, mode, comm, info, ncidp) ;
-    }
-    return status;
+    return ::nc_open_par(path, mode, comm, info, ncidp) ;
 #else
     ERROR("int nc_open_par(const char *path, int mode, MPI_Comm comm, MPI_Info info,int *ncidp)",
@@ -65 +55 @@
   {
 #if defined(USING_NETCDF_PAR)
-    int status = ::nc_var_par_access(ncid, varid, par_access) ;
-    
-    return status;
+    return ::nc_var_par_access(ncid, varid, par_access) ;
 #else
     ERROR("int nc_var_par_access(int ncid, int varid, int par_access)",

XIOS/dev/branch_openmp/src/io/onetcdf4.cpp

@@ -3 +3 @@
 #include "onetcdf4.hpp"
 #include "group_template.hpp"
-#include "ep_mpi.hpp"
+#include "mpi.hpp"
 #include "netcdf.hpp"
 #include "netCdfInterface.hpp"
@@ -58 +58 @@
             CTimer::get("Files : create").resume();
             if (wmpi)
-               CNetCdfInterface::createPar(filename, mode, to_mpi_comm((*comm)->mpi_comm), to_mpi_info(MPI_INFO_NULL), this->ncidp);
+               CNetCdfInterface::createPar(filename, mode, *comm, EP_INFO_NULL, this->ncidp);
             else
                CNetCdfInterface::create(filename, mode, this->ncidp);
@@ -70 +70 @@
             CTimer::get("Files : open").resume();
             if (wmpi)
-               CNetCdfInterface::openPar(filename, mode, to_mpi_comm((*comm)->mpi_comm), to_mpi_info(MPI_INFO_NULL), this->ncidp);
+               CNetCdfInterface::openPar(filename, mode, *comm, EP_INFO_NULL, this->ncidp);
             else
                CNetCdfInterface::open(filename, mode, this->ncidp);

XIOS/dev/branch_openmp/src/io/onetcdf4.hpp

@@ -4 +4 @@
 /// XIOS headers ///
 #include "xios_spl.hpp"
-#include "mpi_std.hpp"
 #include "exception.hpp"
 #include "data_output.hpp"
 #include "array_new.hpp"
+#include "mpi.hpp"
 #include "netcdf.hpp"
 

XIOS/dev/branch_openmp/src/io/onetcdf4_impl.hpp

@@ -73 +73 @@
     }
     char *PtrArrayStr ;
-    PtrArrayStr=new char[stringArrayLen] ;
+    PtrArrayStr=new char[stringArrayLen*data.numElements()] ;
+    memset (PtrArrayStr,' ',stringArrayLen*data.numElements());
+    size_t offset=0 ;
     Array<StdString,1>::const_iterator it, itb=data.begin(), ite=data.end() ;
-    int lineNb = 0;
-    for(it=itb;it!=ite;++it)
+    for(it=itb;it!=ite;++it, offset+=stringArrayLen)
     {
-      it->copy(PtrArrayStr,it->size()) ;
-      PtrArrayStr[it->size()]='\0' ;
-      sstart[0] = lineNb;
-      sstart[dimArrayLen] = 0;
-      scount[0] = 1;
-      scount[dimArrayLen] = it->size() + 1;
-      CTimer::get("CONetCDF4::writeData writeData_").resume();
-      this->writeData_(grpid, varid, sstart, scount, PtrArrayStr);
-      CTimer::get("CONetCDF4::writeData writeData_").suspend();
-      ++lineNb;
+      it->copy(PtrArrayStr+offset,it->size()) ;
+      PtrArrayStr[offset+it->size()]='\0' ;
     }
+
+     CTimer::get("CONetCDF4::writeData writeData_").resume();
+     this->writeData_(grpid, varid, sstart, scount, PtrArrayStr);
+     CTimer::get("CONetCDF4::writeData writeData_").suspend();
+
     delete []  PtrArrayStr;
   }