Changeset 1205 for XIOS/dev/branch_yushan_merged/src/io

Timestamp:

07/10/17 18:17:04 (7 years ago)

Author:

yushan

Message:

branch merged with trunk @1200

Location:

XIOS/dev/branch_yushan_merged/src/io

Files:

• nc4_data_output.cpp (modified) (9 diffs)
• onetcdf4.cpp (modified) (6 diffs)
• onetcdf4.hpp (modified) (1 diff)
• onetcdf4_impl.hpp (modified) (3 diffs)

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

@@ -11 +11 @@
 #include "netCdfException.hpp"
 #include "exception.hpp"
+#include "timer.hpp"
 #include "uuid.hpp"
 // mpi.hpp
@@ -79 +80 @@
 
 
-         StdString dimXid, dimYid ;
+        StdString dimXid, dimYid ;
 
         nc_type typePrec ;
@@ -1045 +1046 @@
         int zoom_begin_srv = axis->zoom_begin_srv;
         int zoom_size  = (MULTI_FILE == SuperClass::type) ? zoom_size_srv
-                                                              : axis->global_zoom_n;
-        int zoom_begin = (MULTI_FILE == SuperClass::type) ? zoom_begin_srv
-                                                              : axis->global_zoom_begin;
+                                                          : axis->global_zoom_size_srv;
 
         if ((0 == zoom_size_srv) && (MULTI_FILE == SuperClass::type)) return;
@@ -1102 +1101 @@
 
             SuperClassWriter::definition_end();
-            printf("SuperClass::type = %d, typePrec = %d\n", SuperClass::type, typePrec);
+
             switch (SuperClass::type)
             {
@@ -1126 +1125 @@
                 std::vector<StdSize> start(1), startBounds(2) ;
                 std::vector<StdSize> count(1), countBounds(2) ;
-                start[0] = startBounds[0] = zoom_begin_srv-axis->global_zoom_begin;
+                start[0] = startBounds[0] = zoom_begin_srv-axis->global_zoom_begin_srv;
                 count[0] = countBounds[0] = zoom_size_srv;
                 startBounds[1] = 0;
@@ -1832 +1831 @@
 
          singleDomain = (file->nbDomains == 1);
+
+         StdString conv_str ;
+         if (file->convention_str.isEmpty())
+         {
+            if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
+            else conv_str="UGRID" ;
+         }
+         else conv_str=file->convention_str ;
+           
          try
          {
-       if (SuperClassWriter::useCFConvention)
-             this->writeFileAttributes(filename, description,
-                                       StdString("CF-1.6"),
-                                       StdString("An IPSL model"),
-                                       this->getTimeStamp());
-           else
-             this->writeFileAttributes(filename, description,
-                                       StdString("UGRID"),
-                                       StdString("An IPSL model"),
-                                       this->getTimeStamp());
-
+           this->writeFileAttributes(filename, description,
+                                      conv_str,
+                                      StdString("An IPSL model"),
+                                      this->getTimeStamp());
 
            if (!appendMode)
@@ -1989 +1990 @@
         CGrid* grid = field->grid;
 
-        if (field->getNStep()<1) return ;
+        if (field->getNStep()<1) 
+        {
+          return;
+        }
         
         if (!grid->doGridHaveDataToWrite())
-          if (SuperClass::type == MULTI_FILE || !isCollective) return;
-
+          if (SuperClass::type == MULTI_FILE || !isCollective)
+          {
+            return;
+          }
+
+          
         StdString fieldid = field->getFieldOutputName();
 
@@ -2118 +2126 @@
               case (MULTI_FILE) :
               {
+                 CTimer::get("Files : writing data").resume();
                  SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
+                 CTimer::get("Files : writing data").suspend();
                  if (wtime)
                  {
+                   CTimer::get("Files : writing time axis").resume();
                    if ( wtimeData)
                    {
-                     SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
-                     SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
-                   }
+//                     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);
+                  }
                    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::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);
                    }
+                   CTimer::get("Files : writing time axis").suspend();
                  }
                  break;
@@ -2256 +2272 @@
                 }
 
+
+                CTimer::get("Files : writing data").resume();
                 SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
+                CTimer::get("Files : writing data").suspend();
+
                  if (wtime)
                  {
+                   CTimer::get("Files : writing time axis").resume();
                    if ( wtimeData)
                    {
-                     SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
-                     SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
+//                     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);
                    }
                    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::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);
+
                    }
+                   CTimer::get("Files : writing time axis").suspend();  
                  }
 

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

@@ -6 +6 @@
 #include "netCdfInterface.hpp"
 #include "netCdfException.hpp"
-// mpi_std.hpp
+#include "timer.hpp"
 
 namespace xios
@@ -54 +54 @@
          if (!append || !std::ifstream(filename.c_str()))
          {
+            CTimer::get("Files : create").resume();
             if (wmpi)
                CNetCdfInterface::createPar(filename, mode, *comm, MPI_INFO_NULL_STD, this->ncidp);
             else
                CNetCdfInterface::create(filename, mode, this->ncidp);
-
+            CTimer::get("Files : create").suspend();
+ 
             this->appendMode = false;
          }
@@ -64 +66 @@
          {
             mode |= NC_WRITE;
+            CTimer::get("Files : open").resume();
             if (wmpi)
-               //CNetCdfInterface::openPar(filename, mode, static_cast<MPI_Comm>(comm->mpi_comm), MPI_INFO_NULL_STD, this->ncidp);
                CNetCdfInterface::openPar(filename, mode, *comm, MPI_INFO_NULL_STD, this->ncidp);
             else
                CNetCdfInterface::open(filename, mode, this->ncidp);
-
+            CTimer::get("Files : open").suspend();
             this->appendMode = true;
          }
@@ -83 +85 @@
       void CONetCDF4::close()
       {
+        CTimer::get("Files : close").resume();
         CNetCdfInterface::close(this->ncidp);
+        CTimer::get("Files : close").suspend();
       }
 
@@ -558 +562 @@
 
          this->getWriteDataInfos(name, 0, array_size,  sstart, scount, NULL, NULL);
+
          this->writeData_(grpid, varid, sstart, scount, data.dataFirst());
+
       }
 
@@ -584 +590 @@
 
          this->getWriteDataInfos(name, record, array_size,  sstart, scount, NULL, NULL);
-         if (using_netcdf_internal)
-         {
-           if (!isRoot)
-           {
-             sstart[0] = sstart[0] + 1;
-             scount[0] = 0;
-           }
-         }
          this->writeData_(grpid, varid, sstart, scount, data.dataFirst());
        }
 
+      void CONetCDF4::writeTimeAxisDataBounds(const CArray<double, 1>& data, const StdString& name,
+                                        bool collective, StdSize record, bool isRoot)
+      {
+         int grpid = this->getCurrentGroup();
+         int varid = this->getVariable(name);
+
+         map<int,size_t>::iterator it=timeAxis.find(varid);
+         if (it == timeAxis.end()) timeAxis[varid] = record;
+         else
+         {
+           if (it->second >= record) return;
+           else it->second =record;
+         }
+
+         StdSize array_size = 1;
+         std::vector<StdSize> sstart, scount;
+
+         if (this->wmpi && collective)
+            CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE);
+         if (this->wmpi && !collective)
+            CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT);
+
+         this->getWriteDataInfos(name, record, array_size,  sstart, scount, NULL, NULL);
+         this->writeData_(grpid, varid, sstart, scount, data.dataFirst());
+       }
+
+
       //---------------------------------------------------------------
 

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

@@ -73 +73 @@
             void writeTimeAxisData(const CArray<double,1>& data, const StdString& name,
                                    bool collective, StdSize record, bool Isroot);
+            void writeTimeAxisDataBounds(const CArray<double,1>& data, const StdString& name,
+                                   bool collective, StdSize record, bool Isroot);
             /// Accesseur ///
             const CONetCDF4Path& getCurrentPath(void) const;

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

@@ -25 +25 @@
     CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT);
 
+    CTimer::get("Files : get data infos").resume();
     this->getWriteDataInfos
     (name, record, array_size,  sstart, scount, start, count);
+    CTimer::get("Files : get data infos").suspend();
+
     if (data.numElements() != array_size)
     {
@@ -54 +57 @@
     CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT);
 
-    this->getWriteDataInfos
-    (name, record, array_size,  sstart, scount, start, count);
+    CTimer::get("CONetCDF4::writeData getWriteDataInfos").resume();
+    this->getWriteDataInfos(name, record, array_size,  sstart, scount, start, count);
+    CTimer::get("CONetCDF4::writeData getWriteDataInfos").suspend();
+ 
     if (data.numElements()*stringArrayLen != array_size)
     {
@@ -72 +77 @@
       PtrArrayStr[it->size()]='\0' ;
     }
+    CTimer::get("CONetCDF4::writeData writeData_").resume();
     this->writeData_(grpid, varid, sstart, scount, ArrayStr);
+    CTimer::get("CONetCDF4::writeData writeData_").suspend();
     delete [] ArrayStr ;
   }