Changeset 379 for XIOS

Timestamp:

10/22/12 13:47:08 (12 years ago)

Author:

ymipsl

Message:

• zoom can be output in single file without need to patch the netcdf library
• sequential version of netcdf4 are now managed. Can be used to output in multiple_file mode

YM

Location:

XIOS/trunk/src

Files:

• data_output.hpp (modified) (1 diff)
• node/field.cpp (modified) (2 diffs)
• node/file.cpp (modified) (8 diffs)
• node/file.hpp (modified) (3 diffs)
• output/nc4_data_output.cpp (modified) (1 diff)
• output/nc4_data_output.hpp (modified) (2 diffs)
• output/netcdf.hpp (added)
• output/netcdf_version.hpp (added)
• output/onetcdf4.cpp (modified) (3 diffs)
• output/onetcdf4.hpp (modified) (1 diff)

XIOS/trunk/src/data_output.hpp

@@ -8 +8 @@
 #include "field.hpp"
 
-#include <mpi.h>
-#define MPI_INCLUDED
-#include <netcdf.h>
 
 namespace xios

XIOS/trunk/src/node/field.cpp

@@ -187 +187 @@
   void CField::writeField(void)
   {
-//    if (! grid->domain->isEmpty() || getRelFile()->type.getValue()=="one_file")
-    if (! grid->domain->isEmpty() || getRelFile()->type == CFile::type_attr::one_file)
-    {
-      getRelFile()->checkFile();
-      this->incrementNStep();
-      getRelFile()->getDataOutput()->writeFieldData(CField::get(this));
-    }
+    if (! getRelFile()->allDomainEmpty )
+      if (! grid->domain->isEmpty() || getRelFile()->type == CFile::type_attr::one_file)
+      {
+        getRelFile()->checkFile();
+        this->incrementNStep();
+        getRelFile()->getDataOutput()->writeFieldData(CField::get(this));
+      }
   }
    //----------------------------------------------------------------
@@ -411 +411 @@
          const CDuration toffset = this->freq_operation - freq_offset_ - context->getCalendar()->getTimeStep(); 
          *this->last_operation   = *this->last_operation - toffset;  
-         cout<<operation<<endl ;
-         
+          
 #define DECLARE_FUNCTOR(MType, mtype)              \
    if  (operation.getValue().compare(#mtype) == 0) \

XIOS/trunk/src/node/file.cpp

@@ -15 +15 @@
 #include "xmlioserver_spl.hpp"
 #include "context_client.hpp"
+#include <mpi.h>
 
 namespace xios {
@@ -22 +23 @@
    CFile::CFile(void)
       : CObjectTemplate<CFile>(), CFileAttributes()
-      , vFieldGroup(), data_out(), enabledFields()
+      , vFieldGroup(), data_out(), enabledFields(), fileComm(MPI_COMM_NULL)
    { setVirtualFieldGroup() ;}
 
    CFile::CFile(const StdString & id)
       : CObjectTemplate<CFile>(id), CFileAttributes()
-      , vFieldGroup(), data_out(), enabledFields()
+      , vFieldGroup(), data_out(), enabledFields(), fileComm(MPI_COMM_NULL)
    { setVirtualFieldGroup() ;}
 
@@ -146 +147 @@
       CContext* context = CContext::getCurrent() ;
       CDate& currentDate=context->calendar->getCurrentDate() ;
-      
+      CContextServer* server=context->server ;
+            
       if (! sync_freq.isEmpty()) syncFreq = CDuration::FromString(sync_freq.getValue());
       if (! split_freq.isEmpty()) splitFreq = CDuration::FromString(split_freq.getValue());
@@ -153 +155 @@
       lastSplit=new CDate(currentDate) ;
       isOpen=false ;
+
+      allDomainEmpty=true ;
+      set<CDomain*> setDomain ;
+
+      std::vector<CField*>::iterator it, end = this->enabledFields.end();
+      for (it = this->enabledFields.begin() ;it != end; it++)
+      {
+         CField* field = *it;
+         allDomainEmpty&=field->grid->domain->isEmpty() ;
+         setDomain.insert(field->grid->domain) ;
+      }
+      nbDomain=setDomain.size() ;
+
+      // create sub communicator for file  
+      int color=allDomainEmpty?0:1 ;
+      MPI_Comm_split(server->intraComm,color,server->intraCommRank,&fileComm) ;
+      if (allDomainEmpty) MPI_Comm_free(&fileComm) ;
+      //
+      
     }
     
@@ -202 +223 @@
    {
       CContext* context = CContext::getCurrent() ;
-      CDate& currentDate=context->calendar->getCurrentDate() ;
-      
-      std::vector<CField*>::iterator it, end = this->enabledFields.end();
-
-      AllDomainEmpty=true ;
-      set<CDomain*> setDomain ;
-      for (it = this->enabledFields.begin() ;it != end; it++)
-      {
-         CField* field = *it;
-         AllDomainEmpty&=field->grid->domain->isEmpty() ;
-         setDomain.insert(field->grid->domain) ;
-      }
-      nbDomain=setDomain.size() ;
-
-      if (!AllDomainEmpty ||  type == type_attr::one_file)
+      CContextServer* server=context->server ;
+     
+      if (!allDomainEmpty)
       {
          StdString filename = (!name.isEmpty()) ?   name.getValue() : getId();
          StdOStringStream oss;
-//         if (! output_dir.isEmpty()) oss << output_dir.getValue();
          oss << filename;
          if (!name_suffix.isEmpty()) oss << name_suffix.getValue();
-//         if (!split_freq.isEmpty()) oss<<"-["<<currentDate.toString()<<"]" ;
          if (!split_freq.isEmpty()) oss<<"_"<<lastSplit->getStryyyymmdd()<<"-"<< (*lastSplit+(splitFreq-1*Second)).getStryyyymmdd();
          bool multifile=true ;
@@ -230 +237 @@
            if (type==type_attr::one_file) multifile=false ;
            else if (type==type_attr::multiple_file) multifile=true ;
-           else ERROR("void Context::createDataOutput(void)",
-                      "incorrect file <type> attribut : must be <multi_file> or <one_file>, "
-                      <<"having : <"<<type.getValue()<<">") ;
+
          } 
-         
-         CContextServer* server=context->server ;
-
+#ifndef USING_NETCDF_PAR
+         if (!multifile)
+         {
+            info(0)<<"!!! Warning -> Using non parallel version of netcdf, switching in multiple_file mode for file : "<<filename<<" ..."<<endl ;
+            multifile=true ;
+          }
+#endif
          if (multifile) 
          {
+            int commSize, commRank ;
+            MPI_Comm_size(fileComm,&commSize) ;
+            MPI_Comm_rank(fileComm,&commRank) ;
+            
             if (server->intraCommSize > 1) 
             {
               oss << "_"  ;
-              int width=0 ; int n=server->intraCommSize-1 ;
+              int width=0 ; int n=commSize-1 ;
               while(n != 0) { n=n/10 ; width++ ;}
               oss.width(width) ;
               oss.fill('0') ;
-              oss<<right<< server->intraCommRank;
+              oss<<right<< commRank;
             }
          }
@@ -264 +277 @@
            }
          }
-         data_out=shared_ptr<CDataOutput>(new CNc4DataOutput(oss.str(), false,server->intraComm,multifile, isCollective));
+         data_out=shared_ptr<CDataOutput>(new CNc4DataOutput(oss.str(), false, fileComm, multifile, isCollective));
          isOpen=true ;
 
          data_out->writeFile(CFile::get(this));
+         std::vector<CField*>::iterator it, end = this->enabledFields.end();
          for (it = this->enabledFields.begin() ;it != end; it++)
          {
@@ -288 +302 @@
      delete lastSync ;
      delete lastSplit ;
-     if (!AllDomainEmpty ||  type==type_attr::one_file)
+     if (!allDomainEmpty)
        if (isOpen) 
        {
          this->data_out->closeFile();
        }
+      if (fileComm != MPI_COMM_NULL) MPI_Comm_free(&fileComm) ;
    }
    //----------------------------------------------------------------

XIOS/trunk/src/node/file.hpp

@@ -10 +10 @@
 #include "attribute_enum.hpp"
 #include "attribute_enum_impl.hpp"
+#include <mpi.h>
 
 
@@ -93 +94 @@
          static ENodeType GetType(void);
          
-         bool AllDomainEmpty ;
+         bool allDomainEmpty ;
          CField* addField(const string& id="") ;
          CFieldGroup* addFieldGroup(const string& id="") ;
@@ -115 +116 @@
          int nbDomain ;
          bool isOpen ;
+         MPI_Comm fileComm ;
       private :
 

XIOS/trunk/src/output/nc4_data_output.cpp

@@ -27 +27 @@
 
       CNc4DataOutput::CNc4DataOutput
-         (const StdString & filename, bool exist, MPI_Comm comm_server,bool multifile, bool isCollective)
+         (const StdString & filename, bool exist, MPI_Comm comm_file,bool multifile, bool isCollective)
             : SuperClass()
-            , SuperClassWriter(filename, exist, &comm_server,multifile)
-            , comm_server(comm_server)
+            , SuperClassWriter(filename, exist, &comm_file,multifile)
+            , comm_file(comm_file)
             , filename(filename)
             , isCollective(isCollective)

XIOS/trunk/src/output/nc4_data_output.hpp

@@ -25 +25 @@
                (const StdString & filename, bool exist);
             CNc4DataOutput
-               (const StdString & filename, bool exist, MPI_Comm comm_server, bool multifile, bool isCollective=true);
+               (const StdString & filename, bool exist, MPI_Comm comm_file, bool multifile, bool isCollective=true);
 
             CNc4DataOutput(const CNc4DataOutput & dataoutput);       // Not implemented.
@@ -88 +88 @@
 
             /// Propriétés privées ///
-            MPI_Comm comm_server;
+            MPI_Comm comm_file;
             const StdString filename;
 

XIOS/trunk/src/output/onetcdf4.cpp

@@ -1 +1 @@
 #include "onetcdf4.hpp"
 #include "group_template.hpp"
+#include <mpi.h>
+#include "netcdf.hpp"
 
 namespace xios
@@ -32 +34 @@
             if (comm != NULL)
             {
-               if (!multifile) CheckError(nc_create_par(filename.c_str(), NC_NETCDF4|NC_MPIIO, *comm, MPI_INFO_NULL, &this->ncidp));
+               if (!multifile) CheckError(xios::nc_create_par(filename.c_str(), NC_NETCDF4|NC_MPIIO, *comm, MPI_INFO_NULL, &this->ncidp));
                else CheckError(nc_create(filename.c_str(), NC_NETCDF4, &this->ncidp));
             }
@@ -41 +43 @@
             if (comm != NULL)
             {
-               if (!multifile) CheckError(nc_open_par(filename.c_str(), NC_NETCDF4|NC_MPIIO, *comm, MPI_INFO_NULL, &this->ncidp));
+               if (!multifile) CheckError(xios::nc_open_par(filename.c_str(), NC_NETCDF4|NC_MPIIO, *comm, MPI_INFO_NULL, &this->ncidp));
                else CheckError(nc_open(filename.c_str(), NC_NETCDF4, &this->ncidp));
             }

XIOS/trunk/src/output/onetcdf4.hpp

@@ -7 +7 @@
 #include "data_output.hpp"
 #include "array_new.hpp"
-
 #include <mpi.h>
-#define MPI_INCLUDED
-#include <netcdf.h>
-#ifdef NETCDF_PAR_HEADER
-extern "C" {
-#include <netcdf_par.h>
-}
-#endif
-
+#include "netcdf.hpp"
 
 #ifndef UNLIMITED_DIM