Fixed ElementFileWriter to work in parallel.

AMDiS/src/Debug.cc

@@ -106,7 +106,7 @@ namespace AMDiS {
 	elInfo = stack.traverseNext(elInfo);
       }
 
-      ElementFileWriter::writeFile(vec, mesh, filename, level);
+      ElementFileWriter::writeFile(vec, mesh, filename, "", level);
     }
 
 

AMDiS/src/io/ElementFileWriter.cc

@@ -14,7 +14,9 @@
 #include <boost/iostreams/device/file_descriptor.hpp>
 #include <boost/filesystem/operations.hpp>
 #include <boost/filesystem/convenience.hpp>
+#include <boost/lexical_cast.hpp>
 
+#include "io/VtkWriter.h"
 #include "ElementFileWriter.h"
 #include "BasisFunction.h"
 #include "Initfile.h"
@@ -93,7 +95,7 @@ namespace AMDiS {
     if (writeVtkFormat) {
       TEST_EXIT(mesh)("no mesh\n");
 
-      writeVtkValues(const_cast<char*>((fn + vtkExt).c_str()));
+      writeVtkValues(fn, vtkExt);
       MSG("VTK file written to %s\n", (fn + vtkExt).c_str());		     
     }
   }
@@ -102,10 +104,11 @@ namespace AMDiS {
   void ElementFileWriter::writeFile(map<int, double> &vec,
 				    Mesh *mesh,
 				    string filename,
+				    string postfix,
 				    int level)
   {
     ElementFileWriter efw("", mesh, vec);
-    efw.writeVtkValues(filename, level);
+    efw.writeVtkValues(filename, postfix, level);
   }
   
 
@@ -213,10 +216,21 @@ namespace AMDiS {
   }
 
 
-  void ElementFileWriter::writeVtkValues(string filename, int level)
+  void ElementFileWriter::writeVtkValues(string fname, 
+					 string postfix, 
+					 int level)
   {
     FUNCNAME("ElementFileWriter::writeVtkValues()");
 
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+    string filename = 
+      fname  + 
+      "-p" + boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank()) + "-" +
+      postfix;
+#else
+    string filename = fname + postfix;
+#endif
+
     boost::iostreams::filtering_ostream file;
     {
       //boost::iostreams seems not to truncate the file
@@ -237,7 +251,7 @@ namespace AMDiS {
       nElements = 0;
 
       TraverseStack stack;
-      ElInfo *elInfo = stack.traverseFirst(mesh, level, Mesh::CALL_EL_LEVEL);      
+      ElInfo *elInfo = stack.traverseFirst(mesh, level, Mesh::CALL_EL_LEVEL);
       while (elInfo) {
 	nElements++;
 	elInfo = stack.traverseNext(elInfo);
@@ -339,5 +353,11 @@ namespace AMDiS {
     file << "    </Piece>\n";
     file << "  </UnstructuredGrid>\n";
     file << "</VTKFile>\n";
+
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+    if (MPI::COMM_WORLD.Get_rank() == 0)
+      VtkWriter::writeParallelFile(fname + ".pvtu", MPI::COMM_WORLD.Get_size(),
+				   fname, ".vtu", 1);
+#endif
   }
 }

AMDiS/src/io/ElementFileWriter.h

@@ -30,6 +30,8 @@
 
 namespace AMDiS {
 
+  using namespace std;
+
   /** \brief
    * Filewriter that make it possible to create mesh files, where the values
    * are not defined on DOFs, but instead are defined on the elements.
@@ -43,9 +45,9 @@ namespace AMDiS {
   {
   public:
     /// Constructor.
-    ElementFileWriter(std::string name, 
+    ElementFileWriter(string name, 
 		      Mesh *mesh,
-		      std::map<int, double> &vec);
+		      map<int, double> &vec);
 
     /// Implementation of FileWriterInterface::writeFiles().
     void writeFiles(AdaptInfo *adaptInfo, bool force,
@@ -54,30 +56,32 @@ namespace AMDiS {
 		    bool (*writeElem)(ElInfo*) = NULL);
 
     /// Simple writing procedure for one element map.
-    static void writeFile(std::map<int, double> &vec,
+    static void writeFile(map<int, double> &vec,
 			  Mesh *mesh,
-			  std::string filename,
+			  string filename,
+			  string postfix = ".vtu",
 			  int level = -1);
 
   protected:
     /// Writes element data in AMDiS format (1 file !).
-    void writeMeshDatValues(std::string filename, double time);
+    void writeMeshDatValues(string filename, double time);
 
     /// Writes element data in VTK format.
-    void writeVtkValues(std::string filename, int level = -1);
+    void writeVtkValues(string filename, string postfix,
+			int level = -1);
 
   protected:
     /// Name.
-    std::string name;
+    string name;
 
     /// Used filename prefix.
-    std::string filename;
+    string filename;
 
     /// AMDiS mesh-data-file extension.
-    std::string amdisMeshDatExt;
+    string amdisMeshDatExt;
 
     /// VTK file extension.
-    std::string vtkExt;
+    string vtkExt;
 
     /// 0: Don't write AMDiS files.
     /// 1: Write AMDiS files. 
@@ -107,7 +111,7 @@ namespace AMDiS {
     Mesh *mesh;
 
     /// Vector that stores the solution.
-    std::map<int, double> vec;
+    map<int, double> vec;
   };
 
 }

AMDiS/src/io/FileWriter.cc

@@ -145,7 +145,8 @@ namespace AMDiS {
       if (MPI::COMM_WORLD.Get_rank() == 0)
 	vtkWriter.writeParallelFile(paraFilename + paraviewParallelFileExt,
 				    MPI::COMM_WORLD.Get_size(),
-				    filename, postfix);
+				    filename, postfix,
+				    dataCollectors.size());
 #endif
 
       MSG("ParaView file written to %s\n", (fn + paraviewFileExt).c_str());
@@ -185,11 +186,9 @@ namespace AMDiS {
       dofWriter.writeFile(fn + ".dof", solutionVecs);
     }
 
-
     if (writeArhFormat)
       ArhWriter::write(fn + ".arh", feSpace->getMesh(), solutionVecs);
 
-
 #ifdef HAVE_PNG
     if (writePngFormat) {
       PngWriter pngWriter(dataCollectors[0]);

AMDiS/src/io/VtkWriter.cc

@@ -32,7 +32,9 @@
 
 namespace AMDiS { 
 
-  int VtkWriter::writeFile(std::string name)
+  using namespace std;
+
+  int VtkWriter::writeFile(string name)
   {
     FUNCNAME("VtkWriter::writeFile()");
     
@@ -51,32 +53,33 @@ namespace AMDiS {
     }
 
     {
-      std::ofstream swapfile(name.c_str(), std::ios::out | std::ios::trunc);
+      ofstream swapfile(name.c_str(), ios::out | ios::trunc);
       TEST_EXIT(swapfile.is_open())
 	("Cannot open file %s for writing!\n", name.c_str());
       swapfile.close();
     }
 
-    file.push(boost::iostreams::file_descriptor_sink(name, std::ios::trunc));
+    file.push(boost::iostreams::file_descriptor_sink(name, ios::trunc));
     writeFileToStream(file);
 
     return 0;
   }
 
 
-  void VtkWriter::writeParallelFile(std::string name, int nRanks,
-				    std::string fnPrefix, std::string fnPostfix)
+  void VtkWriter::writeParallelFile(string name, int nRanks,
+				    string fnPrefix, string fnPostfix,
+				    int nComponents)
   {
     FUNCNAME("VtkWriter::writeParallelFile()");
 
     boost::iostreams::filtering_ostream file;
     {
-      std::ofstream swapfile(name.c_str(), std::ios::out | std::ios::trunc);
+      ofstream swapfile(name.c_str(), ios::out | ios::trunc);
       TEST_EXIT(swapfile.is_open())
 	("Cannot open file %s for writing!\n", name.c_str());
       swapfile.close();
     }
-    file.push(boost::iostreams::file_descriptor_sink(name, std::ios::trunc)); 
+    file.push(boost::iostreams::file_descriptor_sink(name, ios::trunc)); 
 
     file << "<?xml version=\"1.0\"?>\n";
     file << "<VTKFile type=\"PUnstructuredGrid\">\n";
@@ -91,14 +94,14 @@ namespace AMDiS {
 	 << "    </PCells>\n";
     file << "    <PPointData>\n";
 
-    for (int i = 0; i < static_cast<int>(dataCollector->size()); i++)
+    for (int i = 0; i < nComponents; i++)
       file << "      <PDataArray type=\"Float32\" Name=\"value" 
 	   << i << "\" format=\"ascii\"/>\n";
 
     file << "    </PPointData>\n";
 
     for (int i = 0; i < nRanks; i++) {
-      std::stringstream oss;
+      stringstream oss;
       oss << fnPrefix << "-p" << i << "-" << fnPostfix;
       boost::filesystem::path filepath(oss.str());
       file << "    <Piece Source=\"" 
@@ -113,9 +116,9 @@ namespace AMDiS {
 
 
   int VtkWriter::updateAnimationFile(AdaptInfo *adaptInfo,
-				     std::string valueFilename,
-				     std::vector< pair<double, std::string> > *paraViewAnimationFrames,
-				     std::string animationFilename)
+				     string valueFilename,
+				     vector< pair<double, string> > *paraViewAnimationFrames,
+				     string animationFilename)
   {
     FUNCNAME("VtkWriter::updateAnimationFile()");
 
@@ -125,14 +128,14 @@ namespace AMDiS {
 
     boost::iostreams::filtering_ostream file;
     {
-      std::ofstream swapfile(animationFilename.c_str(), 
-			     std::ios::out | std::ios::trunc);
+      ofstream swapfile(animationFilename.c_str(), 
+			     ios::out | ios::trunc);
       TEST_EXIT(swapfile.is_open())
 	("Cannot open file %s for writing!\n", animationFilename.c_str());
       swapfile.close();
     }
     file.push(boost::iostreams::file_descriptor_sink(animationFilename, 
-						     std::ios::trunc)); 
+						     ios::trunc)); 
 
     file << "<?xml version=\"1.0\"?>\n";
     file << "<VTKFile type=\"Collection\" version=\"0.1\" >"  << "\n";
@@ -152,23 +155,23 @@ namespace AMDiS {
 
 
   void VtkWriter::writeFile(DOFVector<double> *values, 
-			    std::string filename,
+			    string filename,
 			    bool writeParallel)
   {
     FUNCNAME("VtkWriter::writeFile()");
 
     DataCollector<> dc(values->getFeSpace(), values);
-    std::vector<DataCollector<>*> dcList(0);
+    vector<DataCollector<>*> dcList(0);
     dcList.push_back(&dc);
     writeFile(dcList, filename, writeParallel);
   }
 
 
-  void VtkWriter::writeFile(std::vector<DOFVector<double>* > &values,
-			    std::string filename,
+  void VtkWriter::writeFile(vector<DOFVector<double>* > &values,
+			    string filename,
 			    bool writeParallel)
   {
-    std::vector<DataCollector<>*> dcList(0);
+    vector<DataCollector<>*> dcList(0);
     for (unsigned int i = 0; i < values.size(); i++)
       dcList.push_back(new DataCollector<>(values[i]->getFeSpace(), values[i]));	
     writeFile(dcList, filename, writeParallel);
@@ -178,10 +181,10 @@ namespace AMDiS {
 
 
   void VtkWriter::writeFile(WorldVector<DOFVector<double>* > &values,
-			    std::string filename,
+			    string filename,
 			    bool writeParallel)
   {
-    std::vector<DataCollector<>*> dcList(0);
+    vector<DataCollector<>*> dcList(0);
     for (int i = 0; i < values.getSize(); i++)
       dcList.push_back(new DataCollector<>(values[i]->getFeSpace(), values[i]));	
     writeFile(dcList, filename, writeParallel);
@@ -191,7 +194,7 @@ namespace AMDiS {
 
 
   void VtkWriter::writeFile(DOFVector<WorldVector<double> > *values,
-			    std::string filename,
+			    string filename,
 			    bool writeParallel)
   {
     WorldVector<DOFVector<double>*> valuesWV;
@@ -205,10 +208,10 @@ namespace AMDiS {
 
   
   void VtkWriter::writeFile(SystemVector *values, 
-			    std::string filename,
+			    string filename,
 			    bool writeParallel)
   {
-    std::vector<DataCollector<>*> dcList(0);
+    vector<DataCollector<>*> dcList(0);
     for (int i = 0; i < values->getSize(); i++)
       dcList.push_back(new DataCollector<>(values->getDOFVector(i)->getFeSpace(), 
 					 values->getDOFVector(i)));    
@@ -218,8 +221,8 @@ namespace AMDiS {
   }
   
   
-  void VtkWriter::writeFile(std::vector<DataCollector<>*> &dcList,
-			    std::string filename,
+  void VtkWriter::writeFile(vector<DataCollector<>*> &dcList,
+			    string filename,
 			    bool writeParallel)
   {
     VtkWriter writer(&dcList);
@@ -230,12 +233,15 @@ namespace AMDiS {
       
       int sPos = filename.find(".vtu");
       TEST_EXIT(sPos >= 0)("Failed to find file postfix!\n");
-      std::string name = filename.substr(0, sPos);
+      string name = filename.substr(0, sPos);
       
       if (MPI::COMM_WORLD.Get_rank() == 0)
-	writer.writeParallelFile(name + ".pvtu", MPI::COMM_WORLD.Get_size(), name, ".vtu");    
+	writer.writeParallelFile(name + ".pvtu", 
+				 MPI::COMM_WORLD.Get_size(), 
+				 name, ".vtu",
+				 static_cast<int>(dcList.size()));    
       
-      filename = name + "-p" + lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank()) + "-.vtu";
+      filename = name + "-p" + lexical_cast<string>(MPI::COMM_WORLD.Get_rank()) + "-.vtu";
     }
 #endif
     writer.writeFile(filename);

AMDiS/src/io/VtkWriter.h

@@ -36,10 +36,12 @@
 
 namespace AMDiS {
 
+  using namespace std;
+
   class VtkWriter
   {
   public:
-    VtkWriter(std::vector<DataCollector<>*> *dc)
+    VtkWriter(vector<DataCollector<>*> *dc)
       : dataCollector(dc),
 	compress(NONE)
     {
@@ -48,51 +50,52 @@ namespace AMDiS {
     }  
 
     /// Writes a ParaView-VTK file.
-    int writeFile(std::string name);
+    int writeFile(string name);
 
     /// Writes a pvtu file, which contains the links to all the rank files.
-    void writeParallelFile(std::string name, int nRanks,
-			   std::string fnPrefix, std::string fnPostfix);
+    static void writeParallelFile(string name, int nRanks,
+				  string fnPrefix, string fnPostfix,
+				  int nComponents);
 
     /// May be used to simply write ParaView files.
     static void writeFile(DOFVector<double> *values, 
-			  std::string filename, 
+			  string filename, 
 			  bool writeParallel = true);
 
     /// May be used to simply write ParaView files.
     static void writeFile(DOFVector<double> &values, 
-			  std::string filename,
+			  string filename,
 			  bool writeParallel = true)
     {
       writeFile(&values, filename, writeParallel);
     }
 
     /// May be used to simply write ParaView files with a list of values.
-    static void writeFile(std::vector<DOFVector<double>*> &values,
-			  std::string filename, 
+    static void writeFile(vector<DOFVector<double>*> &values,
+			  string filename, 
 			  bool writeParallel = true);
 
     static void writeFile(WorldVector<DOFVector<double>*> &values,
-			  std::string filename, 
+			  string filename, 
 			  bool writeParallel = true);