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Commit 340fd949 authored by Thomas Witkowski's avatar Thomas Witkowski
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Fixed ElementFileWriter to work in parallel.

parent 859d3918
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AMDiS/src/Debug.cc
View file @ 340fd949
......@@ -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
View file @ 340fd949
......@@ -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
View file @ 340fd949
......@@ -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
View file @ 340fd949
......@@ -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
View file @ 340fd949
......@@ -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
View file @ 340fd949
......@@ -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);
static void writeFile(DOFVector<WorldVector<double> > *values,
std::string filename,
string filename,
bool writeParallel = true);
static void writeFile(DOFVector<WorldVector<double> > &values,
std::string filename,
string filename,
bool writeParallel = true)
{
writeFile(&values, filename, writeParallel);
}
static void writeFile(SystemVector *values,
std::string filename,
string filename,
bool writeParallel = true);
static void writeFile(std::vector<DataCollector<>*> &dcList,
std::string filename,
static void writeFile(vector<DataCollector<>*> &dcList,
string filename,
bool writeParallel = true);
/// Set a compressing method for file output.
......@@ -103,15 +106,16 @@ namespace AMDiS {
/// Adds a new entry to a ParaView animation file.
static int 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);
protected:
/// Writes the VTK file to an arbitrary stream.
template<typename T>
void writeFileToStream(T &file);
/// Writes all coordinates of vertices and interpolation points to an output file.
/// Writes all coordinates of vertices and interpolation points to an
/// output file.
template<typename T>
void writeVertexCoords(T &file);
......@@ -123,15 +127,18 @@ namespace AMDiS {
template<typename T>
void writeConnectivity(T &file);
/// Writes the connectivity for the case dim = 2 and degree = 2 to an output file.
/// Writes the connectivity for the case dim = 2 and degree = 2 to an
/// output file.
template<typename T>
void writeConnectivity_dim2_degree2(T &file);
/// Writes the connectivity for the case dim = 2 and degree = 3 to an output file.
/// Writes the connectivity for the case dim = 2 and degree = 3 to an
/// output file.
template<typename T>
void writeConnectivity_dim2_degree3(T &file);
/// Writes the connectivity for the case dim = 2 and degree = 4 to an output file.
/// Writes the connectivity for the case dim = 2 and degree = 4 to an
/// output file.
template<typename T>
void writeConnectivity_dim2_degree4(T &file);
......@@ -140,7 +147,7 @@ namespace AMDiS {
WorldVector<double> coord)
{
for (int i = 0; i < Global::getGeo(WORLD); i++)
file << " " << std::scientific << coord[i];
file << " " << scientific << coord[i];
for (int i = Global::getGeo(WORLD); i < 3; i++)
file << " "<<0.0;
......@@ -148,10 +155,10 @@ namespace AMDiS {
}
/// Writes a world coordinate to a given file.
inline void writeCoord(std::ofstream &file, WorldVector<double> coord)
inline void writeCoord(ofstream &file, WorldVector<double> coord)
{
for (int i = 0; i < Global::getGeo(WORLD); i++)
file << " " << std::scientific << coord[i];
file << " " << scientific << coord[i];
for (int i = Global::getGeo(WORLD); i < 3; i++)
file << " "<<0.0;
......@@ -160,12 +167,10 @@ namespace AMDiS {
private:
/// List of DataCollectors, for each component of the problem one.
std::vector<DataCollector<>*> *dataCollector;
vector<DataCollector<>*> *dataCollector;
/** \brief
* Defines if the file has to be compressed for ouput, and with which
* kind of compress method.
*/
/// Defines if the file has to be compressed for ouput, and with which
/// kind of compress method.
FileCompression compress;
/// Degree of the basis function of the problem.
......
AMDiS/src/parallel/MeshDistributor.cc
View file @ 340fd949
......@@ -132,8 +132,6 @@ namespace AMDiS {
{
FUNCNAME("MeshDistributor::initParallelization()");
MSG("RUN INIT\n");
if (initialized)
return;
......
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