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Commit a89a23f4 authored by Thomas Witkowski's avatar Thomas Witkowski
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* Compressing file output using boost

parent 5d144c00
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Showing with 101 additions and 388 deletions
AMDiS/src/FileWriter.cc
View file @ a89a23f4
......@@ -127,6 +127,7 @@ namespace AMDiS {
writingIsDelayed_ = false;
delayedFilename_ = "";
paraViewAnimationFrames_.resize(0);
compression = NONE;
readParameters();
}
......@@ -152,9 +153,16 @@ namespace AMDiS {
GET_PARAMETER(0, name + "->write every i-th timestep", "%d", &tsModulo);
GET_PARAMETER(0, name + "->delay", "%d", &delayWriting_);
std::string compressionStr = "";
GET_PARAMETER(0, name + "->compression", &compressionStr);
if ((compressionStr == "gzip") || (compressionStr == "gz")) {
compression = GZIP;
} else if ((compressionStr == "bzip2") || (compressionStr == "bz2")) {
compression = BZIP2;
}
TEST_EXIT(!delayWriting_ || amdisHaveOpenMP)
("Delayed writing only possible with OpenMP support!\n");
}
void FileWriter::writeFiles(AdaptInfo *adaptInfo,
......@@ -248,7 +256,8 @@ namespace AMDiS {
if (writeParaViewFormat) {
VtkWriter vtkWriter(&dataCollectors_);
vtkWriter.writeFile(const_cast<char*>((fn + paraViewFileExt).c_str()));
vtkWriter.setCompression(compression);
vtkWriter.writeFile(const_cast<char*>((fn + paraViewFileExt).c_str()));
MSG("ParaView file written to %s\n", (fn + paraViewFileExt).c_str());
}
......
AMDiS/src/FileWriter.h
View file @ a89a23f4
......@@ -44,6 +44,13 @@ namespace AMDiS {
template<typename T> class DOFVector;
typedef enum {
NONE = 0,
GZIP = 1,
BZIP2 = 2
} FileCompression;
// ============================================================================
// ===== class FileWriterInterface ============================================
// ============================================================================
......@@ -311,6 +318,12 @@ namespace AMDiS {
* Here the filename for the file, which should be written to the next, is stored.
*/
std::string delayedFilename_;
/** \brief
* Defines if, and with what kind of compression, the file should be compressed
* during writing.
*/
FileCompression compression;
};
}
......
AMDiS/src/VtkWriter.cc
View file @ a89a23f4
......@@ -13,373 +13,34 @@ namespace AMDiS {
int VtkWriter::writeFile(const char *name)
{
int nVertices = (*dataCollector)[0]->getNumberVertices();
int nElements = (*dataCollector)[0]->getNumberElements();
int vertices = (*dataCollector)[0]->getMesh()->getGeo(VERTEX);
if ((dim == 2) && (degree == 2)) {
nVertices += (*dataCollector)[0]->getNumberInterpPoints();
nElements *= 4;
} else if ((dim == 2) && (degree == 3)) {
nVertices += (*dataCollector)[0]->getNumberInterpPoints();
nElements *= 9;
} else if ((dim == 2) && (degree == 4)) {
nVertices += (*dataCollector)[0]->getNumberInterpPoints();
nElements *= 16;
}
#ifdef HAVE_BOOST
boost::iostreams::filtering_ostream file;
switch (compress) {
case GZIP:
file.push(boost::iostreams::gzip_compressor());
file.push(boost::iostreams::file_descriptor_sink(strcat((char*)name, ".gz")));
break;
case BZIP2:
file.push(boost::iostreams::bzip2_compressor());
file.push(boost::iostreams::file_descriptor_sink(strcat((char*)name, ".bz2")));
break;
default:
file.push(boost::iostreams::file_descriptor_sink(name));
break;
}
writeFile(file);
#else
std::ofstream file;
file.open(name);
file << "<?xml version=\"1.0\"?>\n";
file << "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n";
file << " <UnstructuredGrid>\n";
file << " <Piece NumberOfPoints=\"" << nVertices
<< "\" NumberOfCells=\"" << nElements << "\">\n";
file << " <Points>\n";
file << " <DataArray type=\"Float32\" NumberOfComponents=\"3\" format=\"ascii\">\n";
writeVertexCoords(file);
file << " </DataArray>\n";
file << " </Points>\n";
file << " <Cells>\n";
file << " <DataArray type=\"Int32\" Name=\"offsets\">\n";
for (int i = 0; i < nElements; i++) {
file << " " << (i + 1) * vertices << "\n";
}
file << " </DataArray>\n";
file << " <DataArray type=\"UInt8\" Name=\"types\">\n";
for (int i = 0; i < nElements; i++) {
switch (vertices) {
case 2:
file << " 3\n";
break;
case 3:
file << " 5\n";
break;
case 4:
file << " 10\n";
break;
default:
break;
}
}
file << " </DataArray>\n";
file << " <DataArray type=\"Int32\" Name=\"connectivity\">\n";
writeConnectivity(file);
file << " </DataArray>\n";
file << " </Cells>\n";
file << " <PointData>\n";
for (int i = 0; i < static_cast<int>(dataCollector->size()); i++) {
file << " <DataArray type=\"Float32\" Name=\"value" << i
<< "\" format=\"ascii\">\n";
writeVertexValues(file, i);
file << " </DataArray>\n";
}
file << " </PointData>\n";
file << " </Piece>\n";
file << " </UnstructuredGrid>\n";
file << "</VTKFile>\n";
writeFile(file);
file.close();
return 0;
}
void VtkWriter::writeVertexCoords(std::ofstream &file)
{
DOFVector< std::list<VertexInfo> > *vertexInfos = (*dataCollector)[0]->getVertexInfos();
DOFVector< std::list<VertexInfo> >::Iterator it(vertexInfos, USED_DOFS);
int counter = 0;
// For all DOFs of vertices, write the coordinates.
for (it.reset(); !it.end(); ++it) {
// for all vertex infos of this DOF
std::list<VertexInfo>::iterator it2;
for (it2 = it->begin(); it2 != it->end(); ++it2) {
it2->outputIndex = counter++;
writeCoord(file, it2->coords);
}
}
// For the second dim case, write also the interpolation points.
if ((dim == 2) && (degree > 1)) {
DOFVector< std::list< WorldVector<double> > > *interpPointCoords = (*dataCollector)[0]->getInterpPointCoords();
DOFVector< std::list< WorldVector<double> > >::Iterator pointIt(interpPointCoords, USED_DOFS);
for (pointIt.reset(); !pointIt.end(); ++pointIt) {
std::list< WorldVector<double> >::iterator it2;
for (it2 = pointIt->begin(); it2 != pointIt->end(); ++it2) {
writeCoord(file, *it2);
}
}
}
}
void VtkWriter::writeVertexValues(std::ofstream &file, int componentNo)
{
// DOFVector<int> *interpPointInd;
// DOFVector<double> *values;
// DOFVector< std::list<WorldVector<double> > > *dofCoords;
DOFVector<int> *interpPointInd = (*dataCollector)[componentNo]->getInterpPointInd();
DOFVector<double> *values = (*dataCollector)[componentNo]->getValues();
DOFVector< std::list<WorldVector<double> > > *dofCoords = (*dataCollector)[componentNo]->getDofCoords();
/*
#ifdef _OPENMP
#pragma omp critical
#endif
{
interpPointInd = (*dataCollector)[componentNo]->getInterpPointInd();
values = (*dataCollector)[componentNo]->getValues();
dofCoords = (*dataCollector)[componentNo]->getDofCoords();
}
*/
DOFVector<int>::Iterator intPointIt(interpPointInd, USED_DOFS);
DOFVector<double>::Iterator valueIt(values, USED_DOFS);
DOFVector< std::list<WorldVector<double> > >::Iterator coordIt(dofCoords, USED_DOFS);
// Write the values for all vertex DOFs.
for (intPointIt.reset(), valueIt.reset(), coordIt.reset();
!intPointIt.end();
++intPointIt, ++valueIt, ++coordIt) {
if (*intPointIt == -2) {
for (int i = 0; i < static_cast<int>(coordIt->size()); i++) {
file << " " << (fabs(*valueIt) < 1e-40 ? 0.0 : *valueIt) << "\n";
}
}
}
// For the second dim case, write also the values of the interpolation points.
if ((dim == 2) && (degree > 1)) {
DOFVector< std::list<WorldVector<double> > >::Iterator
interpCoordIt((*dataCollector)[componentNo]->getInterpPointCoords(), USED_DOFS);
for (intPointIt.reset(), valueIt.reset(), interpCoordIt.reset();
!intPointIt.end();
++intPointIt, ++valueIt, ++interpCoordIt) {
if (*intPointIt >= 0) {
for (int i = 0; i < static_cast<int>(interpCoordIt->size()); i++) {
file << " " << (fabs(*valueIt) < 1e-40 ? 0.0 : *valueIt) << "\n";
}
}
}
}
}
void VtkWriter::writeConnectivity(std::ofstream &file)
{
// For the second dim case, and if higher order Lagrange elements are used,
// write the connectivity by extra functions.
if ((dim == 2) && (degree == 2)) {
writeConnectivity_dim2_degree2(file);
} else if ((dim == 2) && (degree == 3)) {
writeConnectivity_dim2_degree3(file);
} else if ((dim == 2) && (degree == 4)) {
writeConnectivity_dim2_degree4(file);
} else {
std::list<ElementInfo> *elements = (*dataCollector)[0]->getElementInfos();
std::list<ElementInfo>::iterator elementIt;
int vertices = (*dataCollector)[0]->getMesh()->getGeo(VERTEX);
for (elementIt = elements->begin(); elementIt != elements->end(); ++elementIt) {
// for all vertices
for (int i = 0; i < vertices; i++) {
file << " " << elementIt->vertexInfo[i]->outputIndex;
}
file << "\n";
}
}
}
void VtkWriter::writeConnectivity_dim2_degree2(std::ofstream &file)
{
std::list<ElementInfo> *elements = (*dataCollector)[0]->getElementInfos();
std::list<ElementInfo>::iterator elementIt;
std::vector< std::vector<int> > *interpPoints = (*dataCollector)[0]->getInterpPoints();
std::vector< std::vector<int> >::iterator pointIt;
int nVertices = (*dataCollector)[0]->getNumberVertices();
for (pointIt = interpPoints->begin(), elementIt = elements->begin();
pointIt != interpPoints->end();
++pointIt, ++elementIt) {
file << " " << elementIt->vertexInfo[0]->outputIndex
<< " " << (*pointIt)[1] + nVertices
<< " " << (*pointIt)[2] + nVertices << "\n";
file << " " << elementIt->vertexInfo[2]->outputIndex
<< " " << (*pointIt)[0] + nVertices
<< " " << (*pointIt)[1] + nVertices << "\n";
file << " " << elementIt->vertexInfo[1]->outputIndex
<< " " << (*pointIt)[0] + nVertices
<< " " << (*pointIt)[2] + nVertices << "\n";
file << " " << (*pointIt)[0] + nVertices
<< " " << (*pointIt)[1] + nVertices
<< " " << (*pointIt)[2] + nVertices << "\n";
}
}
void VtkWriter::writeConnectivity_dim2_degree3(std::ofstream &file)
{
std::list<ElementInfo> *elements = (*dataCollector)[0]->getElementInfos();
std::list<ElementInfo>::iterator elementIt;
std::vector< std::vector<int> > *interpPoints = (*dataCollector)[0]->getInterpPoints();
std::vector< std::vector<int> >::iterator pointIt;
int nVertices = (*dataCollector)[0]->getNumberVertices();
for (pointIt = interpPoints->begin(), elementIt = elements->begin();
pointIt != interpPoints->end();
++pointIt, ++elementIt) {
file << " " << elementIt->vertexInfo[0]->outputIndex
<< " " << (*pointIt)[3] + nVertices
<< " " << (*pointIt)[4] + nVertices << "\n";
file << " " << (*pointIt)[4] + nVertices
<< " " << (*pointIt)[5] + nVertices
<< " " << (*pointIt)[6] + nVertices << "\n";
file << " " << (*pointIt)[3] + nVertices
<< " " << (*pointIt)[4] + nVertices
<< " " << (*pointIt)[6] + nVertices << "\n";
file << " " << (*pointIt)[2] + nVertices
<< " " << (*pointIt)[3] + nVertices
<< " " << (*pointIt)[6] + nVertices << "\n";
file << " " << elementIt->vertexInfo[1]->outputIndex
<< " " << (*pointIt)[0] + nVertices
<< " " << (*pointIt)[5] + nVertices << "\n";
file << " " << (*pointIt)[0] + nVertices
<< " " << (*pointIt)[6] + nVertices
<< " " << (*pointIt)[5] + nVertices << "\n";
file << " " << (*pointIt)[0] + nVertices
<< " " << (*pointIt)[1] + nVertices
<< " " << (*pointIt)[6] + nVertices << "\n";
file << " " << (*pointIt)[1] + nVertices
<< " " << (*pointIt)[2] + nVertices
<< " " << (*pointIt)[6] + nVertices << "\n";
file << " " << elementIt->vertexInfo[2]->outputIndex
<< " " << (*pointIt)[1] + nVertices
<< " " << (*pointIt)[2] + nVertices << "\n";
}
}
void VtkWriter::writeConnectivity_dim2_degree4(std::ofstream &file)
{
std::list<ElementInfo> *elements = (*dataCollector)[0]->getElementInfos();
std::list<ElementInfo>::iterator elementIt;
std::vector< std::vector<int> > *interpPoints = (*dataCollector)[0]->getInterpPoints();
std::vector< std::vector<int> >::iterator pointIt;
int nVertices = (*dataCollector)[0]->getNumberVertices();
for (pointIt = interpPoints->begin(), elementIt = elements->begin();
pointIt != interpPoints->end();
++pointIt, ++elementIt) {
file << " " << elementIt->vertexInfo[0]->outputIndex
<< " " << (*pointIt)[5] + nVertices
<< " " << (*pointIt)[6] + nVertices << "\n";
file << " " << (*pointIt)[5] + nVertices
<< " " << (*pointIt)[9] + nVertices
<< " " << (*pointIt)[6] + nVertices << "\n";
file << " " << (*pointIt)[6] + nVertices
<< " " << (*pointIt)[7] + nVertices
<< " " << (*pointIt)[9] + nVertices << "\n";
file << " " << (*pointIt)[7] + nVertices
<< " " << (*pointIt)[9] + nVertices
<< " " << (*pointIt)[10] + nVertices << "\n";
file << " " << (*pointIt)[7] + nVertices
<< " " << (*pointIt)[8] + nVertices
<< " " << (*pointIt)[10] + nVertices << "\n";
file << " " << (*pointIt)[0] + nVertices
<< " " << (*pointIt)[8] + nVertices
<< " " << (*pointIt)[10] + nVertices << "\n";
file << " " << elementIt->vertexInfo[1]->outputIndex
<< " " << (*pointIt)[0] + nVertices
<< " " << (*pointIt)[8] + nVertices << "\n";
file << " " << (*pointIt)[4] + nVertices
<< " " << (*pointIt)[5] + nVertices
<< " " << (*pointIt)[9] + nVertices << "\n";
file << " " << (*pointIt)[4] + nVertices
<< " " << (*pointIt)[9] + nVertices
<< " " << (*pointIt)[11] + nVertices << "\n";
file << " " << (*pointIt)[9] + nVertices
<< " " << (*pointIt)[10] + nVertices
<< " " << (*pointIt)[11] + nVertices << "\n";
file << " " << (*pointIt)[1] + nVertices
<< " " << (*pointIt)[10] + nVertices
<< " " << (*pointIt)[11] + nVertices << "\n";
file << " " << (*pointIt)[0] + nVertices
<< " " << (*pointIt)[1] + nVertices
<< " " << (*pointIt)[10] + nVertices << "\n";
file << " " << (*pointIt)[3] + nVertices
<< " " << (*pointIt)[4] + nVertices
<< " " << (*pointIt)[11] + nVertices << "\n";
file << " " << (*pointIt)[2] + nVertices
<< " " << (*pointIt)[3] + nVertices
<< " " << (*pointIt)[11] + nVertices << "\n";
file << " " << (*pointIt)[1] + nVertices
<< " " << (*pointIt)[2] + nVertices
<< " " << (*pointIt)[11] + nVertices << "\n";
file << " " << elementIt->vertexInfo[2]->outputIndex
<< " " << (*pointIt)[2] + nVertices
<< " " << (*pointIt)[3] + nVertices << "\n";
}
return 0;
}
int VtkWriter::updateAnimationFile(std::string valueFilename,
......@@ -414,18 +75,4 @@ namespace AMDiS {
}
void VtkWriter::writeFile(DOFVector<double> *values,
const char *filename)
{
DataCollector *dc = NEW DataCollector(values->getFESpace(), values);
std::vector<DataCollector*> dcList(0);
dcList.push_back(dc);
VtkWriter *writer = NEW VtkWriter(&dcList);
writer->writeFile(filename);
DELETE writer;
DELETE dc;
}
}
AMDiS/src/VtkWriter.h
View file @ a89a23f4
......@@ -22,10 +22,17 @@
#ifndef AMDIS_VTKWRITER_H
#define AMDIS_VTKWRITER_H
#include <fstream>
#ifdef HAVE_BOOST
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/device/file_descriptor.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/iostreams/filter/bzip2.hpp>
#endif
#include <fstream>
#include "BasisFunction.h"
#include "DataCollector.h"
#include "FileWriter.h"
namespace AMDiS {
......@@ -33,7 +40,8 @@ namespace AMDiS {
{
public:
VtkWriter(std::vector<DataCollector*> *dc)
: dataCollector(dc)
: dataCollector(dc),
compress(NONE)
{
degree = (*dataCollector)[0]->getFeSpace()->getBasisFcts()->getDegree();
dim = (*dataCollector)[0]->getMesh()->getDim();
......@@ -45,11 +53,13 @@ namespace AMDiS {
*/
int writeFile(const char *name);
/** \brief
* May be used to simply write ParaView files.
* Set a compressing method for file output.
*/
static void writeFile(DOFVector<double> *values,
const char *filename);
void setCompression(FileCompression c) {
compress = c;
}
/** \brief
* Adds a new entry to a ParaView animation file.
......@@ -58,45 +68,71 @@ namespace AMDiS {
std::vector< std::string > *paraViewAnimationFrames,
const char *animationFilename);
protected:
/** \brief
* Writes the VTU file to an arbitrary stream.
*/
template<typename T>
void writeFile(T &file);
/** \brief
* Writes all coordinates of vertices and interpolation points to an
* output file.
*/
void writeVertexCoords(std::ofstream &file);
template<typename T>
void writeVertexCoords(T &file);
/** \brief
* Writes all values of vertices and interpolation point to an output
* file.
*/
void writeVertexValues(std::ofstream &file, int componentNo);
template<typename T>
void writeVertexValues(T &file, int componentNo);
/** \brief
* Writes the connectivity of all simplices to an output file.
*/
void writeConnectivity(std::ofstream &file);
template<typename T>
void writeConnectivity(T &file);
/** \brief
* Writes the connectivity for the case dim = 2 and degree = 2 to
* an output file.
*/
void writeConnectivity_dim2_degree2(std::ofstream &file);
template<typename T>
void writeConnectivity_dim2_degree2(T &file);
/** \brief
* Writes the connectivity for the case dim = 2 and degree = 3 to
* an output file.
*/
void writeConnectivity_dim2_degree3(std::ofstream &file);
template<typename T>
void writeConnectivity_dim2_degree3(T &file);
/** \brief
* Writes the connectivity for the case dim = 2 and degree = 4 to
* an output file.
*/
void writeConnectivity_dim2_degree4(std::ofstream &file);
template<typename T>
void writeConnectivity_dim2_degree4(T &file);
#ifdef HAVE_BOOST
/** \brief
* Writes a world coordinate to a given file.
*/
inline void writeCoord(boost::iostreams::filtering_ostream &file, WorldVector<double> coord) {
for (int i = 0; i < Global::getGeo(WORLD); i++) {
file << " " << std::scientific << coord[i];
}
for (int i = Global::getGeo(WORLD); i < 3; i++) {
file << " 0.0";
}
file << "\n";
}
#endif
/** \brief
* Writes a world coordinate to a given file.
......@@ -112,12 +148,18 @@ namespace AMDiS {
}
private:
/**
/**