From 13ed7ef9f72e7e515667eeee87b31c70c7b14de1 Mon Sep 17 00:00:00 2001
From: Thomas Witkowski <thomas.witkowski@gmx.de>
Date: Wed, 23 Sep 2009 07:34:59 +0000
Subject: [PATCH] Parallel paraview output.
---
AMDiS/src/FileWriter.cc | 85 +++++++++++++++++++++++++----------------
AMDiS/src/FileWriter.h | 23 ++++-------
AMDiS/src/VtkWriter.cc | 46 ++++++++++++++++++++++
AMDiS/src/VtkWriter.h | 4 ++
AMDiS/src/VtkWriter.hh | 17 +--------
5 files changed, 112 insertions(+), 63 deletions(-)
diff --git a/AMDiS/src/FileWriter.cc b/AMDiS/src/FileWriter.cc
index 9b70019e..12f21ce8 100644
--- a/AMDiS/src/FileWriter.cc
+++ b/AMDiS/src/FileWriter.cc
@@ -29,8 +29,8 @@ namespace AMDiS {
feSpace = vec->getFESpace();
- solutionVecs_.resize(1);
- solutionVecs_[0] = vec;
+ solutionVecs.resize(1);
+ solutionVecs[0] = vec;
}
@@ -49,7 +49,7 @@ namespace AMDiS {
("All FESpace have to be equal!\n");
feSpace = vecs[0]->getFESpace();
- solutionVecs_ = vecs;
+ solutionVecs = vecs;
}
@@ -64,21 +64,18 @@ namespace AMDiS {
initialize();
// Create the temporal DOFVectors for all components of WorldVector.
- nTmpSolutions_ = (*vec)[0].getSize();
- solutionVecs_.resize(nTmpSolutions_);
- for (int i = 0; i < nTmpSolutions_; i++) {
- solutionVecs_[i] = new DOFVector<double>(vec->getFESpace(), "");
- }
+ nTmpSolutions = (*vec)[0].getSize();
+ solutionVecs.resize(nTmpSolutions);
+ for (int i = 0; i < nTmpSolutions; i++)
+ solutionVecs[i] = new DOFVector<double>(vec->getFESpace(), "");
// Copy the components of the WorldVectors to different DOFVectors
// of double values.
DOFVector< WorldVector<double> >::Iterator it(vec, USED_DOFS);
int counter = 0;
- for (it.reset(); !it.end(); ++it, counter++) {
- for (int i = 0; i < nTmpSolutions_; i++) {
- (*solutionVecs_[i])[counter] = (*it)[i];
- }
- }
+ for (it.reset(); !it.end(); ++it, counter++)
+ for (int i = 0; i < nTmpSolutions; i++)
+ (*solutionVecs[i])[counter] = (*it)[i];
feSpace = vec->getFESpace();
}
@@ -88,9 +85,9 @@ namespace AMDiS {
{
// Do not forget to delete temporal solution vector, if there have been
// some created in the constructor.
- if (nTmpSolutions_ > 0)
- for (int i = 0; i < nTmpSolutions_; i++)
- delete solutionVecs_[i];
+ if (nTmpSolutions > 0)
+ for (int i = 0; i < nTmpSolutions; i++)
+ delete solutionVecs[i];
}
@@ -99,7 +96,8 @@ namespace AMDiS {
tecplotExt = ".tec";
amdisMeshExt = ".mesh";
amdisDataExt = ".dat";
- paraViewFileExt = ".vtu";
+ paraviewFileExt = ".vtu";
+ paraviewParallelFileExt = ".pvtu";
periodicFileExt = ".per";
writeTecPlotFormat = 0;
writeAMDiSFormat = 0;
@@ -112,8 +110,8 @@ namespace AMDiS {
indexLength = 5;
indexDecimals = 3;
tsModulo = 1;
- nTmpSolutions_ = 0;
- paraViewAnimationFrames_.resize(0),
+ nTmpSolutions = 0;
+ paraviewAnimationFrames.resize(0),
compression = NONE;
readParameters();
@@ -131,7 +129,7 @@ namespace AMDiS {
GET_PARAMETER(0, name + "->AMDiS data ext", &amdisDataExt);
GET_PARAMETER(0, name + "->ParaView format", "%d", &writeParaViewFormat);
GET_PARAMETER(0, name + "->ParaView animation", "%d", &writeParaViewAnimation);
- GET_PARAMETER(0, name + "->ParaView ext", ¶ViewFileExt);
+ GET_PARAMETER(0, name + "->ParaView ext", ¶viewFileExt);
GET_PARAMETER(0, name + "->Periodic format", "%d", &writePeriodicFormat);
GET_PARAMETER(0, name + "->Periodic ext", &periodicFileExt);
GET_PARAMETER(0, name + "->PNG format", "%d", &writePngFormat);
@@ -162,15 +160,15 @@ namespace AMDiS {
return;
// Containers, which store the data to be written;
- std::vector< DataCollector* > dataCollectors(solutionVecs_.size());
+ std::vector< DataCollector* > dataCollectors(solutionVecs.size());
if (writeElem) {
for (int i = 0; i < static_cast<int>(dataCollectors.size()); i++)
- dataCollectors[i] = new DataCollector(feSpace, solutionVecs_[i],
+ dataCollectors[i] = new DataCollector(feSpace, solutionVecs[i],
level, flag, writeElem);
} else {
for (int i = 0; i < static_cast<int>(dataCollectors.size()); i++)
- dataCollectors[i] = new DataCollector(feSpace, solutionVecs_[i],
+ dataCollectors[i] = new DataCollector(feSpace, solutionVecs[i],
traverseLevel,
flag | traverseFlag,
writeElement);
@@ -179,7 +177,9 @@ namespace AMDiS {
std::string fn = filename;
#if HAVE_PARALLEL_DOMAIN_AMDIS
- char f[10];
+ std::string paraFilename = fn;
+ std::string postfix = "";
+ char f[15];
sprintf(f, "-p%d-", MPI::COMM_WORLD.Get_rank());
fn += f;
#endif
@@ -196,12 +196,17 @@ namespace AMDiS {
sprintf(timeStr, formatStr, adaptInfo ? adaptInfo->getTime() : 0.0);
fn += timeStr;
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+ paraFilename += timeStr;
+ postfix += timeStr;
+ postfix += paraviewFileExt;
+#endif
}
if (writeTecPlotFormat) {
- TecPlotWriter<DOFVector<double> >::writeValues(solutionVecs_[0],
+ TecPlotWriter<DOFVector<double> >::writeValues(solutionVecs[0],
const_cast<char*>((fn + tecplotExt).c_str()),
- solutionVecs_[0]->getName().c_str());
+ solutionVecs[0]->getName().c_str());
MSG("TecPlot file written to %s\n", (fn + tecplotExt).c_str());
}
@@ -229,16 +234,33 @@ namespace AMDiS {
if (writeParaViewFormat) {
VtkWriter vtkWriter(&dataCollectors);
vtkWriter.setCompression(compression);
- vtkWriter.writeFile(fn + paraViewFileExt);
+ vtkWriter.writeFile(fn + paraviewFileExt);
+
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+ if (MPI::COMM_WORLD.Get_rank() == 0)
+ vtkWriter.writeParallelFile(paraFilename + paraviewParallelFileExt,
+ MPI::COMM_WORLD.Get_size(),
+ filename, postfix);
+#endif
- MSG("ParaView file written to %s\n", (fn + paraViewFileExt).c_str());
+ MSG("ParaView file written to %s\n", (fn + paraviewFileExt).c_str());
}
if (writeParaViewAnimation) {
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+ if (MPI::COMM_WORLD.Get_rank() == 0) {
+ VtkWriter vtkWriter(&dataCollectors);
+ vtkWriter.updateAnimationFile(paraFilename + paraviewParallelFileExt,
+ ¶viewAnimationFrames,
+ filename + ".pvd");
+
+ }
+#else
VtkWriter vtkWriter(&dataCollectors);
- vtkWriter.updateAnimationFile(fn + paraViewFileExt,
- ¶ViewAnimationFrames_,
+ vtkWriter.updateAnimationFile(fn + paraviewFileExt,
+ ¶viewAnimationFrames,
filename + ".pvd");
+#endif
}
if (writePngFormat) {
@@ -249,9 +271,8 @@ namespace AMDiS {
}
- for (int i = 0; i < static_cast<int>(dataCollectors.size()); i++) {
+ for (int i = 0; i < static_cast<int>(dataCollectors.size()); i++)
delete dataCollectors[i];
- }
}
}
diff --git a/AMDiS/src/FileWriter.h b/AMDiS/src/FileWriter.h
index 216d3bd1..e7397bb4 100644
--- a/AMDiS/src/FileWriter.h
+++ b/AMDiS/src/FileWriter.h
@@ -28,22 +28,12 @@
#include <vector>
#include <string>
-#include "MatrixVector.h"
+#include "AMDiS_fwd.h"
#include "Mesh.h"
#include "DataCollector.h"
namespace AMDiS {
- class ProblemScal;
- class ProblemInstat;
- class Mesh;
- class SystemVector;
- class FiniteElemSpace;
- class AdaptInfo;
-
- template<typename T> class DOFVector;
-
-
typedef enum {
NONE = 0,
GZIP = 1,
@@ -158,7 +148,10 @@ namespace AMDiS {
std::string amdisDataExt;
/// VTK file extension.
- std::string paraViewFileExt;
+ std::string paraviewFileExt;
+
+ /// Parallel VTK file extension.
+ std::string paraviewParallelFileExt;
/// Periodic file extension.
std::string periodicFileExt;
@@ -200,7 +193,7 @@ namespace AMDiS {
int tsModulo;
/// Stores all writen filename to a ParaView animation file.
- std::vector< std::string > paraViewAnimationFrames_;
+ std::vector< std::string > paraviewAnimationFrames;
///
int timestepNumber;
@@ -212,14 +205,14 @@ namespace AMDiS {
const FiniteElemSpace *feSpace;
/// Pointers to the vectors which store the solution.
- std::vector< DOFVector<double>* > solutionVecs_;
+ std::vector< DOFVector<double>* > solutionVecs;
/** \brief
* Stores the number of temporal solutions vectors, which have been created
* in the constructor. If this number is greater than zero, the vectors
* stored in solutionVecs_ must be deleted in the destructor.
*/
- int nTmpSolutions_;
+ int nTmpSolutions;
/** \brief
* Defines if, and with what kind of compression, the file should be compressed
diff --git a/AMDiS/src/VtkWriter.cc b/AMDiS/src/VtkWriter.cc
index 98fa9b78..0230281f 100644
--- a/AMDiS/src/VtkWriter.cc
+++ b/AMDiS/src/VtkWriter.cc
@@ -1,8 +1,11 @@
#include <stdio.h>
#include <string>
#include <fstream>
+#include <sstream>
#include <cmath>
+#include "boost/filesystem.hpp"
+
#include "VtkWriter.h"
#include "DataCollector.h"
#include "DOFVector.h"
@@ -44,6 +47,49 @@ namespace AMDiS {
return 0;
}
+
+ void VtkWriter::writeParallelFile(std::string name, int nRanks,
+ std::string fnPrefix, std::string fnPostfix)
+ {
+ std::ofstream file;
+ file.open(name.c_str());
+
+ file << "<?xml version=\"1.0\"?>\n";
+ file << "<VTKFile type=\"PUnstructuredGrid\">\n";
+ file << " <PUnstructuredGrid GhostLevel=\"0\">\n";
+ file << " <PPoints>\n"
+ << " <PDataArray type=\"Float32\" NumberOfComponents=\"3\" format=\"ascii\"/>\n"
+ << " </PPoints>\n";
+ file << " <PCells>\n"
+ << " <PDataArray type=\"Int32\" Name=\"offsets\"/>\n"
+ << " <PDataArray type=\"UInt8\" Name=\"types\"/>\n"
+ << " <PDataArray type=\"Int32\" Name=\"connectivity\"/>\n"
+ << " </PCells>\n";
+ file << " <PPointData>\n";
+
+ for (int i = 0; i < static_cast<int>(dataCollector->size()); i++)
+ file << " <PDataArray type=\"Float32\" Name=\"value"
+ << i << "\" format=\"ascii\"/>\n";
+
+ file << " </PPointData>\n";
+
+ for (int i = 0; i < nRanks; i++) {
+ std::stringstream oss;
+ oss << fnPrefix << "-p" << i << "-" << fnPostfix;
+ boost::filesystem::path filepath(oss.str());
+ file << " <Piece Source=\""
+ << boost::filesystem::basename(filepath)
+ << boost::filesystem::extension(filepath) << "\"/>\n";
+
+ }
+
+ file << " </PUnstructuredGrid>\n";
+ file << "</VTKFile>\n";
+
+ file.close();
+ }
+
+
int VtkWriter::updateAnimationFile(std::string valueFilename,
std::vector< std::string > *paraViewAnimationFrames,
std::string animationFilename)
diff --git a/AMDiS/src/VtkWriter.h b/AMDiS/src/VtkWriter.h
index 807ad64d..3bb807b3 100644
--- a/AMDiS/src/VtkWriter.h
+++ b/AMDiS/src/VtkWriter.h
@@ -50,6 +50,10 @@ namespace AMDiS {
/// Writes a ParaView-VTK file.
int writeFile(std::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);
+
/// May be used to simply write ParaView files.
static void writeFile(DOFVector<double> *values, std::string filename);
diff --git a/AMDiS/src/VtkWriter.hh b/AMDiS/src/VtkWriter.hh
index 012ebbbe..ff0045fd 100644
--- a/AMDiS/src/VtkWriter.hh
+++ b/AMDiS/src/VtkWriter.hh
@@ -36,9 +36,8 @@ namespace AMDiS {
file << " <Cells>\n";
file << " <DataArray type=\"Int32\" Name=\"offsets\">\n";
- for (int i = 0; i < nElements; i++) {
+ for (int i = 0; i < nElements; i++)
file << " " << (i + 1) * vertices << "\n";
- }
file << " </DataArray>\n";
file << " <DataArray type=\"UInt8\" Name=\"types\">\n";
@@ -119,24 +118,10 @@ namespace AMDiS {
template<typename T>
void VtkWriter::writeVertexValues(T &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);
--
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