From 96d0b4bc501693fdd21bcf6904c8667c7eb253ff Mon Sep 17 00:00:00 2001
From: Siqi Ling <lsq0473@gmail.com>
Date: Tue, 20 Oct 2015 11:39:09 +0000
Subject: [PATCH] change in arh, parh file. update with meshconv
---
AMDiS/src/io/Arh3Writer.h | 36 ++--
AMDiS/src/io/FileWriter.cc | 20 ++-
AMDiS/src/io/FileWriter.h | 9 +
AMDiS/src/io/FileWriter.hh | 3 +
AMDiS/src/io/detail/Arh3Reader.cc | 124 +++++++++-----
AMDiS/src/io/detail/Arh3Reader.h | 5 +-
AMDiS/src/io/detail/Arh3Writer.cc | 274 +++++++++++++++++++-----------
AMDiS/src/io/detail/Arh3Writer.h | 20 ++-
8 files changed, 330 insertions(+), 161 deletions(-)
diff --git a/AMDiS/src/io/Arh3Writer.h b/AMDiS/src/io/Arh3Writer.h
index fffe9b77..4312209b 100644
--- a/AMDiS/src/io/Arh3Writer.h
+++ b/AMDiS/src/io/Arh3Writer.h
@@ -5,6 +5,12 @@
#include "SystemVector.h"
#include "detail/Arh3Writer.h"
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+#define WRITE_MACRO false
+#else
+#define WRITE_MACRO true
+#endif
+
namespace AMDiS { namespace io {
/** \ingroup Output
@@ -45,21 +51,23 @@ namespace AMDiS { namespace io {
std::string filename,
bool writeParallel = true,
Cpsformat cps = NONE,
- std::string dataformat = "SF64")
+ std::string dataformat = "SF64",
+ bool writeMacro = WRITE_MACRO)
{
std::vector<DOFVector<double>*> vecs;
for (int i = 0; i < sysVec->getSize(); i++)
vecs.push_back(sysVec->getDOFVector(i));
- detail::write(filename, NULL, vecs, writeParallel, cps, dataformat);
+ detail::write(filename, NULL, vecs, writeParallel, cps, dataformat, writeMacro);
}
inline void writeFile(SystemVector &sysVec,
std::string filename,
bool writeParallel = true,
Cpsformat cps = NONE,
- std::string dataformat = "SF64")
+ std::string dataformat = "SF64",
+ bool writeMacro = WRITE_MACRO)
{
- writeFile(&sysVec, filename, writeParallel, cps, dataformat);
+ writeFile(&sysVec, filename, writeParallel, cps, dataformat, writeMacro);
}
/// write the meshstructure and the dof values of DOFVectors in vec0
@@ -68,11 +76,12 @@ namespace AMDiS { namespace io {
std::string filename,
bool writeParallel = true,
Cpsformat cps = NONE,
- std::string dataformat = "SF64")
+ std::string dataformat = "SF64",
+ bool writeMacro = WRITE_MACRO)
{
std::vector<DOFVector<double>*> vecs;
vecs.push_back(vec0);
- detail::write(filename, NULL, vecs, writeParallel, cps, dataformat);
+ detail::write(filename, NULL, vecs, writeParallel, cps, dataformat, writeMacro);
}
/// write the meshstructure and the dof values of DOFVectors in vec0
@@ -81,9 +90,10 @@ namespace AMDiS { namespace io {
std::string filename,
bool writeParallel = true,
Cpsformat cps = NONE,
- std::string dataformat = "SF64")
+ std::string dataformat = "SF64",
+ bool writeMacro = WRITE_MACRO)
{
- writeFile(&vec0, filename, writeParallel, cps, dataformat);
+ writeFile(&vec0, filename, writeParallel, cps, dataformat, writeMacro);
}
/// write the meshstructure and the dof values of DOFVectors in vecs
@@ -92,9 +102,10 @@ namespace AMDiS { namespace io {
std::string filename,
bool writeParallel = true,
Cpsformat cps = NONE,
- std::string dataformat = "SF64")
+ std::string dataformat = "SF64",
+ bool writeMacro = WRITE_MACRO)
{
- detail::write(filename, NULL, vecs, writeParallel, cps, dataformat);
+ detail::write(filename, NULL, vecs, writeParallel, cps, dataformat, writeMacro);
}
/// write the meshstructure of the mesh to arh file.
@@ -102,10 +113,11 @@ namespace AMDiS { namespace io {
std::string filename,
bool writeParallel = true,
Cpsformat cps = NONE,
- std::string dataformat = "SF64")
+ std::string dataformat = "SF64",
+ bool writeMacro = WRITE_MACRO)
{
std::vector<DOFVector<double>*> vecs;
- detail::write(filename, mesh, vecs, writeParallel, cps, dataformat);
+ detail::write(filename, mesh, vecs, writeParallel, cps, dataformat, writeMacro);
}
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
diff --git a/AMDiS/src/io/FileWriter.cc b/AMDiS/src/io/FileWriter.cc
index 593fe04b..c2b39ee4 100644
--- a/AMDiS/src/io/FileWriter.cc
+++ b/AMDiS/src/io/FileWriter.cc
@@ -73,6 +73,13 @@ namespace AMDiS
for (size_t i = 0; i < solutionVecs.size(); i++)
solutionNames.push_back(solutionVecs[i]->getName());
+
+ std::set<Mesh*> meshset;
+ for (size_t i = 0; i < solutionVecs.size(); i++)
+ if (solutionVecs[i])
+ meshset.insert(solutionVecs[i]->getFeSpace()->getMesh());
+
+ multiMesh = meshset.size() > 1;
}
@@ -201,8 +208,17 @@ namespace AMDiS
Arh2Writer::writeFile(solutionVecs, fn_ + ".arh");
else if (writeArh1)
ArhWriter::write(fn_ + ".arh", feSpace->getMesh(), solutionVecs);
- else if (writeArh3 || writeArhFormat)
- Arh3Writer::writeFile(solutionVecs, fn_ + ".arh");
+ else if (writeArh3 || writeArhFormat) {
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+ if (MPI::COMM_WORLD.Get_rank() == 0) {
+ TEST_EXIT(!multiMesh) ("Multi mesh arh writer is not supported in parallel.\n");
+ Arh3Writer::detail::writeParallelFile(paraFilename + arhParallelFileExt,
+ feSpace->getMesh(),
+ createSubDir > 0);
+ }
+#endif
+ Arh3Writer::writeFile(solutionVecs, fn + ".arh");
+ }
#ifdef HAVE_PNG
diff --git a/AMDiS/src/io/FileWriter.h b/AMDiS/src/io/FileWriter.h
index 81e6f653..2341b46f 100644
--- a/AMDiS/src/io/FileWriter.h
+++ b/AMDiS/src/io/FileWriter.h
@@ -102,6 +102,9 @@ namespace AMDiS {
/// Reads all file writer dependend parameters from the init file.
virtual void readParameters(std::string name) override;
+
+ /// Multi mesh flag
+ bool multiMesh;
/// Name of the writer.
std::string name;
@@ -117,6 +120,12 @@ namespace AMDiS {
/// Parallel VTK file extension.
std::string paraviewParallelFileExt;
+
+ /// Parallel ARH file extension.
+ std::string arhParallelFileExt;
+
+ /// Time ARH file extension.
+ std::string arhTimeFileExt;
/// Periodic file extension.
std::string periodicFileExt;
diff --git a/AMDiS/src/io/FileWriter.hh b/AMDiS/src/io/FileWriter.hh
index 7e74f233..b060e9ca 100644
--- a/AMDiS/src/io/FileWriter.hh
+++ b/AMDiS/src/io/FileWriter.hh
@@ -119,10 +119,13 @@ namespace AMDiS
template<typename T>
void FileWriter<T>::initialize()
{
+ multiMesh = false;
amdisMeshExt = ".mesh";
amdisDataExt = ".dat";
paraviewFileExt = ".vtu";
paraviewParallelFileExt = ".pvtu";
+ arhParallelFileExt = ".parh";
+ arhTimeFileExt = ".tarh";
periodicFileExt = ".per";
writeAMDiSFormat = 0;
writeParaViewFormat = 0;
diff --git a/AMDiS/src/io/detail/Arh3Reader.cc b/AMDiS/src/io/detail/Arh3Reader.cc
index a45b067a..3cbe5b6c 100644
--- a/AMDiS/src/io/detail/Arh3Reader.cc
+++ b/AMDiS/src/io/detail/Arh3Reader.cc
@@ -24,6 +24,20 @@ namespace AMDiS { namespace io {
{
namespace detail
{
+ void firstRead(std::string id_, uint8_t major_, uint8_t minor_, //version in file
+ std::string id, uint8_t major, uint8_t minor) //class version
+ {
+ TEST_EXIT(id == id_)
+ ("Cannot read Arh format: this file is not \"%s\" format.\n", id.c_str());
+
+ TEST_EXIT(major == major_)
+ ("Cannot read Arh format: Arh2Reader major version is %i, the file major version is %i. \n",
+ major, major_);
+
+ TEST_EXIT(minor >= minor_)
+ ("Cannot read Arh format: ArhReader minor version is %i is smaller than the file minor version %i.\n",
+ minor, minor_);
+ }
void firstRead(ifstream& file, string id, uint8_t major, uint8_t minor)
{
@@ -34,18 +48,10 @@ namespace AMDiS { namespace io {
string typeId(4, ' ');
file.read(const_cast<char*>(typeId.data()), 4);
- TEST_EXIT(typeId == id)
- ("Cannot read Arh format: this file is not \"%s\" format.\n", id.c_str());
-
file.read(reinterpret_cast<char*>(&major_), 1);
- TEST_EXIT(major == major_)
- ("Cannot read Arh format: Arh2Reader major version is %i, the file major version is %i. \n",
- major, major_);
-
file.read(reinterpret_cast<char*>(&minor_), 1);
- TEST_EXIT(minor <= minor_)
- ("Cannot read Arh format: ArhReader minor version is %i is smaller than the file minor version %i.\n",
- minor, minor_);
+
+ firstRead(typeId, major_, minor_, id, major, minor);
}
void setDofValues(int macroElIndex, Mesh *mesh,
@@ -315,7 +321,19 @@ namespace AMDiS { namespace io {
tmpString.resize(4, ' ');
file.read(const_cast<char*>(tmpString.data()), 4);
dataformat.push_back(tmpString);
- }
+ }
+
+ // Read macroFile_nl
+ uint32_t macroFile_nl = 0;
+ file.read(reinterpret_cast<char*>(¯oFile_nl), 4);
+ if (macroFile_nl > 0) {
+ string tmpString("");
+ tmpString.resize(macroFile_nl, ' ');
+ file.read(const_cast<char*>(tmpString.data()), macroFile_nl);
+ }
+
+ //================header is over==================//
+
// Adjust and check vecs
if(byName)
{
@@ -546,38 +564,49 @@ namespace AMDiS { namespace io {
}
if (writeParallel) {
using boost::lexical_cast;
+ using namespace boost::filesystem;
+
+ path file_name = filename;
+ path file_onlyname = file_name.filename();
int sPos = filename.find(".arh");
- TEST_EXIT(sPos >= 0)("Failed to find file postfix!\n");
- string name = filename.substr(0, sPos);
+ string filenameWithoutExt = filename.substr(0, sPos);
+ sPos = file_onlyname.string().find(".arh");
+ string onlynameWithoutExt = file_onlyname.string().substr(0, sPos);
+ string parh = filenameWithoutExt + ".parh";
+ string basedir = "";
+ path file_path = file_name.remove_filename();
+
+ int nProcs_ = 0, nMacros_ = 0, nMacros = 0;
+ vector<int> partition;
+ bool parhExists = exists(parh);
+
+ if (parhExists)
+ basedir = readParallelFile(parh, partition, nProcs_, nMacros_);
+ if (basedir != "")
+ filenameWithoutExt = file_path.string() + '/' + basedir + onlynameWithoutExt;
+
if (nProcs == -1) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- string procFilename = name + "-p" + lexical_cast<string>(MPI::COMM_WORLD.Get_rank()) + "-.arh";
+ string procFilename = filenameWithoutExt + "-p" + lexical_cast<string>(MPI::COMM_WORLD.Get_rank()) + "-.arh";
read(procFilename, mesh, vecs, byName);
MSG("ARH file read from: %s\n", procFilename.c_str());
#else
ERROR_EXIT("Reading parallel ARH files in sequential computations requires to specify the number of nodes on which the ARH file was created!\n");
#endif
} else {
- string parhfn = name + ".parh", filenameType = "";
- int nProcs_ = 0, nMacros_ = 0, nMacros = 0;
- vector<int> partition;
-
- bool parh = boost::filesystem::exists(parhfn);
- if (parh)
- readParallelFile(parhfn, filenameType, partition, nProcs_, nMacros_);
- else {
+ if (!parhExists) {
for (; nProcs_ < nProcs + 1; nProcs_++) {
- string fn = name + "-p" + boost::lexical_cast<string>(nProcs_) + "-.arh";
+ string fn = filenameWithoutExt + "-p" + boost::lexical_cast<string>(nProcs_) + "-.arh";
if(!boost::filesystem::exists(fn)) break;
}
}
TEST_EXIT(nProcs_ == nProcs)
("Number of arh files doesn't match number of processors: %d vs %d\n", nProcs_, nProcs);
- if (!parh) {
+ if (!parhExists) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- if(MPI::COMM_WORLD.Get_rank() == 0)
+ if (MPI::COMM_WORLD.Get_rank() == 0)
#endif
for(int i = 0; i < nProcs; i++)
nMacros_ += readNumOfMacrosFromSgArh(filename, i);
@@ -594,9 +623,9 @@ namespace AMDiS { namespace io {
nMacros, nMacros_);
}
- if (!parh) {
+ if (!parhExists) {
for (int i = 0; i < nProcs; i++) {
- string procFilename = name + "-p" + lexical_cast<string>(i) + "-.arh";
+ string procFilename = filenameWithoutExt + "-p" + lexical_cast<string>(i) + "-.arh";
read(procFilename, mesh, vecs, byName);
}
} else {
@@ -607,7 +636,7 @@ namespace AMDiS { namespace io {
std::set<int>::iterator it2 = needFiles.begin();
for (;it2 != needFiles.end(); it2++) {
- string procFilename = name + "-p" + lexical_cast<string>(*it2) + "-.arh";
+ string procFilename = filenameWithoutExt + "-p" + lexical_cast<string>(*it2) + "-.arh";
read(procFilename, mesh, vecs, byName);
}
}
@@ -693,7 +722,15 @@ namespace AMDiS { namespace io {
tmpString.resize(4, ' ');
file.read(const_cast<char*>(tmpString.data()), 4);
dataformat.push_back(tmpString);
- }
+ }
+
+ // Read macroFile_nl
+ uint32_t macroFile_nl = 0;
+ file.read(reinterpret_cast<char*>(¯oFile_nl), 4);
+ string tmpString("");
+ file.read(const_cast<char*>(tmpString.data()), macroFile_nl);
+
+ //================header is over==================//
for (uint32_t i = 0; i < nMacroElements; i++) {
stringstream dataStream(ios::out | ios::in | ios::binary);
@@ -799,32 +836,41 @@ namespace AMDiS { namespace io {
return nMacroElements;
}
- void readParallelFile(string filename, string& filenameType, vector<int>& partition, int& nFiles, int& nMacros)
+ std::string readParallelFile(string filename, vector<int>& partition, int& nFiles, int& nMacros)
{
ifstream file;
file.open(filename.c_str(), ios::in | ios::binary);
TEST_EXIT(file.is_open())
("Cannot open file %s\n", filename.c_str());
-
- firstRead(file, "parh", 1, 0);
- uint32_t macroFile_nl = 0;
- string macroFilename;
+ string fd(16, ' ');
+ file.read(const_cast<char*>(fd.data()), 16);
+ string Id = fd.substr(0, 4);
+ int major = boost::lexical_cast<int>(fd.substr(5, 1));
+ int minor = boost::lexical_cast<int>(fd.substr(7, 1));
+ firstRead(Id, major, minor, "parh", 1, 0);
- filenameType.resize(4, ' ');
+ uint32_t baseDirLen = 0, macroFile_nl = 0;
+ string baseDir, macroFilename;
+ file.read(reinterpret_cast<char*>(&baseDirLen), 4);
+ baseDir.resize(baseDirLen, ' ');
+ file.read(const_cast<char*>(baseDir.data()), baseDirLen);
file.read(reinterpret_cast<char*>(&nFiles), 4);
- file.read(const_cast<char*>(filenameType.data()), 4);
- file.read(reinterpret_cast<char*>(&nMacros), 4);
file.read(reinterpret_cast<char*>(¯oFile_nl), 4);
- macroFilename.resize(macroFile_nl, ' ');
- file.read(const_cast<char*>(macroFilename.data()), macroFile_nl);
+ if (macroFile_nl > 0) {
+ macroFilename.resize(macroFile_nl, ' ');
+ file.read(const_cast<char*>(macroFilename.data()), macroFile_nl);
+ }
+ file.read(reinterpret_cast<char*>(&nMacros), 4);
uint32_t rank = 0;
for (int i = 0; i < nMacros; i++) {
file.read(reinterpret_cast<char*>(&rank), 4);
partition.push_back(rank);
}
+
+ return baseDir;
}
} // end namespace detail
diff --git a/AMDiS/src/io/detail/Arh3Reader.h b/AMDiS/src/io/detail/Arh3Reader.h
index 6821b1a2..857266c4 100644
--- a/AMDiS/src/io/detail/Arh3Reader.h
+++ b/AMDiS/src/io/detail/Arh3Reader.h
@@ -23,6 +23,8 @@ namespace AMDiS { namespace io {
* 3. the minor version of Arh2Reader is bigger than the one in the file.
* return value: minor version
*/
+ void firstRead(std::string, uint8_t, uint8_t, std::string, uint8_t, uint8_t);
+
void firstRead(std::ifstream& file, std::string, uint8_t, uint8_t);
void setDofValues(int macroElIndex, Mesh *mesh,
@@ -80,8 +82,7 @@ namespace AMDiS { namespace io {
int readNumOfMacrosFromSgArh(std::string filename, int nProc = -1);
- void readParallelFile(std::string filename,
- std::string& filenameType,
+ std::string readParallelFile(std::string filename,
std::vector<int>& partition,
int& nFiles,
int& nMacros);
diff --git a/AMDiS/src/io/detail/Arh3Writer.cc b/AMDiS/src/io/detail/Arh3Writer.cc
index 5003c41c..6d010420 100644
--- a/AMDiS/src/io/detail/Arh3Writer.cc
+++ b/AMDiS/src/io/detail/Arh3Writer.cc
@@ -1,6 +1,7 @@
#include <fstream>
#include <stdint.h>
#include <iostream>
+#include <streambuf>
#include "Arh3Writer.h"
#include "Mesh.h"
@@ -31,7 +32,7 @@ namespace AMDiS { namespace io {
bool writeParallel,
Cpsformat cps,
string dataformat,
- string filenameType)
+ bool writeMacro)
{
vector<DOFVector<double>*> vecs(0);
if (vec0 != NULL)
@@ -41,35 +42,53 @@ namespace AMDiS { namespace io {
if (vec2 != NULL)
vecs.push_back(vec2);
- write(filename, NULL, vecs, writeParallel, cps, dataformat, filenameType);
+ write(filename, NULL, vecs, writeParallel, cps, dataformat, writeMacro);
}
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- void writeParallelFile(string filename, Mesh* mesh, string filenameType)
+ void writeParallelFile(string filename, Mesh* mesh, bool createSubDir, bool writeMacro)
{
- TEST_EXIT(filenameType == "cont")("Unsupported filename type.\n");
-
ofstream file;
file.open(filename.c_str(), ios::out | ios::binary | ios::trunc);
- string typeId = "parh", macroFilename = "";
+ string typeId = "parh", macroFilename = "", perFilename = "";
+ string baseDir = createSubDir ? "./data/" : "";
+ string macroData = "", periodicData = "";
+ uint32_t baseDirLen = baseDir.length();
Parameters::get(mesh->getName() + "->macro file name", macroFilename);
- uint8_t major = 1;
- uint8_t minor = 0;
+ Parameters::get(mesh->getName() + "->periodic file", perFilename);
+
+ int major = 1, minor = 0;
uint32_t nFiles = MPI::COMM_WORLD.Get_size();
- uint32_t macroFile_nl = macroFilename.length();
+ uint32_t macroFile_nl = 0;
map<int, int> partitionMap =
Parallel::MeshDistributor::globalMeshDistributor->getPartitionMap();
- uint32_t nMacros =partitionMap.size();
-
- file.write(typeId.c_str(), 4);
- file.write(reinterpret_cast<char*>(&major), 1);
- file.write(reinterpret_cast<char*>(&minor), 1);
+ uint32_t nMacros = partitionMap.size();
+
+ typeId += '_' + boost::lexical_cast<string>(major) + '.' + boost::lexical_cast<string>(minor);
+ if (typeId.length() <= 16) { // 16 is the Id size
+ string rest(16 - typeId.length(), ' ');
+ typeId.append(rest);
+ }
+ else
+ ERROR_EXIT("Should not happen.\n");
+
+ file.write(typeId.c_str(), 16);
+ file.write(reinterpret_cast<char*>(&baseDirLen), 4);
+ file.write(baseDir.c_str(), baseDirLen);
file.write(reinterpret_cast<char*>(&nFiles), 4);
- file.write(filenameType.c_str(), 4);
- file.write(reinterpret_cast<char*>(&nMacros), 4);
+
+ if (writeMacro && macroFilename.length()) {
+ macroFile_nl = 13;
+ readFileToString(macroFilename, macroData);
+
+ if (perFilename.length()) {
+ macroFile_nl = 27;
+ readFileToString(perFilename, periodicData);
+ }
+ }
file.write(reinterpret_cast<char*>(¯oFile_nl), 4);
- file.write(macroFilename.c_str(), macroFile_nl);
+ file.write(reinterpret_cast<char*>(&nMacros), 4);
map<int, int>::const_iterator it = partitionMap.begin();
uint32_t rank = 0;
@@ -77,6 +96,29 @@ namespace AMDiS { namespace io {
rank = it->second;
file.write(reinterpret_cast<char*>(&rank), 4);
}
+
+ // write macro and periodic file
+ if (writeMacro && macroFilename.length()) {
+ file.seekp(0, ios_base::end);
+ long macroPos = file.tellp(), perPos = 0;
+ file.write(macroData.c_str(), macroData.length());
+
+ if (perFilename.length()) {
+ perPos = file.tellp();
+ file.write(periodicData.c_str(), periodicData.length());
+ }
+
+ // update macroFile_nl
+ int offset = 16 + //typeId
+ 4 + //baseDirLen
+ baseDirLen + //baseDir
+ 4 + //nFiles
+ 4; //macroFile_nl
+ file.seekp(offset);
+ file << "this:" << macroPos;
+ if (perFilename.length())
+ file << ";this:" << perPos;
+ }
}
#endif
@@ -86,100 +128,74 @@ namespace AMDiS { namespace io {
bool writeParallel,
Cpsformat cps,
string dataformat,
- string filenameType)
+ bool writeMacro)
{
FUNCNAME("Arh3Writer::detail::write()");
- if (!mesh && vecs.empty()) {
- WARNING("There is nothing to be writen.\n");
- return;
- }
-
map<string,Valformat>::const_iterator it = dataformatMap.find(dataformat);
TEST_EXIT(it != dataformatMap.end())("Wrong data format.\n");
- std::set<string> nameSet;
- pair<std::set<string>::iterator,bool> ret;
-
- for(size_t i = 0; i < vecs.size(); i++)
- {
+ std::set<Mesh*> meshset;
+ std::set<string> nameset;
+ if (mesh)
+ meshset.insert(mesh);
+ for (size_t i = 0; i < vecs.size(); i++) {
TEST_EXIT(vecs[i] != NULL)("Vecs[%i] is NULL. Please check.\n", i);
- ret = nameSet.insert(vecs[i]->getName());
- TEST_EXIT(ret.second)("DOFVectors in vecs cannot have idential name. Please check.\n");
- }
-
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- if (writeParallel) {
- using boost::lexical_cast;
-
- int sPos = filename.find(".arh");
- TEST_EXIT(sPos >= 0)("Failed to find file postfix!\n");
- string name = filename.substr(0, sPos);
- std::vector<int> macroIdx;
-
- Mesh* mesh_ = mesh ? mesh : vecs[0]->getFeSpace()->getMesh();
-
- if (MPI::COMM_WORLD.Get_rank() == 0) {
- writeParallelFile(name + ".parh", mesh_, filenameType);
- }
+ meshset.insert(vecs[i]->getFeSpace()->getMesh());
+ nameset.insert(vecs[i]->getName());
+ }
- TEST_EXIT(filenameType == "cont")("Only filename type \"cont\".\n");
- filename = name + "-p" + lexical_cast<string>(MPI::COMM_WORLD.Get_rank()) + "-.arh";
+ if (meshset.size() == 0) {
+ WARNING("There is nothing to be writen.\n");
+ return;
}
-#endif
+
+ TEST_EXIT(nameset.size() == vecs.size())
+ ("DOFVectors in vecs cannot have idential name. Please check.\n");
+
+ bool multiMesh = meshset.size() > 1;
+
//if mesh exists, the meshes in vecs should be the same.
- if(mesh)
- {
- for(size_t i = 0; i < vecs.size(); i++)
- {
+ if (mesh) {
+ for (size_t i = 0; i < vecs.size(); i++)
TEST_EXIT(mesh == vecs[i]->getFeSpace()->getMesh())
- ("The mesh of DOFVector %i in vecs is not equal to the second parameter.\n", i);
- }
- writeAux(filename, mesh, vecs, writeParallel, cps, dataformat);
- }
- //multiple meshes are allowed here.
- else
- {
- vector<bool> visited(vecs.size(), false);
- vector<DOFVector<double>*> splitedVecs(0);
- bool moreMesh = false;
- Mesh* tmpMesh = vecs[0]->getFeSpace()->getMesh();
- for(size_t i = 1; i < vecs.size(); i++)
- {
- if(vecs[i]->getFeSpace()->getMesh() != tmpMesh)
- {
- moreMesh = true;
- break;
- }
- }
- for(size_t i = 0; i < vecs.size(); i++)
- {
- if(!visited[i])
- {
- splitedVecs.clear();
- splitedVecs.push_back(vecs[i]);
- visited[i] = true;
- tmpMesh = vecs[i]->getFeSpace()->getMesh();
- for(size_t j = i + 1; j < vecs.size(); j++)
- {
- if(vecs[j]->getFeSpace()->getMesh() == tmpMesh)
- {
- splitedVecs.push_back(vecs[j]);
- visited[j] = true;
- }
+ ("The mesh of DOFVector %i in vecs is not equal to the second parameter.\n", i);
+ writeAux(filename, mesh, vecs, writeParallel, cps, dataformat, writeMacro);
+ } else {
+ if (!multiMesh)
+ writeAux(filename, vecs[0]->getFeSpace()->getMesh(), vecs, writeParallel, cps, dataformat, writeMacro);
+ else {
+ vector<bool> visited(vecs.size(), false);
+ vector<DOFVector<double>*> splitedVecs(0);
+ Mesh* tmpMesh = NULL;
+
+ for(size_t i = 0; i < vecs.size(); i++) {
+ if(!visited[i]) {
+ splitedVecs.clear();
+ splitedVecs.push_back(vecs[i]);
+ visited[i] = true;
+ tmpMesh = vecs[i]->getFeSpace()->getMesh();
+ for(size_t j = i + 1; j < vecs.size(); j++)
+ if(vecs[j]->getFeSpace()->getMesh() == tmpMesh)
+ {
+ splitedVecs.push_back(vecs[j]);
+ visited[j] = true;
+ }
}
string newfilename = filename;
- if(moreMesh)
- {
- if(filename.length() > 4 && filename.substr(filename.length()- 4, filename.length()) == ".arh")
- newfilename = filename.substr(0, filename.length() - 4) +
- "." + tmpMesh->getName() +
- filename.substr(filename.length()-4 , filename.length());
- else
- newfilename = filename + "." + tmpMesh->getName() + ".arh";
-
- }
- writeAux(newfilename, splitedVecs[0]->getFeSpace()->getMesh(), splitedVecs, writeParallel, cps, dataformat);
+ if(filename.length() > 4 && filename.substr(filename.length()- 4, filename.length()) == ".arh")
+ newfilename = filename.substr(0, filename.length() - 4) +
+ "." + tmpMesh->getName() + filename.substr(filename.length()-4 , filename.length());
+ else
+ newfilename = filename + "." + tmpMesh->getName() + ".arh";
+
+ writeAux(newfilename,
+ splitedVecs[0]->getFeSpace()->getMesh(),
+ splitedVecs,
+ writeParallel,
+ cps,
+ dataformat,
+ writeMacro);
}
}
}
@@ -225,7 +241,8 @@ namespace AMDiS { namespace io {
fileNamesLen + //feSpaces table
nFeSpaces * 20 + //feSpaces table
valueNamesLen + //value vector table
- nValueVectors * 12; //also value vector table
+ nValueVectors * 12 + //also value vector table
+ 4; //macroFile_nl
string typeId = "sarh";
#ifndef HAVE_COMPRESSION
cps = NONE;
@@ -300,6 +317,9 @@ namespace AMDiS { namespace io {
file.write(reinterpret_cast<char*>(&feSpaceNumOfVecs[i]), 4);
file.write(dataformat.c_str(), 4);
}
+
+ uint32_t macroFile_nl = 0;
+ file.write(reinterpret_cast<char*>(¯oFile_nl), 4);
return headerLen;
}
@@ -307,10 +327,13 @@ namespace AMDiS { namespace io {
vector<DOFVector<double>*> vecs,
bool writeParallel,
Cpsformat cps,
- string dataformat)
+ string dataformat,
+ bool writeMacro)
{
FUNCNAME("Arh3Writer::detail::writeAux()");
+ TEST_EXIT(mesh)("empty mesh.\n");
+
//initialization
ofstream file;
file.open(filename.c_str(), ios::out | ios::binary | ios::trunc);
@@ -453,6 +476,8 @@ namespace AMDiS { namespace io {
TEST_EXIT(macroSize.size() == (unsigned)mesh->getNumberOfMacros())("Should not happen.\n");
//reset the macro positions in file
setMacrosPos(file, headerLen, macroSize);
+ if (writeMacro)
+ setMacroFile(file, headerLen, mesh);
file.close();
MSG("ARH file written to: %s\n", filename.c_str());
}
@@ -475,6 +500,55 @@ namespace AMDiS { namespace io {
file.seekp(pos + 4);
file.write(reinterpret_cast<char*>(&startPos), 4);
}
+
+ void setMacroFile(std::ofstream& file, int headerLen, Mesh* mesh)
+ {
+ string macroFilename = "", perFilename = "";
+ string macroData = "", periodicData = "";
+
+ Parameters::get(mesh->getName() + "->macro file name", macroFilename);
+ Parameters::get(mesh->getName() + "->periodic file", perFilename);
+
+ if (!macroFilename.length()) {
+ WARNING("macro file not found.\n");
+ return;
+ }
+
+ // write macro file to the end
+ readFileToString(macroFilename, macroData);
+ file.seekp(0, ios_base::end);
+ long macroPos = file.tellp(), perPos = 0;
+ file.write(macroData.c_str(), macroData.length());
+
+ // write periodic file to the end
+ if (perFilename.length()) {
+ readFileToString(perFilename, periodicData);
+ perPos = file.tellp();
+ file.write(periodicData.c_str(), periodicData.length());
+ }
+
+ // update macroFile_nl
+ uint32_t macroFile_nl = perFilename.length() ? 27 : 13;
+ file.seekp(headerLen - 4);
+ file.write(reinterpret_cast<char*>(¯oFile_nl), 4);
+ file << "this:" << macroPos;
+ if (perFilename.length())
+ file << ";this:" << perPos;
+
+ // update headerLen
+ headerLen += macroFile_nl;
+ file.seekp(6);
+ file.write(reinterpret_cast<char*>(&headerLen), 4);
+ }
+
+ void readFileToString(std::string filename, std::string& data)
+ {
+ ifstream file(filename.c_str());
+ file.seekg(0, std::ios::end);
+ data.reserve(file.tellg());
+ file.seekg(0, std::ios::beg);
+ data.assign((istreambuf_iterator<char>(file)), istreambuf_iterator<char>());
+ }
pair<int, int> writeMacroElement(ofstream &file,
MeshStructure &code,
diff --git a/AMDiS/src/io/detail/Arh3Writer.h b/AMDiS/src/io/detail/Arh3Writer.h
index b3e3a378..6e46649d 100644
--- a/AMDiS/src/io/detail/Arh3Writer.h
+++ b/AMDiS/src/io/detail/Arh3Writer.h
@@ -43,7 +43,7 @@ namespace AMDiS { namespace io {
bool writeParallel = true,
Cpsformat cps = NONE,
std::string dataformat = "SF64",
- std::string filenameType = "cont");
+ bool writeMacro = false);
/**
* \ingroup Output
@@ -71,12 +71,13 @@ namespace AMDiS { namespace io {
bool writeParallel = true,
Cpsformat cps = NONE,
std::string dataformat = "SF64",
- std::string filenameType = "cont");
+ bool writeMacro = false);
void writeAux(std::string filename, Mesh *mesh,
std::vector<DOFVector<double>*> vecs,
bool writeParallel, Cpsformat cps,
- std::string dataformat);
+ std::string dataformat,
+ bool writeMacro = false);
///\return the size of the macro block in file
std::pair<int, int> writeMacroElement(std::ofstream &file,
@@ -98,16 +99,23 @@ namespace AMDiS { namespace io {
std::vector<DOFVector<double>*> vecs,
std::map<const FiniteElemSpace*,
std::vector<int> >& feSpaces,
- Cpsformat cps, std::string dataformat);
+ Cpsformat cps,
+ std::string dataformat);
///internal method, don't call
void setMacrosPos(std::ofstream& file, int headerLen,
- std::vector<std::pair<int, int> >& macroSize);
+ std::vector<std::pair<int, int> >& macroSize);
+
+ ///internal method, don't call
+ void setMacroFile(std::ofstream& file, int headerLen, Mesh* mesh);
+
+ void readFileToString(std::string filename, std::string& data);
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
void writeParallelFile(std::string filename,
Mesh* mesh,
- std::string filenameType);
+ bool createSubDir,
+ bool writeMacro = true);
#endif
}//end namespace detail
} // end namespace Arh3Writer
--
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