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added: store spline bases inside the HDF5 files

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this means less files and more contained datasets while at the same time
allowing for using internal refine/order raising without problems

git-svn-id: http://svn.sintef.no/trondheim/IFEM/trunk@1022 e10b68d5-8a6e-419e-a041-bce267b0401d
This commit is contained in:
akva
2011-06-01 13:24:47 +00:00
committed by Knut Morten Okstad
parent 04b04a20f3
commit 63ebd5f00a
3 changed files with 65 additions and 32 deletions
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70
src/Utility/HDF5Writer.C
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@@ -109,7 +109,7 @@ void HDF5Writer::readArray(int group, const std::string& name,
}
void HDF5Writer::writeArray(int group, const std::string& name,
int len, void* data)
int len, const void* data, int type)
{
#ifdef HAS_HDF5
#ifdef PARALLEL_PETSC
@@ -123,15 +123,15 @@ void HDF5Writer::writeArray(int group, const std::string& name,
hsize_t start = 0;
#endif
hid_t space = H5Screate_simple(1,&siz,NULL);
hid_t set = H5Dcreate2(group,name.c_str(),H5T_NATIVE_DOUBLE,space,
H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
hid_t set = H5Dcreate2(group,name.c_str(),
type,space,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
hid_t file_space = H5Dget_space(set);
if (len > 0) {
siz = len;
hsize_t stride = 1;
H5Sselect_hyperslab(file_space,H5S_SELECT_SET,&start,&stride,&siz,NULL);
hid_t mem_space = H5Screate_simple(1,&siz,NULL);
H5Dwrite(set,H5T_NATIVE_DOUBLE,mem_space,file_space,H5P_DEFAULT,data);
H5Dwrite(set,type,mem_space,file_space,H5P_DEFAULT,data);
H5Sclose(mem_space);
}
H5Sclose(file_space);
@@ -149,7 +149,9 @@ bool HDF5Writer::readVector(int level, const DataEntry& entry)
void HDF5Writer::writeVector(int level, const DataEntry& entry)
{
writeArray(level,entry.first,entry.second.size,entry.second.data);
#ifdef HAS_HDF5
writeArray(level,entry.first,entry.second.size,entry.second.data,H5T_NATIVE_DOUBLE);
#endif
}
bool HDF5Writer::readSIM (int level, const DataEntry& entry)
@@ -216,6 +218,12 @@ void HDF5Writer::writeSIM (int level, const DataEntry& entry)
if (!sol) return;
const Integrand* prob = sim->getProblem();
if (level == 0) { // TODO time dependent geometries
writeBasis(sim,sim->getName()+"-1",1,level);
if (prob->mixedFormulation())
writeBasis(sim,sim->getName()+"-2",2,level);
}
for (int i = 0; i < sim->getNoPatches(); ++i) {
std::stringstream str;
str << level;
@@ -235,38 +243,72 @@ void HDF5Writer::writeSIM (int level, const DataEntry& entry)
{
// Mixed methods: The primary solution vector is referring to two bases
size_t ndof2 = psol.size() > ndof1 ? psol.size() - ndof1 : 0;
writeArray(group2,entry.first,psol.size(),psol.ptr());
writeArray(group2,prob->getField1Name(11),ndof1,psol.ptr());
writeArray(group2,prob->getField1Name(12),ndof2,psol.ptr()+ndof1);
writeArray(group2,entry.first,psol.size(),psol.ptr(),H5T_NATIVE_DOUBLE);
writeArray(group2,prob->getField1Name(11),ndof1,psol.ptr(),H5T_NATIVE_DOUBLE);
writeArray(group2,prob->getField1Name(12),ndof2,psol.ptr()+ndof1,H5T_NATIVE_DOUBLE);
}
else
writeArray(group2,prob->getField1Name(11),psol.size(),psol.ptr());
writeArray(group2,prob->getField1Name(11),psol.size(),psol.ptr(),H5T_NATIVE_DOUBLE);
if (entry.second.size == -1) {
Matrix field;
sim->evalSecondarySolution(field,loc-1);
for (size_t j = 0; j < prob->getNoFields(2); ++j)
writeArray(group2,prob->getField2Name(j),field.cols(),
field.getRow(j+1).ptr());
field.getRow(j+1).ptr(),H5T_NATIVE_DOUBLE);
}
}
else // must write empty dummy records for the other patches
{
double dummy;
writeArray(group2,entry.first,0,&dummy);
writeArray(group2,entry.first,0,&dummy,H5T_NATIVE_DOUBLE);
if (prob->mixedFormulation())
{
writeArray(group2,prob->getField1Name(11),0,&dummy);
writeArray(group2,prob->getField1Name(12),0,&dummy);
writeArray(group2,prob->getField1Name(11),0,&dummy,H5T_NATIVE_DOUBLE);
writeArray(group2,prob->getField1Name(12),0,&dummy,H5T_NATIVE_DOUBLE);
}
for (size_t j = 0; j < prob->getNoFields(2); ++j)
writeArray(group2,prob->getField2Name(j),0,&dummy);
writeArray(group2,prob->getField2Name(j),0,&dummy,H5T_NATIVE_DOUBLE);
}
H5Gclose(group2);
}
#endif
}
void HDF5Writer::writeBasis(SIMbase* sim, const std::string& name,
int basis, int level)
{
#ifdef HAS_HDF5
std::stringstream str;
str << "/" << level << "/basis/";
int group;
if (checkGroupExistence(m_file,str.str().c_str()))
group = H5Gopen2(m_file,str.str().c_str(),H5P_DEFAULT);
else
group = H5Gcreate2(m_file,str.str().c_str(),0,H5P_DEFAULT,H5P_DEFAULT);
str << "/"+name;
if (checkGroupExistence(m_file,str.str().c_str()))
{
H5Gclose(group);
return;
}
hid_t group2 = H5Gcreate2(m_file,str.str().c_str(),0,H5P_DEFAULT,H5P_DEFAULT);
for (int i=0;i<sim->getNoPatches();++i) {
std::stringstream str;
int loc = sim->getLocalPatchIndex(i+1);
if (loc > 0)
sim->dumpBasis(str,basis,loc);
std::stringstream str2;
str2 << i+1;
writeArray(group2, str2.str(), str.str().size(), str.str().c_str(),
H5T_NATIVE_CHAR);
}
H5Gclose(group2);
H5Gclose(group);
#endif
}
bool HDF5Writer::checkGroupExistence(int parent, const char* path)
{
bool result = false;

4
src/Utility/HDF5Writer.h
View File

@@ -29,7 +29,9 @@ public:
protected:
void writeArray(int group, const std::string& name,
int len, void* data);
int len, const void* data, int type);
void writeBasis(SIMbase* SIM, const std::string& name,
int basis, int level);
void readArray(int group, const std::string& name,
int& len, double*& data);
bool checkGroupExistence(int parent, const char* group);

23
src/Utility/XMLWriter.C
View File

@@ -118,38 +118,27 @@ void XMLWriter::writeSIM (int level, const DataEntry& entry)
if (prob->mixedFormulation())
{
// primary solution vector
addField(entry.first,entry.second.description,g2file,
addField(entry.first,entry.second.description,sim->getName()+"-0",
prob->getNoFields(1),sim->getNoPatches());
std::string g2file1(m_name);
std::string g2file2(m_name);
std::ofstream os1(replaceAll(g2file1,".xml","_1.g2").c_str());
std::ofstream os2(replaceAll(g2file2,".xml","_2.g2").c_str());
sim->dumpBasis(os1,1);
sim->dumpBasis(os2,2);
g2file = g2file2; // Assuming that basis2 is used for secondary variables
// Assuming that basis2 is used for secondary variables
// primary solution fields
addField(prob->getField1Name(11),"primary",g2file1,
addField(prob->getField1Name(11),"primary",sim->getName()+"-0",
sim->getNoFields(1),sim->getNoPatches());
addField(prob->getField1Name(12),"primary",g2file2,
addField(prob->getField1Name(12),"primary",sim->getName()+"-1",
sim->getNoFields(2),sim->getNoPatches());
}
else
{
g2file = m_name;
std::ofstream os(replaceAll(g2file,".xml",".g2").c_str());
sim->dumpGeometry(os);
// primary solution
addField(prob->getField1Name(11),entry.second.description,g2file,
addField(prob->getField1Name(11),entry.second.description,sim->getName()+"-0",
prob->getNoFields(1),sim->getNoPatches());
}
// secondary solution fields
if (entry.second.size == -1)
for (size_t j = 0; j < prob->getNoFields(2); j++)
addField(prob->getField2Name(j),"secondary",g2file,1,sim->getNoPatches());
addField(prob->getField2Name(j),"secondary",sim->getName()+"-1",1,sim->getNoPatches());
}