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draft for SSV #468

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e2a3228
simplification in DataExporter
akva2 Apr 28, 2021
3649219
draft for SSV
akva2 Apr 27, 2021
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20 changes: 15 additions & 5 deletions Apps/Common/SIMSolver.h
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
#include "TimeStep.h"
#include "HDF5Restart.h"
#include "HDF5Writer.h"
#include "HDF5WriterSSV.h"
#include "tinyxml.h"


Expand Down Expand Up @@ -47,17 +48,23 @@ template<class T1> class SIMSolverStat : public SIMadmin
//! \param[in] hdf5file The file to save to
//! \param[in] modelAdm Process administrator to use
//! \param[in] saveInterval The stride in the output file
//! \param[in] ssv Enable SSV writer
void handleDataOutput(const std::string& hdf5file,
const ProcessAdm& modelAdm,
int saveInterval = 1)
int saveInterval = 1,
bool vis = true,
bool ssv = false)
{
if (IFEM::getOptions().discretization == ASM::Spectral && !hdf5file.empty())
IFEM::cout <<"\n ** HDF5 output is available for spline/lagrangian discretization"
<<" only. Deactivating...\n"<< std::endl;
else
else if (vis || ssv)
{
exporter = new DataExporter(true,saveInterval);
exporter->registerWriter(new HDF5Writer(hdf5file,modelAdm));
if (vis)
exporter->registerWriter(new HDF5Writer(hdf5file,modelAdm));
if (ssv)
exporter->registerWriter(new HDF5WriterSSV(hdf5file,modelAdm));
S1.registerFields(*exporter);
IFEM::registerCallback(*exporter);
}
Expand Down Expand Up @@ -169,15 +176,18 @@ template<class T1> class SIMSolver : public SIMSolverStat<T1>
//! \param[in] modelAdm Process administrator to use
//! \param[in] saveInterval The stride in the output file
//! \param[in] restartInterval The stride in the restart file
//! \param[in] ssv Enable SSV writer
void handleDataOutput(const std::string& hdf5file,
const ProcessAdm& modelAdm,
int saveInterval = 1,
int restartInterval = 0)
int restartInterval = 0,
bool vis = true,
bool ssv = false)
{
if (restartInterval > 0)
restartAdm = new HDF5Restart(hdf5file+"_restart",modelAdm,restartInterval);

this->SIMSolverStat<T1>::handleDataOutput(hdf5file, modelAdm, saveInterval);
this->SIMSolverStat<T1>::handleDataOutput(hdf5file, modelAdm, saveInterval, vis, ssv);
}

//! \brief Serialize internal state for restarting purposes.
Expand Down
5 changes: 5 additions & 0 deletions src/SIM/SIMoptions.C
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Expand Up @@ -52,6 +52,8 @@ SIMoptions::SIMoptions ()
nViz[0] = nViz[1] = nViz[2] = 2;

printPid = 0;
saveHDF5viz = true;
saveHDF5ssv = false;
}


Expand Down Expand Up @@ -174,6 +176,9 @@ bool SIMoptions::parseOutputTag (const TiXmlElement* elem)
}
else // use the default output file name
hdf5 = "(default)";

utl::getAttribute(elem,"ssv",saveHDF5ssv);
utl::getAttribute(elem,"viz",saveHDF5viz);
}

else if (!strcasecmp(elem->Value(),"primarySolOnly"))
Expand Down
2 changes: 2 additions & 0 deletions src/SIM/SIMoptions.h
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,8 @@ class SIMoptions
bool pSolOnly; //!< If \e true, don't save secondary solution variables
bool saveNorms;//!< If \e true, save element norms
bool saveLog; //!< If \e true, export the log
bool saveHDF5viz; //!< If \e true, save HDF5 visualization file
bool saveHDF5ssv; //!< If \e true, save HDF5 SSV file

std::string hdf5; //!< Prefix for HDF5-file
std::string vtf; //!< Prefix for VTF-file
Expand Down
38 changes: 19 additions & 19 deletions src/Utility/DataExporter.C
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Expand Up @@ -77,11 +77,6 @@ bool DataExporter::registerWriter (DataWriter* writer, bool info, bool data)
{
m_writers.push_back(writer);

if (info)
m_infoReader = writer;
if (data)
m_dataReader = writer;

return true;
}

Expand Down Expand Up @@ -124,33 +119,38 @@ bool DataExporter::dumpTimeLevel (const TimeStep* tp, bool geometryUpdated)
if (m_level == -1)
m_level = this->getWritersTimeLevel()+1;

std::map<std::string,FileEntry>::iterator it;
for (DataWriter* writer : m_writers) {
writer->openFile(m_level);
for (it = m_entry.begin(); it != m_entry.end(); ++it) {
if (!it->second.data)
for (const DataEntry& it : m_entry)
if (it.second.field == SIM)
if (!writer->prepare(m_level,it,geometryUpdated,it.second.prefix)) {
std::cerr << "** DataExporter::dumpTimeLevel: Error preparing output for field " << it.first << std::endl;
return false;
}

for (const DataEntry& it : m_entry) {
if (!it.second.data)
return false;
switch (it->second.field) {
switch (it.second.field) {
case INTVECTOR:
case VECTOR:
writer->writeVector(m_level,*it);
writer->writeVector(m_level,it);
break;
case SIM:
if (writeData)
writer->writeSIM(m_level,*it,geometryUpdated,it->second.prefix);
writer->writeSIM(m_level,it,geometryUpdated,it.second.prefix);
break;
case NODALFORCES:
writer->writeNodalForces(m_level,*it);
writer->writeNodalForces(m_level,it);
break;
case KNOTSPAN:
writer->writeKnotspan(m_level,*it,it->second.prefix);
writer->writeKnotspan(m_level,it,it.second.prefix);
break;
case BASIS:
writer->writeBasis(m_level,*it,it->second.prefix);
writer->writeBasis(m_level,it,it.second.prefix);
break;
default:
std::cerr <<" ** DataExporter: Invalid field type registered "
<< it->second.field <<", skipping"<< std::endl;
<< it.second.field <<", skipping"<< std::endl;
break;
}
}
Expand All @@ -162,9 +162,9 @@ bool DataExporter::dumpTimeLevel (const TimeStep* tp, bool geometryUpdated)
m_level++;

// disable fields marked as once
for (it = m_entry.begin(); it != m_entry.end(); ++it)
if (abs(it->second.results) & ONCE)
it->second.enabled = false;
for (auto& it : m_entry)
if (abs(it.second.results) & ONCE)
it.second.enabled = false;

return true;
}
Expand Down
15 changes: 11 additions & 4 deletions src/Utility/DataExporter.h
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Expand Up @@ -81,7 +81,7 @@ class DataExporter : public ControlCallback
//! \param[in] ndump Interval between dumps
DataExporter(bool dynWriters = false, int ndump=1) :
m_delete(dynWriters), m_level(-1), m_ndump(ndump),
m_last_step(-1), m_infoReader(0), m_dataReader(0) {}
m_last_step(-1) {}

//! \brief The destructor deletes the writers if \a dynWriters was \e true.
virtual ~DataExporter();
Expand Down Expand Up @@ -154,9 +154,6 @@ class DataExporter : public ControlCallback
int m_level; //!< Current time level
int m_ndump; //!< Time level stride for dumping
int m_last_step; //!< Last time step we dumped for

DataWriter* m_infoReader; //!< DataWriter to read data information from
DataWriter* m_dataReader; //!< DataWriter to read numerical data from
};

//! \brief Convenience type
Expand Down Expand Up @@ -192,6 +189,16 @@ class DataWriter
//! \param[in] level Level we just wrote to the file
virtual void closeFile(int level) = 0;

//! \brief Prepare writer for writing a time level.
//! \param[in] level The time level to write the data at
//! \param[in] entry The DataEntry describing the vector
//! \param[in] geometryUpdated Whether or not geometries should be written
//! \param[in] prefix Field name prefix
//! \details Used by SVV where we have to preallocate datasets
virtual bool prepare(int level, const DataEntry& entry,
bool geometryUpdated, const std::string& prefix)
{ return true; }

//! \brief Writes a vector to file.
//! \param[in] level The time level to write the vector at
//! \param[in] entry The DataEntry describing the vector
Expand Down
32 changes: 23 additions & 9 deletions src/Utility/HDF5Base.C
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Original file line number Diff line number Diff line change
Expand Up @@ -35,27 +35,40 @@ HDF5Base::HDF5Base (const std::string& name, const ProcessAdm& adm)
}


bool HDF5Base::openFile (unsigned int flags)
bool HDF5Base::openFile (unsigned int flags, bool latest)
{
#ifdef HAS_HDF5
if (m_file != -1)
return true;

hid_t acc_tpl = H5P_DEFAULT;
bool acc_tpl_alloc = false;
if (latest
#ifdef HAVE_MPI
&& m_adm.getProcId() == 0 || !m_adm.dd.isPartitioned()
#endif
) {
acc_tpl = H5Pcreate(H5P_FILE_ACCESS);
acc_tpl_alloc = true;
}

#ifdef HAVE_MPI
hid_t acc_tpl;
if (m_adm.dd.isPartitioned()) {
if (m_adm.getProcId() != 0)
return true;
acc_tpl = H5P_DEFAULT;
} else {
MPI_Info info = MPI_INFO_NULL;
acc_tpl = H5Pcreate(H5P_FILE_ACCESS);
if (!acc_tpl_alloc) {
acc_tpl = H5Pcreate(H5P_FILE_ACCESS);
acc_tpl_alloc = true;
}
H5Pset_fapl_mpio(acc_tpl, *m_adm.getCommunicator(), info);
}
#else
hid_t acc_tpl = H5P_DEFAULT;
#endif

if (latest)
H5Pset_libver_bounds(acc_tpl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);

if (flags == H5F_ACC_TRUNC)
m_file = H5Fcreate(m_hdf5_name.c_str(),flags,H5P_DEFAULT,acc_tpl);
else
Expand All @@ -64,13 +77,14 @@ bool HDF5Base::openFile (unsigned int flags)
if (m_file < 0)
{
std::cerr <<" *** HDF5Base: Failed to open "<< m_hdf5_name << std::endl;
if (acc_tpl_alloc)
H5Pclose(acc_tpl);
return false;
}

#ifdef HAVE_MPI
if (!m_adm.dd.isPartitioned())
if (acc_tpl_alloc)
H5Pclose(acc_tpl);
#endif

return true;
#else
return false;
Expand Down
3 changes: 2 additions & 1 deletion src/Utility/HDF5Base.h
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Expand Up @@ -39,7 +39,8 @@ class HDF5Base
protected:
//! \brief Opens the HDF5 file.
//! \param[in] flag Mode to open file using
bool openFile(unsigned int flag);
//! \param[in] latest If true, open using latest version
bool openFile(unsigned int flag, bool latest = false);
//! \brief Closes the HDF5 file.
void closeFile();

Expand Down
41 changes: 28 additions & 13 deletions src/Utility/HDF5Writer.C
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Original file line number Diff line number Diff line change
Expand Up @@ -168,12 +168,18 @@ void HDF5Writer::writeArray(hid_t group, const std::string& name, int patch,
space = H5Screate_simple(1,&siz,nullptr);
std::stringstream str;
str << patch;
set = H5Dcreate2(group1,str.str().c_str(),
type,space,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
if (checkGroupExistence(group1,str.str().c_str()))
set = H5Dopen2(group1,str.str().c_str(),H5P_DEFAULT);
else
set = H5Dcreate2(group1,str.str().c_str(),
type,space,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
} else {
space = H5Screate_simple(1,&siz,nullptr);
set = H5Dcreate2(group,name.c_str(),
type,space,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
if (checkGroupExistence(group,name.c_str()))
set = H5Dopen2(group,name.c_str(),H5P_DEFAULT);
else
set = H5Dcreate2(group,name.c_str(),
type,space,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
}
if (len > 0) {
hid_t file_space = H5Dget_space(set);
Expand All @@ -185,6 +191,7 @@ void HDF5Writer::writeArray(hid_t group, const std::string& name, int patch,
H5Sclose(mem_space);
H5Sclose(file_space);
}
H5Dflush(set);
H5Dclose(set);
H5Sclose(space);
if (group1 != -1)
Expand Down Expand Up @@ -241,6 +248,14 @@ void HDF5Writer::writeBasis (int level, const DataEntry& entry,

void HDF5Writer::writeSIM (int level, const DataEntry& entry,
bool geometryUpdated, const std::string& prefix)
{
this->writeSIMInt(level, entry, geometryUpdated, prefix, false);
}


void HDF5Writer::writeSIMInt (int level, const DataEntry& entry,
bool geometryUpdated,
const std::string& prefix, bool noData)
{
if (!entry.second.enabled || !entry.second.data || entry.second.data2.empty())
return;
Expand Down Expand Up @@ -336,7 +351,7 @@ void HDF5Writer::writeSIM (int level, const DataEntry& entry,
(!(results & DataExporter::REDUNDANT) || sim->getGlobalProcessID() == 0)) // we own the patch
{
ASMbase* pch = sim->getPatch(loc);
if (results & DataExporter::PRIMARY && !sol->empty()) {
if (results & DataExporter::PRIMARY && !sol->empty() && !noData) {
Vector psol;
size_t ndof1 = sim->extractPatchSolution(*sol,psol,pch,entry.second.ncmps,
usedescription ? 1 : 0);
Expand All @@ -357,7 +372,7 @@ void HDF5Writer::writeSIM (int level, const DataEntry& entry,
i+1, ndof1, data, H5T_NATIVE_DOUBLE);
}

if (results & DataExporter::SECONDARY && !sol->empty()) {
if (results & DataExporter::SECONDARY && !sol->empty() && !noData) {
Matrix field;
SIM::SolutionMode mode = prob->getMode();
const_cast<SIMbase*>(sim)->setMode(SIM::RECOVERY);
Expand All @@ -369,7 +384,7 @@ void HDF5Writer::writeSIM (int level, const DataEntry& entry,
i+1, field.cols(), field.getRow(j+1).ptr(), H5T_NATIVE_DOUBLE);
}

if (proj)
if (proj && !noData)
for (size_t p = 0; p < proj->size(); ++p) {
if (proj->at(p).empty())
continue;
Expand All @@ -394,7 +409,7 @@ void HDF5Writer::writeSIM (int level, const DataEntry& entry,
i+1, field.cols(), field.getRow(j+1).ptr(), H5T_NATIVE_DOUBLE);
}

if (results & DataExporter::NORMS && eNorm) {
if (results & DataExporter::NORMS && eNorm && !noData) {
Matrix patchEnorm;
sim->extractPatchElmRes(*eNorm,patchEnorm,loc-1);
for (size_t j = 1, l = 1; l < eNorm->rows(); j++)
Expand All @@ -405,7 +420,7 @@ void HDF5Writer::writeSIM (int level, const DataEntry& entry,
i+1, patchEnorm.cols(), patchEnorm.getRow(l++).ptr(), H5T_NATIVE_DOUBLE);
}

if (results & DataExporter::EIGENMODES) {
if (results & DataExporter::EIGENMODES && !noData) {
size_t iMode = 0;
const std::vector<Mode>* modes = static_cast<const std::vector<Mode>*>(entry.second.data2.front());
for (const Mode& mode : *modes)
Expand Down Expand Up @@ -440,7 +455,7 @@ void HDF5Writer::writeSIM (int level, const DataEntry& entry,
else // must write empty dummy records for the other patches
{
double dummy=0.0;
if (results & DataExporter::PRIMARY) {
if (results & DataExporter::PRIMARY && !noData) {
if (usedescription)
writeArray(group.front(), entry.second.description,
i+1, 0, &dummy, H5T_NATIVE_DOUBLE);
Expand All @@ -453,18 +468,18 @@ void HDF5Writer::writeSIM (int level, const DataEntry& entry,
i+1, 0, &dummy, H5T_NATIVE_DOUBLE);
}

if (results & DataExporter::SECONDARY)
if (results & DataExporter::SECONDARY && !noData)
for (size_t j = 0; j < prob->getNoFields(2); j++)
writeArray(group.front(), prefix+prob->getField2Name(j),
i+1, 0, &dummy,H5T_NATIVE_DOUBLE);

if (proj)
if (proj && !noData)
for (size_t p = 0; p < proj->size(); p++)
for (size_t j = 0; j < prob->getNoFields(2); j++)
writeArray(group.front(), m_prefix[p]+" "+prob->getField2Name(j),
i+1, 0, &dummy,H5T_NATIVE_DOUBLE);

if (results & DataExporter::NORMS && eNorm)
if (results & DataExporter::NORMS && eNorm && !noData)
for (size_t j = 1; j <= norm->getNoFields(0); j++)
for (size_t k = 1; k <= norm->getNoFields(j); k++)
if (norm->hasElementContributions(j,k))
Expand Down
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