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Making sure Hdf5 is an optional dependency (default to binary writer if not present)

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This commit is contained in:
Michael Marshall 2019-04-28 20:23:44 +01:00
parent adc1eaee68
commit fb74de0798
5 changed files with 51 additions and 35 deletions
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42
Hadrons/Distil.hpp
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@ -242,14 +242,24 @@ inline GridCartesian * MakeLowerDimGrid( GridCartesian * gridHD )
return gridLD;
}
#ifdef HAVE_HDF5
using Default_Reader = Grid::Hdf5Reader;
using Default_Writer = Grid::Hdf5Writer;
static const char * FileExtension = ".h5";
#else
using Default_Reader = Grid::BinaryReader;
using Default_Writer = Grid::BinaryWriter;
static const char * FileExtension = ".dat";
#endif
/******************************************************************************
Perambulator object
NamedTensor object
This is an Eigen::Tensor of type Scalar_ and rank NumIndices_ (row-major order)
They can be persisted to disk, with the on-disk format being big endian.
They can be persisted to disk
Scalar_ objects are assumed to be composite objects of size Endian_Scalar_Size.
(Disable big-endian by setting Endian_Scalar_Size=1)
(Disable big-endian by setting Endian_Scalar_Size=1).
NB: Endian_Scalar_Size will disappear when ReadBinary & WriteBinary retired
IndexNames contains one name for each index, and IndexNames are validated on load.
(NB: Indices of dimension 1 are not saved, and not validated on load)
WHAT TO SAVE / VALIDATE ON LOAD (Override to warn instead of assert on load)
Ensemble string
Configuration number
@ -324,8 +334,8 @@ public:
// load and save - not virtual - probably all changes
template<typename Reader> inline void read (Reader &r, const char * pszTag = nullptr);
template<typename Writer> inline void write(Writer &w, const char * pszTag = nullptr) const;
template<typename Reader> inline void read (const char * filename, const char * pszTag = nullptr);
template<typename Writer> inline void write(const char * filename, const char * pszTag = nullptr) const;
inline void read (const char * filename, const char * pszTag = nullptr);
inline void write(const char * filename, const char * pszTag = nullptr) const;
EIGEN_DEPRECATED inline void ReadBinary (const std::string filename); // To be removed
EIGEN_DEPRECATED inline void WriteBinary(const std::string filename); // To be removed
};
@ -506,11 +516,13 @@ void NamedTensor<Scalar_, NumIndices_, Endian_Scalar_Size>::write(Writer &w, con
}
template<typename Scalar_, int NumIndices_, uint16_t Endian_Scalar_Size>
template<typename Writer>
void NamedTensor<Scalar_, NumIndices_, Endian_Scalar_Size>::write(const char * filename, const char * pszTag)const{
LOG(Message) << "Writing NamedTensor to \"" << filename << "\"" << std::endl;
Writer w(filename);
write(w, pszTag);
const std::string sTag{pszTag == nullptr ? filename : pszTag};
std::string sFileName{filename};
sFileName.append( MDistil::FileExtension );
LOG(Message) << "Writing NamedTensor to " << sFileName << ", tag " << sTag << std::endl;
MDistil::Default_Writer w(sFileName);
write(w, sTag.c_str());
}
/******************************************************************************
@ -534,11 +546,13 @@ void NamedTensor<Scalar_, NumIndices_, Endian_Scalar_Size>::read(Reader &r, cons
}
template<typename Scalar_, int NumIndices_, uint16_t Endian_Scalar_Size>
template<typename Reader>
void NamedTensor<Scalar_, NumIndices_, Endian_Scalar_Size>::read(const char * filename, const char * pszTag) {
LOG(Message) << "Reading NamedTensor from \"" << filename << "\"" << std::endl;
Reader r(filename);
read(r, pszTag);
const std::string sTag{pszTag == nullptr ? filename : pszTag};
std::string sFileName{filename};
sFileName.append( MDistil::FileExtension );
LOG(Message) << "Reading NamedTensor from " << sFileName << ", tag " << sTag << std::endl;
MDistil::Default_Reader r(sFileName);
read(r, sTag.c_str());
}
/******************************************************************************

2
Hadrons/Modules/MDistil/PerambFromSolve.hpp
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@ -241,7 +241,7 @@ void TPerambFromSolve<FImpl>::execute(void)
if(PerambFileName.length()) {
std::string sPerambName{PerambFileName + "." + std::to_string(vm().getTrajectory())};
//perambulator.WriteBinary(sPerambName);
perambulator.template write<Hdf5Writer>((sPerambName + ".h5").c_str(), sPerambName.c_str());
perambulator.write(sPerambName.c_str());
}
}

2
Hadrons/Modules/MDistil/Perambulator.hpp
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@ -289,7 +289,7 @@ void TPerambulator<FImpl>::execute(void)
if(PerambFileName.length()) {
std::string sPerambName{PerambFileName + "." + std::to_string(vm().getTrajectory())};
//perambulator.WriteBinary(sPerambName);
perambulator.template write<Hdf5Writer>((sPerambName + ".h5").c_str(), sPerambName.c_str());
perambulator.write(sPerambName.c_str());
}
}

4
Hadrons/Modules/MIO/LoadPerambulator.hpp
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@ -120,9 +120,7 @@ void TLoadPerambulator<FImpl>::execute(void)
{
auto &perambulator = envGet(MDistil::Perambulator<SpinVector COMMA 6 COMMA sizeof(Real)>, getName());
const std::string sPerambName{par().PerambFileName + "." + std::to_string(vm().getTrajectory())};
const std::string PerambFileName{sPerambName + ".h5"};
std::cout << "reading perambulator from file " << PerambFileName << std::endl;
perambulator.template read<Hdf5Reader>(PerambFileName.c_str(), sPerambName.c_str());
perambulator.read(sPerambName.c_str());
}
END_MODULE_NAMESPACE

36
tests/hadrons/Test_distil.cc
View File

@ -784,20 +784,34 @@ bool DebugEigenTest()
DebugShowTensor(y, "y");
// Now see whether we can read a tensor back from an hdf5 file
const char * pszH5Name = "test.h5";
y.write<Hdf5Writer>(pszH5Name);
const char * pszFileName = "test";
y.write(pszFileName);
{
MyTensor z;
const char * pszName = "z1";
DebugShowTensor(z, pszName);
z.read<Hdf5Reader>(pszH5Name);
z.read(pszFileName);
DebugShowTensor(z, pszName);
}
{
MyTensor z(Names2,2,0,0);
const char * pszName = "z2";
DebugShowTensor(z, pszName);
z.read<Hdf5Reader>(pszH5Name);
z.read(pszFileName);
DebugShowTensor(z, pszName);
}
{
// Now see whether we can read a tensor back from an xml file
const char * pszXmlName = "test.xml";
{
XmlWriter w(pszXmlName);
y.write<XmlWriter>(w);
}
MyTensor z;
const char * pszName = "xml1";
DebugShowTensor(z, pszName);
XmlReader r(pszXmlName);
z.read<XmlReader>(r);
DebugShowTensor(z, pszName);
}
if((0)) // The following tests would fail
@ -807,17 +821,7 @@ bool DebugEigenTest()
//MyTensor z(NamesBad);
const char * pszName = "zFail";
DebugShowTensor(z, pszName);
z.read<Hdf5Reader>(pszH5Name);
DebugShowTensor(z, pszName);
}
// Now see whether we can read a tensor back from an xml file
const char * pszXmlName = "test.xml";
y.write<XmlWriter>(pszXmlName);
{
MyTensor z;
const char * pszName = "xml1";
DebugShowTensor(z, pszName);
z.read<XmlReader>(pszXmlName);
z.read(pszFileName);
DebugShowTensor(z, pszName);
}
@ -1027,7 +1031,7 @@ int main(int argc, char *argv[])
<< ", sizeof(hsize_t) = " << sizeof(hsize_t)
<< ", sizeof(unsigned long long) = " << sizeof(unsigned long long)
<< std::endl;
//if( DebugEigenTest() ) return 0;
if( DebugEigenTest() ) return 0;
//if(DebugGridTensorTest()) return 0;
#endif