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Lattice serialisation, just HDF5 for the moment

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This commit is contained in:
Antonin Portelli
2018-03-26 19:16:16 +01:00
parent 1c680d4b7a
commit 8a0cf0194f
3 changed files with 199 additions and 2 deletions
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93
lib/lattice/Lattice_transfer.h
View File

@@ -599,6 +599,51 @@ unvectorizeToLexOrdArray(std::vector<sobj> &out, const Lattice<vobj> &in)
extract1(in_vobj, out_ptrs, 0);
}
}
template<typename vobj, typename sobj>
typename std::enable_if<isSIMDvectorized<vobj>::value && !isSIMDvectorized<sobj>::value, void>::type
unvectorizeToRevLexOrdArray(std::vector<sobj> &out, const Lattice<vobj> &in)
{
typedef typename vobj::vector_type vtype;
GridBase* in_grid = in._grid;
out.resize(in_grid->lSites());
int ndim = in_grid->Nd();
int in_nsimd = vtype::Nsimd();
std::vector<std::vector<int> > in_icoor(in_nsimd);
for(int lane=0; lane < in_nsimd; lane++){
in_icoor[lane].resize(ndim);
in_grid->iCoorFromIindex(in_icoor[lane], lane);
}
parallel_for(int in_oidx = 0; in_oidx < in_grid->oSites(); in_oidx++){ //loop over outer index
//Assemble vector of pointers to output elements
std::vector<sobj*> out_ptrs(in_nsimd);
std::vector<int> in_ocoor(ndim);
in_grid->oCoorFromOindex(in_ocoor, in_oidx);
std::vector<int> lcoor(in_grid->Nd());
for(int lane=0; lane < in_nsimd; lane++){
for(int mu=0;mu<ndim;mu++)
lcoor[mu] = in_ocoor[mu] + in_grid->_rdimensions[mu]*in_icoor[lane][mu];
int lex;
Lexicographic::IndexFromCoorReversed(lcoor, lex, in_grid->_ldimensions);
out_ptrs[lane] = &out[lex];
}
//Unpack into those ptrs
const vobj & in_vobj = in._odata[in_oidx];
extract1(in_vobj, out_ptrs, 0);
}
}
//Copy SIMD-vectorized lattice to array of scalar objects in lexicographic order
template<typename vobj, typename sobj>
typename std::enable_if<isSIMDvectorized<vobj>::value
@@ -648,6 +693,54 @@ vectorizeFromLexOrdArray( std::vector<sobj> &in, Lattice<vobj> &out)
}
}
template<typename vobj, typename sobj>
typename std::enable_if<isSIMDvectorized<vobj>::value
&& !isSIMDvectorized<sobj>::value, void>::type
vectorizeFromRevLexOrdArray( std::vector<sobj> &in, Lattice<vobj> &out)
{
typedef typename vobj::vector_type vtype;
GridBase* grid = out._grid;
assert(in.size()==grid->lSites());
int ndim = grid->Nd();
int nsimd = vtype::Nsimd();
std::vector<std::vector<int> > icoor(nsimd);
for(int lane=0; lane < nsimd; lane++){
icoor[lane].resize(ndim);
grid->iCoorFromIindex(icoor[lane],lane);
}
parallel_for(uint64_t oidx = 0; oidx < grid->oSites(); oidx++){ //loop over outer index
//Assemble vector of pointers to output elements
std::vector<sobj*> ptrs(nsimd);
std::vector<int> ocoor(ndim);
grid->oCoorFromOindex(ocoor, oidx);
std::vector<int> lcoor(grid->Nd());
for(int lane=0; lane < nsimd; lane++){
for(int mu=0;mu<ndim;mu++){
lcoor[mu] = ocoor[mu] + grid->_rdimensions[mu]*icoor[lane][mu];
}
int lex;
Lexicographic::IndexFromCoorReversed(lcoor, lex, grid->_ldimensions);
ptrs[lane] = &in[lex];
}
//pack from those ptrs
vobj vecobj;
merge1(vecobj, ptrs, 0);
out._odata[oidx] = vecobj;
}
}
//Convert a Lattice from one precision to another
template<class VobjOut, class VobjIn>
void precisionChange(Lattice<VobjOut> &out, const Lattice<VobjIn> &in){

62
lib/serialisation/Hdf5IO.h
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@@ -22,6 +22,8 @@
namespace Grid
{
template<class vobj> class Lattice;
class Hdf5Writer: public Writer<Hdf5Writer>
{
public:
@@ -33,6 +35,8 @@ namespace Grid
template <typename U>
void writeDefault(const std::string &s, const U &x);
template <typename U>
void writeDefault(const std::string &s, const Lattice<U> &field);
template <typename U>
typename std::enable_if<element<std::vector<U>>::is_number, void>::type
writeDefault(const std::string &s, const std::vector<U> &x);
template <typename U>
@@ -60,6 +64,8 @@ namespace Grid
template <typename U>
void readDefault(const std::string &s, U &output);
template <typename U>
void readDefault(const std::string &s, Lattice<U> &field);
template <typename U>
typename std::enable_if<element<std::vector<U>>::is_number, void>::type
readDefault(const std::string &s, std::vector<U> &x);
template <typename U>
@@ -99,6 +105,39 @@ namespace Grid
template <>
void Hdf5Writer::writeDefault(const std::string &s, const std::string &x);
template <typename U>
void Hdf5Writer::writeDefault(const std::string &s, const Lattice<U> &field)
{
// alias scalar types
typedef std::vector<typename U::scalar_object> ScalarLattice;
typedef typename U::scalar_type ScalarType;
ScalarLattice scalField;
unvectorizeToRevLexOrdArray(scalField, field);
std::vector<hsize_t> dim;
std::vector<size_t> tDim;
tensorDim(tDim, scalField[0]);
for (auto &d: field._grid->GlobalDimensions())
{
dim.push_back(d);
}
for (auto &d: tDim)
{
dim.push_back(d);
}
// write to file
H5NS::DataSpace dataSpace(dim.size(), dim.data());
H5NS::DataSet dataSet;
dataSet = group_.createDataSet(s, Hdf5Type<ScalarType>::type(), dataSpace);
dataSet.write(scalField.data(), Hdf5Type<ScalarType>::type());
}
template <typename U>
typename std::enable_if<element<std::vector<U>>::is_number, void>::type
Hdf5Writer::writeDefault(const std::string &s, const std::vector<U> &x)
@@ -169,6 +208,29 @@ namespace Grid
template <>
void Hdf5Reader::readDefault(const std::string &s, std::string &x);
template <typename U>
void Hdf5Reader::readDefault(const std::string &s, Lattice<U> &field)
{
// alias scalar types
typedef std::vector<typename U::scalar_object> ScalarLattice;
typedef typename U::scalar_type ScalarType;
ScalarLattice scalField;
H5NS::DataSet dataSet;
std::vector<hsize_t> dim;
hsize_t size = 1;
dataSet = group_.openDataSet(s);
for (auto &d: field._grid->GlobalDimensions())
{
dim.push_back(d);
size *= d;
}
scalField.resize(size);
dataSet.read(scalField.data(), Hdf5Type<ScalarType>::type());
vectorizeFromRevLexOrdArray(scalField, field);
}
template <typename U>
typename std::enable_if<element<std::vector<U>>::is_number, void>::type
Hdf5Reader::readDefault(const std::string &s, std::vector<U> &x)

42
lib/serialisation/VectorUtils.h
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@@ -78,6 +78,48 @@ namespace Grid {
typedef typename std::vector<std::vector<typename TensorToVec<T>::type>> type;
};
template <typename T>
void tensorDim(std::vector<size_t> &dim, const T &t, const bool wipe = true)
{
if (wipe)
{
dim.clear();
}
}
template <typename T>
void tensorDim(std::vector<size_t> &dim, const iScalar<T> &t, const bool wipe = true)
{
if (wipe)
{
dim.clear();
}
tensorDim(dim, t._internal, false);
}
template <typename T, int N>
void tensorDim(std::vector<size_t> &dim, const iVector<T, N> &t, const bool wipe = true)
{
if (wipe)
{
dim.clear();
}
dim.push_back(N);
tensorDim(dim, t._internal[0], false);
}
template <typename T, int N>
void tensorDim(std::vector<size_t> &dim, const iMatrix<T, N> &t, const bool wipe = true)
{
if (wipe)
{
dim.clear();
}
dim.push_back(N);
dim.push_back(N);
tensorDim(dim, t._internal[0][0], false);
}
template <typename T>
typename TensorToVec<T>::type tensorToVec(const T &t)
{