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Merge pull request #4352 from quantumsteve/hdf5_version
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Use HDF5 1.10 API
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@ye-luo
ye-luo authored Dec 1, 2022
2 parents 2859e58 + 4633aff commit 3c3b92c
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Showing 7 changed files with 27 additions and 26 deletions.
4 changes: 2 additions & 2 deletions CMakeLists.txt
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Expand Up @@ -653,7 +653,7 @@ else()
set(HDF5_USE_STATIC_LIBRARIES off)
endif()

find_package(HDF5 COMPONENTS C)
find_package(HDF5 1.10 COMPONENTS C)

if(HDF5_FOUND)
if(HDF5_IS_PARALLEL)
Expand Down Expand Up @@ -694,7 +694,7 @@ if(HDF5_FOUND)

add_library(IO::HDF5 INTERFACE IMPORTED)
target_include_directories(IO::HDF5 INTERFACE "${HDF5_INCLUDE_DIR}")
target_compile_definitions(IO::HDF5 INTERFACE "H5_USE_16_API")
target_compile_definitions(IO::HDF5 INTERFACE "H5_USE_110_API")
target_link_libraries(IO::HDF5 INTERFACE "${HDF5_LIBRARIES}")
if(ENABLE_PHDF5)
target_compile_definitions(IO::HDF5 INTERFACE "ENABLE_PHDF5")
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -26,7 +26,7 @@ particular emphasis is placed on code quality and reproducibility.
* CMake v3.17.0 or later, build utility, http://www.cmake.org
* BLAS/LAPACK, numerical library. Use vendor and platform-optimized libraries.
* LibXml2, XML parser, http://xmlsoft.org/
* HDF5, portable I/O library, http://www.hdfgroup.org/HDF5/
* HDF5 v1.10.0 or later, portable I/O library, http://www.hdfgroup.org/HDF5/
* BOOST v1.61.0 or newer, peer-reviewed portable C++ source libraries, http://www.boost.org
* FFTW, FFT library, http://www.fftw.org/
* MPI, parallel library. Optional, but a near requirement for production calculations.
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3 changes: 2 additions & 1 deletion src/QMCHamiltonians/SkEstimator.cpp
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Expand Up @@ -128,7 +128,8 @@ void SkEstimator::registerCollectables(std::vector<ObservableHelper>& h5desc, hd
kdims[1] = OHMMS_DIM;
std::string kpath = name_ + "/kpoints";
hid_t k_space = H5Screate_simple(2, kdims, NULL);
hid_t k_set = H5Dcreate(file.getFileID(), kpath.c_str(), H5T_NATIVE_DOUBLE, k_space, H5P_DEFAULT);
hid_t k_set =
H5Dcreate(file.getFileID(), kpath.c_str(), H5T_NATIVE_DOUBLE, k_space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t mem_space = H5Screate_simple(2, kdims, NULL);
auto* ptr = &(sourcePtcl->getSimulationCell().getKLists().kpts_cart[0][0]);
herr_t ret = H5Dwrite(k_set, H5T_NATIVE_DOUBLE, mem_space, k_space, H5P_DEFAULT, ptr);
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4 changes: 2 additions & 2 deletions src/QMCWaveFunctions/PlaneWave/PWParameterSet.cpp
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Expand Up @@ -76,7 +76,7 @@ bool PWParameterSet::getEigVectorType(hid_t h)
oss << "/" << spinTag << 0;
oss << "/eigenvector";
hsize_t dimTot[4];
hid_t dataset = H5Dopen(h, oss.str().c_str());
hid_t dataset = H5Dopen(h, oss.str().c_str(), H5P_DEFAULT);
hid_t dataspace = H5Dget_space(dataset);
rank = H5Sget_simple_extent_ndims(dataspace);
int status_n = H5Sget_simple_extent_dims(dataspace, dimTot, NULL);
Expand Down Expand Up @@ -184,7 +184,7 @@ void PWParameterSet::checkVersion(hdf_archive& h)
{
if (is_manager())
{
hid_t dataset = H5Dopen(h.getFileID(), "version");
hid_t dataset = H5Dopen(h.getFileID(), "version", H5P_DEFAULT);
hid_t datatype = H5Dget_type(dataset);
H5T_class_t classtype = H5Tget_class(datatype);
H5Tclose(datatype);
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2 changes: 1 addition & 1 deletion src/io/hdf/hdf_archive.h
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Expand Up @@ -317,7 +317,7 @@ class hdf_archive
if (Mode[NOIO])
return;
hid_t p = group_id.empty() ? file_id : group_id.top();
herr_t status = H5Gunlink(p, aname.c_str());
herr_t status = H5Ldelete(p, aname.c_str(), H5P_DEFAULT);
}
};

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12 changes: 6 additions & 6 deletions src/io/hdf/hdf_stl.h
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Expand Up @@ -96,7 +96,7 @@ struct h5data_proxy<std::string>

inline bool read(data_type& ref, hid_t grp, const std::string& aname, hid_t xfer_plist = H5P_DEFAULT)
{
hid_t dataset = H5Dopen(grp, aname.c_str());
hid_t dataset = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
if (dataset > -1)
{
hid_t datatype = H5Dget_type(dataset);
Expand Down Expand Up @@ -127,11 +127,11 @@ struct h5data_proxy<std::string>
hsize_t dim = 1;

herr_t ret = -1;
hid_t h1 = H5Dopen(grp, aname.c_str());
hid_t h1 = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
if (h1 < 0) // missing create one
{
hid_t dataspace = H5Screate_simple(1, &dim, NULL);
hid_t dataset = H5Dcreate(grp, aname.c_str(), str80, dataspace, H5P_DEFAULT);
hid_t dataset = H5Dcreate(grp, aname.c_str(), str80, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
ret = H5Dwrite(dataset, str80, H5S_ALL, H5S_ALL, xfer_plist, ref.data());
H5Sclose(dataspace);
H5Dclose(dataset);
Expand All @@ -157,7 +157,7 @@ struct h5data_proxy<std::vector<std::string>>
{
hid_t datatype = H5Tcopy(H5T_C_S1);
H5Tset_size(datatype, H5T_VARIABLE);
hid_t dataset = H5Dopen(grp, aname.c_str());
hid_t dataset = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
std::vector<char*> char_list;
herr_t ret = -1;
if (dataset > -1)
Expand Down Expand Up @@ -198,12 +198,12 @@ struct h5data_proxy<std::vector<std::string>>
for (int i = 0; i < ref.size(); i++)
char_list.push_back(ref[i].data());

hid_t h1 = H5Dopen(grp, aname.c_str());
hid_t h1 = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
herr_t ret = -1;
if (h1 < 0) // missing create one
{
hid_t dataspace = H5Screate_simple(1, &dim, NULL);
hid_t dataset = H5Dcreate(grp, aname.c_str(), datatype, dataspace, H5P_DEFAULT);
hid_t dataset = H5Dcreate(grp, aname.c_str(), datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
ret = H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, xfer_plist, char_list.data());
H5Sclose(dataspace);
H5Dclose(dataset);
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26 changes: 13 additions & 13 deletions src/io/hdf/hdf_wrapper_functions.h
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Expand Up @@ -47,7 +47,7 @@ inline bool getDataShape(hid_t grp, const std::string& aname, std::vector<IT>& s
using TSpaceType = h5_space_type<T, 0>;
TSpaceType TSpace;

hid_t h1 = H5Dopen(grp, aname.c_str());
hid_t h1 = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
hid_t dataspace = H5Dget_space(h1);
int rank = H5Sget_simple_extent_ndims(dataspace);

Expand Down Expand Up @@ -124,7 +124,7 @@ inline bool h5d_read(hid_t grp, const std::string& aname, T* first, hid_t xfer_p
{
if (grp < 0)
return true;
hid_t h1 = H5Dopen(grp, aname.c_str());
hid_t h1 = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
if (h1 < 0)
return false;
hid_t h5d_type_id = get_h5_datatype(*first);
Expand All @@ -144,12 +144,12 @@ inline bool h5d_write(hid_t grp,
if (grp < 0)
return true;
hid_t h5d_type_id = get_h5_datatype(*first);
hid_t h1 = H5Dopen(grp, aname.c_str());
hid_t h1 = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
herr_t ret = -1;
if (h1 < 0) //missing create one
{
hid_t dataspace = H5Screate_simple(ndims, dims, NULL);
hid_t dataset = H5Dcreate(grp, aname.c_str(), h5d_type_id, dataspace, H5P_DEFAULT);
hid_t dataset = H5Dcreate(grp, aname.c_str(), h5d_type_id, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
ret = H5Dwrite(dataset, h5d_type_id, H5S_ALL, H5S_ALL, xfer_plist, first);
H5Sclose(dataspace);
H5Dclose(dataset);
Expand Down Expand Up @@ -180,7 +180,7 @@ bool h5d_read(hid_t grp,
{
if (grp < 0)
return true;
hid_t h1 = H5Dopen(grp, aname.c_str());
hid_t h1 = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
if (h1 < 0)
return false;
//herr_t ret = H5Dread(h1, h5d_type_id, H5S_ALL, H5S_ALL, xfer_plist, first);
Expand Down Expand Up @@ -223,15 +223,15 @@ inline bool h5d_write(hid_t grp,
if (grp < 0)
return true;
hid_t h5d_type_id = get_h5_datatype(*first);
hid_t h1 = H5Dopen(grp, aname.c_str());
hid_t h1 = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
hid_t filespace, memspace;
herr_t ret = -1;

const std::vector<hsize_t> ones(ndims, 1);
if (h1 < 0) //missing create one
{
hid_t dataspace = H5Screate_simple(ndims, gcounts, NULL);
hid_t dataset = H5Dcreate(grp, aname.c_str(), h5d_type_id, dataspace, H5P_DEFAULT);
hid_t dataset = H5Dcreate(grp, aname.c_str(), h5d_type_id, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

hid_t filespace = H5Dget_space(dataset);
ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offsets, NULL, ones.data(), counts);
Expand Down Expand Up @@ -276,7 +276,7 @@ bool h5d_read(hid_t grp,
{
if (grp < 0)
return true;
hid_t h1 = H5Dopen(grp, aname.c_str());
hid_t h1 = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
if (h1 < 0)
return false;

Expand Down Expand Up @@ -320,14 +320,14 @@ inline bool h5d_write(hid_t grp,
<< *(mem_gcounts + 2) << " " << *mem_counts << " " << *(mem_counts + 1) << " " << *(mem_counts + 2) << " "
<< *mem_offsets << " " << *(mem_offsets + 1) << " " << *(mem_offsets + 2) << " " << std::endl;
hid_t h5d_type_id = get_h5_datatype(*first);
hid_t h1 = H5Dopen(grp, aname.c_str());
hid_t h1 = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
herr_t ret = -1;

const std::vector<hsize_t> ones(std::max(ndims, mem_ndims), 1);
if (h1 < 0) //missing create one
{
hid_t dataspace = H5Screate_simple(ndims, gcounts, NULL);
hid_t dataset = H5Dcreate(grp, aname.c_str(), h5d_type_id, dataspace, H5P_DEFAULT);
hid_t dataset = H5Dcreate(grp, aname.c_str(), h5d_type_id, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

hid_t filespace = H5Dget_space(dataset);
ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offsets, NULL, ones.data(), counts);
Expand Down Expand Up @@ -373,7 +373,7 @@ inline bool h5d_append(hid_t grp,
hid_t h5d_type_id = get_h5_datatype(*first);
hid_t dataspace;
hid_t memspace;
hid_t dataset = H5Dopen(grp, aname.c_str());
hid_t dataset = H5Dopen(grp, aname.c_str(), H5P_DEFAULT);
std::vector<hsize_t> max_dims(ndims);
max_dims[0] = H5S_UNLIMITED;
for (int d = 1; d < ndims; ++d)
Expand All @@ -397,7 +397,7 @@ inline bool h5d_append(hid_t grp,
// set chunk size
hid_t cs = H5Pset_chunk(p, ndims, chunk_dims.data());
// create the dataset
dataset = H5Dcreate2(grp, aname.c_str(), h5d_type_id, dataspace, H5P_DEFAULT, p, H5P_DEFAULT);
dataset = H5Dcreate(grp, aname.c_str(), h5d_type_id, dataspace, H5P_DEFAULT, p, H5P_DEFAULT);
// create memory dataspace, size of current buffer
memspace = H5Screate_simple(ndims, dims, NULL);
// write the data for the first time
Expand Down Expand Up @@ -438,7 +438,7 @@ inline bool h5d_append(hid_t grp,
start[0] = current;
end[0] = start[0] + dims[0];
//extend the dataset (file)
herr_t he = H5Dextend(dataset, end.data());
herr_t he = H5Dset_extent(dataset, end.data());
//get the corresponding dataspace (filespace)
dataspace = H5Dget_space(dataset);
//set the extent
Expand Down

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