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Use collective IO for read/write tally results

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This commit is contained in:
Sterling Harper 2019-12-13 11:51:22 -05:00
parent bc08d8a6b8
commit 6a2f3ee2ef
3 changed files with 54 additions and 52 deletions
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32
include/openmc/hdf5_interface.h
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@ -32,10 +32,11 @@ void write_attr(hid_t obj_id, int ndim, const hsize_t* dims, const char* name,
hid_t mem_type_id, const void* buffer);
void read_dataset_lowlevel(hid_t obj_id, const char* name, hid_t mem_type_id,
void* buffer, bool indep);
hid_t mem_space_id, bool indep, void* buffer);
void write_dataset_lowlevel(hid_t group_id, int ndim, const hsize_t* dims,
const char* name, hid_t mem_type_id, const void* buffer, bool indep);
const char* name, hid_t mem_type_id, hid_t mem_space_id, bool indep,
const void* buffer);
bool using_mpio_device(hid_t obj_id);
@ -235,7 +236,8 @@ template<typename T> inline
std::enable_if_t<std::is_scalar<std::decay_t<T>>::value>
read_dataset(hid_t obj_id, const char* name, T& buffer, bool indep=false)
{
read_dataset_lowlevel(obj_id, name, H5TypeMap<T>::type_id, &buffer, indep);
read_dataset_lowlevel(obj_id, name, H5TypeMap<T>::type_id, H5S_ALL, indep,
&buffer);
}
// overload for std::string
@ -256,8 +258,8 @@ template<typename T, std::size_t N> inline void
read_dataset(hid_t dset, const char* name, std::array<T, N>& buffer,
bool indep=false)
{
read_dataset_lowlevel(dset, name, H5TypeMap<T>::type_id, buffer.data(),
indep);
read_dataset_lowlevel(dset, name, H5TypeMap<T>::type_id, H5S_ALL, indep,
buffer.data());
}
// vector version
@ -271,8 +273,8 @@ void read_dataset(hid_t dset, std::vector<T>& vec, bool indep=false)
vec.resize(shape[0]);
// Read data into vector
read_dataset_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, vec.data(),
indep);
read_dataset_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, H5S_ALL, indep,
vec.data());
}
template <typename T>
@ -297,8 +299,8 @@ void read_dataset(hid_t dset, xt::xarray<T>& arr, bool indep=false)
arr.resize(shape);
// Read data from attribute
read_dataset_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, arr.data(),
indep);
read_dataset_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, H5S_ALL, indep,
arr.data());
}
template<>
@ -367,8 +369,8 @@ inline void read_dataset_as_shape(hid_t obj_id, const char* name,
std::vector<T> buffer(size);
// Read data from attribute
read_dataset_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, buffer.data(),
indep);
read_dataset_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, H5S_ALL, indep,
buffer.data());
// Adapt into xarray
arr = xt::adapt(buffer, arr.shape());
@ -443,7 +445,7 @@ std::enable_if_t<std::is_scalar<std::decay_t<T>>::value>
write_dataset(hid_t obj_id, const char* name, T buffer)
{
write_dataset_lowlevel(obj_id, 0, nullptr, name, H5TypeMap<T>::type_id,
&buffer, false);
H5S_ALL, false, &buffer);
}
inline void
@ -457,7 +459,7 @@ write_dataset(hid_t obj_id, const char* name, const std::array<T, N>& buffer)
{
hsize_t dims[] {N};
write_dataset_lowlevel(obj_id, 1, dims, name, H5TypeMap<T>::type_id,
buffer.data(), false);
H5S_ALL, false, buffer.data());
}
inline void
@ -492,7 +494,7 @@ write_dataset(hid_t obj_id, const char* name, const std::vector<T>& buffer)
{
hsize_t dims[] {buffer.size()};
write_dataset_lowlevel(obj_id, 1, dims, name, H5TypeMap<T>::type_id,
buffer.data(), false);
H5S_ALL, false, buffer.data());
}
// Template for xarray, xtensor, etc.
@ -503,7 +505,7 @@ write_dataset(hid_t obj_id, const char* name, const xt::xcontainer<D>& arr)
auto s = arr.shape();
std::vector<hsize_t> dims {s.cbegin(), s.cend()};
write_dataset_lowlevel(obj_id, dims.size(), dims.data(), name,
H5TypeMap<T>::type_id, arr.data(), false);
H5TypeMap<T>::type_id, H5S_ALL, false, arr.data());
}
inline void