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Merge pull request #1435 from smharper/collective_mpio_tally
Use collective MPI I/O for reading and writing tally results to statepoint
This commit is contained in:
Paul Romano
GitHub
commit
2e2a269f10
3 changed files with 115 additions and 87 deletions
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@ -26,13 +26,18 @@ namespace openmc {
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//==============================================================================
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void read_attr(hid_t obj_id, const char* name, hid_t mem_type_id,
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void* buffer);
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void* buffer);
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void write_attr(hid_t obj_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer);
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void read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id,
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void* buffer, bool indep);
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void write_dataset(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer, bool indep);
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hid_t mem_type_id, const void* buffer);
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void read_dataset_lowlevel(hid_t obj_id, const char* name, hid_t mem_type_id,
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hid_t mem_space_id, bool indep, void* buffer);
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void write_dataset_lowlevel(hid_t group_id, int ndim, const hsize_t* dims,
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const char* name, hid_t mem_type_id, hid_t mem_space_id, bool indep,
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const void* buffer);
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bool using_mpio_device(hid_t obj_id);
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//==============================================================================
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@ -86,34 +91,32 @@ extern "C" {
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void read_attr_string(hid_t obj_id, const char* name, size_t slen,
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char* buffer);
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void read_complex(hid_t obj_id, const char* name,
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std::complex<double>* buffer, bool indep);
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void read_double(hid_t obj_id, const char* name, double* buffer,
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bool indep);
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void read_int(hid_t obj_id, const char* name, int* buffer,
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bool indep);
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std::complex<double>* buffer, bool indep);
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void read_double(hid_t obj_id, const char* name, double* buffer, bool indep);
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void read_int(hid_t obj_id, const char* name, int* buffer, bool indep);
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void read_llong(hid_t obj_id, const char* name, long long* buffer,
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bool indep);
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void read_string(hid_t obj_id, const char* name, size_t slen,
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char* buffer, bool indep);
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bool indep);
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void read_string(hid_t obj_id, const char* name, size_t slen, char* buffer,
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bool indep);
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void read_tally_results(hid_t group_id, hsize_t n_filter,
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hsize_t n_score, double* results);
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void read_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score,
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double* results);
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void write_attr_double(hid_t obj_id, int ndim, const hsize_t* dims,
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const char* name, const double* buffer);
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const char* name, const double* buffer);
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void write_attr_int(hid_t obj_id, int ndim, const hsize_t* dims,
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const char* name, const int* buffer);
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const char* name, const int* buffer);
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void write_attr_string(hid_t obj_id, const char* name, const char* buffer);
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void write_double(hid_t group_id, int ndim, const hsize_t* dims,
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const char* name, const double* buffer, bool indep);
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const char* name, const double* buffer, bool indep);
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void write_int(hid_t group_id, int ndim, const hsize_t* dims,
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const char* name, const int* buffer, bool indep);
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const char* name, const int* buffer, bool indep);
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void write_llong(hid_t group_id, int ndim, const hsize_t* dims,
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const char* name, const long long* buffer, bool indep);
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const char* name, const long long* buffer, bool indep);
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void write_string(hid_t group_id, int ndim, const hsize_t* dims, size_t slen,
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const char* name, char const* buffer, bool indep);
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const char* name, char const* buffer, bool indep);
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void write_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score,
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const double* results);
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const double* results);
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} // extern "C"
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//==============================================================================
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@ -233,7 +236,8 @@ template<typename T> inline
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std::enable_if_t<std::is_scalar<std::decay_t<T>>::value>
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read_dataset(hid_t obj_id, const char* name, T& buffer, bool indep=false)
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{
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read_dataset(obj_id, name, H5TypeMap<T>::type_id, &buffer, indep);
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read_dataset_lowlevel(obj_id, name, H5TypeMap<T>::type_id, H5S_ALL, indep,
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&buffer);
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}
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// overload for std::string
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@ -251,9 +255,11 @@ read_dataset(hid_t obj_id, const char* name, std::string& str, bool indep=false)
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// array version
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template<typename T, std::size_t N> inline void
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read_dataset(hid_t dset, const char* name, std::array<T, N>& buffer, bool indep=false)
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read_dataset(hid_t dset, const char* name, std::array<T, N>& buffer,
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bool indep=false)
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{
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read_dataset(dset, name, H5TypeMap<T>::type_id, buffer.data(), indep);
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read_dataset_lowlevel(dset, name, H5TypeMap<T>::type_id, H5S_ALL, indep,
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buffer.data());
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}
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// vector version
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@ -267,11 +273,13 @@ void read_dataset(hid_t dset, std::vector<T>& vec, bool indep=false)
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vec.resize(shape[0]);
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// Read data into vector
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read_dataset(dset, nullptr, H5TypeMap<T>::type_id, vec.data(), indep);
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read_dataset_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, H5S_ALL, indep,
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vec.data());
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}
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template <typename T>
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void read_dataset(hid_t obj_id, const char* name, std::vector<T>& vec, bool indep=false)
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void read_dataset(hid_t obj_id, const char* name, std::vector<T>& vec,
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bool indep=false)
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{
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hid_t dset = open_dataset(obj_id, name);
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read_dataset(dset, vec, indep);
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@ -291,14 +299,17 @@ void read_dataset(hid_t dset, xt::xarray<T>& arr, bool indep=false)
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arr.resize(shape);
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// Read data from attribute
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read_dataset(dset, nullptr, H5TypeMap<T>::type_id, arr.data(), indep);
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read_dataset_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, H5S_ALL, indep,
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arr.data());
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}
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template<>
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void read_dataset(hid_t dset, xt::xarray<std::complex<double>>& arr, bool indep);
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void read_dataset(hid_t dset, xt::xarray<std::complex<double>>& arr,
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bool indep);
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template <typename T>
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void read_dataset(hid_t obj_id, const char* name, xt::xarray<T>& arr, bool indep=false)
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void read_dataset(hid_t obj_id, const char* name, xt::xarray<T>& arr,
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bool indep=false)
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{
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// Open dataset and read array
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hid_t dset = open_dataset(obj_id, name);
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@ -308,7 +319,8 @@ void read_dataset(hid_t obj_id, const char* name, xt::xarray<T>& arr, bool indep
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template <typename T, std::size_t N>
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void read_dataset(hid_t obj_id, const char* name, xt::xtensor<T, N>& arr, bool indep=false)
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void read_dataset(hid_t obj_id, const char* name, xt::xtensor<T, N>& arr,
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bool indep=false)
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{
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// Open dataset and read array
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hid_t dset = open_dataset(obj_id, name);
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@ -346,7 +358,7 @@ read_dataset(hid_t obj_id, const char* name, Position& r, bool indep=false)
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template <typename T, std::size_t N>
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inline void read_dataset_as_shape(hid_t obj_id, const char* name,
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xt::xtensor<T, N>& arr, bool indep=false)
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xt::xtensor<T, N>& arr, bool indep=false)
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{
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hid_t dset = open_dataset(obj_id, name);
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@ -357,7 +369,8 @@ inline void read_dataset_as_shape(hid_t obj_id, const char* name,
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std::vector<T> buffer(size);
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// Read data from attribute
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read_dataset(dset, nullptr, H5TypeMap<T>::type_id, buffer.data(), indep);
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read_dataset_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, H5S_ALL, indep,
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buffer.data());
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// Adapt into xarray
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arr = xt::adapt(buffer, arr.shape());
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@ -367,8 +380,8 @@ inline void read_dataset_as_shape(hid_t obj_id, const char* name,
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template <typename T, std::size_t N>
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inline void read_nd_vector(hid_t obj_id, const char* name, xt::xtensor<T, N>& result,
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bool must_have=false)
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inline void read_nd_vector(hid_t obj_id, const char* name,
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xt::xtensor<T, N>& result, bool must_have=false)
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{
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if (object_exists(obj_id, name)) {
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read_dataset_as_shape(obj_id, name, result, true);
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@ -431,7 +444,8 @@ template<typename T> inline
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std::enable_if_t<std::is_scalar<std::decay_t<T>>::value>
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write_dataset(hid_t obj_id, const char* name, T buffer)
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{
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write_dataset(obj_id, 0, nullptr, name, H5TypeMap<T>::type_id, &buffer, false);
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write_dataset_lowlevel(obj_id, 0, nullptr, name, H5TypeMap<T>::type_id,
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H5S_ALL, false, &buffer);
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}
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inline void
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@ -444,11 +458,13 @@ template<typename T, std::size_t N> inline void
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write_dataset(hid_t obj_id, const char* name, const std::array<T, N>& buffer)
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{
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hsize_t dims[] {N};
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write_dataset(obj_id, 1, dims, name, H5TypeMap<T>::type_id, buffer.data(), false);
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write_dataset_lowlevel(obj_id, 1, dims, name, H5TypeMap<T>::type_id,
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H5S_ALL, false, buffer.data());
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}
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inline void
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write_dataset(hid_t obj_id, const char* name, const std::vector<std::string>& buffer)
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write_dataset(hid_t obj_id, const char* name,
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const std::vector<std::string>& buffer)
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{
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auto n {buffer.size()};
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hsize_t dims[] {n};
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@ -477,7 +493,8 @@ template<typename T> inline void
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write_dataset(hid_t obj_id, const char* name, const std::vector<T>& buffer)
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{
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hsize_t dims[] {buffer.size()};
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write_dataset(obj_id, 1, dims, name, H5TypeMap<T>::type_id, buffer.data(), false);
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write_dataset_lowlevel(obj_id, 1, dims, name, H5TypeMap<T>::type_id,
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H5S_ALL, false, buffer.data());
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}
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// Template for xarray, xtensor, etc.
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@ -487,8 +504,8 @@ write_dataset(hid_t obj_id, const char* name, const xt::xcontainer<D>& arr)
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using T = typename D::value_type;
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auto s = arr.shape();
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std::vector<hsize_t> dims {s.cbegin(), s.cend()};
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write_dataset(obj_id, dims.size(), dims.data(), name, H5TypeMap<T>::type_id,
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arr.data(), false);
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write_dataset_lowlevel(obj_id, dims.size(), dims.data(), name,
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H5TypeMap<T>::type_id, H5S_ALL, false, arr.data());
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}
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inline void
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@ -49,7 +49,8 @@ get_shape(hid_t obj_id, hsize_t* dims)
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} else if (type == H5I_ATTR) {
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dspace = H5Aget_space(obj_id);
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} else {
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throw std::runtime_error{"Expected dataset or attribute in call to get_shape."};
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throw std::runtime_error{
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"Expected dataset or attribute in call to get_shape."};
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}
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H5Sget_simple_extent_dims(dspace, dims, nullptr);
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H5Sclose(dspace);
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@ -74,7 +75,8 @@ std::vector<hsize_t> object_shape(hid_t obj_id)
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} else if (type == H5I_ATTR) {
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dspace = H5Aget_space(obj_id);
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} else {
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throw std::runtime_error{"Expected dataset or attribute in call to object_shape."};
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throw std::runtime_error{
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"Expected dataset or attribute in call to object_shape."};
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}
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int n = H5Sget_simple_extent_ndims(dspace);
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@ -471,8 +473,8 @@ read_attr_string(hid_t obj_id, const char* name, size_t slen, char* buffer)
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void
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read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id,
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void* buffer, bool indep)
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read_dataset_lowlevel(hid_t obj_id, const char* name, hid_t mem_type_id,
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hid_t mem_space_id, bool indep, void* buffer)
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{
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hid_t dset = obj_id;
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if (name) dset = open_dataset(obj_id, name);
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@ -487,11 +489,11 @@ read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id,
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H5Pset_dxpl_mpio(plist, data_xfer_mode);
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// Read data
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H5Dread(dset, mem_type_id, H5S_ALL, H5S_ALL, plist, buffer);
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H5Dread(dset, mem_type_id, mem_space_id, H5S_ALL, plist, buffer);
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H5Pclose(plist);
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#endif
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} else {
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H5Dread(dset, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
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H5Dread(dset, mem_type_id, mem_space_id, H5S_ALL, H5P_DEFAULT, buffer);
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}
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if (name) H5Dclose(dset);
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@ -520,26 +522,28 @@ void read_dataset(hid_t dset, xt::xarray<std::complex<double>>& arr, bool indep)
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void
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read_double(hid_t obj_id, const char* name, double* buffer, bool indep)
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{
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read_dataset(obj_id, name, H5T_NATIVE_DOUBLE, buffer, indep);
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read_dataset_lowlevel(obj_id, name, H5T_NATIVE_DOUBLE, H5S_ALL, indep,
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buffer);
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}
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void
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read_int(hid_t obj_id, const char* name, int* buffer, bool indep)
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{
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read_dataset(obj_id, name, H5T_NATIVE_INT, buffer, indep);
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read_dataset_lowlevel(obj_id, name, H5T_NATIVE_INT, H5S_ALL, indep, buffer);
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}
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void
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read_llong(hid_t obj_id, const char* name, long long* buffer, bool indep)
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{
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read_dataset(obj_id, name, H5T_NATIVE_LLONG, buffer, indep);
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read_dataset_lowlevel(obj_id, name, H5T_NATIVE_LLONG, H5S_ALL, indep, buffer);
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}
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void
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read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, bool indep)
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read_string(hid_t obj_id, const char* name, size_t slen, char* buffer,
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bool indep)
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{
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// Create datatype for a string
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hid_t datatype = H5Tcopy(H5T_C_S1);
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@ -548,7 +552,7 @@ read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, bool inde
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H5Tset_strpad(datatype, H5T_STR_NULLPAD);
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// Read data into buffer
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read_dataset(obj_id, name, datatype, buffer, indep);
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read_dataset_lowlevel(obj_id, name, datatype, H5S_ALL, indep, buffer);
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// Free resources
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H5Tclose(datatype);
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@ -556,7 +560,8 @@ read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, bool inde
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void
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read_complex(hid_t obj_id, const char* name, std::complex<double>* buffer, bool indep)
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read_complex(hid_t obj_id, const char* name, std::complex<double>* buffer,
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bool indep)
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{
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// Create compound datatype for complex numbers
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struct complex_t {
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@ -569,7 +574,7 @@ read_complex(hid_t obj_id, const char* name, std::complex<double>* buffer, bool
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H5Tinsert(complex_id, "i", HOFFSET(complex_t, im), H5T_NATIVE_DOUBLE);
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// Read data
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read_dataset(obj_id, name, complex_id, buffer, indep);
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read_dataset_lowlevel(obj_id, name, complex_id, H5S_ALL, indep, buffer);
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// Free resources
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H5Tclose(complex_id);
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@ -577,21 +582,22 @@ read_complex(hid_t obj_id, const char* name, std::complex<double>* buffer, bool
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void
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read_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score, double* results)
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read_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score,
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double* results)
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{
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// Create dataspace for hyperslab in memory
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hsize_t dims[] {n_filter, n_score, 3};
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hsize_t start[] {0, 0, 1};
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hsize_t count[] {n_filter, n_score, 2};
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hid_t memspace = H5Screate_simple(3, dims, nullptr);
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constexpr int ndim = 3;
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hsize_t dims[ndim] {n_filter, n_score, 3};
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hsize_t start[ndim] {0, 0, 1};
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hsize_t count[ndim] {n_filter, n_score, 2};
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hid_t memspace = H5Screate_simple(ndim, dims, nullptr);
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H5Sselect_hyperslab(memspace, H5S_SELECT_SET, start, nullptr, count, nullptr);
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// Create and write dataset
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hid_t dset = H5Dopen(group_id, "results", H5P_DEFAULT);
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H5Dread(dset, H5T_NATIVE_DOUBLE, memspace, H5S_ALL, H5P_DEFAULT, results);
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||||
// Read the dataset
|
||||
read_dataset_lowlevel(group_id, "results", H5T_NATIVE_DOUBLE, memspace,
|
||||
false, results);
|
||||
|
||||
// Free resources
|
||||
H5Dclose(dset);
|
||||
H5Sclose(memspace);
|
||||
}
|
||||
|
||||
|
|
@ -654,8 +660,9 @@ write_attr_string(hid_t obj_id, const char* name, const char* buffer)
|
|||
|
||||
|
||||
void
|
||||
write_dataset(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
|
||||
hid_t mem_type_id, const void* buffer, bool indep)
|
||||
write_dataset_lowlevel(hid_t group_id, int ndim, const hsize_t* dims,
|
||||
const char* name, hid_t mem_type_id, hid_t mem_space_id, bool indep,
|
||||
const void* buffer)
|
||||
{
|
||||
// If array is given, create a simple dataspace. Otherwise, create a scalar
|
||||
// datascape.
|
||||
|
|
@ -679,11 +686,11 @@ write_dataset(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
|
|||
H5Pset_dxpl_mpio(plist, data_xfer_mode);
|
||||
|
||||
// Write data
|
||||
H5Dwrite(dset, mem_type_id, H5S_ALL, H5S_ALL, plist, buffer);
|
||||
H5Dwrite(dset, mem_type_id, mem_space_id, H5S_ALL, plist, buffer);
|
||||
H5Pclose(plist);
|
||||
#endif
|
||||
} else {
|
||||
H5Dwrite(dset, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
|
||||
H5Dwrite(dset, mem_type_id, mem_space_id, H5S_ALL, H5P_DEFAULT, buffer);
|
||||
}
|
||||
|
||||
// Free resources
|
||||
|
|
@ -696,7 +703,8 @@ void
|
|||
write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
|
||||
const double* buffer, bool indep)
|
||||
{
|
||||
write_dataset(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, buffer, indep);
|
||||
write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, H5S_ALL,
|
||||
indep, buffer);
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -704,7 +712,8 @@ void
|
|||
write_int(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
|
||||
const int* buffer, bool indep)
|
||||
{
|
||||
write_dataset(group_id, ndim, dims, name, H5T_NATIVE_INT, buffer, indep);
|
||||
write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_INT, H5S_ALL,
|
||||
indep, buffer);
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -712,7 +721,8 @@ void
|
|||
write_llong(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
|
||||
const long long* buffer, bool indep)
|
||||
{
|
||||
write_dataset(group_id, ndim, dims, name, H5T_NATIVE_LLONG, buffer, indep);
|
||||
write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_LLONG, H5S_ALL,
|
||||
indep, buffer);
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -725,7 +735,8 @@ write_string(hid_t group_id, int ndim, const hsize_t* dims, size_t slen,
|
|||
hid_t datatype = H5Tcopy(H5T_C_S1);
|
||||
H5Tset_size(datatype, slen);
|
||||
|
||||
write_dataset(group_id, ndim, dims, name, datatype, buffer, indep);
|
||||
write_dataset_lowlevel(group_id, ndim, dims, name, datatype, H5S_ALL, indep,
|
||||
buffer);
|
||||
|
||||
// Free resources
|
||||
H5Tclose(datatype);
|
||||
|
|
@ -734,34 +745,34 @@ write_string(hid_t group_id, int ndim, const hsize_t* dims, size_t slen,
|
|||
|
||||
|
||||
void
|
||||
write_string(hid_t group_id, const char* name, const std::string& buffer, bool indep)
|
||||
write_string(hid_t group_id, const char* name, const std::string& buffer,
|
||||
bool indep)
|
||||
{
|
||||
write_string(group_id, 0, nullptr, buffer.length(), name, buffer.c_str(), indep);
|
||||
write_string(group_id, 0, nullptr, buffer.length(), name, buffer.c_str(),
|
||||
indep);
|
||||
}
|
||||
|
||||
|
||||
void
|
||||
write_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score, const double* results)
|
||||
write_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score,
|
||||
const double* results)
|
||||
{
|
||||
// Set dimensions of sum/sum_sq hyperslab to store
|
||||
hsize_t count[] {n_filter, n_score, 2};
|
||||
hid_t dspace = H5Screate_simple(3, count, nullptr);
|
||||
constexpr int ndim = 3;
|
||||
hsize_t count[ndim] {n_filter, n_score, 2};
|
||||
|
||||
// Set dimensions of results array
|
||||
hsize_t dims[] {n_filter, n_score, 3};
|
||||
hsize_t start[] {0, 0, 1};
|
||||
hid_t memspace = H5Screate_simple(3, dims, nullptr);
|
||||
hsize_t dims[ndim] {n_filter, n_score, 3};
|
||||
hsize_t start[ndim] {0, 0, 1};
|
||||
hid_t memspace = H5Screate_simple(ndim, dims, nullptr);
|
||||
H5Sselect_hyperslab(memspace, H5S_SELECT_SET, start, nullptr, count, nullptr);
|
||||
|
||||
// Create and write dataset
|
||||
hid_t dset = H5Dcreate(group_id, "results", H5T_NATIVE_DOUBLE, dspace,
|
||||
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
H5Dwrite(dset, H5T_NATIVE_DOUBLE, memspace, H5S_ALL, H5P_DEFAULT, results);
|
||||
write_dataset_lowlevel(group_id, ndim, count, "results", H5T_NATIVE_DOUBLE,
|
||||
memspace, false, results);
|
||||
|
||||
// Free resources
|
||||
H5Dclose(dset);
|
||||
H5Sclose(memspace);
|
||||
H5Sclose(dspace);
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -420,8 +420,8 @@ void load_state_point()
|
|||
if (mpi::master) {
|
||||
#endif
|
||||
// Read global tally data
|
||||
read_dataset(file_id, "global_tallies", H5T_NATIVE_DOUBLE,
|
||||
simulation::global_tallies.data(), false);
|
||||
read_dataset_lowlevel(file_id, "global_tallies", H5T_NATIVE_DOUBLE,
|
||||
H5S_ALL, false, simulation::global_tallies.data());
|
||||
|
||||
// Check if tally results are present
|
||||
bool present;
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue