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https://github.com/openmc-dev/openmc.git
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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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