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https://github.com/openmc-dev/openmc.git
synced 2026-07-26 21:25:36 -04:00
Use collective IO for read/write tally results
This commit is contained in:
Sterling Harper
parent
bc08d8a6b8
commit
6a2f3ee2ef
3 changed files with 54 additions and 52 deletions
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@ -32,10 +32,11 @@ 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_lowlevel(hid_t obj_id, const char* name, hid_t mem_type_id,
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void* buffer, bool indep);
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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, const void* buffer, bool indep);
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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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@ -235,7 +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_lowlevel(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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@ -256,8 +258,8 @@ 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,
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bool indep=false)
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{
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read_dataset_lowlevel(dset, name, H5TypeMap<T>::type_id, buffer.data(),
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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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@ -271,8 +273,8 @@ 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_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, vec.data(),
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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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@ -297,8 +299,8 @@ 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_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, arr.data(),
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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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@ -367,8 +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_lowlevel(dset, nullptr, H5TypeMap<T>::type_id, buffer.data(),
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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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@ -443,7 +445,7 @@ 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_lowlevel(obj_id, 0, nullptr, name, H5TypeMap<T>::type_id,
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&buffer, false);
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H5S_ALL, false, &buffer);
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}
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inline void
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@ -457,7 +459,7 @@ 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_lowlevel(obj_id, 1, dims, name, H5TypeMap<T>::type_id,
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buffer.data(), false);
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H5S_ALL, false, buffer.data());
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}
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inline void
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@ -492,7 +494,7 @@ 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_lowlevel(obj_id, 1, dims, name, H5TypeMap<T>::type_id,
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buffer.data(), false);
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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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@ -503,7 +505,7 @@ write_dataset(hid_t obj_id, const char* name, const xt::xcontainer<D>& arr)
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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_lowlevel(obj_id, dims.size(), dims.data(), name,
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H5TypeMap<T>::type_id, arr.data(), false);
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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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@ -474,7 +474,7 @@ 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_lowlevel(hid_t obj_id, const char* name, hid_t mem_type_id,
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void* buffer, bool indep)
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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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@ -489,11 +489,11 @@ read_dataset_lowlevel(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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@ -522,21 +522,22 @@ 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_lowlevel(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_lowlevel(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_lowlevel(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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@ -551,7 +552,7 @@ read_string(hid_t obj_id, const char* name, size_t slen, char* buffer,
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H5Tset_strpad(datatype, H5T_STR_NULLPAD);
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// Read data into buffer
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read_dataset_lowlevel(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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@ -573,7 +574,7 @@ read_complex(hid_t obj_id, const char* name, std::complex<double>* buffer,
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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_lowlevel(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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@ -585,18 +586,18 @@ 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
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read_dataset_lowlevel(group_id, "results", H5T_NATIVE_DOUBLE, memspace,
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false, results);
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// Free resources
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H5Dclose(dset);
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H5Sclose(memspace);
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}
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@ -660,7 +661,8 @@ write_attr_string(hid_t obj_id, const char* name, const char* buffer)
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void
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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, const void* buffer, bool indep)
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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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{
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// If array is given, create a simple dataspace. Otherwise, create a scalar
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// datascape.
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@ -684,11 +686,11 @@ write_dataset_lowlevel(hid_t group_id, int ndim, const hsize_t* dims,
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H5Pset_dxpl_mpio(plist, data_xfer_mode);
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// Write data
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H5Dwrite(dset, mem_type_id, H5S_ALL, H5S_ALL, plist, buffer);
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H5Dwrite(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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H5Dwrite(dset, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
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H5Dwrite(dset, mem_type_id, mem_space_id, H5S_ALL, H5P_DEFAULT, buffer);
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}
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// Free resources
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@ -701,8 +703,8 @@ void
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write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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const double* buffer, bool indep)
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{
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write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, buffer,
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indep);
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write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, H5S_ALL,
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indep, buffer);
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}
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@ -710,8 +712,8 @@ void
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write_int(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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const int* buffer, bool indep)
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{
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write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_INT, buffer,
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indep);
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write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_INT, H5S_ALL,
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indep, buffer);
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}
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@ -719,8 +721,8 @@ void
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write_llong(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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const long long* buffer, bool indep)
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{
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write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_LLONG, buffer,
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indep);
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write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_LLONG, H5S_ALL,
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indep, buffer);
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}
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@ -733,7 +735,8 @@ write_string(hid_t group_id, int ndim, const hsize_t* dims, size_t slen,
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hid_t datatype = H5Tcopy(H5T_C_S1);
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H5Tset_size(datatype, slen);
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write_dataset_lowlevel(group_id, ndim, dims, name, datatype, buffer, indep);
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write_dataset_lowlevel(group_id, ndim, dims, name, datatype, H5S_ALL, indep,
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buffer);
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// Free resources
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H5Tclose(datatype);
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@ -755,24 +758,21 @@ 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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{
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// Set dimensions of sum/sum_sq hyperslab to store
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hsize_t count[] {n_filter, n_score, 2};
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hid_t dspace = H5Screate_simple(3, count, nullptr);
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constexpr int ndim = 3;
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hsize_t count[ndim] {n_filter, n_score, 2};
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// Set dimensions of results array
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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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hid_t memspace = H5Screate_simple(3, dims, nullptr);
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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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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 = H5Dcreate(group_id, "results", H5T_NATIVE_DOUBLE, dspace,
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H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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H5Dwrite(dset, H5T_NATIVE_DOUBLE, memspace, H5S_ALL, H5P_DEFAULT, results);
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write_dataset_lowlevel(group_id, ndim, count, "results", H5T_NATIVE_DOUBLE,
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memspace, false, results);
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// Free resources
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H5Dclose(dset);
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H5Sclose(memspace);
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H5Sclose(dspace);
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}
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@ -419,7 +419,7 @@ void load_state_point()
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#endif
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// Read global tally data
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read_dataset_lowlevel(file_id, "global_tallies", H5T_NATIVE_DOUBLE,
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simulation::global_tallies.data(), false);
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H5S_ALL, false, simulation::global_tallies.data());
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// Check if tally results are present
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bool present;
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