From c74f4738c12c4bf459335508743439efabc1d735 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Tue, 17 Apr 2018 14:08:59 -0500 Subject: [PATCH] Use HDF5 file_open from C side (and remove file_create) --- CMakeLists.txt | 1 + src/error.h | 5 +- src/hdf5_interface.F90 | 98 ++++--------------- src/hdf5_interface.cpp | 212 ++++++++++++++++++++++++++++++++++++++++ src/hdf5_interface.h | 208 +++------------------------------------ src/particle_header.F90 | 2 +- src/plot.F90 | 2 +- src/source.F90 | 4 +- src/state_point.F90 | 8 +- src/summary.F90 | 2 +- src/track_output.F90 | 2 +- src/volume_calc.F90 | 4 +- 12 files changed, 261 insertions(+), 287 deletions(-) create mode 100644 src/hdf5_interface.cpp diff --git a/CMakeLists.txt b/CMakeLists.txt index ca3d83717..ff7a3334b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -435,6 +435,7 @@ set(LIBOPENMC_FORTRAN_SRC set(LIBOPENMC_CXX_SRC src/error.h src/hdf5_interface.h + src/hdf5_interface.cpp src/random_lcg.cpp src/random_lcg.h src/simulation.cpp diff --git a/src/error.h b/src/error.h index 4c3373b3e..91c272745 100644 --- a/src/error.h +++ b/src/error.h @@ -12,18 +12,19 @@ namespace openmc { extern "C" void fatal_error_from_c(const char *message, int message_len); +inline void fatal_error(const char *message) { fatal_error_from_c(message, strlen(message)); } - +inline void fatal_error(const std::string &message) { fatal_error_from_c(message.c_str(), message.length()); } - +inline void fatal_error(const std::stringstream &message) { std::string out {message.str()}; diff --git a/src/hdf5_interface.F90 b/src/hdf5_interface.F90 index 410149d9e..0c8d22239 100644 --- a/src/hdf5_interface.F90 +++ b/src/hdf5_interface.F90 @@ -19,6 +19,7 @@ module hdf5_interface #ifdef PHDF5 use message_passing, only: mpi_intracomm, MPI_INFO_NULL #endif + use string, only: to_c_string implicit none private @@ -84,7 +85,6 @@ module hdf5_interface public :: attribute_exists public :: write_attribute public :: read_attribute - public :: file_create public :: file_open public :: file_close public :: create_group @@ -101,98 +101,36 @@ module hdf5_interface contains -!=============================================================================== -! FILE_CREATE creates HDF5 file -!=============================================================================== - - function file_create(filename, parallel) result(file_id) - character(*), intent(in) :: filename ! name of file - logical, optional, intent(in) :: parallel ! whether to write in serial - integer(HID_T) :: file_id - - integer(HID_T) :: plist ! property list handle - integer :: hdf5_err ! HDF5 error code - logical :: parallel_ - - ! Check for serial option - parallel_ = .false. -#ifdef PHDF5 - if (present(parallel)) parallel_ = parallel -#endif - - if (parallel_) then - ! Setup file access property list with parallel I/O access - call h5pcreate_f(H5P_FILE_ACCESS_F, plist, hdf5_err) -#ifdef PHDF5 -#ifdef OPENMC_MPIF08 - call h5pset_fapl_mpio_f(plist, mpi_intracomm%MPI_VAL, & - MPI_INFO_NULL%MPI_VAL, hdf5_err) -#else - call h5pset_fapl_mpio_f(plist, mpi_intracomm, MPI_INFO_NULL, hdf5_err) -#endif -#endif - - ! Create the file collectively - call h5fcreate_f(trim(filename), H5F_ACC_TRUNC_F, file_id, hdf5_err, & - access_prp = plist) - - ! Close the property list - call h5pclose_f(plist, hdf5_err) - else - ! Create the file - call h5fcreate_f(trim(filename), H5F_ACC_TRUNC_F, file_id, hdf5_err) - end if - - end function file_create - !=============================================================================== ! FILE_OPEN opens HDF5 file !=============================================================================== function file_open(filename, mode, parallel) result(file_id) - character(*), intent(in) :: filename ! name of file - character(*), intent(in) :: mode ! access mode to file - logical, optional, intent(in) :: parallel ! whether to write in serial + character(*), intent(in) :: filename ! name of file + character, value :: mode ! access mode to file + logical, optional, intent(in) :: parallel ! whether to write in serial integer(HID_T) :: file_id - logical :: parallel_ - integer(HID_T) :: plist ! property list handle - integer :: hdf5_err ! HDF5 error code - integer :: open_mode ! HDF5 open mode + character(kind=C_CHAR) :: mode_ + logical(C_BOOL) :: parallel_ - ! Check for serial option + interface + function file_open_c(name, mode, parallel) bind(C, name='file_open') result(file_id) + import HID_T, C_CHAR, C_BOOL, C_INT + character(kind=C_CHAR) :: name(*) + character(kind=C_CHAR), value :: mode + logical(C_BOOL), value :: parallel + integer(HID_T) :: file_id + end function file_open_c + end interface + + mode_ = mode parallel_ = .false. #ifdef PHDF5 if (present(parallel)) parallel_ = parallel #endif - ! Determine access type - open_mode = H5F_ACC_RDONLY_F - if (mode == 'w') open_mode = H5F_ACC_RDWR_F - - if (parallel_) then - ! Setup file access property list with parallel I/O access - call h5pcreate_f(H5P_FILE_ACCESS_F, plist, hdf5_err) -#ifdef PHDF5 -#ifdef OPENMC_MPIF08 - call h5pset_fapl_mpio_f(plist, mpi_intracomm%MPI_VAL, & - MPI_INFO_NULL%MPI_VAL, hdf5_err) -#else - call h5pset_fapl_mpio_f(plist, mpi_intracomm, MPI_INFO_NULL, hdf5_err) -#endif -#endif - - ! Open the file collectively - call h5fopen_f(trim(filename), open_mode, file_id, hdf5_err, & - access_prp = plist) - - ! Close the property list - call h5pclose_f(plist, hdf5_err) - else - ! Open file - call h5fopen_f(trim(filename), open_mode, file_id, hdf5_err) - end if - + file_id = file_open_c(to_c_string(filename), mode, parallel_) end function file_open !=============================================================================== diff --git a/src/hdf5_interface.cpp b/src/hdf5_interface.cpp new file mode 100644 index 000000000..10357c91d --- /dev/null +++ b/src/hdf5_interface.cpp @@ -0,0 +1,212 @@ +#include "hdf5_interface.h" +#include "error.h" + +#include "hdf5.h" +#include "hdf5_hl.h" + +#include +#include +#include + +namespace openmc { + +bool +using_mpio_device(hid_t obj_id) { + // Determine file that this object is part of + hid_t file_id = H5Iget_file_id(obj_id); + + // Get file access property list + hid_t fapl_id = H5Fget_access_plist(file_id); + + // Get low-level driver identifier + hid_t driver = H5Pget_driver(fapl_id); + + // Free resources + H5Pclose(fapl_id); + H5Fclose(file_id); + + return driver == H5FD_MPIO; +} + + +hid_t +create_group(hid_t parent_id, char const *name) +{ + hid_t out = H5Gcreate(parent_id, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if (out < 0) { + std::stringstream err_msg; + err_msg << "Failed to create HDF5 group \"" << name << "\""; + fatal_error(err_msg); + } + return out; +} + +hid_t +create_group(hid_t parent_id, const std::string &name) +{ + return create_group(parent_id, name.c_str()); +} + +void +close_dataset(hid_t dataset_id) +{ + if (H5Dclose(dataset_id) < 0) fatal_error("Failed to close dataset"); +} + + +void +close_group(hid_t group_id) +{ + if (H5Gclose(group_id) < 0) fatal_error("Failed to close group"); +} + + +hid_t +file_open(const char* filename, char mode, bool parallel) +{ + bool create; + unsigned int flags; + switch (mode) { + case 'r': + case 'a': + create = false; + flags = (mode == 'r' ? H5F_ACC_RDONLY : H5F_ACC_RDWR); + break; + case 'w': + case 'x': + create = true; + flags = (mode == 'x' ? H5F_ACC_EXCL : H5F_ACC_TRUNC); + break; + default: + std::stringstream err_msg; + err_msg << "Invalid file mode: " << mode; + fatal_error(err_msg); + } + + hid_t plist = H5P_DEFAULT; +#ifdef PHDF5 + if (parallel) { + // Setup file access property list with parallel I/O access + plist = H5Pcreate(H5P_FILE_ACCESS); + H5Pset_fapl_mpio(plist, mpi_intracomm, MPI_INFO_NULL); + } +#endif + + // Open the file collectively + hid_t file_id; + if (create) { + file_id = H5Fcreate(filename, flags, H5P_DEFAULT, plist); + } else { + file_id = H5Fopen(filename, flags, plist); + } + +#ifdef PHDF5 + // Close the property list + if (parallel) H5Pclose(plist); +#endif + + return file_id; +} + +hid_t +file_open(const std::string& filename, char mode, bool parallel=false) { + file_open(filename.c_str(), mode, parallel); +} + +void file_close(hid_t file_id) { + H5Fclose(file_id); +} + +bool +object_exists(hid_t object_id, const char* name) { + htri_t out = H5LTpath_valid(object_id, name, true); + if (out < 0) { + std::stringstream err_msg; + err_msg << "Failed to check if object \"" << name << "\" exists."; + fatal_error(err_msg); + } + return (out > 0); +} + + +hid_t +open_dataset(hid_t group_id, const char* name){ + if (object_exists(group_id, name)) { + return H5Dopen(group_id, name, H5P_DEFAULT); + } else { + std::stringstream err_msg; + err_msg << "Group \"" << name << "\" does not exist"; + fatal_error(err_msg); + } +} + + +hid_t +open_group(hid_t group_id, const char* name){ + if (object_exists(group_id, name)) { + return H5Gopen(group_id, name, H5P_DEFAULT); + } else { + std::stringstream err_msg; + err_msg << "Group \"" << name << "\" does not exist"; + fatal_error(err_msg); + } +} + + +void +write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name, + double* buffer, bool indep) { + hid_t dspace = H5Screate_simple(ndim, dims, nullptr); + hid_t dset = H5Dcreate(group_id, name, H5T_NATIVE_DOUBLE, dspace, + H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + if (using_mpio_device(group_id)) { +#ifdef PHDF5 + // Set up collective vs independent I/O + auto data_xfer_mode {indep ? H5FD_MPIO_INDEPENDENT : H5FD_MPIO_COLLECTIVE}; + + // Create dataset transfer property list + hid_t plist = H5Pcreate(H5P_DATASET_XFER); + H5Pset_dxpl_mpio(plist, data_xfer_mode); + + // Write data + H5Dwrite(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, plist, buffer); + H5Pclose(plist); +#endif + } else { + H5Dwrite(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer); + } + + // Free resources + H5Dclose(dset); + H5Sclose(dspace); +} + + +void +write_string(hid_t group_id, char const *name, char const *buffer) +{ + size_t buffer_len = strlen(buffer); + hid_t datatype = H5Tcopy(H5T_C_S1); + H5Tset_size(datatype, buffer_len); + + hid_t dataspace = H5Screate(H5S_SCALAR); + + hid_t dataset = H5Dcreate(group_id, name, datatype, dataspace, + H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer); + + H5Tclose(datatype); + H5Sclose(dataspace); + H5Dclose(dataset); +} + + +void +write_string(hid_t group_id, char const *name, const std::string &buffer) +{ + write_string(group_id, name, buffer.c_str()); +} + +} diff --git a/src/hdf5_interface.h b/src/hdf5_interface.h index 8a445b21e..b79e0a29c 100644 --- a/src/hdf5_interface.h +++ b/src/hdf5_interface.h @@ -1,8 +1,6 @@ #ifndef HDF5_INTERFACE_H #define HDF5_INTERFACE_H -#include "error.h" - #include "hdf5.h" #include "hdf5_hl.h" @@ -13,143 +11,17 @@ namespace openmc { -bool -using_mpio_device(hid_t obj_id) { - // Determine file that this object is part of - hid_t file_id = H5Iget_file_id(obj_id); - - // Get file access property list - hid_t fapl_id = H5Fget_access_plist(file_id); - - // Get low-level driver identifier - hid_t driver = H5Pget_driver(fapl_id); - - // Free resources - H5Pclose(fapl_id); - H5Fclose(file_id); - - return driver == H5FD_MPIO; -} - - -hid_t -create_group(hid_t parent_id, char const *name) -{ - hid_t out = H5Gcreate(parent_id, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - if (out < 0) { - std::stringstream err_msg; - err_msg << "Failed to create HDF5 group \"" << name << "\""; - fatal_error(err_msg); - } - return out; -} - -hid_t -create_group(hid_t parent_id, const std::string &name) -{ - return create_group(parent_id, name.c_str()); -} - -void -close_dataset(hid_t dataset_id) -{ - if (H5Dclose(dataset_id) < 0) fatal_error("Failed to close dataset"); -} - - -void -close_group(hid_t group_id) -{ - if (H5Gclose(group_id) < 0) fatal_error("Failed to close group"); -} - - -hid_t -file_open(const char* filename, char mode, bool parallel=false) -{ - bool create; - unsigned int flags; - switch (mode) { - case 'r': - case 'a': - create = false; - flags = (mode == 'r' ? H5F_ACC_RDONLY : H5F_ACC_RDWR); - break; - case 'w': - case 'x': - create = true; - flags = (mode == 'x' ? H5F_ACC_EXCL : H5F_ACC_TRUNC); - break; - } - - hid_t plist; - if (parallel) { - // Setup file access property list with parallel I/O access - plist = H5Pcreate(H5P_FILE_ACCESS); -#ifdef PHDF5 - H5Pset_fapl_mpio(plist, mpi_intracomm, MPI_INFO_NULL); -#endif - } else { - plist = H5P_DEFAULT; - } - - // Open the file collectively - hid_t file_id; - if (create) { - file_id = H5Fopen(filename, flags, plist); - } else { - file_id = H5Fcreate(filename, flags, H5P_DEFAULT, plist); - } - - // Close the property list - if (parallel) H5Pclose(plist); - - return file_id; -} - -hid_t -file_open(const std::string& filename, char mode, bool parallel=false) { - file_open(filename.c_str(), mode, parallel); -} - -void file_close(hid_t file_id) { - H5Fclose(file_id); -} - -bool -object_exists(hid_t object_id, const char* name) { - htri_t out = H5LTpath_valid(object_id, name, true); - if (out < 0) { - std::stringstream err_msg; - err_msg << "Failed to check if object \"" << name << "\" exists."; - fatal_error(err_msg); - } - return (out > 0); -} - - -hid_t -open_dataset(hid_t group_id, const char* name){ - if (object_exists(group_id, name)) { - return H5Dopen(group_id, name, H5P_DEFAULT); - } else { - std::stringstream err_msg; - err_msg << "Group \"" << name << "\" does not exist"; - fatal_error(err_msg); - } -} - - -hid_t -open_group(hid_t group_id, const char* name){ - if (object_exists(group_id, name)) { - return H5Gopen(group_id, name, H5P_DEFAULT); - } else { - std::stringstream err_msg; - err_msg << "Group \"" << name << "\" does not exist"; - fatal_error(err_msg); - } -} +bool using_mpio_device(hid_t obj_id); +hid_t create_group(hid_t parent_id, const char* name); +hid_t create_group(hid_t parent_id, const std::string& name); +void close_dataset(hid_t dataset_id); +void close_group(hid_t group_id); +extern "C" hid_t file_open(const char* filename, char mode, bool parallel); +hid_t file_open(const std::string& filename, char mode, bool parallel); +void file_close(hid_t file_id); +bool object_exists(hid_t object_id, const char* name); +hid_t open_dataset(hid_t group_id, const char* name); +hid_t open_group(hid_t group_id, const char* name); template void @@ -169,61 +41,11 @@ write_double_1D(hid_t group_id, char const *name, H5Dclose(dataset); } -void -write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name, - double* buffer, bool indep) { - hid_t dspace = H5Screate_simple(ndim, dims, nullptr); - hid_t dset = H5Dcreate(group_id, name, H5T_NATIVE_DOUBLE, dspace, - H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); +void write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name, + double* buffer, bool indep); - if (using_mpio_device(group_id)) { -#ifdef PHDF5 - // Set up collective vs independent I/O - auto data_xfer_mode {indep ? H5FD_MPIO_INDEPENDENT : H5FD_MPIO_COLLECTIVE}; - - // Create dataset transfer property list - hid_t plist = H5Pcreate(H5P_DATASET_XFER); - H5Pset_dxpl_mpio(plist, data_xfer_mode); - - // Write data - H5Dwrite(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, plist, buffer); - H5Pclose(plist); -#endif - } else { - H5Dwrite(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer); - } - - // Free resources - H5Dclose(dset); - H5Sclose(dspace); -} - - -void -write_string(hid_t group_id, char const *name, char const *buffer) -{ - size_t buffer_len = strlen(buffer); - hid_t datatype = H5Tcopy(H5T_C_S1); - H5Tset_size(datatype, buffer_len); - - hid_t dataspace = H5Screate(H5S_SCALAR); - - hid_t dataset = H5Dcreate(group_id, name, datatype, dataspace, - H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - - H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer); - - H5Tclose(datatype); - H5Sclose(dataspace); - H5Dclose(dataset); -} - - -void -write_string(hid_t group_id, char const *name, const std::string &buffer) -{ - write_string(group_id, name, buffer.c_str()); -} +void write_string(hid_t group_id, char const *name, char const *buffer); +void write_string(hid_t group_id, char const *name, const std::string &buffer); } // namespace openmc #endif //HDF5_INTERFACE_H diff --git a/src/particle_header.F90 b/src/particle_header.F90 index 552f9b042..02fb55405 100644 --- a/src/particle_header.F90 +++ b/src/particle_header.F90 @@ -312,7 +312,7 @@ contains !$omp critical (WriteParticleRestart) ! Create file - file_id = file_create(filename) + file_id = file_open(filename, 'w') associate (src => source_bank(current_work)) ! Write filetype and version info diff --git a/src/plot.F90 b/src/plot.F90 index 5eb894ce8..92b8f350d 100644 --- a/src/plot.F90 +++ b/src/plot.F90 @@ -371,7 +371,7 @@ contains p % coord(1) % universe = root_universe ! Open binary plot file for writing - file_id = file_create(pl%path_plot) + file_id = file_open(pl%path_plot, 'w') ! write header info call write_attribute(file_id, "filetype", 'voxel') diff --git a/src/source.F90 b/src/source.F90 index 5beecd887..9e3a0831d 100644 --- a/src/source.F90 +++ b/src/source.F90 @@ -12,7 +12,7 @@ module source use distribution_multivariate, only: SpatialBox use error, only: fatal_error use geometry, only: find_cell - use hdf5_interface, only: file_create, file_open, file_close, read_dataset + use hdf5_interface, only: file_open, file_close, read_dataset use math use message_passing, only: rank use mgxs_header, only: rev_energy_bins, num_energy_groups @@ -88,7 +88,7 @@ contains if (write_initial_source) then call write_message('Writing out initial source...', 5) filename = trim(path_output) // 'initial_source.h5' - file_id = file_create(filename, parallel=.true.) + file_id = file_open(filename, 'w', parallel=.true.) call write_source_bank(file_id) call file_close(file_id) end if diff --git a/src/state_point.F90 b/src/state_point.F90 index 980a7333c..62240f110 100644 --- a/src/state_point.F90 +++ b/src/state_point.F90 @@ -76,7 +76,7 @@ contains if (master) then ! Create statepoint file - file_id = file_create(filename_) + file_id = file_open(filename_, 'w') ! Write file type call write_attribute(file_id, "filetype", "statepoint") @@ -476,7 +476,7 @@ contains ! Create separate source file if (master .or. parallel) then - file_id = file_create(filename, parallel=.true.) + file_id = file_open(filename, 'w', parallel=.true.) call write_dataset(file_id, "filetype", 'source') end if else @@ -485,7 +485,7 @@ contains filename = trim(filename) // '.h5' if (master .or. parallel) then - file_id = file_open(filename, 'w', parallel=.true.) + file_id = file_open(filename, 'a', parallel=.true.) end if end if @@ -498,7 +498,7 @@ contains filename = trim(path_output) // 'source' // '.h5' call write_message("Creating source file " // trim(filename) // "...", 5) if (master .or. parallel) then - file_id = file_create(filename, parallel=.true.) + file_id = file_open(filename, 'w', parallel=.true.) call write_dataset(file_id, "filetype", 'source') end if diff --git a/src/summary.F90 b/src/summary.F90 index 3aeb42178..9f27694d1 100644 --- a/src/summary.F90 +++ b/src/summary.F90 @@ -38,7 +38,7 @@ contains call write_message("Writing summary.h5 file...", 5) ! Create a new file using default properties. - file_id = file_create("summary.h5") + file_id = file_open("summary.h5", 'w') call write_header(file_id) call write_nuclides(file_id) diff --git a/src/track_output.F90 b/src/track_output.F90 index 244bf182e..350e687b1 100644 --- a/src/track_output.F90 +++ b/src/track_output.F90 @@ -115,7 +115,7 @@ contains end do !$omp critical (FinalizeParticleTrack) - file_id = file_create(fname) + file_id = file_open(fname, 'w') call write_attribute(file_id, 'filetype', 'track') call write_attribute(file_id, 'version', VERSION_TRACK) call write_attribute(file_id, 'n_particles', n_particle_tracks) diff --git a/src/volume_calc.F90 b/src/volume_calc.F90 index e374f2106..ac813a94a 100644 --- a/src/volume_calc.F90 +++ b/src/volume_calc.F90 @@ -11,7 +11,7 @@ module volume_calc use error, only: write_message use geometry, only: find_cell use geometry_header, only: universes, cells - use hdf5_interface, only: file_create, file_close, write_attribute, & + use hdf5_interface, only: file_open, file_close, write_attribute, & create_group, close_group, write_dataset use output, only: header, time_stamp use material_header, only: materials @@ -435,7 +435,7 @@ contains character(MAX_WORD_LEN), allocatable :: nucnames(:) ! names of nuclides ! Create HDF5 file - file_id = file_create(filename) + file_id = file_open(filename, 'w') ! Write header info call write_attribute(file_id, "filetype", "volume")