#ifndef __H5PART_H #define __H5PART_H #ifdef __cplusplus extern "C" { #endif /*! \ingroup h5part_model Set the number of particles for the current time-step. After you call this subroutine, all subsequent operations will assume this number of particles will be written. For the parallel library, the \c nparticles value is the number of particles that the \e individual task will write. You can use a different value on different tasks. This function uses an \c MPI_Allgather call to aggregate each tasks number of particles and determine the appropiate offsets. Because of the use of this MPI collective, it is advisable to call this function as few times as possible when running at large concurrency. This function assumes that your particles' data fields are in stored in contiguous 1D arrays. For instance, the fields \e x and \e y for your particles are stored in separate arrays \c x[] and \c y[]. If instead you store your particles as tuples, so that the values are arranged \f$ x_1,y_1,x_2,y_2\f$... than you need to setup striding (in this case with value 2) using \ref H5PartSetNumParticlesStrided. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartSetNumParticles ( h5_file_t *f, /*!< [in] Handle to open file */ h5_size_t nparticles /*!< [in] Number of particles */ ) { H5_API_ENTER (h5_err_t, "f=%p, nparticles=%llu", f, (long long unsigned)nparticles); h5_size_t stride = 1; H5_API_RETURN (h5u_set_num_particles(f, nparticles, stride)); } /*! \ingroup h5part_model Set the number of particles for the current time-step. After you call this subroutine, all subsequent operations will assume this number of particles will be written. For the parallel library, the \c nparticles value is the number of particles that the \e individual task will write. You can use a different value on different tasks. This function uses an \c MPI_Allgather call to aggregate each tasks number of particles and determine the appropiate offsets. Because of the use of this MPI collective, it is advisable to call this function as few times as possible when running at large concurrency. This function assumes that your particles' data fields are stored tuples. For instance, the fields \e x and \e y of your particles are arranged \f$x_1,y_1,x_2,y_2\f$... in a single data array. In this example, the stride value would be 2. If you instead have a separate array for each fields, such as \c x[] and \c y[], use \ref H5PartSetNumParticles. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartSetNumParticlesStrided ( h5_file_t *f, /*!< [in] Handle to open file */ h5_size_t nparticles, /*!< [in] Number of particles */ h5_size_t stride /*!< [in] Stride value (e.g. number of fields in the particle array) */ ) { H5_API_ENTER (h5_err_t, "f=%p, nparticles=%llu, stride=%llu", f, (long long unsigned)nparticles, (long long unsigned)stride); H5_API_RETURN (h5u_set_num_particles (f, nparticles, stride)); } /*! \ingroup h5part_model Define the chunk \c size and enables chunking in the underlying HDF5 layer. Note that this policy wastes disk space, but can improve write bandwidth on parallel filesystems that are sensitive to write alignment (e.g. lustre). It is only recommended when using the MPI-POSIX or MPI-IO independent VFDs (see \ref H5OpenFile). \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartSetChunk ( h5_file_t *f, h5_size_t size ) { H5_API_ENTER (h5_err_t, "f=%p, size=%llu", f, (long long unsigned)size); H5_API_RETURN (h5u_set_chunk (f, size)); } /*! \ingroup h5part_data Write array of 64 bit floating point data to file. After setting the number of particles with \c H5PartSetNumParticles() and the current timestep using \c H5SetStep(), you can start writing datasets into the file. Each dataset has a name associated with it (chosen by the user) in order to facilitate later retrieval. The name of the dataset is specified in the parameter \c name, which must be a null-terminated string. There are no restrictions on naming of datasets, but it is useful to arrive at some common naming convention when sharing data with other groups. The writing routines also implicitly store the datatype of the array so that the array can be reconstructed properly on other systems with incompatible type representations. All data that is written after setting the timestep is associated with that timestep. While the number of particles can change for each timestep, you cannot change the number of particles in the middle of a given timestep. The data is committed to disk before the routine returns. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartWriteDataFloat64 ( h5_file_t *f, /*!< [in] Handle to open file */ const char *name, /*!< [in] Name to associate array with */ const h5_float64_t *data /*!< [in] Array to commit to disk */ ) { H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data); H5_API_RETURN (h5u_write_data (f, name, (void*)data, H5T_NATIVE_DOUBLE)); } /*! \ingroup h5part_data Write array of 32 bit floating point data to file. After setting the number of particles with \c H5PartSetNumParticles() and the current timestep using \c H5SetStep(), you can start writing datasets into the file. Each dataset has a name associated with it (chosen by the user) in order to facilitate later retrieval. The name of the dataset is specified in the parameter \c name, which must be a null-terminated string. There are no restrictions on naming of datasets, but it is useful to arrive at some common naming convention when sharing data with other groups. The writing routines also implicitly store the datatype of the array so that the array can be reconstructed properly on other systems with incompatible type representations. All data that is written after setting the timestep is associated with that timestep. While the number of particles can change for each timestep, you cannot change the number of particles in the middle of a given timestep. The data is committed to disk before the routine returns. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartWriteDataFloat32 ( h5_file_t *f, /*!< [in] Handle to open file */ const char *name, /*!< [in] Name to associate array with */ const h5_float32_t *data /*!< [in] Array to commit to disk */ ) { H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data); h5_err_t h5err = h5u_write_data( f, name, (void*)data, H5T_NATIVE_FLOAT ); H5_API_RETURN (h5err); } /*! \ingroup h5part_data Write array of 64 bit integer data to file. After setting the number of particles with \c H5PartSetNumParticles() and the current timestep using \c H5SetStep(), you can start writing datasets into the file. Each dataset has a name associated with it (chosen by the user) in order to facilitate later retrieval. The name of the dataset is specified in the parameter \c name, which must be a null-terminated string. There are no restrictions on naming of datasets, but it is useful to arrive at some common naming convention when sharing data with other groups. The writing routines also implicitly store the datatype of the array so that the array can be reconstructed properly on other systems with incompatible type representations. All data that is written after setting the timestep is associated with that timestep. While the number of particles can change for each timestep, you cannot change the number of particles in the middle of a given timestep. The data is committed to disk before the routine returns. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartWriteDataInt64 ( h5_file_t *f, /*!< [in] Handle to open file */ const char *name, /*!< [in] Name to associate array with */ const h5_int64_t *data /*!< [in] Array to commit to disk */ ) { H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data); H5_API_RETURN (h5u_write_data (f, name, (void*)data, H5T_NATIVE_INT64)); } /*! \ingroup h5part_data Write array of 32 bit integer data to file. After setting the number of particles with \c H5PartSetNumParticles() and the current timestep using \c H5SetStep(), you can start writing datasets into the file. Each dataset has a name associated with it (chosen by the user) in order to facilitate later retrieval. The name of the dataset is specified in the parameter \c name, which must be a null-terminated string. There are no restrictions on naming of datasets, but it is useful to arrive at some common naming convention when sharing data with other groups. The writing routines also implicitly store the datatype of the array so that the array can be reconstructed properly on other systems with incompatible type representations. All data that is written after setting the timestep is associated with that timestep. While the number of particles can change for each timestep, you cannot change the number of particles in the middle of a given timestep. The data is committed to disk before the routine returns. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartWriteDataInt32 ( h5_file_t *f, /*!< [in] Handle to open file */ const char *name, /*!< [in] Name to associate array with */ const h5_int32_t *data /*!< [in] Array to commit to disk */ ) { H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data); H5_API_RETURN (h5u_write_data (f, name, (void*)data, H5T_NATIVE_INT32)); } /*! \ingroup h5part_data Read array of 64 bit floating point data from file. When retrieving datasets from disk, you ask for them by name. There are no restrictions on naming of arrays, but it is useful to arrive at some common naming convention when sharing data with other groups. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartReadDataFloat64 ( h5_file_t *f, /*!< [in] Handle to open file */ const char *name, /*!< [in] Name to associate dataset with */ h5_float64_t *data /*!< [out] Array of data */ ) { H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data); H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_DOUBLE)); } /*! \ingroup h5part_data Read array of 32 bit floating point data from file. When retrieving datasets from disk, you ask for them by name. There are no restrictions on naming of arrays, but it is useful to arrive at some common naming convention when sharing data with other groups. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartReadDataFloat32 ( h5_file_t *f, /*!< [in] Handle to open file */ const char *name, /*!< [in] Name to associate dataset with */ h5_float32_t *data /*!< [out] Array of data */ ) { H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data); H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_FLOAT)); } /*! \ingroup h5part_data Read array of 64 bit integer data from file. When retrieving datasets from disk, you ask for them by name. There are no restrictions on naming of arrays, but it is useful to arrive at some common naming convention when sharing data with other groups. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartReadDataInt64 ( h5_file_t *f, /*!< [in] Handle to open file */ const char *name, /*!< [in] Name to associate dataset with */ h5_int64_t *data /*!< [out] Array of data */ ) { H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data); H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_INT64)); } /*! \ingroup h5part_data Read array of 32 bit integer data from file. When retrieving datasets from disk, you ask for them by name. There are no restrictions on naming of arrays, but it is useful to arrive at some common naming convention when sharing data with other groups. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartReadDataInt32 ( h5_file_t *f, /*!< [in] Handle to open file */ const char *name, /*!< [in] Name to associate dataset with */ h5_int32_t *data /*!< [out] Array of data */ ) { H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data); H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_INT32)); } /*! \ingroup h5part_model Get the number of datasets that are stored at the current time-step. \return number of datasets in current timestep or error code */ static inline h5_ssize_t H5PartGetNumDatasets ( h5_file_t *f /*!< [in] Handle to open file */ ) { H5_API_ENTER (h5_err_t, "f=%p", f); H5_API_RETURN (h5u_get_num_datasets(f)); } /*! \ingroup h5part_model This reads the name of a dataset specified by it's index in the current time-step. If the number of datasets is \c n, the range of \c _index is \c 0 to \c n-1. \result \c H5_SUCCESS */ static inline h5_err_t H5PartGetDatasetName ( h5_file_t *f, /*!< [in] Handle to open file */ const h5_id_t idx, /*!< [in] Index of the dataset */ char *name, /*!< [out] Name of dataset */ const h5_size_t len /*!< [in] Size of buffer \c name */ ) { H5_API_ENTER (h5_err_t, "f=%p, " "idx=%lld, " "name='%p', len=%llu, ", f, (long long)idx, name, (unsigned long long)len); H5_API_RETURN (h5u_get_dataset_info(f, idx, name, len, NULL, NULL)); } /*! \ingroup h5part_model Gets the name, type and number of elements of a dataset based on its index in the current timestep. Type is one of the following values: - \c H5_FLOAT64_T (for \c h5_float64_t) - \c H5_FLOAT32_T (for \c h5_float32_t) - \c H5_INT64_T (for \c h5_int64_t) - \c H5_INT32_T (for \c h5_int32_t) \return \c H5_SUCCESS */ static inline h5_err_t H5PartGetDatasetInfo ( h5_file_t *f, /*!< [in] Handle to open file */ const h5_id_t idx, /*!< [in] Index of the dataset */ char *dataset_name, /*!< [out] Name of dataset */ const h5_size_t len_dataset_name, /*!< [in] Size of buffer \c dataset_name */ h5_int64_t *type, /*!< [out] Type of data in dataset */ h5_size_t *nelem /*!< [out] Number of elements. */ ) { H5_API_ENTER (h5_int64_t, "f=%p, " "idx=%lld, " "dataset_name='%p', len_dataset_name=%llu, " "type=%p, nelem=%p", f, (long long)idx, dataset_name, (long long unsigned)len_dataset_name, type, nelem); H5_API_RETURN (h5u_get_dataset_info ( f, idx, dataset_name, len_dataset_name, type, nelem)); } /*! \ingroup h5part_model This function returns the number of particles in this processor's view, if a view has been set. If not, it returns the total number of particles across all processors from the last \ref H5PartSetNumParticles call. If you have neither set the number of particles nor set a view, then this returns the total number of particles in the first data set of the current time step. Note that H5Part assumes that all data sets within a given time step have the same number of particles (although the number particles can vary across time steps). If none of these conditions are met, an error is thrown. \return number of particles in current timestep or an error code. */ static inline h5_ssize_t H5PartGetNumParticles ( h5_file_t *f /*!< [in] Handle to open file */ ) { H5_API_ENTER (h5_ssize_t, "f=%p", f); CHECK_FILEHANDLE( f ); H5_API_RETURN (h5u_get_num_particles (f)); } /*! \ingroup h5part_model Reset the view. \return \c H5_SUCCESS */ static inline h5_err_t H5PartResetView ( h5_file_t *f /*!< [in] Handle to open file */ ) { H5_API_ENTER (h5_ssize_t, "f=%p", f); H5_API_RETURN (h5u_reset_view (f)); } /*! \ingroup h5part_model Check whether a view has been set, either automatically with \ref H5PartSetNumParticles or manually with \ref H5PartSetView or \ref H5PartSetViewIndices. \return 0 for false or 1 for true */ static inline h5_err_t H5PartHasView ( h5_file_t *f /*!< [in] Handle to open file */ ) { H5_API_ENTER (h5_err_t, "f=%p", f); H5_API_RETURN (h5u_has_view (f)); } /*! \ingroup h5part_model For parallel I/O or for subsetting operations on the datafile, this function allows you to define a subset of the total particle dataset to operate on. The concept of "view" works for both serial and for parallel I/O. The "view" will remain in effect until a new view is set, or the number of particles in a dataset changes, or the view is "unset" by calling \c H5PartSetView(file,-1,-1); Before you set a view, \ref H5PartGetNumParticles will return the total number of particles in the current time-step (even for the parallel reads). However, after you set a view, it will return the number of particles contained in the view. The range is \e inclusive: the end value is the last index of the data. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartSetView ( h5_file_t *f, /*!< [in] Handle to open file */ h5_int64_t start, /*!< [in] Start particle */ h5_int64_t end /*!< [in] End particle */ ) { H5_API_ENTER (h5_err_t, "f=%p, start=%lld, end=%lld", f, (long long)start, (long long)end); H5_API_RETURN (h5u_set_view (f, start, end)); } /*! \ingroup h5part_model For parallel I/O or for subsetting operations on the datafile, this function allows you to define a subset of the total dataset to operate on by specifying a list of indices. The concept of "view" works for both serial and for parallel I/O. The "view" will remain in effect until a new view is set, or the number of particles in a dataset changes, or the view is "unset" by calling \c H5PartSetViewIndices(NULL,0); When you perform a read or write on a view consisting of indices, it is assumed that your buffer is \b unpacked, meaning that there is room for all the intermediate values (which will not be touched by the read or write). Before you set a view, the \c H5PartGetNumParticles() will return the total number of particles in the current time-step (even for the parallel reads). However, after you set a view, it will return the number of particles contained in the view. \return \c H5_SUCCESS or error code */ static inline h5_err_t H5PartSetViewIndices ( h5_file_t *f, /*!< [in] Handle to open file */ const h5_size_t *indices, /*!< [in] List of indices */ h5_size_t nelems /*!< [in] Size of list */ ) { H5_API_ENTER (h5_err_t, "f=%p, indices=%p, nelems=%llu", f, indices, (long long unsigned)nelems); H5_API_RETURN (h5u_set_view_indices (f, indices, nelems)); } /*! \ingroup h5part_model Allows you to query the current view. Start and End will be \c -1 if there is no current view established. Use \c H5PartHasView() to see if the view is smaller than the total dataset. \return number of elements in the view or error code */ static inline h5_err_t H5PartGetView ( h5_file_t *f, /*!< [in] Handle to open file */ h5_int64_t *start, /*!< [out] Start particle */ h5_int64_t *end /*!< [out] End particle */ ) { H5_API_ENTER (h5_err_t, "f=%p, start=%p, end=%p", f, start, end); H5_API_RETURN (h5u_get_view (f, start, end)); } /*! \ingroup h5part_model If it is too tedious to manually set the start and end coordinates for a view, the \c H5SetCanonicalView() will automatically select an appropriate domain decomposition of the data arrays for the degree of parallelism and set the "view" accordingly. \return H5_SUCCESS or error code */ static inline h5_err_t H5PartSetCanonicalView ( h5_file_t *f /*!< [in] Handle to open file */ ) { H5_API_ENTER (h5_err_t, "f=%p", f); H5_API_RETURN (h5u_set_canonical_view (f)); } #ifdef __cplusplus } #endif #endif