/* Copyright 2003-2018, University Corporation for Atmospheric * Research. See COPYRIGHT file for copying and redistribution * conditions. */ /** * @file * @internal The netCDF-4 file functions relating to file creation. * * @author Ed Hartnett */ #include "config.h" #include "hdf5internal.h" /* From hdf5file.c. */ extern size_t nc4_chunk_cache_size; extern size_t nc4_chunk_cache_nelems; extern float nc4_chunk_cache_preemption; /** @internal These flags may not be set for create. */ static const int ILLEGAL_CREATE_FLAGS = (NC_NOWRITE|NC_MMAP|NC_64BIT_OFFSET|NC_CDF5); /* From nc4mem.c */ extern int NC4_create_image_file(NC_FILE_INFO_T* h5, size_t); /** * @internal Create a netCDF-4/HDF5 file. * * @param path The file name of the new file. * @param cmode The creation mode flag. * @param initialsz The proposed initial file size (advisory) * @param parameters extra parameter info (like MPI communicator) * @param nc Pointer to an instance of NC. * * @return ::NC_NOERR No error. * @return ::NC_EINVAL Invalid input (check cmode). * @return ::NC_EEXIST File exists and NC_NOCLOBBER used. * @return ::NC_EHDFERR HDF5 returned error. * @ingroup netcdf4 * @author Ed Hartnett, Dennis Heimbigner */ static int nc4_create_file(const char *path, int cmode, size_t initialsz, void* parameters, NC *nc) { hid_t fcpl_id, fapl_id = -1; unsigned flags; FILE *fp; int retval = NC_NOERR; NC_FILE_INFO_T* nc4_info = NULL; NC_HDF5_FILE_INFO_T *hdf5_info; NC_HDF5_GRP_INFO_T *hdf5_grp; #ifdef USE_PARALLEL4 NC_MPI_INFO *mpiinfo = NULL; MPI_Comm comm; MPI_Info info; int comm_duped = 0; /* Whether the MPI Communicator was duplicated */ int info_duped = 0; /* Whether the MPI Info object was duplicated */ #endif /* !USE_PARALLEL4 */ assert(nc && path); LOG((3, "%s: path %s mode 0x%x", __func__, path, cmode)); /* Add necessary structs to hold netcdf-4 file data. */ if ((retval = nc4_nc4f_list_add(nc, path, (NC_WRITE | cmode)))) BAIL(retval); nc4_info = NC4_DATA(nc); assert(nc4_info && nc4_info->root_grp); /* Add struct to hold HDF5-specific file metadata. */ if (!(nc4_info->format_file_info = calloc(1, sizeof(NC_HDF5_FILE_INFO_T)))) BAIL(NC_ENOMEM); hdf5_info = (NC_HDF5_FILE_INFO_T *)nc4_info->format_file_info; /* Add struct to hold HDF5-specific group info. */ if (!(nc4_info->root_grp->format_grp_info = calloc(1, sizeof(NC_HDF5_GRP_INFO_T)))) return NC_ENOMEM; hdf5_grp = (NC_HDF5_GRP_INFO_T *)nc4_info->root_grp->format_grp_info; nc4_info->mem.inmemory = (cmode & NC_INMEMORY) == NC_INMEMORY; nc4_info->mem.diskless = (cmode & NC_DISKLESS) == NC_DISKLESS; nc4_info->mem.persist = (cmode & NC_PERSIST) == NC_PERSIST; nc4_info->mem.created = 1; nc4_info->mem.initialsize = initialsz; /* diskless => !inmemory */ if(nc4_info->mem.inmemory && nc4_info->mem.diskless) BAIL(NC_EINTERNAL); if(nc4_info->mem.inmemory && parameters) nc4_info->mem.memio = *(NC_memio*)parameters; #ifdef USE_PARALLEL4 else if(parameters) { mpiinfo = (NC_MPI_INFO *)parameters; comm = mpiinfo->comm; info = mpiinfo->info; } #endif if(nc4_info->mem.diskless) flags = H5F_ACC_TRUNC; else if(cmode & NC_NOCLOBBER) flags = H5F_ACC_EXCL; else flags = H5F_ACC_TRUNC; /* If this file already exists, and NC_NOCLOBBER is specified, return an error (unless diskless|inmemory) */ if (!nc4_info->mem.diskless && !nc4_info->mem.inmemory) { if ((cmode & NC_NOCLOBBER) && (fp = fopen(path, "r"))) { fclose(fp); BAIL(NC_EEXIST); } } /* Need this access plist to control how HDF5 handles open objects * on file close. Setting H5F_CLOSE_SEMI will cause H5Fclose to * fail if there are any open objects in the file. */ if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) BAIL(NC_EHDFERR); if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI)) BAIL(NC_EHDFERR); #ifdef USE_PARALLEL4 /* If this is a parallel file create, set up the file creation property list. */ if (mpiinfo != NULL) { nc4_info->parallel = NC_TRUE; LOG((4, "creating parallel file with MPI/IO")); if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) BAIL(NC_EPARINIT); /* Keep copies of the MPI Comm & Info objects */ if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm)) BAIL(NC_EMPI); comm_duped++; if (MPI_INFO_NULL != info) { if (MPI_SUCCESS != MPI_Info_dup(info, &nc4_info->info)) BAIL(NC_EMPI); info_duped++; } else { /* No dup, just copy it. */ nc4_info->info = info; } } #else /* only set cache for non-parallel... */ if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size, nc4_chunk_cache_preemption) < 0) BAIL(NC_EHDFERR); LOG((4, "%s: set HDF raw chunk cache to size %d nelems %d preemption %f", __func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption)); #endif /* USE_PARALLEL4 */ #ifdef HDF5_HAS_LIBVER_BOUNDS #if H5_VERSION_GE(1,10,2) if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_V18) < 0) #else if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_LATEST) < 0) #endif BAIL(NC_EHDFERR); #endif /* Create the property list. */ if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) BAIL(NC_EHDFERR); /* RJ: this suppose to be FALSE that is defined in H5 private.h as 0 */ if (H5Pset_obj_track_times(fcpl_id,0)<0) BAIL(NC_EHDFERR); /* Set latest_format in access propertly list and * H5P_CRT_ORDER_TRACKED in the creation property list. This turns * on HDF5 creation ordering. */ if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED)) < 0) BAIL(NC_EHDFERR); if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED)) < 0) BAIL(NC_EHDFERR); #ifdef HDF5_HAS_COLL_METADATA_OPS /* If HDF5 supports collective metadata operations, turn them * on. This is only relevant for parallel I/O builds of HDF5. */ if (H5Pset_all_coll_metadata_ops(fapl_id, 1) < 0) BAIL(NC_EHDFERR); if (H5Pset_coll_metadata_write(fapl_id, 1) < 0) BAIL(NC_EHDFERR); #endif if(nc4_info->mem.inmemory) { retval = NC4_create_image_file(nc4_info,initialsz); if(retval) BAIL(retval); } else if(nc4_info->mem.diskless) { size_t alloc_incr; /* Buffer allocation increment */ size_t min_incr = 65536; /* Minimum buffer increment */ double buf_prcnt = 0.1f; /* Percentage of buffer size to set as increment */ /* set allocation increment to a percentage of the supplied buffer size, or * a pre-defined minimum increment value, whichever is larger */ if ((buf_prcnt * initialsz) > min_incr) alloc_incr = (size_t)(buf_prcnt * initialsz); else alloc_incr = min_incr; /* Configure FAPL to use the core file driver */ if (H5Pset_fapl_core(fapl_id, alloc_incr, (nc4_info->mem.persist?1:0)) < 0) BAIL(NC_EHDFERR); if ((hdf5_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0) BAIL(EACCES); } else /* Normal file */ { /* Create the HDF5 file. */ if ((hdf5_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0) BAIL(EACCES); } /* Open the root group. */ if ((hdf5_grp->hdf_grpid = H5Gopen2(hdf5_info->hdfid, "/", H5P_DEFAULT)) < 0) BAIL(NC_EFILEMETA); /* Release the property lists. */ if (H5Pclose(fapl_id) < 0 || H5Pclose(fcpl_id) < 0) BAIL(NC_EHDFERR); /* Define mode gets turned on automatically on create. */ nc4_info->flags |= NC_INDEF; /* Save the HDF5 superblock number and set the _NCProperties attribute. */ if ((retval = NC4_set_provenance(nc4_info, &globalpropinfo))) BAIL(retval); return NC_NOERR; exit: /*failure exit*/ #ifdef USE_PARALLEL4 if (comm_duped) MPI_Comm_free(&nc4_info->comm); if (info_duped) MPI_Info_free(&nc4_info->info); #endif if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id); if(!nc4_info) return retval; nc4_close_hdf5_file(nc4_info, 1, NULL); /* treat like abort */ return retval; } /** * @internal Create a netCDF-4/HDF5 file. * * @param path The file name of the new file. * @param cmode The creation mode flag. * @param initialsz Ignored by this function. * @param basepe Ignored by this function. * @param chunksizehintp Ignored by this function. * @param parameters pointer to struct holding extra data (e.g. for * parallel I/O) layer. Ignored if NULL. * @param dispatch Pointer to the dispatch table for this file. * @param nc_file Pointer to an instance of NC. * * @return ::NC_NOERR No error. * @return ::NC_EINVAL Invalid input (check cmode). * @ingroup netcdf4 * @author Ed Hartnett */ int NC4_create(const char* path, int cmode, size_t initialsz, int basepe, size_t *chunksizehintp, void *parameters, NC_Dispatch *dispatch, NC *nc_file) { int res; assert(nc_file && path); LOG((1, "%s: path %s cmode 0x%x parameters %p", __func__, path, cmode, parameters)); /* If this is our first file, turn off HDF5 error messages. */ if (!nc4_hdf5_initialized) nc4_hdf5_initialize(); #ifdef LOGGING /* If nc logging level has changed, see if we need to turn on * HDF5's error messages. */ hdf5_set_log_level(); #endif /* LOGGING */ /* Check the cmode for validity. */ if((cmode & ILLEGAL_CREATE_FLAGS) != 0) {res = NC_EINVAL; goto done;} /* check parallel against NC_DISKLESS already done in NC_create() */ nc_file->int_ncid = nc_file->ext_ncid; res = nc4_create_file(path, cmode, initialsz, parameters, nc_file); done: return res; }