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netcdf-c/libhdf5/hdf5create.c
Ed Hartnett bf7ad679f7 finished fixes
2018-08-06 16:33:44 -06:00

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/* 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;
#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;
nc4_info->mem.inmemory = (cmode & NC_INMEMORY) == NC_INMEMORY;
nc4_info->mem.diskless = (cmode & NC_DISKLESS) == NC_DISKLESS;
nc4_info->mem.created = 1;
nc4_info->mem.initialsize = initialsz;
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) {
if((cmode & NC_WRITE) && (cmode & NC_NOCLOBBER) == 0)
nc4_info->mem.persist = 1;
} else if (nc4_info->mem.inmemory) {
/* ok */
} else 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 ((cmode & NC_MPIIO) || (cmode & NC_MPIPOSIX)) {
nc4_info->parallel = NC_TRUE;
if (cmode & NC_MPIIO) /* MPI/IO */
{
LOG((4, "creating parallel file with MPI/IO"));
if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
BAIL(NC_EPARINIT);
}
#ifdef USE_PARALLEL_POSIX
else /* MPI/POSIX */
{
LOG((4, "creating parallel file with MPI/posix"));
if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0)
BAIL(NC_EPARINIT);
}
#else /* USE_PARALLEL_POSIX */
/* Should not happen! Code in NC4_create/NC4_open should alias
* the NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not
* available in HDF5. -QAK */
else /* MPI/POSIX */
BAIL(NC_EPARINIT);
#endif /* USE_PARALLEL_POSIX */
/* 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(cmode & NC_DISKLESS) {
if (H5Pset_fapl_core(fapl_id, 4096, nc4_info->mem.persist))
BAIL(NC_EDISKLESS);
}
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
{
/* Create the HDF5 file. */
if ((hdf5_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0)
BAIL(EACCES);
}
/* Open the root group. */
if ((nc4_info->root_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;
/* Get the HDF5 superblock and read and parse the special
* _NCProperties attribute. */
if ((retval = NC4_get_fileinfo(nc4_info, &globalpropinfo)))
BAIL(retval);
/* Write the _NCProperties attribute. */
if ((retval = NC4_put_propattr(nc4_info)))
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_netcdf4_file(nc4_info, 1, 0); /* 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 use_parallel 0 for sequential, non-zero for parallel I/O.
* @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, int use_parallel, 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;}
/* Cannot have both */
if((cmode & (NC_MPIIO|NC_MPIPOSIX)) == (NC_MPIIO|NC_MPIPOSIX))
{res = NC_EINVAL; goto done;}
/* Currently no parallel diskless io */
if((cmode & (NC_MPIIO | NC_MPIPOSIX)) && (cmode & NC_DISKLESS))
{res = NC_EINVAL; goto done;}
#ifndef USE_PARALLEL_POSIX
/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias
* the NC_MPIPOSIX flag to NC_MPIIO. -QAK
*/
if(cmode & NC_MPIPOSIX)
{
cmode &= ~NC_MPIPOSIX;
cmode |= NC_MPIIO;
}
#endif /* USE_PARALLEL_POSIX */
cmode |= NC_NETCDF4;
/* Apply default create format. */
if (nc_get_default_format() == NC_FORMAT_CDF5)
cmode |= NC_CDF5;
else if (nc_get_default_format() == NC_FORMAT_64BIT_OFFSET)
cmode |= NC_64BIT_OFFSET;
else if (nc_get_default_format() == NC_FORMAT_NETCDF4_CLASSIC)
cmode |= NC_CLASSIC_MODEL;
LOG((2, "cmode after applying default format: 0x%x", cmode));
nc_file->int_ncid = nc_file->ext_ncid;
res = nc4_create_file(path, cmode, initialsz, parameters, nc_file);
done:
return res;
}
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