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netcdf-c/libdispatch/dfile.c
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/**
* @file
*
* File create and open functions
*
* These functions end up calling functions in one of the dispatch
* layers (netCDF-4, dap server, etc).
*
* Copyright 2018 University Corporation for Atmospheric
* Research/Unidata. See COPYRIGHT file for more info.
*/
#include "config.h"
#include <stdlib.h>
#ifdef HAVE_STRING_H
#include <string.h>
#endif
#ifdef HAVE_SYS_RESOURCE_H
#include <sys/resource.h>
#endif
#ifdef HAVE_SYS_TYPES_H
#include <sys/types.h>
#endif
#ifdef HAVE_SYS_STAT_H
#include <sys/stat.h>
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h> /* lseek() */
#endif
#ifdef HAVE_STDIO_H
#include <stdio.h>
#endif
#include "ncdispatch.h"
#include "netcdf_mem.h"
#include "ncpathmgr.h"
#include "fbits.h"
#undef DEBUG
#ifndef nulldup
#define nulldup(s) ((s)?strdup(s):NULL)
#endif
extern int NC_initialized; /**< True when dispatch table is initialized. */
/* User-defined formats. */
NC_Dispatch *UDF0_dispatch_table = NULL;
char UDF0_magic_number[NC_MAX_MAGIC_NUMBER_LEN + 1] = "";
NC_Dispatch *UDF1_dispatch_table = NULL;
char UDF1_magic_number[NC_MAX_MAGIC_NUMBER_LEN + 1] = "";
/**************************************************/
/** \defgroup datasets NetCDF File and Data I/O
NetCDF opens datasets as files or remote access URLs.
A netCDF dataset that has not yet been opened can only be referred to
by its dataset name. Once a netCDF dataset is opened, it is referred
to by a netCDF ID, which is a small non-negative integer returned when
you create or open the dataset. A netCDF ID is much like a file
descriptor in C or a logical unit number in FORTRAN. In any single
program, the netCDF IDs of distinct open netCDF datasets are
distinct. A single netCDF dataset may be opened multiple times and
will then have multiple distinct netCDF IDs; however at most one of
the open instances of a single netCDF dataset should permit
writing. When an open netCDF dataset is closed, the ID is no longer
associated with a netCDF dataset.
Functions that deal with the netCDF library include:
- Get version of library.
- Get error message corresponding to a returned error code.
The operations supported on a netCDF dataset as a single object are:
- Create, given dataset name and whether to overwrite or not.
- Open for access, given dataset name and read or write intent.
- Put into define mode, to add dimensions, variables, or attributes.
- Take out of define mode, checking consistency of additions.
- Close, writing to disk if required.
- Inquire about the number of dimensions, number of variables,
number of global attributes, and ID of the unlimited dimension, if
any.
- Synchronize to disk to make sure it is current.
- Set and unset nofill mode for optimized sequential writes.
- After a summary of conventions used in describing the netCDF
interfaces, the rest of this chapter presents a detailed description
of the interfaces for these operations.
*/
/**
* Add handling of user-defined format.
*
* User-defined formats allow users to write a library which can read
* their own proprietary format as if it were netCDF. This allows
* existing netCDF codes to work on non-netCDF data formats.
*
* User-defined formats work by specifying a netCDF dispatch
* table. The dispatch table is a struct of (mostly) C function
* pointers. It contains pointers to the key functions of the netCDF
* API. Once these functions are provided, and the dispatch table is
* specified, the netcdf-c library can read any format.
*
* @note Unlike the public netCDF API, the dispatch table may not be
* backward compatible between netCDF releases. Instead, it contains a
* dispatch version number. If this number is not correct (i.e. does
* not match the current dispatch table version), then ::NC_EINVAL
* will be returned.
*
* @param mode_flag NC_UDF0 or NC_UDF1
* @param dispatch_table Pointer to dispatch table to use for this user format.
* @param magic_number Magic number used to identify file. Ignored if
* NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL Invalid input.
* @author Ed Hartnett
* @ingroup datasets
*/
int
nc_def_user_format(int mode_flag, NC_Dispatch *dispatch_table, char *magic_number)
{
/* Check inputs. */
if (!dispatch_table)
return NC_EINVAL;
if (magic_number && strlen(magic_number) > NC_MAX_MAGIC_NUMBER_LEN)
return NC_EINVAL;
/* Check the version of the dispatch table provided. */
if (dispatch_table->dispatch_version != NC_DISPATCH_VERSION)
return NC_EINVAL;
/* user defined magic numbers not allowed with netcdf3 modes */
if (magic_number && (fIsSet(mode_flag, NC_64BIT_OFFSET) ||
fIsSet(mode_flag, NC_64BIT_DATA) ||
(fIsSet(mode_flag, NC_CLASSIC_MODEL) &&
!fIsSet(mode_flag, NC_NETCDF4))))
return NC_EINVAL;
/* Retain a pointer to the dispatch_table and a copy of the magic
* number, if one was provided. */
if (fIsSet(mode_flag,NC_UDF0))
{
UDF0_dispatch_table = dispatch_table;
if (magic_number)
strncpy(UDF0_magic_number, magic_number, NC_MAX_MAGIC_NUMBER_LEN);
}
else if(fIsSet(mode_flag, NC_UDF1))
{
UDF1_dispatch_table = dispatch_table;
if (magic_number)
strncpy(UDF1_magic_number, magic_number, NC_MAX_MAGIC_NUMBER_LEN);
}
else
{
return NC_EINVAL;
}
return NC_NOERR;
}
/**
* Inquire about user-defined format.
*
* @param mode_flag NC_UDF0 or NC_UDF1
* @param dispatch_table Pointer that gets pointer to dispatch table
* to use for this user format, or NULL if this user-defined format is
* not defined. Ignored if NULL.
* @param magic_number Pointer that gets magic number used to identify
* file, if one has been set. Magic number will be of max size
* NC_MAX_MAGIC_NUMBER_LEN. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL Invalid input.
* @author Ed Hartnett
* @ingroup datasets
*/
int
nc_inq_user_format(int mode_flag, NC_Dispatch **dispatch_table, char *magic_number)
{
/* Check inputs. */
if (fIsSet(mode_flag,NC_UDF0))
{
if (dispatch_table)
*dispatch_table = UDF0_dispatch_table;
if (magic_number)
strncpy(magic_number, UDF0_magic_number, NC_MAX_MAGIC_NUMBER_LEN);
}
else if(fIsSet(mode_flag,NC_UDF1))
{
if (dispatch_table)
*dispatch_table = UDF1_dispatch_table;
if (magic_number)
strncpy(magic_number, UDF1_magic_number, NC_MAX_MAGIC_NUMBER_LEN);
}
else
{
return NC_EINVAL;
}
return NC_NOERR;
}
/** \ingroup datasets
Create a new netCDF file.
This function creates a new netCDF dataset, returning a netCDF ID that
can subsequently be used to refer to the netCDF dataset in other
netCDF function calls. The new netCDF dataset opened for write access
and placed in define mode, ready for you to add dimensions, variables,
and attributes.
\param path The file name of the new netCDF dataset.
\param cmode The creation mode flag. The following flags are available:
NC_CLOBBER (overwrite existing file),
NC_NOCLOBBER (do not overwrite existing file),
NC_SHARE (limit write caching - netcdf classic files only),
NC_64BIT_OFFSET (create 64-bit offset file),
NC_64BIT_DATA (alias NC_CDF5) (create CDF-5 file),
NC_NETCDF4 (create netCDF-4/HDF5 file),
NC_CLASSIC_MODEL (enforce netCDF classic mode on netCDF-4/HDF5 files),
NC_DISKLESS (store data in memory), and
NC_PERSIST (force the NC_DISKLESS data from memory to a file),
NC_MMAP (use MMAP for NC_DISKLESS instead of NC_INMEMORY -- deprecated).
See discussion below.
\param ncidp Pointer to location where returned netCDF ID is to be
stored.
<h2>The cmode Flag</h2>
The cmode flag is used to control the type of file created, and some
aspects of how it may be used.
Setting NC_NOCLOBBER means you do not want to clobber (overwrite) an
existing dataset; an error (NC_EEXIST) is returned if the specified
dataset already exists.
The NC_SHARE flag is appropriate when one process may be writing the
dataset and one or more other processes reading the dataset
concurrently; it means that dataset accesses are not buffered and
caching is limited. Since the buffering scheme is optimized for
sequential access, programs that do not access data sequentially may
see some performance improvement by setting the NC_SHARE flag. This
flag is ignored for netCDF-4 files.
Setting NC_64BIT_OFFSET causes netCDF to create a 64-bit offset format
file, instead of a netCDF classic format file. The 64-bit offset
format imposes far fewer restrictions on very large (i.e. over 2 GB)
data files. See Large File Support.
Setting NC_64BIT_DATA (alias NC_CDF5) causes netCDF to create a CDF-5
file format that supports large files (i.e. over 2GB) and large
variables (over 2B array elements.). See Large File Support.
A zero value (defined for convenience as NC_CLOBBER) specifies the
default behavior: overwrite any existing dataset with the same file
name and buffer and cache accesses for efficiency. The dataset will be
in netCDF classic format. See NetCDF Classic Format Limitations.
Setting NC_NETCDF4 causes netCDF to create a HDF5/NetCDF-4 file.
Setting NC_CLASSIC_MODEL causes netCDF to enforce the classic data
model in this file. (This only has effect for netCDF-4/HDF5 files, as
CDF-1, 2 and 5 files always use the classic model.) When
used with NC_NETCDF4, this flag ensures that the resulting
netCDF-4/HDF5 file may never contain any new constructs from the
enhanced data model. That is, it cannot contain groups, user defined
types, multiple unlimited dimensions, or new atomic types. The
advantage of this restriction is that such files are guaranteed to
work with existing netCDF software.
Setting NC_DISKLESS causes netCDF to create the file only in
memory and to optionally write the final contents to the
correspondingly named disk file. This allows for the use of
files that have no long term purpose. Operating on an existing file
in memory may also be faster. The decision on whether
or not to "persist" the memory contents to a disk file is
described in detail in the file docs/inmemory.md, which is
definitive. By default, closing a diskless fill will cause it's
contents to be lost.
If NC_DISKLESS is going to be used for creating a large classic
file, it behooves one to use nc__create and specify an
appropriately large value of the initialsz parameter to avoid to
many extensions to the in-memory space for the file. This flag
applies to files in classic format and to file in extended
format (netcdf-4).
Note that nc_create(path,cmode,ncidp) is equivalent to the invocation of
nc__create(path,cmode,NC_SIZEHINT_DEFAULT,NULL,ncidp).
\returns ::NC_NOERR No error.
\returns ::NC_EEXIST Specifying a file name of a file that exists and also specifying NC_NOCLOBBER.
\returns ::NC_EPERM Attempting to create a netCDF file in a directory where you do not have permission to create files.
\returns ::NC_ENOMEM System out of memory.
\returns ::NC_ENFILE Too many files open.
\returns ::NC_EHDFERR HDF5 error (netCDF-4 files only).
\returns ::NC_EFILEMETA Error writing netCDF-4 file-level metadata in
HDF5 file. (netCDF-4 files only).
\returns ::NC_EDISKLESS if there was an error in creating the
in-memory file.
\note When creating a netCDF-4 file HDF5 error reporting is turned
off, if it is on. This doesn't stop the HDF5 error stack from
recording the errors, it simply stops their display to the user
through stderr.
<h1>Examples</h1>
In this example we create a netCDF dataset named foo.nc; we want the
dataset to be created in the current directory only if a dataset with
that name does not already exist:
@code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
...
status = nc_create("foo.nc", NC_NOCLOBBER, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
In this example we create a netCDF dataset named foo_large.nc. It will
be in the 64-bit offset format.
@code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
...
status = nc_create("foo_large.nc", NC_NOCLOBBER|NC_64BIT_OFFSET, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
In this example we create a netCDF dataset named foo_HDF5.nc. It will
be in the HDF5 format.
@code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
...
status = nc_create("foo_HDF5.nc", NC_NOCLOBBER|NC_NETCDF4, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
In this example we create a netCDF dataset named
foo_HDF5_classic.nc. It will be in the HDF5 format, but will not allow
the use of any netCDF-4 advanced features. That is, it will conform to
the classic netCDF-3 data model.
@code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
...
status = nc_create("foo_HDF5_classic.nc", NC_NOCLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
In this example we create an in-memory netCDF classic dataset named
diskless.nc whose content will be lost when nc_close() is called.
@code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
...
status = nc_create("diskless.nc", NC_DISKLESS, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
In this example we create a in-memory netCDF classic dataset named
diskless.nc and specify that it should be made persistent
in a file named diskless.nc when nc_close() is called.
@code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
...
status = nc_create("diskless.nc", NC_DISKLESS|NC_PERSIST, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
A variant of nc_create(), nc__create() (note the double underscore) allows
users to specify two tuning parameters for the file that it is
creating. */
int
nc_create(const char *path, int cmode, int *ncidp)
{
return nc__create(path,cmode,NC_SIZEHINT_DEFAULT,NULL,ncidp);
}
/**
* Create a netCDF file with some extra parameters controlling classic
* file caching.
*
* Like nc_create(), this function creates a netCDF file.
*
* @param path The file name of the new netCDF dataset.
* @param cmode The creation mode flag, the same as in nc_create().
* @param initialsz On some systems, and with custom I/O layers, it
* may be advantageous to set the size of the output file at creation
* time. This parameter sets the initial size of the file at creation
* time. This only applies to classic CDF-1, 2, and 5 files. The
* special value NC_SIZEHINT_DEFAULT (which is the value 0), lets the
* netcdf library choose a suitable initial size.
* @param chunksizehintp A pointer to the chunk size hint, which
* controls a space versus time tradeoff, memory allocated in the
* netcdf library versus number of system calls. Because of internal
* requirements, the value may not be set to exactly the value
* requested. The actual value chosen is returned by reference. Using
* a NULL pointer or having the pointer point to the value
* NC_SIZEHINT_DEFAULT causes the library to choose a default. How the
* system chooses the default depends on the system. On many systems,
* the "preferred I/O block size" is available from the stat() system
* call, struct stat member st_blksize. If this is available it is
* used. Lacking that, twice the system pagesize is used. Lacking a
* call to discover the system pagesize, we just set default bufrsize
* to 8192. The bufrsize is a property of a given open netcdf
* descriptor ncid, it is not a persistent property of the netcdf
* dataset. This only applies to classic files.
* @param ncidp Pointer to location where returned netCDF ID is to be
* stored.
*
* @note This function uses the same return codes as the nc_create()
* function.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_ENOMEM System out of memory.
* @returns ::NC_EHDFERR HDF5 error (netCDF-4 files only).
* @returns ::NC_EFILEMETA Error writing netCDF-4 file-level metadata in
* HDF5 file. (netCDF-4 files only).
* @returns ::NC_EDISKLESS if there was an error in creating the
* in-memory file.
*
* <h1>Examples</h1>
*
* In this example we create a netCDF dataset named foo_large.nc; we
* want the dataset to be created in the current directory only if a
* dataset with that name does not already exist. We also specify that
* bufrsize and initial size for the file.
*
* @code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
int intialsz = 2048;
int *bufrsize;
...
*bufrsize = 1024;
status = nc__create("foo.nc", NC_NOCLOBBER, initialsz, bufrsize, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
*
* @ingroup datasets
* @author Glenn Davis
*/
int
nc__create(const char *path, int cmode, size_t initialsz,
size_t *chunksizehintp, int *ncidp)
{
return NC_create(path, cmode, initialsz, 0,
chunksizehintp, 0, NULL, ncidp);
}
/** \ingroup datasets
Create a netCDF file with the contents stored in memory.
\param path Must be non-null, but otherwise only used to set the dataset name.
\param mode the mode flags; Note that this procedure uses a limited set of flags because it forcibly sets NC_INMEMORY.
\param initialsize (advisory) size to allocate for the created file
\param ncidp Pointer to location where returned netCDF ID is to be
stored.
\returns ::NC_NOERR No error.
\returns ::NC_ENOMEM Out of memory.
\returns ::NC_EDISKLESS diskless io is not enabled for fails.
\returns ::NC_EINVAL, etc. other errors also returned by nc_open.
<h1>Examples</h1>
In this example we use nc_create_mem() to create a classic netCDF dataset
named foo.nc. The initial size is set to 4096.
@code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
int mode = 0;
size_t initialsize = 4096;
...
status = nc_create_mem("foo.nc", mode, initialsize, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
*/
int
nc_create_mem(const char* path, int mode, size_t initialsize, int* ncidp)
{
if(mode & NC_MMAP) return NC_EINVAL;
mode |= NC_INMEMORY; /* Specifically, do not set NC_DISKLESS */
return NC_create(path, mode, initialsize, 0, NULL, 0, NULL, ncidp);
}
/**
* @internal Create a file with special (deprecated) Cray settings.
*
* @deprecated This function was used in the old days with the Cray at
* NCAR. The Cray is long gone, and this call is supported only for
* backward compatibility. Use nc_create() instead.
*
* @param path File name.
* @param cmode Create mode.
* @param initialsz Initial size of metadata region for classic files,
* ignored for other files.
* @param basepe Deprecated parameter from the Cray days.
* @param chunksizehintp A pointer to the chunk size hint. This only
* applies to classic files.
* @param ncidp Pointer that gets ncid.
*
* @return ::NC_NOERR No error.
* @author Glenn Davis
*/
int
nc__create_mp(const char *path, int cmode, size_t initialsz,
int basepe, size_t *chunksizehintp, int *ncidp)
{
return NC_create(path, cmode, initialsz, basepe,
chunksizehintp, 0, NULL, ncidp);
}
/**
* Open an existing netCDF file.
*
* This function opens an existing netCDF dataset for access. It
* determines the underlying file format automatically. Use the same
* call to open a netCDF classic or netCDF-4 file.
*
* @param path File name for netCDF dataset to be opened. When the dataset
* is located on some remote server, then the path may be an OPeNDAP URL
* rather than a file path.
* @param omode The open mode flag may include NC_WRITE (for read/write
* access) and NC_SHARE (see below) and NC_DISKLESS (see below).
* @param ncidp Pointer to location where returned netCDF ID is to be
* stored.
*
* <h2>Open Mode</h2>
*
* A zero value (or ::NC_NOWRITE) specifies the default behavior: open
* the dataset with read-only access, buffering and caching accesses
* for efficiency.
*
* Otherwise, the open mode is ::NC_WRITE, ::NC_SHARE, or
* ::NC_WRITE|::NC_SHARE. Setting the ::NC_WRITE flag opens the
* dataset with read-write access. ("Writing" means any kind of change
* to the dataset, including appending or changing data, adding or
* renaming dimensions, variables, and attributes, or deleting
* attributes.)
*
* The NC_SHARE flag is only used for netCDF classic
* files. It is appropriate when one process may be writing the
* dataset and one or more other processes reading the dataset
* concurrently; it means that dataset accesses are not buffered and
* caching is limited. Since the buffering scheme is optimized for
* sequential access, programs that do not access data sequentially
* may see some performance improvement by setting the NC_SHARE flag.
*
* This procedure may also be invoked with the NC_DISKLESS flag set in
* the omode argument if the file to be opened is a classic format
* file. For nc_open(), this flag applies only to files in classic
* format. If the file is of type NC_NETCDF4, then the NC_DISKLESS
* flag will be ignored.
*
* If NC_DISKLESS is specified, then the whole file is read completely
* into memory. In effect this creates an in-memory cache of the file.
* If the omode flag also specifies NC_PERSIST, then the in-memory cache
* will be re-written to the disk file when nc_close() is called. For
* some kinds of manipulations, having the in-memory cache can speed
* up file processing. But in simple cases, non-cached processing may
* actually be faster than using cached processing. You will need to
* experiment to determine if the in-memory caching is worthwhile for
* your application.
*
* Normally, NC_DISKLESS allocates space in the heap for storing the
* in-memory file. If, however, the ./configure flags --enable-mmap is
* used, and the additional omode flag NC_MMAP is specified, then the
* file will be opened using the operating system MMAP facility. This
* flag only applies to files in classic format. Extended format
* (netcdf-4) files will ignore the NC_MMAP flag.
*
* In most cases, using MMAP provides no advantage for just
* NC_DISKLESS. The one case where using MMAP is an advantage is when
* a file is to be opened and only a small portion of its data is to
* be read and/or written. In this scenario, MMAP will cause only the
* accessed data to be retrieved from disk. Without MMAP, NC_DISKLESS
* will read the whole file into memory on nc_open. Thus, MMAP will
* provide some performance improvement in this case.
*
* It is not necessary to pass any information about the format of the
* file being opened. The file type will be detected automatically by
* the netCDF library.
*
* If a the path is a DAP URL, then the open mode is read-only.
* Setting NC_WRITE will be ignored.
*
* As of version 4.3.1.2, multiple calls to nc_open with the same
* path will return the same ncid value.
*
* @note When opening a netCDF-4 file HDF5 error reporting is turned
* off, if it is on. This doesn't stop the HDF5 error stack from
* recording the errors, it simply stops their display to the user
* through stderr.
*
* nc_open()returns the value NC_NOERR if no errors
* occurred. Otherwise, the returned status indicates an
* error. Possible causes of errors include:
*
* Note that nc_open(path,omode,ncidp) is equivalent to the invocation
* of nc__open(path,omode,NC_SIZEHINT_DEFAULT,NULL,ncidp).
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EPERM Attempting to create a netCDF file in a directory where you do not have permission to open files.
* @returns ::NC_ENFILE Too many files open
* @returns ::NC_ENOMEM Out of memory.
* @returns ::NC_EHDFERR HDF5 error. (NetCDF-4 files only.)
* @returns ::NC_EDIMMETA Error in netCDF-4 dimension metadata. (NetCDF-4 files only.)
*
* <h1>Examples</h1>
*
* Here is an example using nc_open()to open an existing netCDF dataset
* named foo.nc for read-only, non-shared access:
*
* @code
* #include <netcdf.h>
* ...
* int status = NC_NOERR;
* int ncid;
* ...
* status = nc_open("foo.nc", 0, &ncid);
* if (status != NC_NOERR) handle_error(status);
* @endcode
* @ingroup datasets
* @author Glenn Davis, Ed Hartnett, Dennis Heimbigner
*/
int
nc_open(const char *path, int omode, int *ncidp)
{
return NC_open(path, omode, 0, NULL, 0, NULL, ncidp);
}
/** \ingroup datasets
Open a netCDF file with extra performance parameters for the classic
library.
\param path File name for netCDF dataset to be opened. When DAP
support is enabled, then the path may be an OPeNDAP URL rather than a
file path.
\param omode The open mode flag may include NC_WRITE (for read/write
access) and NC_SHARE as in nc_open().
\param chunksizehintp A size hint for the classic library. Only
applies to classic files. See below for more
information.
\param ncidp Pointer to location where returned netCDF ID is to be
stored.
<h1>The chunksizehintp Parameter</h1>
The argument referenced by bufrsizehintp controls a space versus time
tradeoff, memory allocated in the netcdf library versus number of
system calls.
Because of internal requirements, the value may not be set to exactly
the value requested. The actual value chosen is returned by reference.
Using a NULL pointer or having the pointer point to the value
NC_SIZEHINT_DEFAULT causes the library to choose a default.
How the system chooses the default depends on the system. On
many systems, the "preferred I/O block size" is available from the
stat() system call, struct stat member st_blksize. If this is
available it is used. Lacking that, twice the system pagesize is used.
Lacking a call to discover the system pagesize, we just set default
bufrsize to 8192.
The bufrsize is a property of a given open netcdf descriptor ncid, it
is not a persistent property of the netcdf dataset.
\returns ::NC_NOERR No error.
\returns ::NC_ENOMEM Out of memory.
\returns ::NC_EHDFERR HDF5 error. (NetCDF-4 files only.)
\returns ::NC_EDIMMETA Error in netCDF-4 dimension metadata. (NetCDF-4
files only.)
*/
int
nc__open(const char *path, int omode,
size_t *chunksizehintp, int *ncidp)
{
/* this API is for non-parallel access.
* Note nc_open_par() also calls NC_open().
*/
return NC_open(path, omode, 0, chunksizehintp, 0, NULL, ncidp);
}
/** \ingroup datasets
Open a netCDF file with the contents taken from a block of memory.
\param path Must be non-null, but otherwise only used to set the dataset name.
\param omode the open mode flags; Note that this procedure uses a limited set of flags because it forcibly sets NC_INMEMORY.
\param size The length of the block of memory being passed.
\param memory Pointer to the block of memory containing the contents
of a netcdf file.
\param ncidp Pointer to location where returned netCDF ID is to be
stored.
\returns ::NC_NOERR No error.
\returns ::NC_ENOMEM Out of memory.
\returns ::NC_EDISKLESS diskless io is not enabled for fails.
\returns ::NC_EINVAL, etc. other errors also returned by nc_open.
<h1>Examples</h1>
Here is an example using nc_open_mem() to open an existing netCDF dataset
named foo.nc for read-only, non-shared access. It differs from the nc_open()
example in that it assumes the contents of foo.nc have been read into memory.
@code
#include <netcdf.h>
#include <netcdf_mem.h>
...
int status = NC_NOERR;
int ncid;
size_t size;
void* memory;
...
size = <compute file size of foo.nc in bytes>;
memory = malloc(size);
...
status = nc_open_mem("foo.nc", 0, size, memory, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
*/
int
nc_open_mem(const char* path, int omode, size_t size, void* memory, int* ncidp)
{
NC_memio meminfo;
/* Sanity checks */
if(memory == NULL || size < MAGIC_NUMBER_LEN || path == NULL)
return NC_EINVAL;
if(omode & (NC_WRITE|NC_MMAP))
return NC_EINVAL;
omode |= (NC_INMEMORY); /* Note: NC_INMEMORY and NC_DISKLESS are mutually exclusive*/
meminfo.size = size;
meminfo.memory = memory;
meminfo.flags = NC_MEMIO_LOCKED;
return NC_open(path, omode, 0, NULL, 0, &meminfo, ncidp);
}
/** \ingroup datasets
Open a netCDF file with the contents taken from a block of memory.
Similar to nc_open_mem, but with parameters. Warning: if you do
specify that the provided memory is locked, then <b>never</b>
pass in non-heap allocated memory. Additionally, if not locked,
then do not assume that the memory returned by nc_close_mem
is the same as passed to nc_open_memio. You <b>must</b> check
before attempting to free the original memory.
\param path Must be non-null, but otherwise only used to set the dataset name.
\param omode the open mode flags; Note that this procedure uses a limited set of flags because it forcibly sets NC_INMEMORY.
\param params controlling parameters
\param ncidp Pointer to location where returned netCDF ID is to be
stored.
\returns ::NC_NOERR No error.
\returns ::NC_ENOMEM Out of memory.
\returns ::NC_EDISKLESS diskless io is not enabled for fails.
\returns ::NC_EINVAL, etc. other errors also returned by nc_open.
<h1>Examples</h1>
Here is an example using nc_open_memio() to open an existing netCDF dataset
named foo.nc for read-only, non-shared access. It differs from the nc_open_mem()
example in that it uses a parameter block.
@code
#include <netcdf.h>
#include <netcdf_mem.h>
...
int status = NC_NOERR;
int ncid;
NC_memio params;
...
params.size = <compute file size of foo.nc in bytes>;
params.memory = malloc(size);
params.flags = <see netcdf_mem.h>
...
status = nc_open_memio("foo.nc", 0, &params, &ncid);
if (status != NC_NOERR) handle_error(status);
@endcode
*/
int
nc_open_memio(const char* path, int omode, NC_memio* params, int* ncidp)
{
/* Sanity checks */
if(path == NULL || params == NULL)
return NC_EINVAL;
if(params->memory == NULL || params->size < MAGIC_NUMBER_LEN)
return NC_EINVAL;
if(omode & NC_MMAP)
return NC_EINVAL;
omode |= (NC_INMEMORY);
return NC_open(path, omode, 0, NULL, 0, params, ncidp);
}
/**
* @internal Open a netCDF file with extra parameters for Cray.
*
* @deprecated This function was used in the old days with the Cray at
* NCAR. The Cray is long gone, and this call is supported only for
* backward compatibility. Use nc_open() instead.
*
* @param path The file name of the new netCDF dataset.
* @param omode Open mode.
* @param basepe Deprecated parameter from the Cray days.
* @param chunksizehintp A pointer to the chunk size hint. This only
* applies to classic files.
* @param ncidp Pointer to location where returned netCDF ID is to be
* stored.
*
* @return ::NC_NOERR
* @author Glenn Davis
*/
int
nc__open_mp(const char *path, int omode, int basepe,
size_t *chunksizehintp, int *ncidp)
{
return NC_open(path, omode, basepe, chunksizehintp, 0, NULL, ncidp);
}
/** \ingroup datasets
Get the file pathname (or the opendap URL) which was used to
open/create the ncid's file.
\param ncid NetCDF ID, from a previous call to nc_open() or
nc_create().
\param pathlen Pointer where length of path will be returned. Ignored
if NULL.
\param path Pointer where path name will be copied. Space must already
be allocated. Ignored if NULL.
\returns ::NC_NOERR No error.
\returns ::NC_EBADID Invalid ncid passed.
*/
int
nc_inq_path(int ncid, size_t *pathlen, char *path)
{
NC* ncp;
int stat = NC_NOERR;
if ((stat = NC_check_id(ncid, &ncp)))
return stat;
if(ncp->path == NULL) {
if(pathlen) *pathlen = 0;
if(path) path[0] = '\0';
} else {
if (pathlen) *pathlen = strlen(ncp->path);
if (path) strcpy(path, ncp->path);
}
return stat;
}
/** \ingroup datasets
Put open netcdf dataset into define mode
The function nc_redef puts an open netCDF dataset into define mode, so
dimensions, variables, and attributes can be added or renamed and
attributes can be deleted.
For netCDF-4 files (i.e. files created with NC_NETCDF4 in the cmode in
their call to nc_create()), it is not necessary to call nc_redef()
unless the file was also created with NC_STRICT_NC3. For straight-up
netCDF-4 files, nc_redef() is called automatically, as needed.
For all netCDF-4 files, the root ncid must be used. This is the ncid
returned by nc_open() and nc_create(), and points to the root of the
hierarchy tree for netCDF-4 files.
\param ncid NetCDF ID, from a previous call to nc_open() or
nc_create().
\returns ::NC_NOERR No error.
\returns ::NC_EBADID Bad ncid.
\returns ::NC_EBADGRPID The ncid must refer to the root group of the
file, that is, the group returned by nc_open() or nc_create().
\returns ::NC_EINDEFINE Already in define mode.
\returns ::NC_EPERM File is read-only.
<h1>Example</h1>
Here is an example using nc_redef to open an existing netCDF dataset
named foo.nc and put it into define mode:
\code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
...
status = nc_open("foo.nc", NC_WRITE, &ncid);
if (status != NC_NOERR) handle_error(status);
...
status = nc_redef(ncid);
if (status != NC_NOERR) handle_error(status);
\endcode
*/
int
nc_redef(int ncid)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
return ncp->dispatch->redef(ncid);
}
/** \ingroup datasets
Leave define mode
The function nc_enddef() takes an open netCDF dataset out of define
mode. The changes made to the netCDF dataset while it was in define
mode are checked and committed to disk if no problems
occurred. Non-record variables may be initialized to a "fill value" as
well with nc_set_fill(). The netCDF dataset is then placed in data
mode, so variable data can be read or written.
It's not necessary to call nc_enddef() for netCDF-4 files. With netCDF-4
files, nc_enddef() is called when needed by the netcdf-4 library. User
calls to nc_enddef() for netCDF-4 files still flush the metadata to
disk.
This call may involve copying data under some circumstances. For a
more extensive discussion see File Structure and Performance.
For netCDF-4/HDF5 format files there are some variable settings (the
compression, endianness, fletcher32 error correction, and fill value)
which must be set (if they are going to be set at all) between the
nc_def_var() and the next nc_enddef(). Once the nc_enddef() is called,
these settings can no longer be changed for a variable.
\param ncid NetCDF ID, from a previous call to nc_open() or
nc_create().
If you use a group id (in a netCDF-4/HDF5 file), the enddef
will apply to the entire file. That means the enddef will not just end
define mode in one group, but in the entire file.
\returns ::NC_NOERR no error
\returns ::NC_EBADID Invalid ncid passed.
<h1>Example</h1>
Here is an example using nc_enddef() to finish the definitions of a new
netCDF dataset named foo.nc and put it into data mode:
\code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
...
status = nc_create("foo.nc", NC_NOCLOBBER, &ncid);
if (status != NC_NOERR) handle_error(status);
... create dimensions, variables, attributes
status = nc_enddef(ncid);
if (status != NC_NOERR) handle_error(status);
\endcode
*/
int
nc_enddef(int ncid)
{
int status = NC_NOERR;
NC *ncp;
status = NC_check_id(ncid, &ncp);
if(status != NC_NOERR) return status;
return ncp->dispatch->_enddef(ncid,0,1,0,1);
}
/** \ingroup datasets
Leave define mode with performance tuning
The function nc__enddef takes an open netCDF dataset out of define
mode. The changes made to the netCDF dataset while it was in define
mode are checked and committed to disk if no problems
occurred. Non-record variables may be initialized to a "fill value" as
well with nc_set_fill(). The netCDF dataset is then placed in data mode,
so variable data can be read or written.
This call may involve copying data under some circumstances. For a
more extensive discussion see File Structure and Performance.
\warning This function exposes internals of the netcdf version 1 file
format. Users should use nc_enddef() in most circumstances. This
function may not be available on future netcdf implementations.
The classic netcdf file format has three sections, the "header"
section, the data section for fixed size variables, and the data
section for variables which have an unlimited dimension (record
variables).
The header begins at the beginning of the file. The index (offset) of
the beginning of the other two sections is contained in the
header. Typically, there is no space between the sections. This causes
copying overhead to accrue if one wishes to change the size of the
sections, as may happen when changing names of things, text attribute
values, adding attributes or adding variables. Also, for buffered i/o,
there may be advantages to aligning sections in certain ways.
The minfree parameters allow one to control costs of future calls to
nc_redef, nc_enddef() by requesting that minfree bytes be available at
the end of the section.
The align parameters allow one to set the alignment of the beginning
of the corresponding sections. The beginning of the section is rounded
up to an index which is a multiple of the align parameter. The flag
value ALIGN_CHUNK tells the library to use the bufrsize (see above) as
the align parameter. It has nothing to do with the chunking
(multidimensional tiling) features of netCDF-4.
The file format requires mod 4 alignment, so the align parameters are
silently rounded up to multiples of 4. The usual call,
\code
nc_enddef(ncid);
\endcode
is equivalent to
\code
nc__enddef(ncid, 0, 4, 0, 4);
\endcode
The file format does not contain a "record size" value, this is
calculated from the sizes of the record variables. This unfortunate
fact prevents us from providing minfree and alignment control of the
"records" in a netcdf file. If you add a variable which has an
unlimited dimension, the third section will always be copied with the
new variable added.
\param ncid NetCDF ID, from a previous call to nc_open() or
nc_create().
\param h_minfree Sets the pad at the end of the "header" section.
\param v_align Controls the alignment of the beginning of the data
section for fixed size variables.
\param v_minfree Sets the pad at the end of the data section for fixed
size variables.
\param r_align Controls the alignment of the beginning of the data
section for variables which have an unlimited dimension (record
variables).
\returns ::NC_NOERR No error.
\returns ::NC_EBADID Invalid ncid passed.
*/
int
nc__enddef(int ncid, size_t h_minfree, size_t v_align, size_t v_minfree,
size_t r_align)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
return ncp->dispatch->_enddef(ncid,h_minfree,v_align,v_minfree,r_align);
}
/** \ingroup datasets
Synchronize an open netcdf dataset to disk
The function nc_sync() offers a way to synchronize the disk copy of a
netCDF dataset with in-memory buffers. There are two reasons you might
want to synchronize after writes:
- To minimize data loss in case of abnormal termination, or
- To make data available to other processes for reading immediately
after it is written. But note that a process that already had the
dataset open for reading would not see the number of records
increase when the writing process calls nc_sync(); to accomplish this,
the reading process must call nc_sync.
This function is backward-compatible with previous versions of the
netCDF library. The intent was to allow sharing of a netCDF dataset
among multiple readers and one writer, by having the writer call
nc_sync() after writing and the readers call nc_sync() before each
read. For a writer, this flushes buffers to disk. For a reader, it
makes sure that the next read will be from disk rather than from
previously cached buffers, so that the reader will see changes made by
the writing process (e.g., the number of records written) without
having to close and reopen the dataset. If you are only accessing a
small amount of data, it can be expensive in computer resources to
always synchronize to disk after every write, since you are giving up
the benefits of buffering.
An easier way to accomplish sharing (and what is now recommended) is
to have the writer and readers open the dataset with the NC_SHARE
flag, and then it will not be necessary to call nc_sync() at
all. However, the nc_sync() function still provides finer granularity
than the NC_SHARE flag, if only a few netCDF accesses need to be
synchronized among processes.
It is important to note that changes to the ancillary data, such as
attribute values, are not propagated automatically by use of the
NC_SHARE flag. Use of the nc_sync() function is still required for this
purpose.
Sharing datasets when the writer enters define mode to change the data
schema requires extra care. In previous releases, after the writer
left define mode, the readers were left looking at an old copy of the
dataset, since the changes were made to a new copy. The only way
readers could see the changes was by closing and reopening the
dataset. Now the changes are made in place, but readers have no
knowledge that their internal tables are now inconsistent with the new
dataset schema. If netCDF datasets are shared across redefinition,
some mechanism external to the netCDF library must be provided that
prevents access by readers during redefinition and causes the readers
to call nc_sync before any subsequent access.
When calling nc_sync(), the netCDF dataset must be in data mode. A
netCDF dataset in define mode is synchronized to disk only when
nc_enddef() is called. A process that is reading a netCDF dataset that
another process is writing may call nc_sync to get updated with the
changes made to the data by the writing process (e.g., the number of
records written), without having to close and reopen the dataset.
Data is automatically synchronized to disk when a netCDF dataset is
closed, or whenever you leave define mode.
\param ncid NetCDF ID, from a previous call to nc_open() or
nc_create().
\returns ::NC_NOERR No error.
\returns ::NC_EBADID Invalid ncid passed.
*/
int
nc_sync(int ncid)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
return ncp->dispatch->sync(ncid);
}
/** \ingroup datasets
No longer necessary for user to invoke manually.
\warning Users no longer need to call this function since it is called
automatically by nc_close() in case the dataset is in define mode and
something goes wrong with committing the changes. The function
nc_abort() just closes the netCDF dataset, if not in define mode. If
the dataset is being created and is still in define mode, the dataset
is deleted. If define mode was entered by a call to nc_redef(), the
netCDF dataset is restored to its state before definition mode was
entered and the dataset is closed.
\param ncid NetCDF ID, from a previous call to nc_open() or
nc_create().
\returns ::NC_NOERR No error.
<h1>Example</h1>
Here is an example using nc_abort to back out of redefinitions of a
dataset named foo.nc:
\code
#include <netcdf.h>
...
int ncid, status, latid;
...
status = nc_open("foo.nc", NC_WRITE, &ncid);
if (status != NC_NOERR) handle_error(status);
...
status = nc_redef(ncid);
if (status != NC_NOERR) handle_error(status);
...
status = nc_def_dim(ncid, "lat", 18L, &latid);
if (status != NC_NOERR) {
handle_error(status);
status = nc_abort(ncid);
if (status != NC_NOERR) handle_error(status);
}
\endcode
*/
int
nc_abort(int ncid)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
stat = ncp->dispatch->abort(ncid);
del_from_NCList(ncp);
free_NC(ncp);
return stat;
}
/** \ingroup datasets
Close an open netCDF dataset
If the dataset in define mode, nc_enddef() will be called before
closing. (In this case, if nc_enddef() returns an error, nc_abort() will
automatically be called to restore the dataset to the consistent state
before define mode was last entered.) After an open netCDF dataset is
closed, its netCDF ID may be reassigned to the next netCDF dataset
that is opened or created.
\param ncid NetCDF ID, from a previous call to nc_open() or nc_create().
\returns ::NC_NOERR No error.
\returns ::NC_EBADID Invalid id passed.
\returns ::NC_EBADGRPID ncid did not contain the root group id of this
file. (NetCDF-4 only).
<h1>Example</h1>
Here is an example using nc_close to finish the definitions of a new
netCDF dataset named foo.nc and release its netCDF ID:
\code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
...
status = nc_create("foo.nc", NC_NOCLOBBER, &ncid);
if (status != NC_NOERR) handle_error(status);
... create dimensions, variables, attributes
status = nc_close(ncid);
if (status != NC_NOERR) handle_error(status);
\endcode
*/
int
nc_close(int ncid)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
stat = ncp->dispatch->close(ncid,NULL);
/* Remove from the nc list */
if (!stat)
{
del_from_NCList(ncp);
free_NC(ncp);
}
return stat;
}
/** \ingroup datasets
Do a normal close (see nc_close()) on an in-memory dataset,
then return a copy of the final memory contents of the dataset.
\param ncid NetCDF ID, from a previous call to nc_open() or nc_create().
\param memio a pointer to an NC_memio object into which the final valid memory
size and memory will be returned.
\returns ::NC_NOERR No error.
\returns ::NC_EBADID Invalid id passed.
\returns ::NC_ENOMEM Out of memory.
\returns ::NC_EDISKLESS if the file was not created as an inmemory file.
\returns ::NC_EBADGRPID ncid did not contain the root group id of this
file. (NetCDF-4 only).
<h1>Example</h1>
Here is an example using nc_close_mem to finish the definitions of a new
netCDF dataset named foo.nc, return the final memory,
and release its netCDF ID:
\code
#include <netcdf.h>
...
int status = NC_NOERR;
int ncid;
NC_memio finalmem;
size_t initialsize = 65000;
...
status = nc_create_mem("foo.nc", NC_NOCLOBBER, initialsize, &ncid);
if (status != NC_NOERR) handle_error(status);
... create dimensions, variables, attributes
status = nc_close_memio(ncid,&finalmem);
if (status != NC_NOERR) handle_error(status);
\endcode
*/
int
nc_close_memio(int ncid, NC_memio* memio)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
stat = ncp->dispatch->close(ncid,memio);
/* Remove from the nc list */
if (!stat)
{
del_from_NCList(ncp);
free_NC(ncp);
}
return stat;
}
/** \ingroup datasets
Change the fill-value mode to improve write performance.
This function is intended for advanced usage, to optimize writes under
some circumstances described below. The function nc_set_fill() sets the
fill mode for a netCDF dataset open for writing and returns the
current fill mode in a return parameter. The fill mode can be
specified as either ::NC_FILL or ::NC_NOFILL. The default behavior
corresponding to ::NC_FILL is that data is pre-filled with fill values,
that is fill values are written when you create non-record variables
or when you write a value beyond data that has not yet been
written. This makes it possible to detect attempts to read data before
it was written. For more information on the use of fill values see
Fill Values. For information about how to define your own fill values
see Attribute Conventions.
The behavior corresponding to ::NC_NOFILL overrides the default behavior
of prefilling data with fill values. This can be used to enhance
performance, because it avoids the duplicate writes that occur when
the netCDF library writes fill values that are later overwritten with
data.
A value indicating which mode the netCDF dataset was already in is
returned. You can use this value to temporarily change the fill mode
of an open netCDF dataset and then restore it to the previous mode.
After you turn on ::NC_NOFILL mode for an open netCDF dataset, you must
be certain to write valid data in all the positions that will later be
read. Note that nofill mode is only a transient property of a netCDF
dataset open for writing: if you close and reopen the dataset, it will
revert to the default behavior. You can also revert to the default
behavior by calling nc_set_fill() again to explicitly set the fill mode
to ::NC_FILL.
There are three situations where it is advantageous to set nofill
mode:
- Creating and initializing a netCDF dataset. In this case, you should
set nofill mode before calling nc_enddef() and then write completely
all non-record variables and the initial records of all the record
variables you want to initialize.
- Extending an existing record-oriented netCDF dataset. Set nofill
mode after opening the dataset for writing, then append the
additional records to the dataset completely, leaving no intervening
unwritten records.
- Adding new variables that you are going to initialize to an existing
netCDF dataset. Set nofill mode before calling nc_enddef() then write
all the new variables completely.
If the netCDF dataset has an unlimited dimension and the last record
was written while in nofill mode, then the dataset may be shorter than
if nofill mode was not set, but this will be completely transparent if
you access the data only through the netCDF interfaces.
The use of this feature may not be available (or even needed) in
future releases. Programmers are cautioned against heavy reliance upon
this feature.
\param ncid NetCDF ID, from a previous call to nc_open() or
nc_create().
\param fillmode Desired fill mode for the dataset, either ::NC_NOFILL or
::NC_FILL.
\param old_modep Pointer to location for returned current fill mode of
the dataset before this call, either ::NC_NOFILL or ::NC_FILL.
\returns ::NC_NOERR No error.
\returns ::NC_EBADID The specified netCDF ID does not refer to an open
netCDF dataset.
\returns ::NC_EPERM The specified netCDF ID refers to a dataset open for
read-only access.
\returns ::NC_EINVAL The fill mode argument is neither ::NC_NOFILL nor
::NC_FILL.
<h1>Example</h1>
Here is an example using nc_set_fill() to set nofill mode for subsequent
writes of a netCDF dataset named foo.nc:
\code
#include <netcdf.h>
...
int ncid, status, old_fill_mode;
...
status = nc_open("foo.nc", NC_WRITE, &ncid);
if (status != NC_NOERR) handle_error(status);
... write data with default prefilling behavior
status = nc_set_fill(ncid, ::NC_NOFILL, &old_fill_mode);
if (status != NC_NOERR) handle_error(status);
... write data with no prefilling
\endcode
*/
int
nc_set_fill(int ncid, int fillmode, int *old_modep)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
return ncp->dispatch->set_fill(ncid,fillmode,old_modep);
}
/**
* @internal Learn base PE.
*
* @deprecated This function was used in the old days with the Cray at
* NCAR. The Cray is long gone, and this call is now meaningless. The
* value returned for pe is always 0.
*
* @param ncid File and group ID.
* @param pe Pointer for base PE.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Invalid ncid passed.
* @author Glenn Davis
*/
int
nc_inq_base_pe(int ncid, int *pe)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
if (pe) *pe = 0;
return NC_NOERR;
}
/**
* @internal Sets base processing element (ignored).
*
* @deprecated This function was used in the old days with the Cray at
* NCAR. The Cray is long gone, and this call is supported only for
* backward compatibility.
*
* @param ncid File ID.
* @param pe Base PE.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Invalid ncid passed.
* @author Glenn Davis
*/
int
nc_set_base_pe(int ncid, int pe)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
return NC_NOERR;
}
/**
* @ingroup datasets
* Inquire about the binary format of a netCDF file
* as presented by the API.
*
* This function returns the (rarely needed) format version.
*
* @param ncid NetCDF ID, from a previous call to nc_open() or
* nc_create().
* @param formatp Pointer to location for returned format version, one
* of NC_FORMAT_CLASSIC, NC_FORMAT_64BIT_OFFSET, NC_FORMAT_CDF5,
* NC_FORMAT_NETCDF4, NC_FORMAT_NETCDF4_CLASSIC.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Invalid ncid passed.
* @author Dennis Heimbigner
*/
int
nc_inq_format(int ncid, int *formatp)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
return ncp->dispatch->inq_format(ncid,formatp);
}
/** \ingroup datasets
Obtain more detailed (vis-a-vis nc_inq_format)
format information about an open dataset.
Note that the netcdf API will present the file
as if it had the format specified by nc_inq_format.
The true file format, however, may not even be
a netcdf file; it might be DAP, HDF4, or PNETCDF,
for example. This function returns that true file type.
It also returns the effective mode for the file.
\param ncid NetCDF ID, from a previous call to nc_open() or
nc_create().
\param formatp Pointer to location for returned true format.
\param modep Pointer to location for returned mode flags.
Refer to the actual list in the file netcdf.h to see the
currently defined set.
\returns ::NC_NOERR No error.
\returns ::NC_EBADID Invalid ncid passed.
*/
int
nc_inq_format_extended(int ncid, int *formatp, int *modep)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
return ncp->dispatch->inq_format_extended(ncid,formatp,modep);
}
/**\ingroup datasets
Inquire about a file or group.
\param ncid NetCDF or group ID, from a previous call to nc_open(),
nc_create(), nc_def_grp(), or associated inquiry functions such as
nc_inq_ncid().
\param ndimsp Pointer to location for returned number of dimensions
defined for this netCDF dataset. Ignored if NULL.
\param nvarsp Pointer to location for returned number of variables
defined for this netCDF dataset. Ignored if NULL.
\param nattsp Pointer to location for returned number of global
attributes defined for this netCDF dataset. Ignored if NULL.
\param unlimdimidp Pointer to location for returned ID of the
unlimited dimension, if there is one for this netCDF dataset. If no
unlimited length dimension has been defined, -1 is returned. Ignored
if NULL. If there are multiple unlimited dimensions (possible only
for netCDF-4 files), only a pointer to the first is returned, for
backward compatibility. If you want them all, use nc_inq_unlimids().
\returns ::NC_NOERR No error.
\returns ::NC_EBADID Invalid ncid passed.
<h1>Example</h1>
Here is an example using nc_inq to find out about a netCDF dataset
named foo.nc:
\code
#include <netcdf.h>
...
int status, ncid, ndims, nvars, ngatts, unlimdimid;
...
status = nc_open("foo.nc", NC_NOWRITE, &ncid);
if (status != NC_NOERR) handle_error(status);
...
status = nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdimid);
if (status != NC_NOERR) handle_error(status);
\endcode
*/
int
nc_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
return ncp->dispatch->inq(ncid,ndimsp,nvarsp,nattsp,unlimdimidp);
}
/**
* Learn the number of variables in a file or group.
*
* @param ncid File and group ID.
* @param nvarsp Pointer that gets number of variables. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @author Glenn Davis, Ed Hartnett, Dennis Heimbigner
*/
int
nc_inq_nvars(int ncid, int *nvarsp)
{
NC* ncp;
int stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) return stat;
return ncp->dispatch->inq(ncid, NULL, nvarsp, NULL, NULL);
}
/**\ingroup datasets
Inquire about a type.
Given an ncid and a typeid, get the information about a type. This
function will work on any type, including atomic and any user defined
type, whether compound, opaque, enumeration, or variable length array.
For even more information about a user defined type nc_inq_user_type().
\param ncid The ncid for the group containing the type (ignored for
atomic types).
\param xtype The typeid for this type, as returned by nc_def_compound,
nc_def_opaque, nc_def_enum, nc_def_vlen, or nc_inq_var, or as found in
netcdf.h in the list of atomic types (NC_CHAR, NC_INT, etc.).
\param name If non-NULL, the name of the user defined type will be
copied here. It will be NC_MAX_NAME bytes or less. For atomic types,
the type name from CDL will be given.
\param size If non-NULL, the (in-memory) size of the type in bytes
will be copied here. VLEN type size is the size of nc_vlen_t. String
size is returned as the size of a character pointer. The size may be
used to malloc space for the data, no matter what the type.
\returns ::NC_NOERR No error.
\returns ::NC_EBADTYPE Bad typeid.
\returns ::NC_ENOTNC4 Seeking a user-defined type in a netCDF-3 file.
\returns ::NC_ESTRICTNC3 Seeking a user-defined type in a netCDF-4 file
for which classic model has been turned on.
\returns ::NC_EBADGRPID Bad group ID in ncid.
\returns ::NC_EBADID Type ID not found.
\returns ::NC_EHDFERR An error was reported by the HDF5 layer.
<h1>Example</h1>
This example is from the test program tst_enums.c, and it uses all the
possible inquiry functions on an enum type.
\code
if (nc_inq_user_type(ncid, typeids[0], name_in, &base_size_in, &base_nc_type_in,
&nfields_in, &class_in)) ERR;
if (strcmp(name_in, TYPE_NAME) || base_size_in != sizeof(int) ||
base_nc_type_in != NC_INT || nfields_in != NUM_MEMBERS || class_in != NC_ENUM) ERR;
if (nc_inq_type(ncid, typeids[0], name_in, &base_size_in)) ERR;
if (strcmp(name_in, TYPE_NAME) || base_size_in != sizeof(int)) ERR;
if (nc_inq_enum(ncid, typeids[0], name_in, &base_nc_type, &base_size_in, &num_members)) ERR;
if (strcmp(name_in, TYPE_NAME) || base_nc_type != NC_INT || num_members != NUM_MEMBERS) ERR;
for (i = 0; i < NUM_MEMBERS; i++)
{
if (nc_inq_enum_member(ncid, typeid, i, name_in, &value_in)) ERR;
if (strcmp(name_in, member_name[i]) || value_in != member_value[i]) ERR;
if (nc_inq_enum_ident(ncid, typeid, member_value[i], name_in)) ERR;
if (strcmp(name_in, member_name[i])) ERR;
}
if (nc_close(ncid)) ERR;
\endcode
*/
int
nc_inq_type(int ncid, nc_type xtype, char *name, size_t *size)
{
NC* ncp;
int stat;
/* Do a quick triage on xtype */
if(xtype <= NC_NAT) return NC_EBADTYPE;
/* For compatibility, we need to allow inq about
atomic types, even if ncid is ill-defined */
if(xtype <= ATOMICTYPEMAX4) {
if(name) strncpy(name,NC_atomictypename(xtype),NC_MAX_NAME);
if(size) *size = NC_atomictypelen(xtype);
return NC_NOERR;
}
/* Apparently asking about a user defined type, so we need
a valid ncid */
stat = NC_check_id(ncid, &ncp);
if(stat != NC_NOERR) /* bad ncid */
return NC_EBADTYPE;
/* have good ncid */
return ncp->dispatch->inq_type(ncid,xtype,name,size);
}
/**
Check the create mode parameter for sanity.
Some create flags cannot be used if corresponding library features are
enabled during the build. This function does a pre-check of the mode
flag before calling the dispatch layer nc_create functions.
\param mode The creation mode flag.
\returns ::NC_NOERR No error.
\returns ::NC_ENOTBUILT Requested feature not built into library
\returns ::NC_EINVAL Invalid combination of modes.
\internal
\ingroup dispatch
\author Ed Hartnett
*/
static int
check_create_mode(int mode)
{
int mode_format;
int mmap = 0;
int inmemory = 0;
int diskless = 0;
/* This is a clever check to see if more than one format bit is
* set. */
mode_format = (mode & NC_NETCDF4) | (mode & NC_64BIT_OFFSET) |
(mode & NC_CDF5);
if (mode_format && (mode_format & (mode_format - 1)))
return NC_EINVAL;
mmap = ((mode & NC_MMAP) == NC_MMAP);
inmemory = ((mode & NC_INMEMORY) == NC_INMEMORY);
diskless = ((mode & NC_DISKLESS) == NC_DISKLESS);
/* NC_INMEMORY and NC_DISKLESS and NC_MMAP are all mutually exclusive */
if(diskless && inmemory) return NC_EDISKLESS;
if(diskless && mmap) return NC_EDISKLESS;
if(inmemory && mmap) return NC_EINMEMORY;
/* mmap is not allowed for netcdf-4 */
if(mmap && (mode & NC_NETCDF4)) return NC_EINVAL;
#ifndef USE_NETCDF4
/* If the user asks for a netCDF-4 file, and the library was built
* without netCDF-4, then return an error.*/
if (mode & NC_NETCDF4)
return NC_ENOTBUILT;
#endif /* USE_NETCDF4 undefined */
/* Well I guess there is some sanity in the world after all. */
return NC_NOERR;
}
/**
* @internal Create a file, calling the appropriate dispatch create
* call.
*
* For create, we have the following pieces of information to use to
* determine the dispatch table:
* - path
* - cmode
*
* @param path0 The file name of the new netCDF dataset.
* @param cmode The creation mode flag, the same as in nc_create().
* @param initialsz This parameter sets the initial size of the file
* at creation time. This only applies to classic
* files.
* @param basepe Deprecated parameter from the Cray days.
* @param chunksizehintp A pointer to the chunk size hint. This only
* applies to classic files.
* @param useparallel Non-zero if parallel I/O is to be used on this
* file.
* @param parameters Pointer to MPI comm and info.
* @param ncidp Pointer to location where returned netCDF ID is to be
* stored.
*
* @returns ::NC_NOERR No error.
* @ingroup dispatch
* @author Dennis Heimbigner, Ed Hartnett, Ward Fisher
*/
int
NC_create(const char *path0, int cmode, size_t initialsz,
int basepe, size_t *chunksizehintp, int useparallel,
void* parameters, int *ncidp)
{
int stat = NC_NOERR;
NC* ncp = NULL;
const NC_Dispatch* dispatcher = NULL;
char* path = NULL;
NCmodel model;
char* newpath = NULL;
TRACE(nc_create);
if(path0 == NULL)
{stat = NC_EINVAL; goto done;}
/* Check mode flag for sanity. */
if ((stat = check_create_mode(cmode))) goto done;
/* Initialize the library. The available dispatch tables
* will depend on how netCDF was built
* (with/without netCDF-4, DAP, CDMREMOTE). */
if(!NC_initialized) {
if ((stat = nc_initialize())) goto done;
}
{
/* Skip past any leading whitespace in path */
const unsigned char* p;
for(p=(const unsigned char*)path0;*p;p++) {if(*p > ' ') break;}
path = nulldup((const char*)p);
}
memset(&model,0,sizeof(model));
newpath = NULL;
if((stat = NC_infermodel(path,&cmode,1,useparallel,NULL,&model,&newpath))) goto done;
if(newpath) {
nullfree(path);
path = newpath;
newpath = NULL;
}
assert(model.format != 0 && model.impl != 0);
/* Now, check for NC_ENOTBUILT cases limited to create (so e.g. HDF4 is not listed) */
#ifndef USE_HDF5
if (model.impl == NC_FORMATX_NC4)
{stat = NC_ENOTBUILT; goto done;}
#endif
#ifndef USE_PNETCDF
if (model.impl == NC_FORMATX_PNETCDF)
{stat = NC_ENOTBUILT; goto done;}
#endif
#ifndef ENABLE_CDF5
if (model.impl == NC_FORMATX_NC3 && (cmode & NC_64BIT_DATA))
{stat = NC_ENOTBUILT; goto done;}
#endif
/* Figure out what dispatcher to use */
switch (model.impl) {
#ifdef USE_HDF5
case NC_FORMATX_NC4:
dispatcher = HDF5_dispatch_table;
break;
#endif
#ifdef USE_PNETCDF
case NC_FORMATX_PNETCDF:
dispatcher = NCP_dispatch_table;
break;
#endif
#ifdef USE_NETCDF4
case NC_FORMATX_UDF0:
dispatcher = UDF0_dispatch_table;
break;
case NC_FORMATX_UDF1:
dispatcher = UDF1_dispatch_table;
break;
#endif /* USE_NETCDF4 */
#ifdef ENABLE_NCZARR
case NC_FORMATX_NCZARR:
dispatcher = NCZ_dispatch_table;
break;
#endif
case NC_FORMATX_NC3:
dispatcher = NC3_dispatch_table;
break;
default:
{stat = NC_ENOTNC; goto done;}
}
/* Create the NC* instance and insert its dispatcher and model */
if((stat = new_NC(dispatcher,path,cmode,&ncp))) goto done;
/* Add to list of known open files and define ext_ncid */
add_to_NCList(ncp);
/* Assume create will fill in remaining ncp fields */
if ((stat = dispatcher->create(ncp->path, cmode, initialsz, basepe, chunksizehintp,
parameters, dispatcher, ncp->ext_ncid))) {
del_from_NCList(ncp); /* oh well */
free_NC(ncp);
} else {
if(ncidp)*ncidp = ncp->ext_ncid;
}
done:
nullfree(path);
nullfree(newpath);
return stat;
}
/**
* @internal Open a netCDF file (or remote dataset) calling the
* appropriate dispatch function.
*
* For open, we have the following pieces of information to use to
* determine the dispatch table.
* - table specified by override
* - path
* - omode
* - the contents of the file (if it exists), basically checking its magic number.
*
* @param path0 Path to the file to open.
* @param omode Open mode.
* @param basepe Base processing element (ignored).
* @param chunksizehintp Size hint for classic files.
* @param useparallel If true use parallel I/O.
* @param parameters Extra parameters for the open.
* @param ncidp Pointer that gets ncid.
*
* @returns ::NC_NOERR No error.
* @ingroup dispatch
* @author Dennis Heimbigner
*/
int
NC_open(const char *path0, int omode, int basepe, size_t *chunksizehintp,
int useparallel, void* parameters, int *ncidp)
{
int stat = NC_NOERR;
NC* ncp = NULL;
const NC_Dispatch* dispatcher = NULL;
int inmemory = 0;
int diskless = 0;
int mmap = 0;
char* path = NULL;
NCmodel model;
char* newpath = NULL;
TRACE(nc_open);
if(!NC_initialized) {
stat = nc_initialize();
if(stat) goto done;
}
/* Check inputs. */
if (!path0)
{stat = NC_EINVAL; goto done;}
/* Capture the inmemory related flags */
mmap = ((omode & NC_MMAP) == NC_MMAP);
diskless = ((omode & NC_DISKLESS) == NC_DISKLESS);
inmemory = ((omode & NC_INMEMORY) == NC_INMEMORY);
/* NC_INMEMORY and NC_DISKLESS and NC_MMAP are all mutually exclusive */
if(diskless && inmemory) {stat = NC_EDISKLESS; goto done;}
if(diskless && mmap) {stat = NC_EDISKLESS; goto done;}
if(inmemory && mmap) {stat = NC_EINMEMORY; goto done;}
/* mmap is not allowed for netcdf-4 */
if(mmap && (omode & NC_NETCDF4)) {stat = NC_EINVAL; goto done;}
/* Attempt to do file path conversion: note that this will do
nothing if path is a 'file:...' url, so it will need to be
repeated in protocol code (e.g. libdap2, libdap4, etc).
*/
{
/* Skip past any leading whitespace in path */
const char* p;
for(p=(const char*)path0;*p;p++) {if(*p < 0 || *p > ' ') break;}
path = nulldup(p);
}
memset(&model,0,sizeof(model));
/* Infer model implementation and format, possibly by reading the file */
if((stat = NC_infermodel(path,&omode,0,useparallel,parameters,&model,&newpath)))
goto done;
if(newpath) {
nullfree(path);
path = newpath;
newpath = NULL;
}
/* Still no implementation, give up */
if(model.impl == 0) {
#ifdef DEBUG
fprintf(stderr,"implementation == 0\n");
#endif
{stat = NC_ENOTNC; goto done;}
}
/* Suppress unsupported formats */
#if 0
/* (should be more compact, table-driven, way to do this) */
{
int hdf5built = 0;
int hdf4built = 0;
int cdf5built = 0;
int udf0built = 0;
int udf1built = 0;
int nczarrbuilt = 0;
#ifdef USE_NETCDF4
hdf5built = 1;
#endif
#ifdef USE_HDF4
hdf4built = 1;
#endif
#ifdef ENABLE_CDF5
cdf5built = 1;
#endif
#ifdef ENABLE_NCZARR
nczarrbuilt = 1;
#endif
if(UDF0_dispatch_table != NULL)
udf0built = 1;
if(UDF1_dispatch_table != NULL)
udf1built = 1;
if(!hdf5built && model.impl == NC_FORMATX_NC4)
{stat = NC_ENOTBUILT; goto done;}
if(!hdf4built && model.impl == NC_FORMATX_NC_HDF4)
{stat = NC_ENOTBUILT; goto done;}
if(!cdf5built && model.impl == NC_FORMATX_NC3 && model.format == NC_FORMAT_CDF5)
{stat = NC_ENOTBUILT; goto done;}
if(!nczarrbuilt && model.impl == NC_FORMATX_NCZARR)
{stat = NC_ENOTBUILT; goto done;}
if(!udf0built && model.impl == NC_FORMATX_UDF0)
{stat = NC_ENOTBUILT; goto done;}
if(!udf1built && model.impl == NC_FORMATX_UDF1)
{stat = NC_ENOTBUILT; goto done;}
}
#else
{
unsigned built = 0 /* leave off the trailing semicolon so we can build constant */
| (1<<NC_FORMATX_NC3) /* NC3 always supported */
#ifdef USE_HDF5
| (1<<NC_FORMATX_NC_HDF5)
#endif
#ifdef USE_HDF4
| (1<<NC_FORMATX_NC_HDF4)
#endif
#ifdef ENABLE_NCZARR
| (1<<NC_FORMATX_NCZARR)
#endif
#ifdef ENABLE_DAP
| (1<<NC_FORMATX_DAP2)
#endif
#ifdef ENABLE_DAP4
| (1<<NC_FORMATX_DAP4)
#endif
#ifdef USE_PNETCDF
| (1<<NC_FORMATX_PNETCDF)
#endif
; /* end of the built flags */
if(UDF0_dispatch_table != NULL)
built |= (1<<NC_FORMATX_UDF0);
if(UDF1_dispatch_table != NULL)
built |= (1<<NC_FORMATX_UDF1);
/* Verify */
if((built & (1 << model.impl)) == 0)
{stat = NC_ENOTBUILT; goto done;}
#ifndef ENABLE_CDF5
/* Special case because there is no separate CDF5 dispatcher */
if(model.impl == NC_FORMATX_NC3 && (omode & NC_64BIT_DATA))
{stat = NC_ENOTBUILT; goto done;}
#endif
}
#endif
/* Figure out what dispatcher to use */
if (!dispatcher) {
switch (model.impl) {
#ifdef ENABLE_DAP
case NC_FORMATX_DAP2:
dispatcher = NCD2_dispatch_table;
break;
#endif
#ifdef ENABLE_DAP4
case NC_FORMATX_DAP4:
dispatcher = NCD4_dispatch_table;
break;
#endif
#ifdef ENABLE_NCZARR
case NC_FORMATX_NCZARR:
dispatcher = NCZ_dispatch_table;
break;
#endif
#ifdef USE_PNETCDF
case NC_FORMATX_PNETCDF:
dispatcher = NCP_dispatch_table;
break;
#endif
#ifdef USE_HDF5
case NC_FORMATX_NC4:
dispatcher = HDF5_dispatch_table;
break;
#endif
#ifdef USE_HDF4
case NC_FORMATX_NC_HDF4:
dispatcher = HDF4_dispatch_table;
break;
#endif
#ifdef USE_NETCDF4
case NC_FORMATX_UDF0:
dispatcher = UDF0_dispatch_table;
break;
case NC_FORMATX_UDF1:
dispatcher = UDF1_dispatch_table;
break;
#endif /* USE_NETCDF4 */
case NC_FORMATX_NC3:
dispatcher = NC3_dispatch_table;
break;
default:
stat = NC_ENOTNC;
goto done;
}
}
/* If we can't figure out what dispatch table to use, give up. */
if (!dispatcher) {stat = NC_ENOTNC; goto done;}
/* Create the NC* instance and insert its dispatcher */
if((stat = new_NC(dispatcher,path,omode,&ncp))) goto done;
/* Add to list of known open files. This assigns an ext_ncid. */
add_to_NCList(ncp);
/* Assume open will fill in remaining ncp fields */
stat = dispatcher->open(ncp->path, omode, basepe, chunksizehintp,
parameters, dispatcher, ncp->ext_ncid);
if(stat == NC_NOERR) {
if(ncidp) *ncidp = ncp->ext_ncid;
} else {
del_from_NCList(ncp);
free_NC(ncp);
}
done:
nullfree(path);
nullfree(newpath);
return stat;
}
/*Provide an internal function for generating pseudo file descriptors
for systems that are not file based (e.g. dap, memio).
*/
/** @internal Static counter for pseudo file descriptors (incremented) */
static int pseudofd = 0;
/**
* @internal Create a pseudo file descriptor that does not
* overlap real file descriptors
*
* @return pseudo file number
* @author Dennis Heimbigner
*/
int
nc__pseudofd(void)
{
if(pseudofd == 0) {
#ifdef HAVE_GETRLIMIT
int maxfd = 32767; /* default */
struct rlimit rl;
if(getrlimit(RLIMIT_NOFILE,&rl) == 0) {
if(rl.rlim_max != RLIM_INFINITY)
maxfd = (int)rl.rlim_max;
if(rl.rlim_cur != RLIM_INFINITY)
maxfd = (int)rl.rlim_cur;
}
pseudofd = maxfd+1;
#endif
}
return pseudofd++;
}
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