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Merge pull request #2183 from DennisHeimbigner/modeflags.dmh

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Make sure mode flags are properly defined in netcdf.h
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Ward Fisher 2022-01-13 11:19:59 -07:00 committed by GitHub
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8 changed files with 89 additions and 75 deletions
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1
RELEASE_NOTES.md
View File

@ -7,6 +7,7 @@ This file contains a high-level description of this package's evolution. Release
## 4.8.2 - TBD
* [Bug Fix] Make sure that netcdf.h accurately defines the flags in the open/create mode flags. See [Github #2183](https://github.com/Unidata/netcdf-c/pull/2183).
* [Enhancement] Improve support for msys2+mingw platform. See [Github #2171](https://github.com/Unidata/netcdf-c/pull/2171).
* [Bug Fix] Clean up the various inter-test dependencies in ncdump for CMake. See [Github #2168](https://github.com/Unidata/netcdf-c/pull/2168).
* [Enhancement] Added options to suppress the new behavior from [Github #2135](https://github.com/Unidata/netcdf-c/pull/2135). The options for `cmake` and `configure` are, respectively `-DENABLE_LIBXML2` and `--(enable/disable)-libxml2`. Both of these options defaul to 'on/enabled'. When disabled, the bundled `ezxml` XML interpreter is used regardless of whether `libxml2` is present on the system.

39
include/nc3internal.h
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@ -224,15 +224,18 @@ NC_lookupvar(NC3_INFO* ncp, int varid, NC_var **varp);
struct NC3_INFO {
/* contains the previous NC during redef. */
NC3_INFO *old;
/* flags */
#define NC_CREAT 2 /* in create phase, cleared by ncendef */
#define NC_INDEF 8 /* in define mode, cleared by ncendef */
#define NC_NSYNC 0x10 /* synchronise numrecs on change */
#define NC_HSYNC 0x20 /* synchronise whole header on change */
#define NC_NDIRTY 0x40 /* numrecs has changed */
#define NC_HDIRTY 0x80 /* header info has changed */
/* NC_NOFILL in netcdf.h, historical interface */
int flags;
int flags; /* mode flags */
int state; /* state transitions flags */
# define NC_CREAT 0x1 /* in create phase, cleared by ncendef */
# define NC_INDEF 0x2 /* in define mode, cleared by ncendef */
# define NC_NSYNC 0x4 /* synchronise numrecs on change */
# define NC_HSYNC 0x8 /* synchronise whole header on change */
# define NC_NDIRTY 0x10 /* numrecs has changed */
# define NC_HDIRTY 0x20 /* header info has changed */
/* NC_NOFILL defined in netcdf.h, historical interface */
#if 0
# define NC_NOFILL 0x100 /**< Argument to nc_set_fill() to turn off filling of data. */
#endif
struct ncio* nciop;
size_t chunk; /* largest extent this layer will request from ncio->get() */
size_t xsz; /* external size of this header, == var[0].begin */
@ -258,31 +261,31 @@ struct NC3_INFO {
fClr((ncp)->flags, NC_WRITE)
#define NC_IsNew(ncp) \
fIsSet((ncp)->flags, NC_CREAT)
fIsSet((ncp)->state, NC_CREAT)
#define NC_indef(ncp) \
(NC_IsNew(ncp) || fIsSet((ncp)->flags, NC_INDEF))
(NC_IsNew(ncp) || fIsSet((ncp)->state, NC_INDEF))
#define set_NC_ndirty(ncp) \
fSet((ncp)->flags, NC_NDIRTY)
fSet((ncp)->state, NC_NDIRTY)
#define NC_ndirty(ncp) \
fIsSet((ncp)->flags, NC_NDIRTY)
fIsSet((ncp)->state, NC_NDIRTY)
#define set_NC_hdirty(ncp) \
fSet((ncp)->flags, NC_HDIRTY)
fSet((ncp)->state, NC_HDIRTY)
#define NC_hdirty(ncp) \
fIsSet((ncp)->flags, NC_HDIRTY)
fIsSet((ncp)->state, NC_HDIRTY)
#define NC_dofill(ncp) \
(!fIsSet((ncp)->flags, NC_NOFILL))
(!fIsSet((ncp)->state, NC_NOFILL))
#define NC_doHsync(ncp) \
fIsSet((ncp)->flags, NC_HSYNC)
fIsSet((ncp)->state, NC_HSYNC)
#define NC_doNsync(ncp) \
fIsSet((ncp)->flags, NC_NSYNC)
fIsSet((ncp)->state, NC_NSYNC)
# define NC_get_numrecs(nc3i) \
((nc3i)->numrecs)

16
include/nc4internal.h
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@ -276,20 +276,14 @@ typedef struct NC_GRP_INFO
NCindex* vars; /**< NCindex<NC_VAR_INFO_T> * */
} NC_GRP_INFO_T;
/* These constants apply to the cmode parameter in the
/* These constants apply to the flags field in the
* HDF5_FILE_INFO_T defined below. */
/* Make sure they do not conflict with defined flags in netcdf.h */
#define NC_CREAT 0x10002 /**< in create phase, cleared by ncendef */
#define NC_INDEF 0x10008 /**< in define mode, cleared by ncendef */
#define NC_NSYNC 0x10010 /**< synchronise numrecs on change */
#define NC_HSYNC 0x10020 /**< synchronise whole header on change */
#define NC_NDIRTY 0x10040 /**< numrecs has changed */
#define NC_HDIRTY 0x10080 /**< header info has changed */
#define NC_INDEF 0x01 /**< in define mode, cleared by ncendef */
/** This is the metadata we need to keep track of for each
* netcdf-4/HDF5 file. */
typedef struct NC_FILE_INFO
typedef struct NC_FILE_INFO
{
NC_OBJ hdr;
NC *controller; /**< Pointer to containing NC. */
@ -297,8 +291,8 @@ typedef struct NC_FILE_INFO
MPI_Comm comm; /**< Copy of MPI Communicator used to open the file. */
MPI_Info info; /**< Copy of MPI Information Object used to open the file. */
#endif
int flags; /**< Flags used to open the file. */
int cmode; /**< Create mode used to create the file. */
int cmode; /**< Create/Open mode for the file. */
int flags; /**< State transition flags . */
nc_bool_t parallel; /**< True if file is open for parallel access */
nc_bool_t redef; /**< True if redefining an existing file */
nc_bool_t no_attr_create_order; /**< True if the creation order tracking of attributes is disabled (netcdf-4 only) */

12
include/netcdf.h
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@ -115,13 +115,14 @@ extern "C" {
#define NC_NOFILL 0x100 /**< Argument to nc_set_fill() to turn off filling of data. */
/* Define the ioflags bits for nc_create and nc_open.
currently unused:
Currently unused in lower 16 bits:
0x0002
and the whole upper 16 bits
Note: nc4internal also defines flags in this space even tho it should not.
so check there around #define NC_CREAT.
All upper 16 bits are unused except
0x20000
*/
/* Lower 16 bits */
#define NC_NOWRITE 0x0000 /**< Set read-only access for nc_open(). */
#define NC_WRITE 0x0001 /**< Set read-write access for nc_open(). */
@ -161,7 +162,8 @@ Use this in mode flags for both nc_create() and nc_open(). */
#define NC_PERSIST 0x4000 /**< Save diskless contents to disk. Mode flag for nc_open() or nc_create() */
#define NC_INMEMORY 0x8000 /**< Read from memory. Mode flag for nc_open() or nc_create() */
#define NC_NOATTCREORD 0x20000 /**< Disable the netcdf-4 (hdf5) attribute creation order tracking */
/* Upper 16 bits */
#define NC_NOATTCREORD 0x20000 /**< Disable the netcdf-4 (hdf5) attribute creation order tracking */
#define NC_MAX_MAGIC_NUMBER_LEN 8 /**< Max len of user-defined format magic number. */

49
libsrc/nc3internal.c
View File

@ -413,7 +413,7 @@ write_numrecs(NC3_INFO *ncp)
(void) ncio_rel(ncp->nciop, NC_NUMRECS_OFFSET, RGN_MODIFIED);
if(status == NC_NOERR)
fClr(ncp->flags, NC_NDIRTY);
fClr(ncp->state, NC_NDIRTY);
return status;
}
@ -435,7 +435,7 @@ read_NC(NC3_INFO *ncp)
status = nc_get_NC(ncp);
if(status == NC_NOERR)
fClr(ncp->flags, NC_NDIRTY | NC_HDIRTY);
fClr(ncp->state, NC_NDIRTY | NC_HDIRTY);
return status;
}
@ -454,7 +454,7 @@ write_NC(NC3_INFO *ncp)
status = ncx_put_NC(ncp, NULL, 0, 0);
if(status == NC_NOERR)
fClr(ncp->flags, NC_NDIRTY | NC_HDIRTY);
fClr(ncp->state, NC_NDIRTY | NC_HDIRTY);
return status;
}
@ -864,7 +864,7 @@ NC_endef(NC3_INFO *ncp,
{
/* a plain redef, not a create */
assert(!NC_IsNew(ncp));
assert(fIsSet(ncp->flags, NC_INDEF));
assert(fIsSet(ncp->state, NC_INDEF));
assert(ncp->begin_rec >= ncp->old->begin_rec);
assert(ncp->begin_var >= ncp->old->begin_var);
@ -937,7 +937,7 @@ NC_endef(NC3_INFO *ncp,
ncp->old = NULL;
}
fClr(ncp->flags, NC_CREAT | NC_INDEF);
fClr(ncp->state, NC_CREAT | NC_INDEF);
return ncio_sync(ncp->nciop);
}
@ -1071,7 +1071,7 @@ NC3_create(const char *path, int ioflags, size_t initialsz, int basepe,
goto unwind_alloc;
}
fSet(nc3->flags, NC_CREAT);
fSet(nc3->state, NC_CREAT);
if(fIsSet(nc3->nciop->ioflags, NC_SHARE))
{
@ -1082,7 +1082,7 @@ NC3_create(const char *path, int ioflags, size_t initialsz, int basepe,
* automatically. Some sort of IPC (external to this package)
* would be used to trigger a call to nc_sync().
*/
fSet(nc3->flags, NC_NSYNC);
fSet(nc3->state, NC_NSYNC);
}
status = ncx_put_NC(nc3, &xp, sizeof_off_t, nc3->xsz);
@ -1173,29 +1173,12 @@ NC3_open(const char *path, int ioflags, int basepe, size_t *chunksizehintp,
goto unwind_alloc;
}
#ifdef ENABLE_BYTERANGE
{
NCURI* uri = NULL;
ncuriparse(path,&uri);
if(uri) {
/* If the model specified the use of byte-ranges, then signal by
a temporary hack using one of the flags in the ioflags. */
if(NC_testmode(uri,"bytes")) {
# ifdef ENABLE_S3_SDK
if(NC_iss3(uri)) ioflags |= NC_S3SDK; else
# endif
ioflags |= NC_HTTP;
}
ncurifree(uri);
}
}
#endif /*ENABLE_BYTERANGE*/
status = ncio_open(path, ioflags, 0, 0, &nc3->chunk, parameters,
&nc3->nciop, NULL);
if(status)
goto unwind_alloc;
assert(nc3->flags == 0);
assert(nc3->state == 0);
if(fIsSet(nc3->nciop->ioflags, NC_SHARE))
{
@ -1206,7 +1189,7 @@ NC3_open(const char *path, int ioflags, int basepe, size_t *chunksizehintp,
* automatically. Some sort of IPC (external to this package)
* would be used to trigger a call to nc_sync().
*/
fSet(nc3->flags, NC_NSYNC);
fSet(nc3->state, NC_NSYNC);
}
status = nc_get_NC(nc3);
@ -1279,10 +1262,10 @@ NC3_abort(int ncid)
{
/* a plain redef, not a create */
assert(!NC_IsNew(nc3));
assert(fIsSet(nc3->flags, NC_INDEF));
assert(fIsSet(nc3->state, NC_INDEF));
free_NC3INFO(nc3->old);
nc3->old = NULL;
fClr(nc3->flags, NC_INDEF);
fClr(nc3->state, NC_INDEF);
}
else if(!NC_readonly(nc3))
{
@ -1397,7 +1380,7 @@ NC3_redef(int ncid)
if(nc3->old == NULL)
return NC_ENOMEM;
fSet(nc3->flags, NC_INDEF);
fSet(nc3->state, NC_INDEF);
return NC_NOERR;
}
@ -1509,15 +1492,15 @@ NC3_set_fill(int ncid,
if(NC_readonly(nc3))
return NC_EPERM;
oldmode = fIsSet(nc3->flags, NC_NOFILL) ? NC_NOFILL : NC_FILL;
oldmode = fIsSet(nc3->state, NC_NOFILL) ? NC_NOFILL : NC_FILL;
if(fillmode == NC_NOFILL)
{
fSet(nc3->flags, NC_NOFILL);
fSet(nc3->state, NC_NOFILL);
}
else if(fillmode == NC_FILL)
{
if(fIsSet(nc3->flags, NC_NOFILL))
if(fIsSet(nc3->state, NC_NOFILL))
{
/*
* We are changing back to fill mode
@ -1527,7 +1510,7 @@ NC3_set_fill(int ncid,
if(status != NC_NOERR)
return status;
}
fClr(nc3->flags, NC_NOFILL);
fClr(nc3->state, NC_NOFILL);
}
else
{

38
libsrc/ncio.c
View File

@ -12,6 +12,8 @@
#include "netcdf.h"
#include "ncio.h"
#include "fbits.h"
#include "ncuri.h"
#include "ncrc.h"
/* With the advent of diskless io, we need to provide
for multiple ncio packages at the same time,
@ -46,6 +48,9 @@ extern int ffio_open(const char*,int,off_t,size_t,size_t*,void*,ncio**,void** co
extern int memio_create(const char*,int,size_t,off_t,size_t,size_t*,void*,ncio**,void** const);
extern int memio_open(const char*,int,off_t,size_t,size_t*,void*,ncio**,void** const);
/* Forward */
static int urlmodetest(const char* path);
int
ncio_create(const char *path, int ioflags, size_t initialsz,
off_t igeto, size_t igetsz, size_t *sizehintp,
@ -78,6 +83,8 @@ ncio_open(const char *path, int ioflags,
void* parameters,
ncio** iopp, void** const mempp)
{
int modetest = urlmodetest(path);
/* Diskless open has the following constraints:
1. file must be classic version 1 or 2 or 5
*/
@ -93,12 +100,11 @@ ncio_open(const char *path, int ioflags,
}
# endif /*USE_MMAP*/
# ifdef ENABLE_BYTERANGE
/* The NC_HTTP flag is a big hack until we can reorganize the ncio interface */
if(fIsSet(ioflags,NC_HTTP)) {
if(modetest == NC_HTTP) {
return httpio_open(path,ioflags,igeto,igetsz,sizehintp,parameters,iopp,mempp);
}
# ifdef ENABLE_S3_SDK
if(fIsSet(ioflags,NC_S3SDK)) {
if(modetest == NC_S3SDK) {
return s3io_open(path,ioflags,igeto,igetsz,sizehintp,parameters,iopp,mempp);
}
# endif
@ -162,3 +168,29 @@ ncio_close(ncio* const nciop, int doUnlink)
int status = nciop->close(nciop,doUnlink);
return status;
}
/* URL utilities */
/*
Check mode flags and return:
NC_HTTP => byterange
NC_S3SDK => s3
0 => Not URL
*/
static int
urlmodetest(const char* path)
{
int kind = 0;
NCURI* uri = NULL;
ncuriparse(path,&uri);
if(uri == NULL) return 0; /* Not URL */
if(NC_testmode(uri, "bytes"))
kind = NC_HTTP;
else if(NC_testmode(uri, "s3"))
kind = NC_S3SDK;
else
kind = 0;
ncurifree(uri);
return kind;
}

8
libsrc/ncio.h
View File

@ -11,11 +11,9 @@
#include <sys/types.h> /* off_t */
#include "netcdf.h"
/* Define internal use only flags to signal use of byte ranges and S3.
This is temporary until we can re-organize the ncio open/create API.
*/
#define NC_HTTP 0x80000000
#define NC_S3SDK 0x40000000
/* Define internal use only flags to signal use of byte ranges and S3. */
#define NC_HTTP 1
#define NC_S3SDK 2
typedef struct ncio ncio; /* forward reference */

1
libsrc/s3io.c
View File

@ -36,6 +36,7 @@
#include "fbits.h"
#include "rnd.h"
#include "ncs3sdk.h"
#include "ncuri.h"
#define DEFAULTPAGESIZE 16384