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Merge branch 'master' into bigend.dmh

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Ward Fisher 2019-02-07 14:28:39 -07:00 committed by GitHub
commit 3a14251dd9
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24 changed files with 378 additions and 118 deletions
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9
CMakeInstallation.cmake
View File

@ -38,6 +38,7 @@ SET(CPACK_SOURCE_IGNORE_FILES "${CPACK_SOURCE_IGNORE_FILES}"
"/obsolete/"
"/unknown/"
".*~"
".git/"
)
###
@ -56,9 +57,9 @@ IF(WIN32)
SET(CPACK_NSIS_CONTACT "support-netcdf@unidata.ucar.edu")
SET(CPACK_NSIS_ENABLE_UNINSTALL_BEFORE_INSTALL ON)
SET(CPACK_NSIS_MENU_LINKS
"http://www.unidata.ucar.edu/netcdf" "Unidata Website"
"http://www.unidata.ucar.edu/netcdf/docs" "NetCDF Stable Documentation"
"http://www.unidata.ucar.edu/netcdf/docs_rc" "NetCDF Unstable Documentation")
"http://www.unidata.ucar.edu/software/netcdf" "Unidata Website"
"http://www.unidata.ucar.edu/software/netcdf/docs" "NetCDF Stable Documentation"
"http://www.unidata.ucar.edu/software/netcdf/docs_rc" "NetCDF Unstable Documentation")
ENDIF()
@ -103,7 +104,7 @@ ENDIF()
IF(APPLE)
SET(CPACK_SOURCE_GENERATOR "TGZ")
SET(CPACK_GENERATOR "PackageMaker" "STGZ" "TBZ2" "TGZ" "ZIP")
SET(CPACK_GENERATOR "productbuild" "STGZ" "TBZ2" "TGZ" "ZIP")
ENDIF()
##

2
CMakeLists.txt
View File

@ -82,7 +82,7 @@ IF(MSVC)
ENDIF()
#Add custom CMake Module
SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/"
SET(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules/"
CACHE INTERNAL "Location of our custom CMake modules.")
# auto-configure style checks, other CMake modules.

9
include/hdf5internal.h
View File

@ -135,7 +135,14 @@ int nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_IN
extern hid_t NC4_image_init(NC_FILE_INFO_T* h5);
extern void NC4_image_finalize(void*);
/* These functions are internal to the libhdf5 directory. */
/* Create HDF5 dataset for dim without a coord var. */
extern int nc4_create_dim_wo_var(NC_DIM_INFO_T *dim);
/* Give a var a secret HDF5 name, for use when there is a dim of this
* name, but the var is not a coord var of that dim. */
extern int nc4_give_var_secret_name(NC_VAR_INFO_T *var);
/* Get the fill value for a var. */
int nc4_get_fill_value(NC_FILE_INFO_T *h5, NC_VAR_INFO_T *var, void **fillp);

4
include/nc4internal.h
View File

@ -153,7 +153,7 @@ typedef struct NC_VAR_INFO
nc_bool_t created; /* Variable has already been created (_not_ that it was just created) */
nc_bool_t written_to; /* True if variable has data written to it */
struct NC_TYPE_INFO *type_info;
int atts_not_read; /* If true, the atts have not yet been read. */
int atts_read; /* If true, the atts have been read. */
nc_bool_t meta_read; /* True if this vars metadata has been completely read. */
nc_bool_t coords_read; /* True if this var has hidden coordinates att, and it has been read. */
NCindex *att; /* NCindex<NC_ATT_INFO_T*> */
@ -229,7 +229,7 @@ typedef struct NC_GRP_INFO
void *format_grp_info;
struct NC_FILE_INFO *nc4_info;
struct NC_GRP_INFO *parent;
int atts_not_read;
int atts_read; /* True if atts have been read for this group. */
NCindex* children; /* NCindex<struct NC_GRP_INFO*> */
NCindex* dim; /* NCindex<NC_DIM_INFO_T> * */
NCindex* att; /* NCindex<NC_ATT_INFO_T> * */

4
include/ncconfigure.h
View File

@ -89,4 +89,8 @@ typedef unsigned short ushort;
typedef unsigned int uint;
#endif
#ifndef NC_UNUSED
#define NC_UNUSED(var) (void)var
#endif
#endif /* NCCONFIGURE_H */

23
libdispatch/dparallel.c
View File

@ -102,6 +102,11 @@ int nc_create_par(const char *path, int cmode, MPI_Comm comm,
MPI_Info info, int *ncidp)
{
#ifndef USE_PARALLEL
NC_UNUSED(path);
NC_UNUSED(cmode);
NC_UNUSED(comm);
NC_UNUSED(info);
NC_UNUSED(ncidp);
return NC_ENOPAR;
#else
NC_MPI_INFO data;
@ -201,6 +206,11 @@ nc_open_par(const char *path, int omode, MPI_Comm comm,
MPI_Info info, int *ncidp)
{
#ifndef USE_PARALLEL
NC_UNUSED(path);
NC_UNUSED(omode);
NC_UNUSED(comm);
NC_UNUSED(info);
NC_UNUSED(ncidp);
return NC_ENOPAR;
#else
NC_MPI_INFO mpi_data;
@ -249,6 +259,11 @@ nc_open_par_fortran(const char *path, int omode, int comm,
int info, int *ncidp)
{
#ifndef USE_PARALLEL
NC_UNUSED(path);
NC_UNUSED(omode);
NC_UNUSED(comm);
NC_UNUSED(info);
NC_UNUSED(ncidp);
return NC_ENOPAR;
#else
MPI_Comm comm_c;
@ -348,6 +363,9 @@ int
nc_var_par_access(int ncid, int varid, int par_access)
{
#ifndef USE_PARALLEL
NC_UNUSED(ncid);
NC_UNUSED(varid);
NC_UNUSED(par_access);
return NC_ENOPAR;
#else
int stat = NC_NOERR;
@ -403,6 +421,11 @@ nc_create_par_fortran(const char *path, int cmode, int comm,
int info, int *ncidp)
{
#ifndef USE_PARALLEL
NC_UNUSED(path);
NC_UNUSED(cmode);
NC_UNUSED(comm);
NC_UNUSED(info);
NC_UNUSED(ncidp);
return NC_ENOPAR;
#else
MPI_Comm comm_c;

4
libdispatch/drc.c
View File

@ -396,8 +396,8 @@ rcsearch(const char* prefix, const char* rcname, char** pathp)
{
char* path = NULL;
FILE* f = NULL;
int plen = strlen(prefix);
int rclen = strlen(rcname);
size_t plen = strlen(prefix);
size_t rclen = strlen(rcname);
int ret = NC_NOERR;
size_t pathlen = plen+rclen+1; /*+1 for '/' */

2
libdispatch/dutil.c
View File

@ -210,7 +210,7 @@ NC_mktmp(const char* base)
char spid[7];
if(rno < 0) rno = -rno;
snprintf(spid,sizeof(spid),"%06d",rno);
strncat(tmp,spid,sizeof(tmp));
strncat(tmp,spid,sizeof(tmp) - strlen(tmp) - 1);
}
#endif /* HAVE_MKTEMP */
#ifdef _MSC_VER

1
libdispatch/nclog.c
View File

@ -213,6 +213,7 @@ Each line will be sent using nclog with the specified tag.
void
nclogtextn(int tag, const char* text, size_t count)
{
NC_UNUSED(tag);
if(!nclogging || nclogstream == NULL) return;
fwrite(text,1,count,nclogstream);
fflush(nclogstream);

4
libdispatch/nctime.c
View File

@ -23,6 +23,7 @@
#include <string.h>
#include <stdarg.h>
#include <assert.h>
#include "ncconfigure.h"
#include "nctime.h"
static int cuErrOpts; /* Error options */
@ -309,7 +310,7 @@ cdParseRelunits(cdCalenType timetype, char* relunits, cdUnitTime* unit, cdCompTi
char charunits[CD_MAX_RELUNITS];
char basetime_1[CD_MAX_CHARTIME];
char basetime_2[CD_MAX_CHARTIME];
char basetime[CD_MAX_CHARTIME];
char basetime[2 * CD_MAX_CHARTIME + 1];
int nconv1, nconv2, nconv;
/* Parse the relunits */
@ -659,6 +660,7 @@ Cdh2e(CdTime *htime, double *etime)
static int
cdValidateTime(cdCalenType timetype, cdCompTime comptime)
{
NC_UNUSED(timetype);
if(comptime.month<1 || comptime.month>12){
cdError("Error on time conversion: invalid month = %hd\n",comptime.month);
return 1;

4
libdispatch/ncuri.c
View File

@ -67,7 +67,7 @@ static char* queryallow =
static char* userpwdallow =
"0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ!$&'()*+,-.;=_~?#/";
#ifndef HAVE_STRNCMP
#ifndef HAVE_STRNDUP
#define strndup ncstrndup
/* Not all systems have strndup, so provide one*/
char*
@ -258,7 +258,7 @@ ncuriparse(const char* uri0, NCURI** durip)
isfile = (strcmp(tmp.protocol,"file")==0);
if(isfile) {
int l = strlen(p); /* to test if we have enough characters */
size_t l = strlen(p); /* to test if we have enough characters */
hashost = 0; /* always */
if(l >= 2 && p[1] == ':' && strchr(DRIVELETTERS,p[0]) != NULL) { /* case 1 */
; /* p points to the start of the path */

2
libhdf4/hdf4file.c
View File

@ -415,6 +415,7 @@ nc4_var_list_add_full(NC_GRP_INFO_T* grp, const char* name, int ndims, nc_type x
(*var)->created = NC_TRUE;
(*var)->written_to = NC_TRUE;
(*var)->format_var_info = format_var_info;
(*var)->atts_read = 1;
/* Fill special type_info struct for variable type information. */
if ((retval = nc4_set_var_type(xtype, endianness, type_size, type_name,
@ -630,6 +631,7 @@ NC_HDF4_open(const char *path, int mode, int basepe, size_t *chunksizehintp,
assert(nc4_info && nc4_info->root_grp);
h5 = nc4_info;
h5->no_write = NC_TRUE;
h5->root_grp->atts_read = 1;
/* Allocate data to hold HDF4 specific file data. */
if (!(hdf4_file = malloc(sizeof(NC_HDF4_FILE_INFO_T))))

9
libhdf5/hdf5attr.c
View File

@ -27,13 +27,14 @@ static int
getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp,
NCindex **attlist)
{
NC_VAR_INFO_T* var;
int retval;
assert(grp && attlist);
if (varid == NC_GLOBAL)
{
/* Do we need to read the atts? */
if (grp->atts_not_read)
if (!grp->atts_read)
if ((retval = nc4_read_atts(grp, NULL)))
return retval;
@ -43,12 +44,14 @@ getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp,
}
else
{
NC_VAR_INFO_T *var;
if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid)))
return NC_ENOTVAR;
assert(var->hdr.id == varid);
/* Do we need to read the atts? */
if (var->atts_not_read)
if (!var->atts_read)
if ((retval = nc4_read_atts(grp, var)))
return retval;

1
libhdf5/hdf5create.c
View File

@ -66,6 +66,7 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
BAIL(retval);
nc4_info = NC4_DATA(nc);
assert(nc4_info && nc4_info->root_grp);
nc4_info->root_grp->atts_read = 1;
/* Add struct to hold HDF5-specific file metadata. */
if (!(nc4_info->format_file_info = calloc(1, sizeof(NC_HDF5_FILE_INFO_T))))

2
libhdf5/hdf5file.c
View File

@ -727,7 +727,7 @@ NC4_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp)
if (nattsp)
{
/* Do we need to read the atts? */
if (grp->atts_not_read)
if (!grp->atts_read)
if ((retval = nc4_read_atts(grp, NULL)))
return retval;

5
libhdf5/hdf5grp.c
View File

@ -67,6 +67,11 @@ NC4_def_grp(int parent_ncid, const char *name, int *new_ncid)
return retval;
if (!(g->format_grp_info = calloc(1, sizeof(NC_HDF5_GRP_INFO_T))))
return NC_ENOMEM;
/* For new groups, there are no atts to read from file. */
g->atts_read = 1;
/* Return the ncid to the user. */
if (new_ncid)
*new_ncid = grp->nc4_info->controller->ext_ncid | g->hdr.id;

37
libhdf5/hdf5internal.c
View File

@ -385,7 +385,7 @@ delete_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim)
* @param dim Pointer to dimension info struct.
*
* @return ::NC_NOERR No error.
* @author Quincey Koziol
* @author Quincey Koziol, Ed Hartnett
*/
int
nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
@ -406,14 +406,14 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Detach dimscales from the [new] coordinate variable */
/* Detach dimscales from the [new] coordinate variable. */
if (var->dimscale_attached)
{
int dims_detached = 0;
int finished = 0;
int d;
/* Loop over all dimensions for variable */
/* Loop over all dimensions for variable. */
for (d = 0; d < var->ndims && !finished; d++)
{
/* Is there a dimscale attached to this axis? */
@ -439,7 +439,8 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
/* Find dataset ID for dimension */
if (dim1->coord_var)
dim_datasetid = ((NC_HDF5_VAR_INFO_T *)(dim1->coord_var->format_var_info))->hdf_datasetid;
dim_datasetid = ((NC_HDF5_VAR_INFO_T *)
(dim1->coord_var->format_var_info))->hdf_datasetid;
else
dim_datasetid = hdf5_dim1->hdf_dimscaleid;
@ -450,7 +451,8 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
if (dim_datasetid > 0)
{
LOG((3, "detaching scale from %s", var->hdr.name));
if (H5DSdetach_scale(hdf5_var->hdf_datasetid, dim_datasetid, d) < 0)
if (H5DSdetach_scale(hdf5_var->hdf_datasetid,
dim_datasetid, d) < 0)
BAIL(NC_EHDFERR);
}
var->dimscale_attached[d] = NC_FALSE;
@ -462,7 +464,7 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
}
} /* next variable dimension */
/* Release & reset the array tracking attached dimscales */
/* Release & reset the array tracking attached dimscales. */
free(var->dimscale_attached);
var->dimscale_attached = NULL;
need_to_reattach_scales++;
@ -476,31 +478,32 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
BAIL(NC_EHDFERR);
hdf5_dim->hdf_dimscaleid = 0;
/* Now delete the dimscale's dataset
(it will be recreated later, if necessary) */
/* Now delete the dimscale's dataset (it will be recreated
later, if necessary). */
if (H5Gunlink(hdf5_grp->hdf_grpid, dim->hdr.name) < 0)
return NC_EDIMMETA;
}
/* Attach variable to dimension */
/* Attach variable to dimension. */
var->dimscale = NC_TRUE;
dim->coord_var = var;
/* Check if this variable used to be a coord. var */
if (need_to_reattach_scales || (var->was_coord_var && grp != NULL))
{
/* Reattach the scale everywhere it is used. */
/* (Recall that netCDF dimscales are always 1-D) */
/* Reattach the scale everywhere it is used. (Recall that netCDF
* dimscales are always 1-D) */
if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
var->dimids[0], hdf5_var->hdf_datasetid)))
return retval;
/* Set state transition indicator (cancels earlier transition) */
/* Set state transition indicator (cancels earlier
* transition). */
var->was_coord_var = NC_FALSE;
}
else
/* Set state transition indicator */
var->became_coord_var = NC_TRUE;
/* Set state transition indicator */
var->became_coord_var = NC_TRUE;
exit:
return retval;
@ -837,7 +840,7 @@ nc4_hdf5_find_grp_var_att(int ncid, int varid, const char *name, int attnum,
if (varid == NC_GLOBAL)
{
/* Do we need to read the atts? */
if (my_grp->atts_not_read)
if (!my_grp->atts_read)
if ((retval = nc4_read_atts(my_grp, NULL)))
return retval;
@ -849,7 +852,7 @@ nc4_hdf5_find_grp_var_att(int ncid, int varid, const char *name, int attnum,
return NC_ENOTVAR;
/* Do we need to read the var attributes? */
if (my_var->atts_not_read)
if (!my_var->atts_read)
if ((retval = nc4_read_atts(my_grp, my_var)))
return retval;

9
libhdf5/hdf5open.c
View File

@ -1308,7 +1308,7 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
H5Iinc_ref(hdf5_var->hdf_datasetid); /* Increment number of objects using ID */
incr_id_rc++; /* Indicate that we've incremented the ref. count (for errors) */
var->created = NC_TRUE;
var->atts_not_read = 1; /* Don't read var atts until user asks for one. */
var->atts_read = 0;
/* Try and read the dimids from the COORDINATES attribute. If it's
* not present, we will have to do dimsscale matching to locate the
@ -2112,9 +2112,9 @@ nc4_read_atts(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
/* Remember that we have read the atts for this var or group. */
if (var)
var->atts_not_read = 0;
var->atts_read = 1;
else
grp->atts_not_read = 0;
grp->atts_read = 1;
return NC_NOERR;
}
@ -2569,9 +2569,6 @@ rec_read_metadata(NC_GRP_INFO_T *grp)
BAIL(retval);
}
/* Defer the reading of global atts until someone asks for one. */
grp->atts_not_read = 1;
/* When reading existing file, mark all variables as written. */
for (i = 0; i < ncindexsize(grp->vars); i++)
((NC_VAR_INFO_T *)ncindexith(grp->vars, i))->written_to = NC_TRUE;

69
libhdf5/hdf5var.c
View File

@ -220,6 +220,36 @@ nc4_find_default_chunksizes2(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
return NC_NOERR;
}
/**
* @internal Give a var a secret HDF5 name. This is needed when a var
* is defined with the same name as a dim, but it is not a coord var
* of that dim. In that case, the var uses a secret name inside the
* HDF5 file.
*
* @param var Pointer to var info.
* @param name Name to use for base of secret name.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EMAXNAME Name too long to fit secret prefix.
* @returns ::NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
static int
give_var_secret_name(NC_VAR_INFO_T *var, const char *name)
{
/* Set a different hdf5 name for this variable to avoid name
* clash. */
if (strlen(name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME)
return NC_EMAXNAME;
if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) +
strlen(name) + 1) * sizeof(char))))
return NC_ENOMEM;
sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, name);
return NC_NOERR;
}
/**
* @internal This is called when a new netCDF-4 variable is defined
* with nc_def_var().
@ -410,6 +440,7 @@ NC4_def_var(int ncid, const char *name, nc_type xtype,
var->is_new_var = NC_TRUE;
var->meta_read = NC_TRUE;
var->atts_read = NC_TRUE;
/* Point to the type, and increment its ref. count */
var->type_info = type;
@ -501,17 +532,8 @@ NC4_def_var(int ncid, const char *name, nc_type xtype,
* and this var has the same name. */
dim = (NC_DIM_INFO_T*)ncindexlookup(grp->dim,norm_name);
if (dim && (!var->ndims || dimidsp[0] != dim->hdr.id))
{
/* Set a different hdf5 name for this variable to avoid name
* clash. */
if (strlen(norm_name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME)
BAIL(NC_EMAXNAME);
if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) +
strlen(norm_name) + 1) * sizeof(char))))
BAIL(NC_ENOMEM);
sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, norm_name);
}
if ((retval = give_var_secret_name(var, var->hdr.name)))
BAIL(retval);
/* If this is a coordinate var, it is marked as a HDF5 dimension
* scale. (We found dim above.) Otherwise, allocate space to
@ -1038,6 +1060,8 @@ NC4_rename_var(int ncid, int varid, const char *name)
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *other_dim;
int use_secret_name = 0;
int retval = NC_NOERR;
if (!name)
@ -1081,10 +1105,31 @@ NC4_rename_var(int ncid, int varid, const char *name)
(h5->cmode & NC_CLASSIC_MODEL))
return NC_ENOTINDEFINE;
/* Is there another dim with this name, for which this var will not
* be a coord var? If so, we have to create a dim without a
* variable for the old name. */
if ((other_dim = (NC_DIM_INFO_T *)ncindexlookup(grp->dim, name)) &&
strcmp(name, var->dim[0]->hdr.name))
{
/* Create a dim without var dataset for old dim. */
if ((retval = nc4_create_dim_wo_var(other_dim)))
return retval;
/* Give this var a secret HDF5 name so it can co-exist in file
* with dim wp var dataset. Base the secret name on the new var
* name. */
if ((retval = give_var_secret_name(var, name)))
return retval;
use_secret_name++;
}
/* Change the HDF5 file, if this var has already been created
there. */
if (var->created)
{
char *hdf5_name;
hdf5_name = use_secret_name ? var->hdf5_name: (char *)name;
/* Do we need to read var metadata? */
if (!var->meta_read)
if ((retval = nc4_get_var_meta(var)))
@ -1106,7 +1151,7 @@ NC4_rename_var(int ncid, int varid, const char *name)
}
LOG((3, "Moving dataset %s to %s", var->hdr.name, name));
if (H5Gmove(hdf5_grp->hdf_grpid, var->hdr.name, name) < 0)
if (H5Gmove(hdf5_grp->hdf_grpid, var->hdr.name, hdf5_name) < 0)
BAIL(NC_EHDFERR);
}

153
libhdf5/nc4hdf.c
View File

@ -1707,6 +1707,92 @@ write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
return NC_NOERR;
}
/**
* @internal Write a HDF5 dataset which is a dimension without a
* coordinate variable. This is a special 1-D dataset.
*
* @param dim Pointer to dim info struct.
* @param grp Pointer to group info struct.
* @param write_dimid
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EPERM Read-only file.
* @returns ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
*/
int
nc4_create_dim_wo_var(NC_DIM_INFO_T *dim)
{
NC_HDF5_DIM_INFO_T *hdf5_dim;
NC_HDF5_GRP_INFO_T *hdf5_grp;
hid_t spaceid = -1, create_propid = -1;
hsize_t dims[1], max_dims[1], chunk_dims[1] = {1};
char dimscale_wo_var[NC_MAX_NAME];
int retval = NC_NOERR;
LOG((4, "%s: creating dim %s", __func__, dim->hdr.name));
/* Sanity check */
assert(!dim->coord_var);
/* Get HDF5-specific dim and group info. */
hdf5_grp = (NC_HDF5_GRP_INFO_T *)dim->container->format_grp_info;
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
/* Create a property list. */
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
BAIL(NC_EHDFERR);
/* Turn off recording of times associated with this object. */
if (H5Pset_obj_track_times(create_propid, 0) < 0)
BAIL(NC_EHDFERR);
/* Set size of dataset to size of dimension. */
dims[0] = dim->len;
max_dims[0] = dim->len;
/* If this dimension scale is unlimited (i.e. it's an unlimited
* dimension), then set up chunking, with a chunksize of 1. */
if (dim->unlimited)
{
max_dims[0] = H5S_UNLIMITED;
if (H5Pset_chunk(create_propid, 1, chunk_dims) < 0)
BAIL(NC_EHDFERR);
}
/* Set up space. */
if ((spaceid = H5Screate_simple(1, dims, max_dims)) < 0)
BAIL(NC_EHDFERR);
/* Turn on creation-order tracking. */
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
/* Create the dataset that will be the dimension scale. */
LOG((4, "%s: about to H5Dcreate1 a dimscale dataset %s", __func__,
dim->hdr.name));
if ((hdf5_dim->hdf_dimscaleid = H5Dcreate2(hdf5_grp->hdf_grpid, dim->hdr.name,
H5T_IEEE_F32BE, spaceid,
H5P_DEFAULT, create_propid,
H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
/* Indicate that this is a scale. Also indicate that not
* be shown to the user as a variable. It is hidden. It is
* a DIM WITHOUT A VARIABLE! */
sprintf(dimscale_wo_var, "%s%10d", DIM_WITHOUT_VARIABLE, (int)dim->len);
if (H5DSset_scale(hdf5_dim->hdf_dimscaleid, dimscale_wo_var) < 0)
BAIL(NC_EHDFERR);
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (create_propid > 0 && H5Pclose(create_propid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal Write a dimension.
*
@ -1722,76 +1808,21 @@ write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
static int
write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
{
hid_t spaceid = -1, create_propid = -1;
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_HDF5_DIM_INFO_T *hdf5_dim;
hsize_t *new_size = NULL;
int retval = NC_NOERR;
assert(dim && dim->format_dim_info && grp && grp->format_grp_info);
/* Get HDF5-specific dim and group info. */
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
/* If there's no dimscale dataset for this dim, create one,
* and mark that it should be hidden from netCDF as a
* variable. (That is, it should appear as a dimension
* without an associated variable.) */
if (!hdf5_dim->hdf_dimscaleid)
{
hsize_t dims[1], max_dims[1], chunk_dims[1] = {1};
char dimscale_wo_var[NC_MAX_NAME];
LOG((4, "%s: creating dim %s", __func__, dim->hdr.name));
/* Sanity check */
assert(!dim->coord_var);
/* Create a property list. If this dimension scale is
* unlimited (i.e. it's an unlimited dimension), then set
* up chunking, with a chunksize of 1. */
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
BAIL(NC_EHDFERR);
/* Turn off recording of times associated with this object. */
if (H5Pset_obj_track_times(create_propid,0)<0)
BAIL(NC_EHDFERR);
dims[0] = dim->len;
max_dims[0] = dim->len;
if (dim->unlimited)
{
max_dims[0] = H5S_UNLIMITED;
if (H5Pset_chunk(create_propid, 1, chunk_dims) < 0)
BAIL(NC_EHDFERR);
}
/* Set up space. */
if ((spaceid = H5Screate_simple(1, dims, max_dims)) < 0)
BAIL(NC_EHDFERR);
/* Turn on creation-order tracking. */
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
/* Create the dataset that will be the dimension scale. */
LOG((4, "%s: about to H5Dcreate1 a dimscale dataset %s", __func__,
dim->hdr.name));
if ((hdf5_dim->hdf_dimscaleid = H5Dcreate2(hdf5_grp->hdf_grpid, dim->hdr.name,
H5T_IEEE_F32BE, spaceid,
H5P_DEFAULT, create_propid,
H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
/* Indicate that this is a scale. Also indicate that not
* be shown to the user as a variable. It is hidden. It is
* a DIM WITHOUT A VARIABLE! */
sprintf(dimscale_wo_var, "%s%10d", DIM_WITHOUT_VARIABLE, (int)dim->len);
if (H5DSset_scale(hdf5_dim->hdf_dimscaleid, dimscale_wo_var) < 0)
BAIL(NC_EHDFERR);
}
if ((retval = nc4_create_dim_wo_var(dim)))
BAIL(retval);
/* Did we extend an unlimited dimension? */
if (dim->extended)
@ -1806,6 +1837,7 @@ write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
if (v1)
{
NC_HDF5_VAR_INFO_T *hdf5_v1;
hsize_t *new_size;
int d1;
hdf5_v1 = (NC_HDF5_VAR_INFO_T *)v1->format_var_info;
@ -1821,6 +1853,7 @@ write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
}
if (H5Dset_extent(hdf5_v1->hdf_datasetid, new_size) < 0)
BAIL(NC_EHDFERR);
free(new_size);
}
}
@ -1833,12 +1866,6 @@ write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
BAIL(retval);
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (create_propid > 0 && H5Pclose(create_propid) < 0)
BAIL2(NC_EHDFERR);
if (new_size)
free(new_size);
return retval;
}

10
libsrc/posixio.c
View File

@ -184,7 +184,11 @@ blksize(int fd)
return 8192;
}
/* else, silent in the face of error */
#else
NC_UNUSED(fd);
#endif
#else
NC_UNUSED(fd);
#endif
return (size_t) 2 * pagesize();
}
@ -445,6 +449,7 @@ px_rel(ncio_px *const pxp, off_t offset, int rflags)
&& offset < pxp->bf_offset + (off_t) pxp->bf_extent);
assert(pIf(fIsSet(rflags, RGN_MODIFIED),
fIsSet(pxp->bf_rflags, RGN_WRITE)));
NC_UNUSED(offset);
if(fIsSet(rflags, RGN_MODIFIED))
{
@ -797,6 +802,7 @@ px_double_buffer(ncio *const nciop, off_t to, off_t from,
int status = NC_NOERR;
void *src;
void *dest;
NC_UNUSED(rflags);
#if INSTRUMENT
fprintf(stderr, "\tdouble_buffr %ld %ld %ld\n",
@ -1152,6 +1158,7 @@ ncio_spx_rel(ncio *const nciop, off_t offset, int rflags)
assert(offset < pxp->bf_offset + X_ALIGN);
assert(pxp->bf_cnt % X_ALIGN == 0 );
#endif
NC_UNUSED(offset);
if(fIsSet(rflags, RGN_MODIFIED))
{
@ -1400,6 +1407,7 @@ ncio_spx_move(ncio *const nciop, off_t to, off_t from,
static int
ncio_spx_sync(ncio *const nciop)
{
NC_UNUSED(nciop);
/* NOOP */
return NC_NOERR;
}
@ -1592,6 +1600,7 @@ posixio_create(const char *path, int ioflags,
int oflags = (O_RDWR|O_CREAT);
int fd;
int status;
NC_UNUSED(parameters);
if(initialsz < (size_t)igeto + igetsz)
initialsz = (size_t)igeto + igetsz;
@ -1736,6 +1745,7 @@ posixio_open(const char *path,
int oflags = fIsSet(ioflags, NC_WRITE) ? O_RDWR : O_RDONLY;
int fd = -1;
int status = 0;
NC_UNUSED(parameters);
if(path == NULL || *path == 0)
return EINVAL;

3
libsrc4/nc4var.c
View File

@ -390,6 +390,9 @@ int
NC4_var_par_access(int ncid, int varid, int par_access)
{
#ifndef USE_PARALLEL4
NC_UNUSED(ncid);
NC_UNUSED(varid);
NC_UNUSED(par_access);
return NC_ENOPAR;
#else
NC *nc;

4
nc_test4/Makefile.am
View File

@ -144,10 +144,10 @@ tst_floats2_*.cdl tst_ints2_*.cdl tst_shorts2_*.cdl tst_elena_*.cdl \
tst_simple*.cdl tst_chunks.cdl pr_A1.* tauu_A1.* usi_01.* thetau_01.* \
tst_*.h5 tst_grp_rename.cdl tst_grp_rename.dmp ref_grp_rename.cdl \
foo1.nc tst_*.h4 test.nc testszip.nc test.h5 szip_dump.cdl \
perftest.txt bigmeta.nc bigvars.nc run_par_test.sh *.gz MSGCPP_*.nc \
perftest.txt bigmeta.nc bigvars.nc *.gz MSGCPP_*.nc \
floats*.nc floats*.cdl shorts*.nc shorts*.cdl ints*.nc ints*.cdl
DISTCLEANFILES = findplugin.sh
DISTCLEANFILES = findplugin.sh run_par_test.sh
# If valgrind is present, add valgrind targets.
@VALGRIND_CHECK_RULES@

126
nc_test4/tst_rename2.c
View File

@ -25,11 +25,18 @@ See \ref copyright file for more info.
#define DIM_X "x"
#define DIM_Y "y"
#define DIM_Z "z"
#define VAR_NAME_START "lon"
#define VAR_NAME_END "lo"
#define DIM_NAME_START "lon"
#define DIM_NAME_END "lo"
#define DIM1_LEN 4
#define NDIM1 1
#define NDIM3 3
#define NUM_ENDDEF_SETTINGS 2
#define D1_NAME "d1"
#define D2_NAME "d2"
#define TMP_NAME "t1"
int
main(int argc, char **argv)
@ -147,5 +154,124 @@ main(int argc, char **argv)
SUMMARIZE_ERR;
} /* next format */
#define FILE_NAME1 "tst_dims_foo1.nc"
#define DIM_NAME "lat_T42"
#define VAR_NAME DIM_NAME
#define DIM_NAME2 "lat"
#define VAR_NAME2 DIM_NAME2
#define RANK_lat_T42 1
fprintf(stderr,"*** test renaming with sync...");
{
int ncid, dimid, varid;
char file_name[NC_MAX_NAME + 1];
char name[NC_MAX_NAME + 1];
/* Create file with dim and associated coordinate var. */
sprintf(file_name, "%s_sync.nc", TEST_NAME);
if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
if (nc_def_dim(ncid, DIM_NAME_END, DIM1_LEN, &dimid)) ERR;
if (nc_def_var(ncid, DIM_NAME_END, NC_INT, NDIM1, &dimid, &varid)) ERR;
if (nc_close(ncid)) ERR;
if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
if (nc_def_dim(ncid, DIM_NAME_START, DIM1_LEN, &dimid)) ERR;
if (nc_def_var(ncid, DIM_NAME_END, NC_INT, NDIM1, &dimid, &varid)) ERR;
if (nc_close(ncid)) ERR;
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
if (nc_rename_dim(ncid, dimid, DIM_NAME_END)) ERR;
if (nc_close(ncid)) ERR;
/* Reopen file and check, */
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
if (nc_inq_dimid(ncid, DIM_NAME_END, &dimid)) ERR;
if (nc_inq_varid(ncid, DIM_NAME_END, &varid)) ERR;
if (nc_inq_dimname(ncid, dimid, name)) ERR;
if (strcmp(name, DIM_NAME_END)) ERR;
if (nc_inq_varname(ncid, varid, name)) ERR;
if (strcmp(name, DIM_NAME_END)) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
fprintf(stderr,"*** test renaming with sync...");
{
int ncid, dimid, varid;
char file_name[NC_MAX_NAME + 1];
char name[NC_MAX_NAME + 1];
/* Create file with dim and associated coordinate var. */
sprintf(file_name, "%s_sync.nc", TEST_NAME);
if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
if (nc_def_dim(ncid, DIM_NAME_START, DIM1_LEN, &dimid)) ERR;
if (nc_def_var(ncid, VAR_NAME_START, NC_INT, NDIM1, &dimid, &varid)) ERR;
if (nc_close(ncid)) ERR;
/* nc_set_log_level(4); */
/* Open the file and rename the var. */
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
if (nc_inq_dimid(ncid, DIM_NAME_START, &dimid)) ERR;
if (nc_inq_varid(ncid, VAR_NAME_START, &varid)) ERR;
if (nc_rename_var(ncid, varid, VAR_NAME_END)) ERR;
/* Sync to disk. Now the file has one dim and one var. The dim
* is a dimscale only dataset, and the var is a dataset with a
* dimscale attached pointing to the dim. */
/* if (nc_sync(ncid)) ERR; */
if (nc_close(ncid)) ERR;
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
/* Now rename the dim to the same name as the var. After this
* there will be one dataset, called DIM_NAME_END, which will be
* a dimscale. */
if (nc_rename_dim(ncid, dimid, DIM_NAME_END)) ERR;
if (nc_close(ncid)) ERR;
/* Reopen file and check, */
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
if (nc_inq_dimid(ncid, DIM_NAME_END, &dimid)) ERR;
if (nc_inq_varid(ncid, VAR_NAME_END, &varid)) ERR;
if (nc_inq_dimname(ncid, dimid, name)) ERR;
if (strcmp(name, DIM_NAME_END)) ERR;
if (nc_inq_varname(ncid, varid, name)) ERR;
if (strcmp(name, VAR_NAME_END)) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
fprintf(stderr,"*** test renaming non-coord var to same name as dim...");
{
int ncid, dimid1, dimid2, varid1, varid2;
int dimid_in, varid_in;
char file_name[NC_MAX_NAME + 1];
/* Create file with dim and associated coordinate var. */
sprintf(file_name, "%s_non_coord_to_dim.nc", TEST_NAME);
if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
if (nc_def_dim(ncid, D1_NAME, DIM1_LEN, &dimid1)) ERR;
if (nc_def_dim(ncid, D2_NAME, DIM1_LEN, &dimid2)) ERR;
if (nc_def_var(ncid, D1_NAME, NC_INT, NDIM1, &dimid1, &varid1)) ERR;
if (nc_def_var(ncid, D2_NAME, NC_INT, NDIM1, &dimid2, &varid2)) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and rename the vars. */
/* nc_set_log_level(4); */
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
if (nc_rename_var(ncid, varid1, TMP_NAME)) ERR;
if (nc_rename_var(ncid, varid2, D1_NAME)) ERR;
if (nc_close(ncid)) ERR;
/* Reopen file and check, */
if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
if (nc_inq_dimid(ncid, D1_NAME, &dimid_in)) ERR;
if (dimid_in != dimid1) ERR;
if (nc_inq_dimid(ncid, D2_NAME, &dimid_in)) ERR;
if (dimid_in != dimid2) ERR;
if (nc_inq_dimid(ncid, TMP_NAME, &dimid_in) != NC_EBADDIM) ERR;
if (nc_inq_varid(ncid, TMP_NAME, &varid_in)) ERR;
if (varid_in != varid1) ERR;
if (nc_inq_varid(ncid, D1_NAME, &varid_in)) ERR;
if (varid_in != varid2) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}