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netcdf-c/libsrc/nc3internal.c

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/*
* Copyright 2018, Unuiversity Corporation for Atmospheric Research
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*/
#if HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <sys/types.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include "nc3internal.h"
#include "netcdf_mem.h"
#include "rnd.h"
#include "ncx.h"
#include "ncrc.h"
/* These have to do with version numbers. */
#define MAGIC_NUM_LEN 4
#define VER_CLASSIC 1
#define VER_64BIT_OFFSET 2
#define VER_HDF5 3
#define NC_NUMRECS_OFFSET 4
/* For netcdf classic */
#define NC_NUMRECS_EXTENT3 4
/* For cdf5 */
#define NC_NUMRECS_EXTENT5 8
/* Internal function; breaks ncio abstraction */
extern int memio_extract(ncio* const nciop, size_t* sizep, void** memoryp);
static void
free_NC3INFO(NC3_INFO *nc3)
{
if(nc3 == NULL)
return;
free_NC_dimarrayV(&nc3->dims);
free_NC_attrarrayV(&nc3->attrs);
free_NC_vararrayV(&nc3->vars);
free(nc3);
}
static NC3_INFO *
new_NC3INFO(const size_t *chunkp)
{
NC3_INFO *ncp;
ncp = (NC3_INFO*)calloc(1,sizeof(NC3_INFO));
if(ncp == NULL) return ncp;
ncp->chunk = chunkp != NULL ? *chunkp : NC_SIZEHINT_DEFAULT;
/* Note that ncp->xsz is not set yet because we do not know the file format */
return ncp;
}
static NC3_INFO *
dup_NC3INFO(const NC3_INFO *ref)
{
NC3_INFO *ncp;
ncp = (NC3_INFO*)calloc(1,sizeof(NC3_INFO));
if(ncp == NULL) return ncp;
if(dup_NC_dimarrayV(&ncp->dims, &ref->dims) != NC_NOERR)
goto err;
if(dup_NC_attrarrayV(&ncp->attrs, &ref->attrs) != NC_NOERR)
goto err;
if(dup_NC_vararrayV(&ncp->vars, &ref->vars) != NC_NOERR)
goto err;
ncp->xsz = ref->xsz;
ncp->begin_var = ref->begin_var;
ncp->begin_rec = ref->begin_rec;
ncp->recsize = ref->recsize;
NC_set_numrecs(ncp, NC_get_numrecs(ref));
return ncp;
err:
free_NC3INFO(ncp);
return NULL;
}
/*
* Verify that this is a user nc_type
* Formerly NCcktype()
* Sense of the return is changed.
*/
int
nc3_cktype(int mode, nc_type type)
{
#ifdef NETCDF_ENABLE_CDF5
if (mode & NC_CDF5) { /* CDF-5 format */
if (type >= NC_BYTE && type < NC_STRING) return NC_NOERR;
} else
#endif
if (mode & NC_64BIT_OFFSET) { /* CDF-2 format */
if (type >= NC_BYTE && type <= NC_DOUBLE) return NC_NOERR;
} else if ((mode & NC_64BIT_OFFSET) == 0) { /* CDF-1 format */
if (type >= NC_BYTE && type <= NC_DOUBLE) return NC_NOERR;
}
return(NC_EBADTYPE);
}
/*
* How many objects of 'type'
* will fit into xbufsize?
*/
size_t
ncx_howmany(nc_type type, size_t xbufsize)
{
switch(type){
case NC_BYTE:
case NC_CHAR:
return xbufsize;
case NC_SHORT:
return xbufsize/X_SIZEOF_SHORT;
case NC_INT:
return xbufsize/X_SIZEOF_INT;
case NC_FLOAT:
return xbufsize/X_SIZEOF_FLOAT;
case NC_DOUBLE:
return xbufsize/X_SIZEOF_DOUBLE;
case NC_UBYTE:
return xbufsize;
case NC_USHORT:
return xbufsize/X_SIZEOF_USHORT;
case NC_UINT:
return xbufsize/X_SIZEOF_UINT;
case NC_INT64:
return xbufsize/X_SIZEOF_LONGLONG;
case NC_UINT64:
return xbufsize/X_SIZEOF_ULONGLONG;
default:
assert("ncx_howmany: Bad type" == 0);
return(0);
}
}
#define D_RNDUP(x, align) _RNDUP(x, (off_t)(align))
/*
* Compute each variable's 'begin' offset,
* update 'begin_rec' as well.
*/
static int
NC_begins(NC3_INFO* ncp,
size_t h_minfree, size_t v_align,
size_t v_minfree, size_t r_align)
{
size_t ii, j;
size_t sizeof_off_t;
off_t index = 0;
off_t old_ncp_begin_var;
NC_var **vpp;
NC_var *last = NULL;
NC_var *first_var = NULL; /* first "non-record" var */
if(v_align == NC_ALIGN_CHUNK)
v_align = ncp->chunk;
if(r_align == NC_ALIGN_CHUNK)
r_align = ncp->chunk;
if (fIsSet(ncp->flags, NC_64BIT_OFFSET) || fIsSet(ncp->flags, NC_64BIT_DATA)) {
sizeof_off_t = 8;
} else {
sizeof_off_t = 4;
}
ncp->xsz = ncx_len_NC(ncp,sizeof_off_t);
if(ncp->vars.nelems == 0)
return NC_NOERR;
old_ncp_begin_var = ncp->begin_var;
/* only (re)calculate begin_var if there is not sufficient space in header
or start of non-record variables is not aligned as requested by valign */
if (ncp->begin_var < ncp->xsz + h_minfree ||
ncp->begin_var != D_RNDUP(ncp->begin_var, v_align) )
{
index = (off_t) ncp->xsz;
ncp->begin_var = D_RNDUP(index, v_align);
if(ncp->begin_var < index + (off_t)h_minfree)
{
ncp->begin_var = D_RNDUP(index + (off_t)h_minfree, v_align);
}
}
if (ncp->old != NULL) {
/* check whether the new begin_var is smaller */
if (ncp->begin_var < ncp->old->begin_var)
ncp->begin_var = ncp->old->begin_var;
}
index = ncp->begin_var;
/* loop thru vars, first pass is for the 'non-record' vars */
j = 0;
vpp = ncp->vars.value;
for(ii = 0; ii < ncp->vars.nelems ; ii++, vpp++)
{
if( IS_RECVAR(*vpp) )
{
/* skip record variables on this pass */
continue;
}
if (first_var == NULL) first_var = *vpp;
#if 0
fprintf(stderr, " VAR %d %s: %ld\n", ii, (*vpp)->name->cp, (long)index);
#endif
if( sizeof_off_t == 4 && (index > X_OFF_MAX || index < 0) )
{
ncp->begin_var = old_ncp_begin_var;
return NC_EVARSIZE;
}
(*vpp)->begin = index;
if (ncp->old != NULL) {
/* move to the next fixed variable */
for (; j<ncp->old->vars.nelems; j++) {
if (!IS_RECVAR(ncp->old->vars.value[j]))
break;
}
if (j < ncp->old->vars.nelems) {
if ((*vpp)->begin < ncp->old->vars.value[j]->begin) {
/* the first ncp->vars.nelems fixed variables
should be the same. If the new begin is smaller,
reuse the old begin */
(*vpp)->begin = ncp->old->vars.value[j]->begin;
index = (*vpp)->begin;
}
j++;
}
}
index += (*vpp)->len;
}
if (ncp->old != NULL) {
/* check whether the new begin_rec is smaller */
if (ncp->begin_rec < ncp->old->begin_rec)
ncp->begin_rec = ncp->old->begin_rec;
}
/* only (re)calculate begin_rec if there is not sufficient
space at end of non-record variables or if start of record
variables is not aligned as requested by r_align */
if (ncp->begin_rec < index + (off_t)v_minfree ||
ncp->begin_rec != D_RNDUP(ncp->begin_rec, r_align) )
{
ncp->begin_rec = D_RNDUP(index, r_align);
if(ncp->begin_rec < index + (off_t)v_minfree)
{
ncp->begin_rec = D_RNDUP(index + (off_t)v_minfree, r_align);
}
}
if (first_var != NULL)
ncp->begin_var = first_var->begin;
else
ncp->begin_var = ncp->begin_rec;
index = ncp->begin_rec;
ncp->recsize = 0;
/* loop thru vars, second pass is for the 'record' vars */
j = 0;
vpp = (NC_var **)ncp->vars.value;
for(ii = 0; ii < ncp->vars.nelems; ii++, vpp++)
{
if( !IS_RECVAR(*vpp) )
{
/* skip non-record variables on this pass */
continue;
}
#if 0
fprintf(stderr, " REC %d %s: %ld\n", ii, (*vpp)->name->cp, (long)index);
#endif
if( sizeof_off_t == 4 && (index > X_OFF_MAX || index < 0) )
{
ncp->begin_var = old_ncp_begin_var;
return NC_EVARSIZE;
}
(*vpp)->begin = index;
if (ncp->old != NULL) {
/* move to the next record variable */
for (; j<ncp->old->vars.nelems; j++)
if (IS_RECVAR(ncp->old->vars.value[j]))
break;
if (j < ncp->old->vars.nelems) {
if ((*vpp)->begin < ncp->old->vars.value[j]->begin)
/* if the new begin is smaller, use the old begin */
(*vpp)->begin = ncp->old->vars.value[j]->begin;
j++;
}
}
index += (*vpp)->len;
/* check if record size must fit in 32-bits */
#if SIZEOF_OFF_T == SIZEOF_SIZE_T && SIZEOF_SIZE_T == 4
if( ncp->recsize > X_UINT_MAX - (*vpp)->len )
{
ncp->begin_var = old_ncp_begin_var;
return NC_EVARSIZE;
}
#endif
ncp->recsize += (*vpp)->len;
last = (*vpp);
}
/*
* for special case (Check CDF-1 and CDF-2 file format specifications.)
* "A special case: Where there is exactly one record variable, we drop the
* requirement that each record be four-byte aligned, so in this case there
* is no record padding."
*/
if (last != NULL) {
if (ncp->recsize == last->len) {
/* exactly one record variable, pack value */
ncp->recsize = *last->dsizes * last->xsz;
}
}
if(NC_IsNew(ncp))
NC_set_numrecs(ncp, 0);
return NC_NOERR;
}
/*
* Read just the numrecs member.
* (A relatively expensive way to do things.)
*/
int
read_numrecs(NC3_INFO *ncp)
{
int status = NC_NOERR;
const void *xp = NULL;
size_t new_nrecs = 0;
size_t old_nrecs = NC_get_numrecs(ncp);
size_t nc_numrecs_extent = NC_NUMRECS_EXTENT3; /* CDF-1 and CDF-2 */
assert(!NC_indef(ncp));
if (fIsSet(ncp->flags, NC_64BIT_DATA))
nc_numrecs_extent = NC_NUMRECS_EXTENT5; /* CDF-5 */
status = ncio_get(ncp->nciop,
NC_NUMRECS_OFFSET, nc_numrecs_extent, 0, (void **)&xp);/* cast away const */
if(status != NC_NOERR)
return status;
if (fIsSet(ncp->flags, NC_64BIT_DATA)) {
unsigned long long tmp=0;
status = ncx_get_uint64(&xp, &tmp);
new_nrecs = (size_t)tmp;
} else
status = ncx_get_size_t(&xp, &new_nrecs);
(void) ncio_rel(ncp->nciop, NC_NUMRECS_OFFSET, 0);
if(status == NC_NOERR && old_nrecs != new_nrecs)
{
NC_set_numrecs(ncp, new_nrecs);
fClr(ncp->flags, NC_NDIRTY);
}
return status;
}
/*
* Write out just the numrecs member.
* (A relatively expensive way to do things.)
*/
int
write_numrecs(NC3_INFO *ncp)
{
int status = NC_NOERR;
void *xp = NULL;
size_t nc_numrecs_extent = NC_NUMRECS_EXTENT3; /* CDF-1 and CDF-2 */
assert(!NC_readonly(ncp));
assert(!NC_indef(ncp));
if (fIsSet(ncp->flags, NC_64BIT_DATA))
nc_numrecs_extent = NC_NUMRECS_EXTENT5; /* CDF-5 */
status = ncio_get(ncp->nciop,
NC_NUMRECS_OFFSET, nc_numrecs_extent, RGN_WRITE, &xp);
if(status != NC_NOERR)
return status;
{
const size_t nrecs = NC_get_numrecs(ncp);
if (fIsSet(ncp->flags, NC_64BIT_DATA))
status = ncx_put_uint64(&xp, (unsigned long long)nrecs);
else
status = ncx_put_size_t(&xp, &nrecs);
}
(void) ncio_rel(ncp->nciop, NC_NUMRECS_OFFSET, RGN_MODIFIED);
if(status == NC_NOERR)
fClr(ncp->state, NC_NDIRTY);
return status;
}
/*
* Read in the header
* It is expensive.
*/
static int
read_NC(NC3_INFO *ncp)
{
int status = NC_NOERR;
free_NC_dimarrayV(&ncp->dims);
free_NC_attrarrayV(&ncp->attrs);
free_NC_vararrayV(&ncp->vars);
status = nc_get_NC(ncp);
if(status == NC_NOERR)
fClr(ncp->state, NC_NDIRTY | NC_HDIRTY);
return status;
}
/*
* Write out the header
*/
static int
write_NC(NC3_INFO *ncp)
{
int status = NC_NOERR;
assert(!NC_readonly(ncp));
status = ncx_put_NC(ncp, NULL, 0, 0);
if(status == NC_NOERR)
fClr(ncp->state, NC_NDIRTY | NC_HDIRTY);
return status;
}
/*
* Write the header or the numrecs if necessary.
*/
int
NC_sync(NC3_INFO *ncp)
{
assert(!NC_readonly(ncp));
if(NC_hdirty(ncp))
{
return write_NC(ncp);
}
/* else */
if(NC_ndirty(ncp))
{
return write_numrecs(ncp);
}
/* else */
return NC_NOERR;
}
/*
* Initialize the 'non-record' variables.
*/
static int
fillerup(NC3_INFO *ncp)
{
int status = NC_NOERR;
size_t ii;
NC_var **varpp;
assert(!NC_readonly(ncp));
/* loop thru vars */
varpp = ncp->vars.value;
for(ii = 0; ii < ncp->vars.nelems; ii++, varpp++)
{
if ((*varpp)->no_fill) continue;
if(IS_RECVAR(*varpp))
{
/* skip record variables */
continue;
}
status = fill_NC_var(ncp, *varpp, (*varpp)->len, 0);
if(status != NC_NOERR)
break;
}
return status;
}
/* Begin endef */
/*
*/
static int
fill_added_recs(NC3_INFO *gnu, NC3_INFO *old)
{
NC_var ** const gnu_varpp = (NC_var **)gnu->vars.value;
const size_t old_nrecs = NC_get_numrecs(old);
size_t recno = 0;
NC_var **vpp = gnu_varpp;
NC_var *const *const end = &vpp[gnu->vars.nelems];
int numrecvars = 0;
/* Determine if there is only one record variable. If so, we
must treat as a special case because there's no record padding */
for(; vpp < end; vpp++) {
if(IS_RECVAR(*vpp)) {
numrecvars++;
}
}
for(; recno < old_nrecs; recno++)
{
int varid = (int)old->vars.nelems;
for(; varid < (int)gnu->vars.nelems; varid++)
{
const NC_var *const gnu_varp = *(gnu_varpp + varid);
if (gnu_varp->no_fill) continue;
if(!IS_RECVAR(gnu_varp))
{
/* skip non-record variables */
continue;
}
/* else */
{
long long varsize = numrecvars == 1 ? gnu->recsize : gnu_varp->len;
const int status = fill_NC_var(gnu, gnu_varp, varsize, recno);
if(status != NC_NOERR)
return status;
}
}
}
return NC_NOERR;
}
/*
*/
static int
fill_added(NC3_INFO *gnu, NC3_INFO *old)
{
NC_var ** const gnu_varpp = (NC_var **)gnu->vars.value;
int varid = (int)old->vars.nelems;
for(; varid < (int)gnu->vars.nelems; varid++)
{
const NC_var *const gnu_varp = *(gnu_varpp + varid);
if (gnu_varp->no_fill) continue;
if(IS_RECVAR(gnu_varp))
{
/* skip record variables */
continue;
}
/* else */
{
const int status = fill_NC_var(gnu, gnu_varp, gnu_varp->len, 0);
if(status != NC_NOERR)
return status;
}
}
return NC_NOERR;
}
/*
* Move the records "out".
* Fill as needed.
*/
static int
move_recs_r(NC3_INFO *gnu, NC3_INFO *old)
{
int status;
int recno;
int varid;
NC_var **gnu_varpp = (NC_var **)gnu->vars.value;
NC_var **old_varpp = (NC_var **)old->vars.value;
NC_var *gnu_varp;
NC_var *old_varp;
off_t gnu_off;
off_t old_off;
const size_t old_nrecs = NC_get_numrecs(old);
/* Don't parallelize this loop */
for(recno = (int)old_nrecs -1; recno >= 0; recno--)
{
/* Don't parallelize this loop */
for(varid = (int)old->vars.nelems -1; varid >= 0; varid--)
{
gnu_varp = *(gnu_varpp + varid);
if(!IS_RECVAR(gnu_varp))
{
/* skip non-record variables on this pass */
continue;
}
/* else */
/* else, a pre-existing variable */
old_varp = *(old_varpp + varid);
gnu_off = gnu_varp->begin + (off_t)(gnu->recsize * (size_t)recno);
old_off = old_varp->begin + (off_t)(old->recsize * (size_t)recno);
if(gnu_off == old_off)
continue; /* nothing to do */
assert(gnu_off > old_off);
status = ncio_move(gnu->nciop, gnu_off, old_off,
old_varp->len, 0);
if(status != NC_NOERR)
return status;
}
}
NC_set_numrecs(gnu, old_nrecs);
return NC_NOERR;
}
/*
* Move the "non record" variables "out".
* Fill as needed.
*/
static int
move_vars_r(NC3_INFO *gnu, NC3_INFO *old)
{
int err, status=NC_NOERR;
int varid;
NC_var **gnu_varpp = (NC_var **)gnu->vars.value;
NC_var **old_varpp = (NC_var **)old->vars.value;
NC_var *gnu_varp;
NC_var *old_varp;
off_t gnu_off;
off_t old_off;
/* Don't parallelize this loop */
for(varid = (int)old->vars.nelems -1;
varid >= 0; varid--)
{
gnu_varp = *(gnu_varpp + varid);
if(IS_RECVAR(gnu_varp))
{
/* skip record variables on this pass */
continue;
}
/* else */
old_varp = *(old_varpp + varid);
gnu_off = gnu_varp->begin;
old_off = old_varp->begin;
if (gnu_off > old_off) {
err = ncio_move(gnu->nciop, gnu_off, old_off,
old_varp->len, 0);
if (status == NC_NOERR) status = err;
}
}
return status;
}
/*
* Given a valid ncp, return NC_EVARSIZE if any variable has a bad len
* (product of non-rec dim sizes too large), else return NC_NOERR.
*/
int
NC_check_vlens(NC3_INFO *ncp)
{
NC_var **vpp;
/* maximum permitted variable size (or size of one record's worth
of a record variable) in bytes. This is different for format 1
and format 2. */
long long vlen_max;
size_t ii;
size_t large_vars_count;
size_t rec_vars_count;
int last = 0;
if(ncp->vars.nelems == 0)
return NC_NOERR;
if (fIsSet(ncp->flags,NC_64BIT_DATA)) /* CDF-5 */
vlen_max = X_INT64_MAX - 3; /* "- 3" handles rounded-up size */
else if (fIsSet(ncp->flags,NC_64BIT_OFFSET) && sizeof(off_t) > 4)
/* CDF2 format and LFS */
vlen_max = X_UINT_MAX - 3; /* "- 3" handles rounded-up size */
else /* CDF1 format */
vlen_max = X_INT_MAX - 3;
/* Loop through vars, first pass is for non-record variables. */
large_vars_count = 0;
rec_vars_count = 0;
vpp = ncp->vars.value;
for (ii = 0; ii < ncp->vars.nelems; ii++, vpp++) {
assert(vpp != NULL && *vpp != NULL);
if( !IS_RECVAR(*vpp) ) {
last = 0;
if( NC_check_vlen(*vpp, vlen_max) == 0 ) {
if (fIsSet(ncp->flags,NC_64BIT_DATA)) /* too big for CDF-5 */
return NC_EVARSIZE;
large_vars_count++;
last = 1;
}
} else {
rec_vars_count++;
}
}
/* OK if last non-record variable size too large, since not used to
compute an offset */
if( large_vars_count > 1) { /* only one "too-large" variable allowed */
return NC_EVARSIZE;
}
/* and it has to be the last one */
if( large_vars_count == 1 && last == 0) {
return NC_EVARSIZE;
}
if( rec_vars_count > 0 ) {
/* and if it's the last one, there can't be any record variables */
if( large_vars_count == 1 && last == 1) {
return NC_EVARSIZE;
}
/* Loop through vars, second pass is for record variables. */
large_vars_count = 0;
vpp = ncp->vars.value;
for (ii = 0; ii < ncp->vars.nelems; ii++, vpp++) {
if( IS_RECVAR(*vpp) ) {
last = 0;
if( NC_check_vlen(*vpp, vlen_max) == 0 ) {
if (fIsSet(ncp->flags,NC_64BIT_DATA)) /* too big for CDF-5 */
return NC_EVARSIZE;
large_vars_count++;
last = 1;
}
}
}
/* OK if last record variable size too large, since not used to
compute an offset */
if( large_vars_count > 1) { /* only one "too-large" variable allowed */
return NC_EVARSIZE;
}
/* and it has to be the last one */
if( large_vars_count == 1 && last == 0) {
return NC_EVARSIZE;
}
}
return NC_NOERR;
}
/*----< NC_check_voffs() >---------------------------------------------------*/
/*
* Given a valid ncp, check whether the file starting offsets (begin) of all
* variables follows the same increasing order as they were defined.
*/
int
NC_check_voffs(NC3_INFO *ncp)
{
size_t i;
off_t prev_off;
NC_var *varp;
if (ncp->vars.nelems == 0) return NC_NOERR;
/* Loop through vars, first pass is for non-record variables */
prev_off = ncp->begin_var;
for (i=0; i<ncp->vars.nelems; i++) {
varp = ncp->vars.value[i];
if (IS_RECVAR(varp)) continue;
if (varp->begin < prev_off) {
#if 0
fprintf(stderr,"Variable \"%s\" begin offset (%lld) is less than previous variable end offset (%lld)\n", varp->name->cp, varp->begin, prev_off);
#endif
return NC_ENOTNC;
}
prev_off = varp->begin + varp->len;
}
if (ncp->begin_rec < prev_off) {
#if 0
fprintf(stderr,"Record variable section begin offset (%lld) is less than fix-sized variable section end offset (%lld)\n", varp->begin, prev_off);
#endif
return NC_ENOTNC;
}
/* Loop through vars, second pass is for record variables */
prev_off = ncp->begin_rec;
for (i=0; i<ncp->vars.nelems; i++) {
varp = ncp->vars.value[i];
if (!IS_RECVAR(varp)) continue;
if (varp->begin < prev_off) {
#if 0
fprintf(stderr,"Variable \"%s\" begin offset (%lld) is less than previous variable end offset (%lld)\n", varp->name->cp, varp->begin, prev_off);
#endif
return NC_ENOTNC;
}
prev_off = varp->begin + varp->len;
}
return NC_NOERR;
}
/*
* End define mode.
* Common code for ncendef, ncclose(endef)
* Flushes I/O buffers.
*/
static int
NC_endef(NC3_INFO *ncp,
size_t h_minfree, size_t v_align,
size_t v_minfree, size_t r_align)
{
int status = NC_NOERR;
assert(!NC_readonly(ncp));
assert(NC_indef(ncp));
status = NC_check_vlens(ncp);
if(status != NC_NOERR)
return status;
status = NC_begins(ncp, h_minfree, v_align, v_minfree, r_align);
if(status != NC_NOERR)
return status;
status = NC_check_voffs(ncp);
if(status != NC_NOERR)
return status;
if(ncp->old != NULL)
{
/* a plain redef, not a create */
assert(!NC_IsNew(ncp));
assert(fIsSet(ncp->state, NC_INDEF));
assert(ncp->begin_rec >= ncp->old->begin_rec);
assert(ncp->begin_var >= ncp->old->begin_var);
if(ncp->vars.nelems != 0)
{
if(ncp->begin_rec > ncp->old->begin_rec)
{
status = move_recs_r(ncp, ncp->old);
if(status != NC_NOERR)
return status;
if(ncp->begin_var > ncp->old->begin_var)
{
status = move_vars_r(ncp, ncp->old);
if(status != NC_NOERR)
return status;
}
/* else if (ncp->begin_var == ncp->old->begin_var) { NOOP } */
}
else
{
/* due to fixed variable alignment, it is possible that header
grows but begin_rec did not change */
if(ncp->begin_var > ncp->old->begin_var)
{
status = move_vars_r(ncp, ncp->old);
if(status != NC_NOERR)
return status;
}
/* Even if (ncp->begin_rec == ncp->old->begin_rec)
and (ncp->begin_var == ncp->old->begin_var)
might still have added a new record variable */
if(ncp->recsize > ncp->old->recsize)
{
status = move_recs_r(ncp, ncp->old);
if(status != NC_NOERR)
return status;
}
}
}
}
status = write_NC(ncp);
if(status != NC_NOERR)
return status;
/* fill mode is now per variable */
{
if(NC_IsNew(ncp))
{
status = fillerup(ncp);
if(status != NC_NOERR)
return status;
}
else if(ncp->old == NULL ? 0
: (ncp->vars.nelems > ncp->old->vars.nelems))
{
status = fill_added(ncp, ncp->old);
if(status != NC_NOERR)
return status;
status = fill_added_recs(ncp, ncp->old);
if(status != NC_NOERR)
return status;
}
}
if(ncp->old != NULL)
{
free_NC3INFO(ncp->old);
ncp->old = NULL;
}
fClr(ncp->state, NC_CREAT | NC_INDEF);
return ncio_sync(ncp->nciop);
}
/*
* Compute the expected size of the file.
*/
int
NC_calcsize(const NC3_INFO *ncp, off_t *calcsizep)
{
NC_var **vpp = (NC_var **)ncp->vars.value;
NC_var *last_fix = NULL; /* last "non-record" var */
int numrecvars = 0; /* number of record variables */
if(ncp->vars.nelems == 0) { /* no non-record variables and
no record variables */
*calcsizep = (off_t)ncp->xsz; /* size of header */
return NC_NOERR;
}
if (vpp)
{
NC_var *const *const end = &vpp[ncp->vars.nelems];
for( /*NADA*/; vpp < end; vpp++) {
if(IS_RECVAR(*vpp)) {
numrecvars++;
} else {
last_fix = *vpp;
}
}
}
if(numrecvars == 0) {
off_t varsize;
assert(last_fix != NULL);
varsize = last_fix->len;
if(last_fix->len == X_UINT_MAX) { /* huge last fixed var */
varsize = 1;
for(size_t i = 0; i < last_fix->ndims; i++ ) {
varsize *= (last_fix->shape ? last_fix->shape[i] : 1);
}
}
*calcsizep = last_fix->begin + varsize;
/*last_var = last_fix;*/
} else { /* we have at least one record variable */
*calcsizep = ncp->begin_rec + (off_t)(ncp->numrecs * ncp->recsize);
}
return NC_NOERR;
}
/* Public */
#if 0 /* no longer needed */
int NC3_new_nc(NC3_INFO** ncpp)
{
NC *nc;
NC3_INFO* nc3;
ncp = (NC *) malloc(sizeof(NC));
if(ncp == NULL)
return NC_ENOMEM;
(void) memset(ncp, 0, sizeof(NC));
ncp->xsz = MIN_NC_XSZ;
assert(ncp->xsz == ncx_len_NC(ncp,0));
if(ncpp) *ncpp = ncp;
return NC_NOERR;
}
#endif
/* WARNING: SIGNATURE CHANGE */
int
NC3_create(const char *path, int ioflags, size_t initialsz, int basepe,
size_t *chunksizehintp, void *parameters,
const NC_Dispatch *dispatch, int ncid)
{
int status = NC_NOERR;
void *xp = NULL;
size_t sizeof_off_t = 0;
NC *nc;
NC3_INFO* nc3 = NULL;
/* Find NC struct for this file. */
if ((status = NC_check_id(ncid, &nc)))
return status;
/* Create our specific NC3_INFO instance */
nc3 = new_NC3INFO(chunksizehintp);
#if ALWAYS_NC_SHARE /* DEBUG */
fSet(ioflags, NC_SHARE);
#endif
/*
* Only pe 0 is valid
*/
if(basepe != 0) {
if(nc3) free(nc3);
return NC_EINVAL;
}
assert(nc3->flags == 0);
/* Now we can set min size */
if (fIsSet(ioflags, NC_64BIT_DATA))
nc3->xsz = MIN_NC5_XSZ; /* CDF-5 has minimum 16 extra bytes */
else
nc3->xsz = MIN_NC3_XSZ;
if (fIsSet(ioflags, NC_64BIT_OFFSET)) {
fSet(nc3->flags, NC_64BIT_OFFSET);
sizeof_off_t = 8;
} else if (fIsSet(ioflags, NC_64BIT_DATA)) {
fSet(nc3->flags, NC_64BIT_DATA);
sizeof_off_t = 8;
} else {
sizeof_off_t = 4;
}
assert(nc3->xsz == ncx_len_NC(nc3,sizeof_off_t));
status = ncio_create(path, ioflags, initialsz,
0, nc3->xsz, &nc3->chunk, NULL,
&nc3->nciop, &xp);
if(status != NC_NOERR)
{
/* translate error status */
if(status == EEXIST)
status = NC_EEXIST;
goto unwind_alloc;
}
fSet(nc3->state, NC_CREAT);
if(fIsSet(nc3->nciop->ioflags, NC_SHARE))
{
/*
* NC_SHARE implies sync up the number of records as well.
* (File format version one.)
* Note that other header changes are not shared
* automatically. Some sort of IPC (external to this package)
* would be used to trigger a call to nc_sync().
*/
fSet(nc3->state, NC_NSYNC);
}
status = ncx_put_NC(nc3, &xp, sizeof_off_t, nc3->xsz);
if(status != NC_NOERR)
goto unwind_ioc;
if(chunksizehintp != NULL)
*chunksizehintp = nc3->chunk;
/* Link nc3 and nc */
NC3_DATA_SET(nc,nc3);
nc->int_ncid = nc3->nciop->fd;
return NC_NOERR;
unwind_ioc:
if(nc3 != NULL) {
(void) ncio_close(nc3->nciop, 1); /* N.B.: unlink */
nc3->nciop = NULL;
}
/*FALLTHRU*/
unwind_alloc:
free_NC3INFO(nc3);
if(nc)
NC3_DATA_SET(nc,NULL);
return status;
}
#if 0
/* This function sets a default create flag that will be logically
or'd to whatever flags are passed into nc_create for all future
calls to nc_create.
Valid default create flags are NC_64BIT_OFFSET, NC_CDF5, NC_CLOBBER,
NC_LOCK, NC_SHARE. */
int
nc_set_default_format(int format, int *old_formatp)
{
/* Return existing format if desired. */
if (old_formatp)
*old_formatp = default_create_format;
/* Make sure only valid format is set. */
#ifdef USE_NETCDF4
if (format != NC_FORMAT_CLASSIC && format != NC_FORMAT_64BIT_OFFSET &&
format != NC_FORMAT_NETCDF4 && format != NC_FORMAT_NETCDF4_CLASSIC)
return NC_EINVAL;
#else
if (format != NC_FORMAT_CLASSIC && format != NC_FORMAT_64BIT_OFFSET
#ifdef NETCDF_ENABLE_CDF5
&& format != NC_FORMAT_CDF5
#endif
)
return NC_EINVAL;
#endif
default_create_format = format;
return NC_NOERR;
}
#endif
int
NC3_open(const char *path, int ioflags, int basepe, size_t *chunksizehintp,
void *parameters, const NC_Dispatch *dispatch, int ncid)
{
int status;
NC3_INFO* nc3 = NULL;
NC *nc;
/* Find NC struct for this file. */
if ((status = NC_check_id(ncid, &nc)))
return status;
/* Create our specific NC3_INFO instance */
nc3 = new_NC3INFO(chunksizehintp);
#if ALWAYS_NC_SHARE /* DEBUG */
fSet(ioflags, NC_SHARE);
#endif
/*
* Only pe 0 is valid.
*/
if(basepe != 0) {
if(nc3) {
free(nc3);
nc3 = NULL;
}
status = NC_EINVAL;
goto unwind_alloc;
}
status = ncio_open(path, ioflags, 0, 0, &nc3->chunk, parameters,
&nc3->nciop, NULL);
if(status)
goto unwind_alloc;
assert(nc3->state == 0);
if(fIsSet(nc3->nciop->ioflags, NC_SHARE))
{
/*
* NC_SHARE implies sync up the number of records as well.
* (File format version one.)
* Note that other header changes are not shared
* automatically. Some sort of IPC (external to this package)
* would be used to trigger a call to nc_sync().
*/
fSet(nc3->state, NC_NSYNC);
}
status = nc_get_NC(nc3);
if(status != NC_NOERR)
goto unwind_ioc;
if(chunksizehintp != NULL)
*chunksizehintp = nc3->chunk;
/* Link nc3 and nc */
NC3_DATA_SET(nc,nc3);
nc->int_ncid = nc3->nciop->fd;
return NC_NOERR;
unwind_ioc:
if(nc3) {
(void) ncio_close(nc3->nciop, 0);
nc3->nciop = NULL;
}
/*FALLTHRU*/
unwind_alloc:
free_NC3INFO(nc3);
if(nc)
NC3_DATA_SET(nc,NULL);
return status;
}
int
NC3__enddef(int ncid,
size_t h_minfree, size_t v_align,
size_t v_minfree, size_t r_align)
{
int status;
NC *nc;
NC3_INFO* nc3;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
nc3 = NC3_DATA(nc);
if(!NC_indef(nc3))
return(NC_ENOTINDEFINE);
return (NC_endef(nc3, h_minfree, v_align, v_minfree, r_align));
}
/*
* In data mode, same as ncclose.
* In define mode, restore previous definition.
* In create, remove the file.
*/
int
NC3_abort(int ncid)
{
int status;
NC *nc;
NC3_INFO* nc3;
int doUnlink = 0;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
nc3 = NC3_DATA(nc);
doUnlink = NC_IsNew(nc3);
if(nc3->old != NULL)
{
/* a plain redef, not a create */
assert(!NC_IsNew(nc3));
assert(fIsSet(nc3->state, NC_INDEF));
free_NC3INFO(nc3->old);
nc3->old = NULL;
fClr(nc3->state, NC_INDEF);
}
else if(!NC_readonly(nc3))
{
status = NC_sync(nc3);
if(status != NC_NOERR)
return status;
}
(void) ncio_close(nc3->nciop, doUnlink);
nc3->nciop = NULL;
free_NC3INFO(nc3);
if(nc)
NC3_DATA_SET(nc,NULL);
return NC_NOERR;
}
int
NC3_close(int ncid, void* params)
{
int status = NC_NOERR;
NC *nc;
NC3_INFO* nc3;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
nc3 = NC3_DATA(nc);
if(NC_indef(nc3))
{
status = NC_endef(nc3, 0, 1, 0, 1); /* TODO: defaults */
if(status != NC_NOERR )
{
(void) NC3_abort(ncid);
return status;
}
}
else if(!NC_readonly(nc3))
{
status = NC_sync(nc3);
/* flush buffers before any filesize comparisons */
(void) ncio_sync(nc3->nciop);
}
/*
* If file opened for writing and filesize is less than
* what it should be (due to previous use of NOFILL mode),
* pad it to correct size, as reported by NC_calcsize().
*/
if (status == NC_NOERR) {
off_t filesize; /* current size of open file */
off_t calcsize; /* calculated file size, from header */
status = ncio_filesize(nc3->nciop, &filesize);
if(status != NC_NOERR)
return status;
status = NC_calcsize(nc3, &calcsize);
if(status != NC_NOERR)
return status;
if(filesize < calcsize && !NC_readonly(nc3)) {
status = ncio_pad_length(nc3->nciop, calcsize);
if(status != NC_NOERR)
return status;
}
}
if(params != NULL && (nc->mode & NC_INMEMORY) != 0) {
NC_memio* memio = (NC_memio*)params;
/* Extract the final memory size &/or contents */
status = memio_extract(nc3->nciop,&memio->size,&memio->memory);
}
(void) ncio_close(nc3->nciop, 0);
nc3->nciop = NULL;
free_NC3INFO(nc3);
NC3_DATA_SET(nc,NULL);
return status;
}
int
NC3_redef(int ncid)
{
int status;
NC *nc;
NC3_INFO* nc3;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
nc3 = NC3_DATA(nc);
if(NC_readonly(nc3))
return NC_EPERM;
if(NC_indef(nc3))
return NC_EINDEFINE;
if(fIsSet(nc3->nciop->ioflags, NC_SHARE))
{
/* read in from disk */
status = read_NC(nc3);
if(status != NC_NOERR)
return status;
}
nc3->old = dup_NC3INFO(nc3);
if(nc3->old == NULL)
return NC_ENOMEM;
fSet(nc3->state, NC_INDEF);
return NC_NOERR;
}
int
NC3_inq(int ncid,
int *ndimsp,
int *nvarsp,
int *nattsp,
int *xtendimp)
{
int status;
NC *nc;
NC3_INFO* nc3;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
nc3 = NC3_DATA(nc);
if(ndimsp != NULL)
*ndimsp = (int) nc3->dims.nelems;
if(nvarsp != NULL)
*nvarsp = (int) nc3->vars.nelems;
if(nattsp != NULL)
*nattsp = (int) nc3->attrs.nelems;
if(xtendimp != NULL)
*xtendimp = find_NC_Udim(&nc3->dims, NULL);
return NC_NOERR;
}
int
NC3_inq_unlimdim(int ncid, int *xtendimp)
{
int status;
NC *nc;
NC3_INFO* nc3;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
nc3 = NC3_DATA(nc);
if(xtendimp != NULL)
*xtendimp = find_NC_Udim(&nc3->dims, NULL);
return NC_NOERR;
}
int
NC3_sync(int ncid)
{
int status;
NC *nc;
NC3_INFO* nc3;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
nc3 = NC3_DATA(nc);
if(NC_indef(nc3))
return NC_EINDEFINE;
if(NC_readonly(nc3))
{
return read_NC(nc3);
}
/* else, read/write */
status = NC_sync(nc3);
if(status != NC_NOERR)
return status;
status = ncio_sync(nc3->nciop);
if(status != NC_NOERR)
return status;
#ifdef USE_FSYNC
/* may improve concurrent access, but slows performance if
* called frequently */
#ifndef _WIN32
status = fsync(nc3->nciop->fd);
#else
status = _commit(nc3->nciop->fd);
#endif /* _WIN32 */
#endif /* USE_FSYNC */
return status;
}
int
NC3_set_fill(int ncid,
int fillmode, int *old_mode_ptr)
{
int i, status;
NC *nc;
NC3_INFO* nc3;
int oldmode;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
nc3 = NC3_DATA(nc);
if(NC_readonly(nc3))
return NC_EPERM;
oldmode = fIsSet(nc3->state, NC_NOFILL) ? NC_NOFILL : NC_FILL;
if(fillmode == NC_NOFILL)
{
fSet(nc3->state, NC_NOFILL);
}
else if(fillmode == NC_FILL)
{
if(fIsSet(nc3->state, NC_NOFILL))
{
/*
* We are changing back to fill mode
* so do a sync
*/
status = NC_sync(nc3);
if(status != NC_NOERR)
return status;
}
fClr(nc3->state, NC_NOFILL);
}
else
{
return NC_EINVAL; /* Invalid fillmode */
}
if(old_mode_ptr != NULL)
*old_mode_ptr = oldmode;
/* loop thru all variables to set/overwrite its fill mode */
for (i=0; i<nc3->vars.nelems; i++)
nc3->vars.value[i]->no_fill = (fillmode == NC_NOFILL);
/* once the file's fill mode is set, any new variables defined after
* this call will check NC_dofill(nc3) and set their no_fill accordingly.
* See NC3_def_var() */
return NC_NOERR;
}
/**
* Return the file format.
*
* \param ncid the ID of the open file.
* \param formatp a pointer that gets the format. Ignored if NULL.
*
* \returns NC_NOERR No error.
* \returns NC_EBADID Bad ncid.
* \internal
* \author Ed Hartnett, Dennis Heimbigner
*/
int
NC3_inq_format(int ncid, int *formatp)
{
int status;
NC *nc;
NC3_INFO* nc3;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
nc3 = NC3_DATA(nc);
/* Why even call this function with no format pointer? */
if (!formatp)
return NC_NOERR;
/* only need to check for netCDF-3 variants, since this is never called for netCDF-4 files */
#ifdef NETCDF_ENABLE_CDF5
if (fIsSet(nc3->flags, NC_64BIT_DATA))
*formatp = NC_FORMAT_CDF5;
else
#endif
if (fIsSet(nc3->flags, NC_64BIT_OFFSET))
*formatp = NC_FORMAT_64BIT_OFFSET;
else
*formatp = NC_FORMAT_CLASSIC;
return NC_NOERR;
}
/**
* Return the extended format (i.e. the dispatch model), plus the mode
* associated with an open file.
*
* \param ncid the ID of the open file.
* \param formatp a pointer that gets the extended format. Note that
* this is not the same as the format provided by nc_inq_format(). The
* extended format indicates the dispatch layer model. Classic, 64-bit
* offset, and CDF5 files all have an extended format of
* ::NC_FORMATX_NC3. Ignored if NULL.
* \param modep a pointer that gets the open/create mode associated with
* this file. Ignored if NULL.
*
* \returns NC_NOERR No error.
* \returns NC_EBADID Bad ncid.
* \internal
* \author Dennis Heimbigner
*/
int
NC3_inq_format_extended(int ncid, int *formatp, int *modep)
{
int status;
NC *nc;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR)
return status;
if(formatp) *formatp = NC_FORMATX_NC3;
if(modep) *modep = nc->mode;
return NC_NOERR;
}
/**
* Determine name and size of netCDF type. This netCDF-4 function
* proved so popular that a netCDF-classic version is provided. You're
* welcome.
*
* \param ncid The ID of an open file.
* \param typeid The ID of a netCDF type.
* \param name Pointer that will get the name of the type. Maximum
* size will be NC_MAX_NAME. Ignored if NULL.
* \param size Pointer that will get size of type in bytes. Ignored if
* null.
*
* \returns NC_NOERR No error.
* \returns NC_EBADID Bad ncid.
* \returns NC_EBADTYPE Bad typeid.
* \internal
* \author Ed Hartnett
*/
int
NC3_inq_type(int ncid, nc_type typeid, char *name, size_t *size)
{
NC *ncp;
int stat = NC_check_id(ncid, &ncp);
if (stat != NC_NOERR)
return stat;
if(typeid < NC_BYTE || typeid > NC_STRING)
return NC_EBADTYPE;
/* Give the user the values they want. */
if (name)
strcpy(name, NC_atomictypename(typeid));
if (size)
*size = NC_atomictypelen(typeid);
return NC_NOERR;
}
/**
* This is an obsolete form of nc_delete(), supported for backwards
* compatibility.
*
* @param path Filename to delete.
* @param basepe Must be 0.
*
* @return ::NC_NOERR No error.
* @return ::NC_EIO Couldn't delete file.
* @return ::NC_EINVAL Invaliod basepe. Must be 0.
* @author Glenn Davis, Ed Hartnett
*/
int
nc_delete_mp(const char * path, int basepe)
{
NC *nc;
int status;
int ncid;
status = nc_open(path,NC_NOWRITE,&ncid);
if(status) return status;
status = NC_check_id(ncid,&nc);
if(status) return status;
/*
* Only pe 0 is valid.
*/
if(basepe != 0)
return NC_EINVAL;
(void) nc_close(ncid);
if(unlink(path) == -1) {
return NC_EIO; /* No more specific error code is appropriate */
}
return NC_NOERR;
}
int
nc_delete(const char * path)
{
return nc_delete_mp(path, 0);
}
/*----< NC3_inq_default_fill_value() >---------------------------------------*/
/* copy the default fill value to the memory space pointed by fillp */
int
NC3_inq_default_fill_value(int xtype, void *fillp)
{
if (fillp == NULL) return NC_NOERR;
switch(xtype) {
case NC_CHAR : *(char*)fillp = NC_FILL_CHAR; break;
case NC_BYTE : *(signed char*)fillp = NC_FILL_BYTE; break;
case NC_SHORT : *(short*)fillp = NC_FILL_SHORT; break;
case NC_INT : *(int*)fillp = NC_FILL_INT; break;
case NC_FLOAT : *(float*)fillp = NC_FILL_FLOAT; break;
case NC_DOUBLE : *(double*)fillp = NC_FILL_DOUBLE; break;
case NC_UBYTE : *(unsigned char*)fillp = NC_FILL_UBYTE; break;
case NC_USHORT : *(unsigned short*)fillp = NC_FILL_USHORT; break;
case NC_UINT : *(unsigned int*)fillp = NC_FILL_UINT; break;
case NC_INT64 : *(long long*)fillp = NC_FILL_INT64; break;
case NC_UINT64 : *(unsigned long long*)fillp = NC_FILL_UINT64; break;
default : return NC_EBADTYPE;
}
return NC_NOERR;
}
/*----< NC3_inq_var_fill() >-------------------------------------------------*/
/* inquire the fill value of a variable */
int
NC3_inq_var_fill(const NC_var *varp, void *fill_value)
{
NC_attr **attrpp = NULL;
if (fill_value == NULL) return NC_EINVAL;
/*
* find fill value
*/
attrpp = NC_findattr(&varp->attrs, NC_FillValue);
if ( attrpp != NULL ) {
const void *xp;
/* User defined fill value */
if ( (*attrpp)->type != varp->type || (*attrpp)->nelems != 1 )
return NC_EBADTYPE;
xp = (*attrpp)->xvalue;
/* value stored in xvalue is in external representation, may need byte-swap */
switch(varp->type) {
case NC_CHAR: return ncx_getn_text (&xp, 1, (char*)fill_value);
case NC_BYTE: return ncx_getn_schar_schar (&xp, 1, (signed char*)fill_value);
case NC_UBYTE: return ncx_getn_uchar_uchar (&xp, 1, (unsigned char*)fill_value);
case NC_SHORT: return ncx_getn_short_short (&xp, 1, (short*)fill_value);
case NC_USHORT: return ncx_getn_ushort_ushort (&xp, 1, (unsigned short*)fill_value);
case NC_INT: return ncx_getn_int_int (&xp, 1, (int*)fill_value);
case NC_UINT: return ncx_getn_uint_uint (&xp, 1, (unsigned int*)fill_value);
case NC_FLOAT: return ncx_getn_float_float (&xp, 1, (float*)fill_value);
case NC_DOUBLE: return ncx_getn_double_double (&xp, 1, (double*)fill_value);
case NC_INT64: return ncx_getn_longlong_longlong (&xp, 1, (long long*)fill_value);
case NC_UINT64: return ncx_getn_ulonglong_ulonglong(&xp, 1, (unsigned long long*)fill_value);
default: return NC_EBADTYPE;
}
}
else {
/* use the default */
switch(varp->type){
case NC_CHAR: *(char *)fill_value = NC_FILL_CHAR;
break;
case NC_BYTE: *(signed char *)fill_value = NC_FILL_BYTE;
break;
case NC_SHORT: *(short *)fill_value = NC_FILL_SHORT;
break;
case NC_INT: *(int *)fill_value = NC_FILL_INT;
break;
case NC_UBYTE: *(unsigned char *)fill_value = NC_FILL_UBYTE;
break;
case NC_USHORT: *(unsigned short *)fill_value = NC_FILL_USHORT;
break;
case NC_UINT: *(unsigned int *)fill_value = NC_FILL_UINT;
break;
case NC_INT64: *(long long *)fill_value = NC_FILL_INT64;
break;
case NC_UINT64: *(unsigned long long *)fill_value = NC_FILL_UINT64;
break;
case NC_FLOAT: *(float *)fill_value = NC_FILL_FLOAT;
break;
case NC_DOUBLE: *(double *)fill_value = NC_FILL_DOUBLE;
break;
default:
return NC_EINVAL;
}
}
return NC_NOERR;
}
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