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Applied Wei-keng Liao's patch for fixing bug NCF-234, fixing variable offsets in files created by pnetcdf but rewritten by calling nc_enddef.

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This commit is contained in:
Russ Rew 2013-03-10 01:09:06 +00:00
parent 1ca3153d96
commit 4b89b3c392
2 changed files with 78 additions and 16 deletions
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5
RELEASE_NOTES
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@ -8,6 +8,11 @@ VERSION COMMENTS
------- --------
4.3 Released 201?-??-??
Fixed bug with incorrect fixed-size variable offsets in header
getting written when schema changed for files created
by parallel-netcdf. Thanks to Wei-keng Liao for
developing and contributing the fix. [NCF-234]
fsync: Changed default in autotools config
file; fsync must now be explicitely enabled
instead of explicitely disabled.

89
libsrc/nc3internal.c
View File

@ -138,11 +138,13 @@ NC_begins(NC3_INFO* ncp,
size_t h_minfree, size_t v_align,
size_t v_minfree, size_t r_align)
{
size_t ii;
size_t ii, j;
int sizeof_off_t;
off_t index = 0;
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;
@ -172,9 +174,17 @@ NC_begins(NC3_INFO* ncp,
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++)
{
@ -183,6 +193,8 @@ NC_begins(NC3_INFO* ncp,
/* 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
@ -191,9 +203,31 @@ fprintf(stderr, " VAR %d %s: %ld\n", ii, (*vpp)->name->cp, (long)index);
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;
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 */
@ -206,11 +240,18 @@ fprintf(stderr, " VAR %d %s: %ld\n", ii, (*vpp)->name->cp, (long)index);
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++)
{
@ -228,6 +269,20 @@ fprintf(stderr, " REC %d %s: %ld\n", ii, (*vpp)->name->cp, (long)index);
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
@ -557,7 +612,7 @@ move_recs_r(NC3_INFO *gnu, NC3_INFO *old)
static int
move_vars_r(NC3_INFO *gnu, NC3_INFO *old)
{
int status;
int i, err, status=NC_NOERR;
int varid;
NC_var **gnu_varpp = (NC_var **)gnu->vars.value;
NC_var **old_varpp = (NC_var **)old->vars.value;
@ -582,20 +637,13 @@ move_vars_r(NC3_INFO *gnu, NC3_INFO *old)
gnu_off = gnu_varp->begin;
old_off = old_varp->begin;
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;
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 NC_NOERR;
return status;
}
@ -727,7 +775,16 @@ NC_endef(NC3_INFO *ncp,
/* else if (ncp->begin_var == ncp->old->begin_var) { NOOP } */
}
else
{ /* Even if (ncp->begin_rec == ncp->old->begin_rec)
{
/* 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)