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Replace linked list with array for var storage in netcdf-4 format #328

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merged 7 commits into from
Nov 28, 2016
Merged

Replace linked list with array for var storage in netcdf-4 format #328

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dee1bac
Store vars in array instead of linked list (linked list still active)
gsjaardema Jul 7, 2016
c84b475
Remove var linked list
gsjaardema Jul 7, 2016
8698e57
Compile with c89 -- eliminate init in for-loop
gsjaardema Jul 13, 2016
d16f5a8
Whitespace cleanup
gsjaardema Aug 24, 2016
207a2ee
Fix stdc violation
gsjaardema Aug 25, 2016
a55d96e
Clean-up build after changes -- remove unused variables
gsjaardema Aug 25, 2016
b9c50ae
Create var correctly for hdf4 files
gdsjaar Nov 16, 2016
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13 changes: 9 additions & 4 deletions include/nc4internal.h
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Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,6 @@ typedef struct NC_ATT_INFO
/* This is a struct to handle the var metadata. */
typedef struct NC_VAR_INFO
{
NC_LIST_NODE_T l; /* Use generic doubly-linked list (must be first) */
char *name;
char *hdf5_name; /* used if different from name */
int ndims;
Expand Down Expand Up @@ -262,6 +261,12 @@ typedef struct NC_TYPE_INFO
} u; /* Union of structs, for each type/class */
} NC_TYPE_INFO_T;

typedef struct NC_VAR_ARRAY_T {
size_t nalloc; /* number allocated >= nelems */
size_t nelems; /* length of the array */
NC_VAR_INFO_T **value;
} NC_VAR_ARRAY_T;

/* This holds information for one group. Groups reproduce with
* parthenogenesis. */
typedef struct NC_GRP_INFO
Expand All @@ -273,7 +278,7 @@ typedef struct NC_GRP_INFO
struct NC_HDF5_FILE_INFO *nc4_info;
struct NC_GRP_INFO *parent;
struct NC_GRP_INFO *children;
NC_VAR_INFO_T *var;
NC_VAR_ARRAY_T vars;
NC_DIM_INFO_T *dim;
NC_ATT_INFO_T *att;
NC_TYPE_INFO_T *type;
Expand Down Expand Up @@ -385,8 +390,8 @@ int nc4_type_free(NC_TYPE_INFO_T *type);

/* These list functions add and delete vars, atts. */
int nc4_nc4f_list_add(NC *nc, const char *path, int mode);
int nc4_var_list_add(NC_VAR_INFO_T **list, NC_VAR_INFO_T **var);
int nc4_var_list_del(NC_VAR_INFO_T **list, NC_VAR_INFO_T *var);
int nc4_var_add(NC_VAR_INFO_T **var);
int nc4_var_del(NC_VAR_INFO_T *var);
int nc4_dim_list_add(NC_DIM_INFO_T **list, NC_DIM_INFO_T **dim);
int nc4_dim_list_del(NC_DIM_INFO_T **list, NC_DIM_INFO_T *dim);
int nc4_att_list_add(NC_ATT_INFO_T **list, NC_ATT_INFO_T **att);
Expand Down
46 changes: 18 additions & 28 deletions libsrc4/nc4attr.c
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,6 @@ nc4_get_att(int ncid, NC *nc, int varid, const char *name,
char norm_name[NC_MAX_NAME + 1];
int i;
int retval = NC_NOERR;
const char** sp;

if (attnum) {
my_attnum = *attnum;
Expand Down Expand Up @@ -261,14 +260,12 @@ nc4_put_att(int ncid, NC *nc, int varid, const char *name,
attlist = &grp->att;
else
{
for (var = grp->var; var; var = var->l.next)
if (var->varid == varid)
{
attlist = &var->att;
break;
}
if (!var)
return NC_ENOTVAR;
if (varid < 0 || varid >= grp->vars.nelems)
return NC_ENOTVAR;
var = grp->vars.value[varid];
if (!var) return NC_ENOTVAR;
attlist = &var->att;
assert(var->varid == varid);
}

for (att = *attlist; att; att = att->l.next)
Expand Down Expand Up @@ -364,7 +361,6 @@ nc4_put_att(int ncid, NC *nc, int varid, const char *name,
* attribute). */
if (!strcmp(att->name, _FillValue) && varid != NC_GLOBAL)
{
NC_ATT_INFO_T *varatt;
int size;

/* Fill value must be same type and have exactly one value */
Expand Down Expand Up @@ -666,14 +662,12 @@ NC4_rename_att(int ncid, int varid, const char *name,
}
else
{
for (var = grp->var; var; var = var->l.next)
if (var->varid == varid)
{
list = var->att;
break;
}
if (!var)
return NC_ENOTVAR;
if (varid < 0 || varid >= grp->vars.nelems)
return NC_ENOTVAR;
var = grp->vars.value[varid];
if (!var) return NC_ENOTVAR;
assert(var->varid == varid);
list = var->att;
}
for (att = list; att; att = att->l.next)
if (!strncmp(att->name, norm_newname, NC_MAX_NAME))
Expand Down Expand Up @@ -777,16 +771,12 @@ NC4_del_att(int ncid, int varid, const char *name)
}
else
{
for(var = grp->var; var; var = var->l.next)
{
if (var->varid == varid)
{
attlist = &var->att;
break;
}
}
if (!var)
return NC_ENOTVAR;
if (varid < 0 || varid >= grp->vars.nelems)
return NC_ENOTVAR;
var = grp->vars.value[varid];
if (!var) return NC_ENOTVAR;
attlist = &var->att;
assert(var->varid == varid);
if (var->created)
locid = var->hdf_datasetid;
}
Expand Down
25 changes: 17 additions & 8 deletions libsrc4/nc4file.c
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,9 @@ COPYRIGHT file for copying and redistribution conditions.
#include "nc4internal.h"
#include "nc4dispatch.h"

extern int nc4_vararray_add(NC_GRP_INFO_T *grp,
NC_VAR_INFO_T *var);

/* must be after nc4internal.h */
#include <H5DSpublic.h>
#include <H5Fpublic.h>
Expand Down Expand Up @@ -506,7 +509,6 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe,
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
int res;
NC* nc;

assert(nc_file && path);

Expand Down Expand Up @@ -1534,7 +1536,7 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
LOG((4, "%s: obj_name %s", __func__, obj_name));

/* Add a variable to the end of the group's var list. */
if ((retval = nc4_var_list_add(&grp->var, &var)))
if ((retval = nc4_var_add(&var)))
BAIL(retval);

/* Fill in what we already know. */
Expand Down Expand Up @@ -1810,6 +1812,8 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
} /* endif not HDF5 att */
} /* next attribute */

nc4_vararray_add(grp, var);

/* Is this a deflated variable with a chunksize greater than the
* current cache size? */
if ((retval = nc4_adjust_var_cache(grp, var)))
Expand All @@ -1820,7 +1824,7 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
{
if (incr_id_rc && H5Idec_ref(datasetid) < 0)
BAIL2(NC_EHDFERR);
if (var && nc4_var_list_del(&grp->var, var))
if (var && nc4_var_del(var))
BAIL2(NC_EHDFERR);
}
if (access_pid && H5Pclose(access_pid) < 0)
Expand Down Expand Up @@ -2590,14 +2594,16 @@ nc4_open_hdf4_file(const char *path, int mode, NC *nc)
size_t var_type_size;
int a;

/* Add a variable to the end of the group's var list. */
if ((retval = nc4_var_list_add(&grp->var, &var)))
/* Add a variable. */
if ((retval = nc4_var_add(&var)))
return retval;

var->varid = grp->nvars++;
var->created = NC_TRUE;
var->written_to = NC_TRUE;

nc4_vararray_add(grp, var);

/* Open this dataset in HDF4 file. */
if ((var->sdsid = SDselect(h5->sdid, v)) == FAIL)
return NC_EVARMETA;
Expand Down Expand Up @@ -3205,7 +3211,6 @@ NC4_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp)
NC_GRP_INFO_T *grp;
NC_DIM_INFO_T *dim;
NC_ATT_INFO_T *att;
NC_VAR_INFO_T *var;
int retval;

LOG((2, "%s: ncid 0x%x", __func__, ncid));
Expand All @@ -3225,9 +3230,13 @@ NC4_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp)
}
if (nvarsp)
{
int i;
*nvarsp = 0;
for (var = grp->var; var; var= var->l.next)
(*nvarsp)++;
for (i=0; i < grp->vars.nelems; i++)
{
if (grp->vars.value[i])
(*nvarsp)++;
}
}
if (nattsp)
{
Expand Down
14 changes: 7 additions & 7 deletions libsrc4/nc4grp.c
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Original file line number Diff line number Diff line change
Expand Up @@ -392,6 +392,7 @@ NC4_inq_varids(int ncid, int *nvars, int *varids)
NC_VAR_INFO_T *var;
int v, num_vars = 0;
int retval;
int i;

LOG((2, "nc_inq_varids: ncid 0x%x", ncid));

Expand All @@ -413,14 +414,13 @@ NC4_inq_varids(int ncid, int *nvars, int *varids)
{
/* This is a netCDF-4 group. Round up them doggies and count
* 'em. The list is in correct (i.e. creation) order. */
if (grp->var)
for (i=0; i < grp->vars.nelems; i++)
{
for (var = grp->var; var; var = var->l.next)
{
if (varids)
varids[num_vars] = var->varid;
num_vars++;
}
var = grp->vars.value[i];
if (!var) continue;
if (varids)
varids[num_vars] = var->varid;
num_vars++;
}
}

Expand Down
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