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netcdf-c/ncdump/nccopy.c

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/*********************************************************************
* Copyright 2010, University Corporation for Atmospheric Research
* See netcdf/README file for copying and redistribution conditions.
* Thanks to Philippe Poilbarbe and Antonio S. Cofiño for
* compression additions.
* $Id: nccopy.c 400 2010-08-27 21:02:52Z russ $
*********************************************************************/
#include "config.h" /* for USE_NETCDF4 macro */
#include <stdlib.h>
#ifdef HAVE_GETOPT_H
#include <getopt.h>
#endif
#ifndef _WIN32
#include <unistd.h>
#endif
#include <string.h>
#include <netcdf.h>
#include "nciter.h"
#include "chunkspec.h"
#include "utils.h"
#include "dimmap.h"
/* default bytes of memory we are willing to allocate for variable
* values during copy */
#define COPY_BUFFER_SIZE (5000000)
#define COPY_CHUNKCACHE_PREEMPTION (1.0f) /* for copying, can eject fully read chunks */
#define SAME_AS_INPUT (-1) /* default, if kind not specified */
#define CHUNK_THRESHOLD (1024) /* variables with fewer bytes don't get chunked */
#ifndef USE_NETCDF4
#define NC_CLASSIC_MODEL 0x0100 /* Enforce classic model if netCDF-4 not available. */
#endif
/* Global variables for command-line requests */
char *progname; /* for error messages */
static int option_kind = SAME_AS_INPUT;
static int option_deflate_level = -1; /* default, compress output only if input compressed */
static int option_shuffle_vars = NC_NOSHUFFLE; /* default, no shuffling on compression */
static int option_fix_unlimdims = 0; /* default, preserve unlimited dimensions */
static char* option_chunkspec = 0; /* default, no chunk specification */
static size_t option_copy_buffer_size = COPY_BUFFER_SIZE;
static size_t option_chunk_cache_size = CHUNK_CACHE_SIZE; /* default from config.h */
static size_t option_chunk_cache_nelems = CHUNK_CACHE_NELEMS; /* default from config.h */
static int option_compute_chunkcaches = 0; /* default, don't try still flaky estimate of
* chunk cache for each variable */
static int option_read_diskless = 0; /* default, don't read input into memory on open */
static int option_write_diskless = 0; /* default, don't write output to diskless file */
/* get group id in output corresponding to group igrp in input,
* given parent group id (or root group id) parid in output. */
static int
get_grpid(int igrp, int parid, int *ogrpp) {
int stat = NC_NOERR;
int ogid = parid; /* like igrp but in output file */
#ifdef USE_NETCDF4
int inparid;
/* if not root group, get corresponding output groupid from group name */
stat = nc_inq_grp_parent(igrp, &inparid);
if(stat == NC_NOERR) { /* not root group */
char grpname[NC_MAX_NAME + 1];
NC_CHECK(nc_inq_grpname(igrp, grpname));
NC_CHECK(nc_inq_grp_ncid(parid, grpname, &ogid));
} else if(stat == NC_ENOGRP) { /* root group */
stat = NC_NOERR;
} else {
NC_CHECK(stat);
}
#endif /* USE_NETCDF4 */
*ogrpp = ogid;
return stat;
}
#ifdef USE_NETCDF4
/* Get parent id needed to define a new group from its full name in an
* open file identified by ncid. Assumes all intermediate groups are
* already defined. */
static int
nc_inq_parid(int ncid, const char *fullname, int *locidp) {
int stat = NC_NOERR;
char *parent = strdup(fullname);
char *slash = "/"; /* groupname separator */
char *last_slash;
if(parent == NULL) {
NC_CHECK(NC_ENOMEM);
} else
last_slash = strrchr(parent, '/');
if(last_slash == parent) { /* parent is root */
free(parent);
parent = strdup(slash);
} else {
*last_slash = '\0'; /* truncate to get parent name */
}
NC_CHECK(nc_inq_grp_full_ncid(ncid, parent, locidp));
free(parent);
return stat;
}
/* Return size of chunk in bytes for a variable varid in a group igrp, or 0 if
* layout is contiguous */
static int
inq_var_chunksize(int igrp, int varid, size_t* chunksizep) {
int stat = NC_NOERR;
int ndims;
size_t *chunksizes;
int dim;
int contig = 1;
nc_type vartype;
size_t value_size;
size_t prod;
NC_CHECK(nc_inq_vartype(igrp, varid, &vartype));
/* from type, get size in memory needed for each value */
NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
prod = value_size;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
chunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
if(ndims > 0) {
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, NULL));
}
if(contig == 1) {
*chunksizep = 0;
} else {
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, chunksizes));
for(dim = 0; dim < ndims; dim++) {
prod *= chunksizes[dim];
}
*chunksizep = prod;
}
free(chunksizes);
return stat;
}
/* Return estimated number of elems required in chunk cache and
* estimated size of chunk cache adequate to efficiently copy input
* variable ivarid to output variable ovarid, which may have different
* chunk size and shape */
static int
inq_var_chunking_params(int igrp, int ivarid, int ogrp, int ovarid,
size_t* chunkcache_sizep,
size_t *chunkcache_nelemsp,
float * chunkcache_preemptionp)
{
int stat = NC_NOERR;
int ndims;
size_t *ichunksizes, *ochunksizes;
int dim;
int icontig = 1, ocontig = 1;
nc_type vartype;
size_t value_size;
size_t prod, iprod, oprod;
size_t nelems;
*chunkcache_nelemsp = CHUNK_CACHE_NELEMS;
*chunkcache_sizep = CHUNK_CACHE_SIZE;
*chunkcache_preemptionp = COPY_CHUNKCACHE_PREEMPTION;
NC_CHECK(nc_inq_varndims(igrp, ivarid, &ndims));
if(ndims > 0) {
NC_CHECK(nc_inq_var_chunking(igrp, ivarid, &icontig, NULL));
NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &ocontig, NULL));
}
if(icontig == 1 && ocontig == 1) { /* no chunking in input or output */
*chunkcache_nelemsp = 0;
*chunkcache_sizep = 0;
*chunkcache_preemptionp = 0;
return stat;
}
NC_CHECK(nc_inq_vartype(igrp, ivarid, &vartype));
NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
iprod = value_size;
if(icontig == 0 && ocontig == 1) { /* chunking only in input */
*chunkcache_nelemsp = 1; /* read one input chunk at a time */
*chunkcache_sizep = iprod;
*chunkcache_preemptionp = 1.0f;
return stat;
}
ichunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
if(icontig == 1) { /* if input contiguous, treat as if chunked on
* first dimension */
ichunksizes[0] = 1;
for(dim = 1; dim < ndims; dim++) {
ichunksizes[dim] = dim;
}
} else {
NC_CHECK(nc_inq_var_chunking(igrp, ivarid, &icontig, ichunksizes));
}
/* now can assume chunking in both input and output */
ochunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &ocontig, ochunksizes));
nelems = 1;
oprod = value_size;
for(dim = 0; dim < ndims; dim++) {
nelems += 1 + (ichunksizes[dim] - 1) / ochunksizes[dim];
iprod *= ichunksizes[dim];
oprod *= ochunksizes[dim];
}
prod = iprod + oprod * (nelems - 1);
*chunkcache_nelemsp = nelems;
*chunkcache_sizep = prod;
free(ichunksizes);
free(ochunksizes);
return stat;
}
/* Forward declaration, because copy_type, copy_vlen_type call each other */
static int copy_type(int igrp, nc_type typeid, int ogrp);
/*
* copy a user-defined variable length type in the group igrp to the
* group ogrp
*/
static int
copy_vlen_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
nc_type ibasetype;
nc_type obasetype; /* base type in target group */
char name[NC_MAX_NAME];
size_t size;
char basename[NC_MAX_NAME];
size_t basesize;
nc_type vlen_type;
NC_CHECK(nc_inq_vlen(igrp, itype, name, &size, &ibasetype));
/* to get base type id in target group, use name of base type in
* source group */
NC_CHECK(nc_inq_type(igrp, ibasetype, basename, &basesize));
stat = nc_inq_typeid(ogrp, basename, &obasetype);
/* if no such type, create it now */
if(stat == NC_EBADTYPE) {
NC_CHECK(copy_type(igrp, ibasetype, ogrp));
stat = nc_inq_typeid(ogrp, basename, &obasetype);
}
NC_CHECK(stat);
/* Now we know base type exists in output and we know its type id */
NC_CHECK(nc_def_vlen(ogrp, name, obasetype, &vlen_type));
return stat;
}
/*
* copy a user-defined opaque type in the group igrp to the group ogrp
*/
static int
copy_opaque_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
nc_type otype;
char name[NC_MAX_NAME];
size_t size;
NC_CHECK(nc_inq_opaque(igrp, itype, name, &size));
NC_CHECK(nc_def_opaque(ogrp, size, name, &otype));
return stat;
}
/*
* copy a user-defined enum type in the group igrp to the group ogrp
*/
static int
copy_enum_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
nc_type otype;
nc_type basetype;
size_t basesize;
size_t nmembers;
char name[NC_MAX_NAME];
int i;
NC_CHECK(nc_inq_enum(igrp, itype, name, &basetype, &basesize, &nmembers));
NC_CHECK(nc_def_enum(ogrp, basetype, name, &otype));
for(i = 0; i < nmembers; i++) { /* insert enum members */
char ename[NC_MAX_NAME];
long long val; /* large enough to hold any integer type */
NC_CHECK(nc_inq_enum_member(igrp, itype, i, ename, &val));
NC_CHECK(nc_insert_enum(ogrp, otype, ename, &val));
}
return stat;
}
/*
* copy a user-defined compound type in the group igrp to the group ogrp
*/
static int
copy_compound_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
char name[NC_MAX_NAME];
size_t size;
size_t nfields;
nc_type otype;
int fid;
NC_CHECK(nc_inq_compound(igrp, itype, name, &size, &nfields));
NC_CHECK(nc_def_compound(ogrp, size, name, &otype));
for (fid = 0; fid < nfields; fid++) {
char fname[NC_MAX_NAME];
char ftypename[NC_MAX_NAME];
size_t foff;
nc_type iftype, oftype;
int fndims;
NC_CHECK(nc_inq_compound_field(igrp, itype, fid, fname, &foff, &iftype, &fndims, NULL));
/* type ids in source don't necessarily correspond to same
* typeids in destination, so look up destination typeid by using
* field type name */
NC_CHECK(nc_inq_type(igrp, iftype, ftypename, NULL));
NC_CHECK(nc_inq_typeid(ogrp, ftypename, &oftype));
if(fndims == 0) {
NC_CHECK(nc_insert_compound(ogrp, otype, fname, foff, oftype));
} else { /* field is array type */
int *fdimsizes;
fdimsizes = (int *) emalloc((fndims + 1) * sizeof(int));
stat = nc_inq_compound_field(igrp, itype, fid, NULL, NULL, NULL,
NULL, fdimsizes);
NC_CHECK(nc_insert_array_compound(ogrp, otype, fname, foff, oftype, fndims, fdimsizes));
free(fdimsizes);
}
}
return stat;
}
/*
* copy a user-defined type in the group igrp to the group ogrp
*/
static int
copy_type(int igrp, nc_type typeid, int ogrp)
{
int stat = NC_NOERR;
nc_type type_class;
NC_CHECK(nc_inq_user_type(igrp, typeid, NULL, NULL, NULL, NULL, &type_class));
switch(type_class) {
case NC_VLEN:
NC_CHECK(copy_vlen_type(igrp, typeid, ogrp));
break;
case NC_OPAQUE:
NC_CHECK(copy_opaque_type(igrp, typeid, ogrp));
break;
case NC_ENUM:
NC_CHECK(copy_enum_type(igrp, typeid, ogrp));
break;
case NC_COMPOUND:
NC_CHECK(copy_compound_type(igrp, typeid, ogrp));
break;
default:
NC_CHECK(NC_EBADTYPE);
}
return stat;
}
/* Copy a group and all its subgroups, recursively, from iroot to
* oroot, the ncids of input file and output file. This just creates
* all the groups in the destination, but doesn't copy anything that's
* in the groups yet. */
static int
copy_groups(int iroot, int oroot)
{
int stat = NC_NOERR;
int numgrps;
int *grpids;
int i;
/* get total number of groups and their ids, including all descendants */
NC_CHECK(nc_inq_grps_full(iroot, &numgrps, NULL));
grpids = emalloc(numgrps * sizeof(int));
NC_CHECK(nc_inq_grps_full(iroot, NULL, grpids));
/* create corresponding new groups in ogrp, except for root group */
for(i = 1; i < numgrps; i++) {
char *grpname_full;
char grpname[NC_MAX_NAME];
size_t len_name;
int ogid, oparid;
/* get full group name of input group */
NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, NULL));
grpname_full = emalloc(len_name + 1);
NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, grpname_full));
/* get id of parent group of corresponding group in output.
* Note that this exists, because nc_inq_groups returned
* grpids in preorder, so parents are always copied before
* their subgroups */
NC_CHECK(nc_inq_parid(oroot, grpname_full, &oparid));
NC_CHECK(nc_inq_grpname(grpids[i], grpname));
/* define corresponding group in output */
NC_CHECK(nc_def_grp(oparid, grpname, &ogid));
free(grpname_full);
}
free(grpids);
return stat;
}
/*
* Copy the user-defined types in this group (igrp) and all its
* subgroups, recursively, to corresponding group in output (ogrp)
*/
static int
copy_types(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ntypes;
nc_type *types = NULL;
int numgrps;
int *grpids = NULL;
int i;
NC_CHECK(nc_inq_typeids(igrp, &ntypes, NULL));
if(ntypes > 0) {
types = (nc_type *) emalloc(ntypes * sizeof(nc_type));
NC_CHECK(nc_inq_typeids(igrp, &ntypes, types));
for (i = 0; i < ntypes; i++) {
NC_CHECK(copy_type(igrp, types[i], ogrp));
}
free(types);
}
/* Copy types from subgroups */
NC_CHECK(nc_inq_grps(igrp, &numgrps, NULL));
if(numgrps > 0) {
grpids = (int *)emalloc(sizeof(int) * numgrps);
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
for(i = 0; i < numgrps; i++) {
int ogid;
/* get groupid in output corresponding to grpids[i] in
* input, given parent group (or root group) ogrp in
* output */
NC_CHECK(get_grpid(grpids[i], ogrp, &ogid));
NC_CHECK(copy_types(grpids[i], ogid));
}
free(grpids);
}
return stat;
}
/* Copy all netCDF-4 specific variable properties such as chunking,
* endianness, deflation, checksumming, fill, etc. */
static int
copy_var_specials(int igrp, int varid, int ogrp, int o_varid)
{
int stat = NC_NOERR;
{ /* handle chunking parameters */
int ndims;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
if (ndims > 0) { /* no chunking for scalar variables */
int contig = 0;
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, NULL));
if(contig == 1) {
NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CONTIGUOUS, NULL));
} else {
size_t *chunkp = (size_t *) emalloc(ndims * sizeof(size_t));
int *dimids = (int *) emalloc(ndims * sizeof(int));
int idim;
NC_CHECK(nc_inq_var_chunking(igrp, varid, NULL, chunkp));
NC_CHECK(nc_inq_vardimid(igrp, varid, dimids));
for(idim = 0; idim < ndims; idim++) {
int dimid = dimids[idim];
size_t chunksize = chunkspec_size(dimid);
if(chunkspec_size(dimid) > 0) { /* found in chunkspec */
chunkp[idim] = chunksize;
}
}
/* explicitly set chunking, even if default */
NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CHUNKED, chunkp));
free(dimids);
free(chunkp);
}
}
}
{ /* handle compression parameters, copying from input, overriding
* with command-line options */
int shuffle, deflate, deflate_level;
NC_CHECK(nc_inq_var_deflate(igrp, varid, &shuffle, &deflate, &deflate_level));
if(option_deflate_level >= 0) { /* change output compression, if requested */
deflate_level = option_deflate_level;
deflate=1;
}
if(shuffle==0 && option_shuffle_vars != 0) {
shuffle = option_shuffle_vars;
}
if(deflate != 0 || shuffle != 0) {
NC_CHECK(nc_def_var_deflate(ogrp, o_varid, shuffle, deflate_level > 0, deflate_level));
}
}
{ /* handle checksum parameters */
int fletcher32 = 0;
NC_CHECK(nc_inq_var_fletcher32(igrp, varid, &fletcher32));
if(fletcher32 != 0) {
NC_CHECK(nc_def_var_fletcher32(ogrp, o_varid, fletcher32));
}
}
{ /* handle endianness */
int endianness = 0;
NC_CHECK(nc_inq_var_endian(igrp, varid, &endianness));
if(endianness != NC_ENDIAN_NATIVE) { /* native is the default */
NC_CHECK(nc_def_var_endian(ogrp, o_varid, endianness));
}
}
return stat;
}
/* Set output variable o_varid (in group ogrp) to use chunking
* specified on command line, only called for classic format input and
* netCDF-4 format output, so no existing chunk lengths to override. */
static int
set_var_chunked(int ogrp, int o_varid)
{
int stat = NC_NOERR;
int ndims;
int odim;
size_t chunk_threshold = CHUNK_THRESHOLD;
if(chunkspec_ndims() == 0) /* no chunking specified on command line */
return stat;
NC_CHECK(nc_inq_varndims(ogrp, o_varid, &ndims));
if (ndims > 0) { /* no chunking for scalar variables */
int chunked = 0;
int *dimids = (int *) emalloc(ndims * sizeof(int));
size_t varsize;
nc_type vartype;
size_t value_size;
int is_unlimited = 0;
NC_CHECK(nc_inq_vardimid (ogrp, o_varid, dimids));
NC_CHECK(nc_inq_vartype(ogrp, o_varid, &vartype));
/* from type, get size in memory needed for each value */
NC_CHECK(nc_inq_type(ogrp, vartype, NULL, &value_size));
varsize = value_size;
/* Determine if this variable should be chunked. A variable
* should be chunked if any of its dims are in command-line
* chunk spec. It will also be chunked if any of its
* dims are unlimited. */
for(odim = 0; odim < ndims; odim++) {
int odimid = dimids[odim];
int idimid = dimmap_idimid(odimid); /* corresponding dimid in input file */
if(dimmap_ounlim(odimid))
is_unlimited = 1;
if(idimid != -1) {
size_t chunksize = chunkspec_size(idimid); /* from chunkspec */
size_t dimlen;
NC_CHECK(nc_inq_dimlen(ogrp, odimid, &dimlen));
if( (chunksize > 0) || dimmap_ounlim(odimid)) {
chunked = 1;
}
varsize *= dimlen;
}
}
/* Don't chunk small variables that don't use an unlimited
* dimension. */
if(varsize < chunk_threshold && !is_unlimited)
chunked = 0;
if(chunked) {
/* Allocate chunksizes and set defaults to dimsize for any
* dimensions not mentioned in chunkspec. */
size_t *chunkp = (size_t *) emalloc(ndims * sizeof(size_t));
for(odim = 0; odim < ndims; odim++) {
int odimid = dimids[odim];
int idimid = dimmap_idimid(odimid);
size_t chunksize = chunkspec_size(idimid);
if(chunksize > 0) {
chunkp[odim] = chunksize;
} else {
NC_CHECK(nc_inq_dimlen(ogrp, odimid, &chunkp[odim]));
}
}
NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CHUNKED, chunkp));
free(chunkp);
}
free(dimids);
}
return stat;
}
/* Set variable to compression specified on command line */
static int
set_var_compressed(int ogrp, int o_varid)
{
int stat = NC_NOERR;
if (option_deflate_level >= 0) {
int deflate = 1;
NC_CHECK(nc_def_var_deflate(ogrp, o_varid, option_shuffle_vars, deflate, option_deflate_level));
}
return stat;
}
/* Release the variable chunk cache allocated for variable varid in
* group grp. This is not necessary, but will save some memory when
* processing one variable at a time. */
#ifdef UNUSED
static int
free_var_chunk_cache(int grp, int varid)
{
int stat = NC_NOERR;
size_t chunk_cache_size = 1;
size_t cache_nelems = 1;
float cache_preemp = 0;
int kind;
NC_CHECK(nc_inq_format(grp, &kind));
if(kind == NC_FORMAT_NETCDF4 || kind == NC_FORMAT_NETCDF4_CLASSIC) {
int contig = 1;
NC_CHECK(nc_inq_var_chunking(grp, varid, &contig, NULL));
if(contig == 0) { /* chunked */
NC_CHECK(nc_set_var_chunk_cache(grp, varid, chunk_cache_size, cache_nelems, cache_preemp));
}
}
return stat;
}
#endif
#endif /* USE_NETCDF4 */
/* Copy dimensions from group igrp to group ogrp, also associate input
* dimids with output dimids (they need not match, because the input
* dimensions may have been defined in a different order than we define
* the output dimensions here. */
static int
copy_dims(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ndims;
int dgrp;
#ifdef USE_NETCDF4
int nunlims;
int *dimids;
int *unlimids;
#else
int unlimid;
#endif /* USE_NETCDF4 */
NC_CHECK(nc_inq_ndims(igrp, &ndims));
#ifdef USE_NETCDF4
/* In netCDF-4 files, dimids may not be sequential because they
* may be defined in various groups, and we are only looking at one
* group at a time. */
/* Find the dimension ids in this group, don't include parents. */
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
NC_CHECK(nc_inq_dimids(igrp, NULL, dimids, 0));
/* Find the number of unlimited dimensions and get their IDs */
NC_CHECK(nc_inq_unlimdims(igrp, &nunlims, NULL));
unlimids = (int *) emalloc((nunlims + 1) * sizeof(int));
NC_CHECK(nc_inq_unlimdims(igrp, NULL, unlimids));
#else
NC_CHECK(nc_inq_unlimdim(igrp, &unlimid));
#endif /* USE_NETCDF4 */
/* Copy each dimension to output, including unlimited dimension(s) */
for (dgrp = 0; dgrp < ndims; dgrp++) {
char name[NC_MAX_NAME];
size_t length;
int i_is_unlim;
int o_is_unlim;
int idimid, odimid;
#ifdef USE_NETCDF4
int uld;
#endif
i_is_unlim = 0;
#ifdef USE_NETCDF4
idimid = dimids[dgrp];
for (uld = 0; uld < nunlims; uld++) {
if(idimid == unlimids[uld]) {
i_is_unlim = 1;
break;
}
}
#else
idimid = dgrp;
if(unlimid != -1 && (idimid == unlimid)) {
i_is_unlim = 1;
}
#endif /* USE_NETCDF4 */
stat = nc_inq_dim(igrp, idimid, name, &length);
if (stat == NC_EDIMSIZE && sizeof(size_t) < 8) {
error("dimension \"%s\" requires 64-bit platform", name);
}
NC_CHECK(stat);
o_is_unlim = i_is_unlim;
if(i_is_unlim && !option_fix_unlimdims) {
NC_CHECK(nc_def_dim(ogrp, name, NC_UNLIMITED, &odimid));
} else {
NC_CHECK(nc_def_dim(ogrp, name, length, &odimid));
o_is_unlim = 0;
}
/* Store (idimid, odimid) mapping for later use, also whether unlimited */
dimmap_store(idimid, odimid, i_is_unlim, o_is_unlim);
}
#ifdef USE_NETCDF4
free(dimids);
free(unlimids);
#endif /* USE_NETCDF4 */
return stat;
}
/* Copy the attributes for variable ivar in group igrp to variable
* ovar in group ogrp. Global (group) attributes are specified by
* using the varid NC_GLOBAL */
static int
copy_atts(int igrp, int ivar, int ogrp, int ovar)
{
int natts;
int iatt;
int stat = NC_NOERR;
NC_CHECK(nc_inq_varnatts(igrp, ivar, &natts));
for(iatt = 0; iatt < natts; iatt++) {
char name[NC_MAX_NAME];
NC_CHECK(nc_inq_attname(igrp, ivar, iatt, name));
NC_CHECK(nc_copy_att(igrp, ivar, name, ogrp, ovar));
}
return stat;
}
/* copy the schema for a single variable in group igrp to group ogrp */
static int
copy_var(int igrp, int varid, int ogrp)
{
int stat = NC_NOERR;
int ndims;
int *idimids; /* ids of dims for input variable */
int *odimids; /* ids of dims for output variable */
char name[NC_MAX_NAME];
nc_type typeid, o_typeid;
int natts;
int i;
int o_varid;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
idimids = (int *) emalloc((ndims + 1) * sizeof(int));
NC_CHECK(nc_inq_var(igrp, varid, name, &typeid, NULL, idimids, &natts));
o_typeid = typeid;
#ifdef USE_NETCDF4
if (typeid > NC_STRING) { /* user-defined type */
/* type ids in source don't necessarily correspond to same
* typeids in destination, so look up destination typeid by
* using type name */
char type_name[NC_MAX_NAME];
NC_CHECK(nc_inq_type(igrp, typeid, type_name, NULL));
NC_CHECK(nc_inq_typeid(ogrp, type_name, &o_typeid));
}
#endif /* USE_NETCDF4 */
/* get the corresponding dimids in the output file */
odimids = (int *) emalloc((ndims + 1) * sizeof(int));
for(i = 0; i < ndims; i++) {
odimids[i] = dimmap_odimid(idimids[i]);
if(odimids[i] == -1) {
error("Oops, no dimension in output associated with input dimid %d", idimids[i]);
}
}
/* define the output variable */
NC_CHECK(nc_def_var(ogrp, name, o_typeid, ndims, odimids, &o_varid));
/* attach the variable attributes to the output variable */
NC_CHECK(copy_atts(igrp, varid, ogrp, o_varid));
#ifdef USE_NETCDF4
{
int inkind;
int outkind;
NC_CHECK(nc_inq_format(igrp, &inkind));
NC_CHECK(nc_inq_format(ogrp, &outkind));
if(outkind == NC_FORMAT_NETCDF4 || outkind == NC_FORMAT_NETCDF4_CLASSIC) {
if((inkind == NC_FORMAT_NETCDF4 || inkind == NC_FORMAT_NETCDF4_CLASSIC)) {
/* Copy all netCDF-4 specific variable properties such as
* chunking, endianness, deflation, checksumming, fill, etc. */
NC_CHECK(copy_var_specials(igrp, varid, ogrp, o_varid));
} else {
/* Set chunking if specified in command line option */
NC_CHECK(set_var_chunked(ogrp, o_varid));
}
/* Set compression if specified in command line option */
NC_CHECK(set_var_compressed(ogrp, o_varid));
}
}
#endif /* USE_NETCDF4 */
free(idimids);
free(odimids);
return stat;
}
/* copy the schema for all the variables in group igrp to group ogrp */
static int
copy_vars(int igrp, int ogrp)
{
int stat = NC_NOERR;
int nvars;
int varid;
NC_CHECK(nc_inq_nvars(igrp, &nvars));
for (varid = 0; varid < nvars; varid++) {
NC_CHECK(copy_var(igrp, varid, ogrp));
}
return stat;
}
/* Copy the schema in a group and all its subgroups, recursively, from
* group igrp in input to parent group ogrp in destination. Use
* dimmap array to map input dimids to output dimids. */
static int
copy_schema(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ogid; /* like igrp but in output file */
/* get groupid in output corresponding to group igrp in input,
* given parent group (or root group) ogrp in output */
NC_CHECK(get_grpid(igrp, ogrp, &ogid));
NC_CHECK(copy_dims(igrp, ogid));
NC_CHECK(copy_atts(igrp, NC_GLOBAL, ogid, NC_GLOBAL));
NC_CHECK(copy_vars(igrp, ogid));
#ifdef USE_NETCDF4
{
int numgrps;
int *grpids;
int i;
/* Copy schema from subgroups */
stat = nc_inq_grps(igrp, &numgrps, NULL);
grpids = (int *)emalloc((numgrps + 1) * sizeof(int));
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
for(i = 0; i < numgrps; i++) {
NC_CHECK(copy_schema(grpids[i], ogid));
}
free(grpids);
}
#endif /* USE_NETCDF4 */
return stat;
}
/* Return number of values for a variable varid in a group igrp */
static int
inq_nvals(int igrp, int varid, long long *nvalsp) {
int stat = NC_NOERR;
int ndims;
int *dimids;
int dim;
long long nvals = 1;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
NC_CHECK(nc_inq_vardimid (igrp, varid, dimids));
for(dim = 0; dim < ndims; dim++) {
size_t len;
NC_CHECK(nc_inq_dimlen(igrp, dimids[dim], &len));
nvals *= len;
}
if(nvalsp)
*nvalsp = nvals;
free(dimids);
return stat;
}
/* Copy data from variable varid in group igrp to corresponding group
* ogrp. */
static int
copy_var_data(int igrp, int varid, int ogrp) {
int stat = NC_NOERR;
nc_type vartype;
long long nvalues; /* number of values for this variable */
size_t ntoget; /* number of values to access this iteration */
size_t value_size; /* size of a single value of this variable */
static void *buf = 0; /* buffer for the variable values */
char varname[NC_MAX_NAME];
int ovarid;
size_t *start;
size_t *count;
nciter_t *iterp; /* opaque structure for iteration status */
int do_realloc = 0;
#ifdef USE_NETCDF4
int okind;
size_t chunksize;
#endif
NC_CHECK(inq_nvals(igrp, varid, &nvalues));
if(nvalues == 0)
return stat;
/* get corresponding output variable */
NC_CHECK(nc_inq_varname(igrp, varid, varname));
NC_CHECK(nc_inq_varid(ogrp, varname, &ovarid));
NC_CHECK(nc_inq_vartype(igrp, varid, &vartype));
/* from type, get size in memory needed for each value */
NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
if(value_size > option_copy_buffer_size) {
option_copy_buffer_size = value_size;
do_realloc = 1;
}
#ifdef USE_NETCDF4
NC_CHECK(nc_inq_format(ogrp, &okind));
if(okind == NC_FORMAT_NETCDF4 || okind == NC_FORMAT_NETCDF4_CLASSIC) {
/* if this variable chunked, set variable chunk cache size */
int contig = 1;
NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &contig, NULL));
if(contig == 0) { /* chunked */
if(option_compute_chunkcaches) {
/* Try to estimate variable-specific chunk cache,
* depending on specific size and shape of this
* variable's chunks. This doesn't work yet. */
size_t chunkcache_size, chunkcache_nelems;
float chunkcache_preemption;
NC_CHECK(inq_var_chunking_params(igrp, varid, ogrp, ovarid,
&chunkcache_size,
&chunkcache_nelems,
&chunkcache_preemption));
NC_CHECK(nc_set_var_chunk_cache(ogrp, ovarid,
chunkcache_size,
chunkcache_nelems,
chunkcache_preemption));
} else {
/* by default, use same chunk cache for all chunked variables */
NC_CHECK(nc_set_var_chunk_cache(ogrp, ovarid,
option_chunk_cache_size,
option_chunk_cache_nelems,
COPY_CHUNKCACHE_PREEMPTION));
}
}
}
/* For chunked variables, option_copy_buffer_size must also be at least as large as
* size of a chunk in input, otherwise resize it. */
{
NC_CHECK(inq_var_chunksize(igrp, varid, &chunksize));
if(chunksize > option_copy_buffer_size) {
option_copy_buffer_size = chunksize;
do_realloc = 1;
}
}
#endif /* USE_NETCDF4 */
if(buf && do_realloc) {
free(buf);
buf = 0;
}
if(buf == 0) { /* first time or needs to grow */
buf = emalloc(option_copy_buffer_size);
memset((void*)buf,0,option_copy_buffer_size);
}
/* initialize variable iteration */
NC_CHECK(nc_get_iter(igrp, varid, option_copy_buffer_size, &iterp));
start = (size_t *) emalloc((iterp->rank + 1) * sizeof(size_t));
count = (size_t *) emalloc((iterp->rank + 1) * sizeof(size_t));
/* nc_next_iter() initializes start and count on first call,
* changes start and count to iterate through whole variable on
* subsequent calls. */
while((ntoget = nc_next_iter(iterp, start, count)) > 0) {
NC_CHECK(nc_get_vara(igrp, varid, start, count, buf));
NC_CHECK(nc_put_vara(ogrp, ovarid, start, count, buf));
#ifdef USE_NETCDF4
/* we have to explicitly free values for strings and vlens */
if(vartype == NC_STRING) {
NC_CHECK(nc_free_string(ntoget, (char **)buf));
} else if(vartype > NC_STRING) { /* user-defined type */
nc_type vclass;
NC_CHECK(nc_inq_user_type(igrp, vartype, NULL, NULL, NULL, NULL, &vclass));
if(vclass == NC_VLEN) {
NC_CHECK(nc_free_vlens(ntoget, (nc_vlen_t *)buf));
}
}
#endif /* USE_NETCDF4 */
} /* end main iteration loop */
#ifdef USE_NETCDF4
/* We're all done with this input and output variable, so if
* either variable is chunked, free up its variable chunk cache */
/* NC_CHECK(free_var_chunk_cache(igrp, varid)); */
/* NC_CHECK(free_var_chunk_cache(ogrp, ovarid)); */
#endif /* USE_NETCDF4 */
free(start);
free(count);
NC_CHECK(nc_free_iter(iterp));
return stat;
}
/* Copy data from variables in group igrp to variables in
* corresponding group with parent ogrp, and all subgroups
* recursively */
static int
copy_data(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ogid;
int nvars;
int varid;
#ifdef USE_NETCDF4
int numgrps;
int *grpids;
int i;
#endif
/* get groupid in output corresponding to group igrp in input,
* given parent group (or root group) ogrp in output */
NC_CHECK(get_grpid(igrp, ogrp, &ogid));
/* Copy data from this group */
NC_CHECK(nc_inq_nvars(igrp, &nvars));
for (varid = 0; varid < nvars; varid++) {
NC_CHECK(copy_var_data(igrp, varid, ogid));
}
#ifdef USE_NETCDF4
/* Copy data from subgroups */
stat = nc_inq_grps(igrp, &numgrps, NULL);
grpids = (int *)emalloc((numgrps + 1) * sizeof(int));
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
for(i = 0; i < numgrps; i++) {
NC_CHECK(copy_data(grpids[i], ogid));
}
free(grpids);
#endif /* USE_NETCDF4 */
return stat;
}
/* Count total number of dimensions in ncid and all its subgroups */
int
count_dims(ncid) {
int numgrps;
int *grpids;
int igrp;
int ndims=0;
/* get total number of groups and their ids, including all descendants */
NC_CHECK(nc_inq_grps_full(ncid, &numgrps, NULL));
grpids = emalloc(numgrps * sizeof(int));
NC_CHECK(nc_inq_grps_full(ncid, NULL, grpids));
for(igrp = 0; igrp < numgrps; igrp++) {
int ndims_local;
nc_inq_ndims(grpids[igrp], &ndims_local);
ndims += ndims_local;
}
free(grpids);
return ndims;
}
/* Test if special case: netCDF-3 file with more than one record
* variable. Performance can be very slow for this case when the disk
* block size is large, there are many record variables, and a
* record's worth of data for some variables is smaller than the disk
* block size. In this case, copying the record variables a variable
* at a time causes much rereading of record data, so instead we want
* to copy data a record at a time. */
static int
nc3_special_case(int ncid, int kind) {
if (kind == NC_FORMAT_CLASSIC || kind == NC_FORMAT_64BIT) {
int recdimid = 0;
NC_CHECK(nc_inq_unlimdim(ncid, &recdimid));
if (recdimid != -1) { /* we have a record dimension */
int nvars;
int varid;
NC_CHECK(nc_inq_nvars(ncid, &nvars));
for (varid = 0; varid < nvars; varid++) {
int *dimids = 0;
int ndims;
NC_CHECK( nc_inq_varndims(ncid, varid, &ndims) );
if (ndims > 0) {
int dimids0;
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_vardimid(ncid, varid, dimids) );
dimids0 = dimids[0];
free(dimids);
if(dimids0 == recdimid) {
return 1; /* found a record variable */
}
}
}
}
}
return 0;
}
/* Classify variables in ncid as either fixed-size variables (with no
* unlimited dimension) or as record variables (with an unlimited
* dimension) */
static int
classify_vars(
int ncid, /* netCDF ID */
size_t *nf, /* for returning number of fixed-size variables */
int **fvars, /* the array of fixed_size variable IDS, caller should free */
size_t *nr, /* for returning number of record variables */
int **rvars) /* the array of record variable IDs, caller should free */
{
int varid;
int nvars;
NC_CHECK(nc_inq_nvars(ncid, &nvars));
*nf = 0;
*fvars = (int *) emalloc(nvars * sizeof(int));
*nr = 0;
*rvars = (int *) emalloc(nvars * sizeof(int));
for (varid = 0; varid < nvars; varid++) {
if (isrecvar(ncid, varid)) {
(*rvars)[*nr] = varid;
(*nr)++;
} else {
(*fvars)[*nf] = varid;
(*nf)++;
}
}
return NC_NOERR;
}
/* Only called for classic format or 64-bit offset format files, to speed up special case */
static int
copy_fixed_size_data(int igrp, int ogrp, size_t nfixed_vars, int *fixed_varids) {
size_t ivar;
/* for each fixed-size variable, copy data */
for (ivar = 0; ivar < nfixed_vars; ivar++) {
int varid = fixed_varids[ivar];
NC_CHECK(copy_var_data(igrp, varid, ogrp));
}
if (fixed_varids)
free(fixed_varids);
return NC_NOERR;
}
/* copy a record's worth of data for a variable from input to output */
static int
copy_rec_var_data(int ncid, /* input */
int ogrp, /* output */
int irec, /* record number */
int varid, /* input variable id */
int ovarid, /* output variable id */
size_t *start, /* start indices for record data */
size_t *count, /* edge lengths for record data */
void *buf /* buffer large enough to hold data */
)
{
NC_CHECK(nc_get_vara(ncid, varid, start, count, buf));
NC_CHECK(nc_put_vara(ogrp, ovarid, start, count, buf));
return NC_NOERR;
}
/* Only called for classic format or 64-bit offset format files, to speed up special case */
static int
copy_record_data(int ncid, int ogrp, size_t nrec_vars, int *rec_varids) {
int unlimid;
size_t nrecs = 0; /* how many records? */
size_t irec;
size_t ivar;
void **buf; /* space for reading in data for each variable */
int *rec_ovarids; /* corresponding varids in output */
size_t **start;
size_t **count;
NC_CHECK(nc_inq_unlimdim(ncid, &unlimid));
NC_CHECK(nc_inq_dimlen(ncid, unlimid, &nrecs));
buf = (void **) emalloc(nrec_vars * sizeof(void *));
rec_ovarids = (int *) emalloc(nrec_vars * sizeof(int));
start = (size_t **) emalloc(nrec_vars * sizeof(size_t*));
count = (size_t **) emalloc(nrec_vars * sizeof(size_t*));
/* get space to hold one record's worth of data for each record variable */
for (ivar = 0; ivar < nrec_vars; ivar++) {
int varid;
int ndims;
int *dimids;
nc_type vartype;
size_t value_size;
int dimid;
int ii;
size_t nvals;
char varname[NC_MAX_NAME];
varid = rec_varids[ivar];
NC_CHECK(nc_inq_varndims(ncid, varid, &ndims));
dimids = (int *) emalloc((1 + ndims) * sizeof(int));
start[ivar] = (size_t *) emalloc(ndims * sizeof(size_t));
count[ivar] = (size_t *) emalloc(ndims * sizeof(size_t));
NC_CHECK(nc_inq_vardimid (ncid, varid, dimids));
NC_CHECK(nc_inq_vartype(ncid, varid, &vartype));
NC_CHECK(nc_inq_type(ncid, vartype, NULL, &value_size));
nvals = 1;
for(ii = 1; ii < ndims; ii++) { /* for rec size, don't include first record dimension */
size_t dimlen;
dimid = dimids[ii];
NC_CHECK(nc_inq_dimlen(ncid, dimid, &dimlen));
nvals *= dimlen;
start[ivar][ii] = 0;
count[ivar][ii] = dimlen;
}
start[ivar][0] = 0;
count[ivar][0] = 1; /* 1 record */
buf[ivar] = (void *) emalloc(nvals * value_size);
NC_CHECK(nc_inq_varname(ncid, varid, varname));
NC_CHECK(nc_inq_varid(ogrp, varname, &rec_ovarids[ivar]));
if(dimids)
free(dimids);
}
/* for each record, copy all variable data */
for(irec = 0; irec < nrecs; irec++) {
for (ivar = 0; ivar < nrec_vars; ivar++) {
int varid, ovarid;
varid = rec_varids[ivar];
ovarid = rec_ovarids[ivar];
start[ivar][0] = irec;
NC_CHECK(copy_rec_var_data(ncid, ogrp, irec, varid, ovarid,
start[ivar], count[ivar], buf[ivar]));
}
}
for (ivar = 0; ivar < nrec_vars; ivar++) {
if(start[ivar])
free(start[ivar]);
if(count[ivar])
free(count[ivar]);
}
if(start)
free(start);
if(count)
free(count);
for (ivar = 0; ivar < nrec_vars; ivar++) {
if(buf[ivar]) {
free(buf[ivar]);
}
}
if (rec_varids)
free(rec_varids);
if(buf)
free(buf);
if(rec_ovarids)
free(rec_ovarids);
return NC_NOERR;
}
/* copy infile to outfile using netCDF API
*/
static int
copy(char* infile, char* outfile)
{
int stat = NC_NOERR;
int igrp, ogrp;
int inkind, outkind;
int open_mode = NC_NOWRITE;
int create_mode = NC_CLOBBER;
size_t ndims;
if(option_read_diskless) {
open_mode |= NC_DISKLESS;
}
NC_CHECK(nc_open(infile, open_mode, &igrp));
NC_CHECK(nc_inq_format(igrp, &inkind));
/* option_kind specifies which netCDF format for output:
* -1 -> same as input,
* 1 -> classic
* 2 -> 64-bit offset
* 3 -> netCDF-4,
* 4 -> netCDF-4 classic model
*
* However, if compression or shuffling was specified and kind was -1,
* kind is changed to format 4 that supports compression for input of
* type 1 or 2.
*/
outkind = option_kind;
if (option_kind == SAME_AS_INPUT) { /* default, kind not specified */
outkind = inkind;
/* Deduce output kind if netCDF-4 features requested */
if (inkind == NC_FORMAT_CLASSIC || inkind == NC_FORMAT_64BIT) {
if (option_deflate_level > 0 ||
option_shuffle_vars == NC_SHUFFLE ||
option_chunkspec)
{
outkind = NC_FORMAT_NETCDF4_CLASSIC;
}
}
}
#ifdef USE_NETCDF4
if(option_chunkspec) {
/* Now that input is open, can parse option_chunkspec into binary
* structure. */
NC_CHECK(chunkspec_parse(igrp, option_chunkspec));
}
#endif /* USE_NETCDF4 */
if(option_write_diskless)
create_mode |= NC_WRITE | NC_DISKLESS; /* NC_WRITE persists diskless file on close */
switch(outkind) {
case NC_FORMAT_CLASSIC:
/* nothing to do */
break;
case NC_FORMAT_64BIT:
create_mode |= NC_64BIT_OFFSET;
break;
#ifdef USE_NETCDF4
case NC_FORMAT_NETCDF4:
create_mode |= NC_NETCDF4;
break;
case NC_FORMAT_NETCDF4_CLASSIC:
create_mode |= NC_NETCDF4 | NC_CLASSIC_MODEL;
break;
#else
case NC_FORMAT_NETCDF4:
case NC_FORMAT_NETCDF4_CLASSIC:
error("nccopy built with --disable-netcdf4, can't create netCDF-4 files");
break;
#endif /* USE_NETCDF4 */
default:
error("bad value (%d) for -k option\n", option_kind);
break;
}
NC_CHECK(nc_create(outfile, create_mode, &ogrp));
NC_CHECK(nc_set_fill(ogrp, NC_NOFILL, NULL));
#ifdef USE_NETCDF4
/* Because types in one group may depend on types in a different
* group, need to create all groups before defining types */
if(inkind == NC_FORMAT_NETCDF4) {
NC_CHECK(copy_groups(igrp, ogrp));
NC_CHECK(copy_types(igrp, ogrp));
}
#endif /* USE_NETCDF4 */
ndims = count_dims(igrp);
NC_CHECK(dimmap_init(ndims));
NC_CHECK(copy_schema(igrp, ogrp));
NC_CHECK(nc_enddef(ogrp));
/* For performance, special case netCDF-3 input or output file with record
* variables, to copy a record-at-a-time instead of a
* variable-at-a-time. */
if(nc3_special_case(igrp, inkind)) {
size_t nfixed_vars, nrec_vars;
int *fixed_varids;
int *rec_varids;
NC_CHECK(classify_vars(igrp, &nfixed_vars, &fixed_varids, &nrec_vars, &rec_varids));
NC_CHECK(copy_fixed_size_data(igrp, ogrp, nfixed_vars, fixed_varids));
NC_CHECK(copy_record_data(igrp, ogrp, nrec_vars, rec_varids));
} else if (nc3_special_case(ogrp, outkind)) {
size_t nfixed_vars, nrec_vars;
int *fixed_varids;
int *rec_varids;
/* classifies output vars, but returns input varids */
NC_CHECK(classify_vars(ogrp, &nfixed_vars, &fixed_varids, &nrec_vars, &rec_varids));
NC_CHECK(copy_fixed_size_data(igrp, ogrp, nfixed_vars, fixed_varids));
NC_CHECK(copy_record_data(igrp, ogrp, nrec_vars, rec_varids));
} else {
NC_CHECK(copy_data(igrp, ogrp)); /* recursive, to handle nested groups */
}
NC_CHECK(nc_close(igrp));
NC_CHECK(nc_close(ogrp));
return stat;
}
static void
usage(void)
{
#define USAGE "\
[-k n] specify kind of netCDF format for output file, default same as input\n\
1 classic, 2 64-bit offset, 3 netCDF-4, 4 netCDF-4 classic model\n\
[-d n] set deflation compression level, default same as input (0=none 9=max)\n\
[-s] add shuffle option to deflation compression\n\
[-c chunkspec] specify chunking for dimensions, e.g. \"dim1/N1,dim2/N2,...\"\n\
[-u] convert unlimited dimensions to fixed-size dimensions in output copy\n\
[-w] write whole output file from diskless netCDF on close\n\
[-m n] set size in bytes of copy buffer, default is 5000000 bytes\n\
[-h n] set size in bytes of chunk_cache for chunked variables\n\
[-e n] set number of elements that chunk_cache can hold\n\
[-r] read whole input file into diskless file on open (classic or 64-bit offset format only)\n\
infile name of netCDF input file\n\
outfile name for netCDF output file\n"
/* Don't document this flaky option until it works better */
/* [-x] use experimental computed estimates for variable-specific chunk caches\n\ */
error("%s [-k n] [-d n] [-s] [-c chunkspec] [-u] [-w] [-m n] [-h n] [-e n] [-r] infile outfile\n%s",
progname, USAGE);
}
/** @page nccopy \b nccopy tool - Copy a netCDF file, optionally changing format, compression, or chunking in the output.
@section SYNOPSIS
\code
nccopy [-k kind] [-d n] [-s] [-u] [-w] [-c chunkspec] [-m bufsize]
[-h chunk_cache] [-e cache_elems] [-r] infile outfile
\endcode
@section DESCRIPTION
The \b nccopy utility copies an input netCDF file in any supported
format variant to an output netCDF file, optionally converting the
output to any compatible netCDF format variant, compressing the data,
or rechunking the data. For example, if built with the netCDF-3
library, a netCDF classic file may be copied to a netCDF 64-bit offset
file, permitting larger variables. If built with the netCDF-4
library, a netCDF classic file may be copied to a netCDF-4 file or to
a netCDF-4 classic model file as well, permitting data compression,
efficient schema changes, larger variable sizes, and use of other
netCDF-4 features.
\b nccopy also serves as an example of a generic netCDF-4 program,
with its ability to read any valid netCDF file and handle nested
groups, strings, and user-defined types, including arbitrarily
nested compound types, variable-length types, and data of any valid
netCDF-4 type.
If DAP support was enabled when \b nccopy was built, the file name may
specify a DAP URL. This may be used to convert data on DAP servers to
local netCDF files.
@section OPTIONS
@par -k \e kind
Specifies the kind of file to be created (that is, the format variant)
and, by inference, the data model (i.e. netcdf-3 (classic) versus
netcdf-4 (enhanced)). The possible arguments are as follows. \n
'1' or 'classic' => netCDF classic format \n
'2', '64-bit-offset', or '64-bit offset' => netCDF 64-bit format \n
'3', 'hdf5', 'netCDF-4', or 'enhanced' => netCDF-4 format (enhanced data model) \n
'4', 'hdf5-nc3', 'netCDF-4 classic model', or 'enhanced-nc3' => netCDF-4 classic model format \n
@par
If no value for -k is specified, then the output will use the same
format as the input, except if the input is classic or 64-bit offset
and either chunking or compression is specified, in which case the
output will be netCDF-4 classic model format. Note that attempting
some kinds of format conversion will result in an error, if the
conversion is not possible. For example, an attempt to copy a
netCDF-4 file that uses features of the enhanced model, such as groups
or variable-length strings, to any of the other kinds of netCDF
formats that use the classic model will result in an error.
@par -d \e n
For netCDF-4 output, including netCDF-4 classic model, specify
deflation level (level of compression) for variable data output. 0
corresponds to no compression and 9 to maximum compression, with
higher levels of compression requiring marginally more time to
compress or uncompress than lower levels. Compression achieved may
also depend on output chunking parameters. If this option is
specified for a classic format or 64-bit offset format input file, it
is not necessary to also specify that the output should be netCDF-4
classic model, as that will be the default. If this option is not
specified and the input file has compressed variables, the compression
will still be preserved in the output, using the same chunking as in
the input by default.
@par
Note that \b nccopy requires all variables to be compressed using the
same compression level, but the API has no such restriction. With a
program you can customize compression for each variable independently.
@par -s
For netCDF-4 output, including netCDF-4 classic model,
specify shuffling of variable data bytes before compression or after
decompression. This option is ignored unless a non-zero deflation
level is specified. Turning shuffling on sometimes improves
compression.
@par -u
Convert any unlimited size dimensions in the input to fixed size
dimensions in the output. This can speed up variable-at-a-time
access, but slow down record-at-a-time access to multiple variables
along an unlimited dimension.
@par -w
Keep output in memory (as a diskless netCDF file) until output is
closed, at which time output file is written to disk. This can
greatly speedup operations such as converting unlimited dimension to
fixed size (-u option), chunking, rechunking, or compressing the
input. It requires that available memory is large enough to hold the
output file. This option may provide a larger speedup than careful
tuning of the -m, -h, or -e options, and it's certainly a lot simpler.
@par -c \e chunkspec
@par
For netCDF-4 output, including netCDF-4 classic model, specify
chunking (multidimensional tiling) for variable data in the output.
This is useful to specify the units of disk access, compression, or
other filters such as checksums. Changing the chunking in a netCDF
file can also greatly speedup access, by choosing chunk shapes that
are appropriate for the most common access patterns.
@par
The chunkspec argument is a string of comma-separated associations,
each specifying a dimension name, a '/' character, and optionally the
corresponding chunk length for that dimension. No blanks should
appear in the chunkspec string, except possibly escaped blanks that
are part of a dimension name. A chunkspec must name at least one
dimension, and may omit dimensions which are not to be chunked or for
which the default chunk length is desired. If a dimension name is
followed by a '/' character but no subsequent chunk length, the actual
dimension length is assumed. If copying a classic model file to a
netCDF-4 output file and not naming all dimensions in the chunkspec,
unnamed dimensions will also use the actual dimension length for the
chunk length. An example of a chunkspec for variables that use
'm' and 'n' dimensions might be 'm/100,n/200' to specify 100 by 200
chunks. To see the chunking resulting from copying with a chunkspec,
use the '-s' option of ncdump on the output file.
@par
Note that \b nccopy requires variables that share a dimension to also
share the chunk size associated with that dimension, but the
programming interface has no such restriction. If you need to
customize chunking for variables independently, you will need to use
the library API in a custom utility program.
@par -m \e bufsize
@par
An integer or floating-point number that specifies the size, in bytes,
of the copy buffer used to copy large variables. A suffix of K, M, G,
or T multiplies the copy buffer size by one thousand, million,
billion, or trillion, respectively. The default is 5 Mbytes,
but will be increased if necessary to hold at least one chunk of
netCDF-4 chunked variables in the input file. You may want to specify
a value larger than the default for copying large files over high
latency networks. Using the '-w' option may provide better
performance, if the output fits in memory.
@par -e \e chunk_cache
@par
For netCDF-4 output, including netCDF-4 classic model, an integer or
floating-point number that specifies the size in bytes of chunk cache
for chunked variables. This is not a property of the file, but merely
a performance tuning parameter for avoiding compressing or
decompressing the same data multiple times while copying and changing
chunk shapes. A suffix of K, M, G, or T multiplies the chunk cache
size by one thousand, million, billion, or trillion, respectively.
The default is 4.194304 Mbytes (or whatever was specified for the
configure-time constant CHUNK_CACHE_SIZE when the netCDF library was
built). Ideally, the \b nccopy utility should accept only one memory
buffer size and divide it optimally between a copy buffer and chunk
cache, but no general algorithm for computing the optimum chunk cache
size has been implemented yet. Using the '-w' option may provide
better performance, if the output fits in memory.
@par -h \e cache_elems
@par
For netCDF-4 output, including netCDF-4 classic model, specifies
number of elements that the chunk cache can hold. This is not a
property of the file, but merely a performance tuning parameter for
avoiding compressing or decompressing the same data multiple times
while copying and changing chunk shapes. The default is 1009 (or
whatever was specified for the configure-time constant
CHUNK_CACHE_NELEMS when the netCDF library was built). Ideally, the
\b nccopy utility should determine an optimum value for this parameter,
but no general algorithm for computing the optimum number of chunk
cache elements has been implemented yet.
@par -r
Read netCDF classic or 64-bit offset input file into a diskless netCDF
file in memory before copying. Requires that input file be small
enough to fit into memory. For \b nccopy, this doesn't seem to provide
any significant speedup, so may not be a useful option.
@section EXAMPLES
@subsection simple_copy Simple Copy
Make a copy of foo1.nc, a netCDF file of any type, to
foo2.nc, a netCDF file of the same type:
\code
nccopy foo1.nc foo2.nc
\endcode
Note that the above copy will not be as fast as use of cp or other
simple copy utility, because the file is copied using only the netCDF
API. If the input file has extra bytes after the end of the netCDF
data, those will not be copied, because they are not accessible
through the netCDF interface. If the original file was generated in
'No fill' mode so that fill values are not stored for padding for data
alignment, the output file may have different padding bytes.
@subsection uncompress Uncompress Data
Convert a netCDF-4 classic model file, compressed.nc, that uses
compression, to a netCDF-3 file classic.nc:
\code
nccopy -k classic compressed.nc classic.nc
\endcode
Note that '1' could be used instead of 'classic'.
@subsection remote_access Remote Access to Data Subset
Download the variable 'time_bnds' and its associated attributes from
an OPeNDAP server and copy the result to a netCDF file named 'tb.nc':
\code
nccopy 'http://test.opendap.org/opendap/data/nc/sst.mnmean.nc.gz?time_bnds' tb.nc
\endcode
Note that URLs that name specific variables as command-line arguments
should generally be quoted, to avoid the shell interpreting special
characters such as '?'.
@subsection compress Compress Data
Compress all the variables in the input file foo.nc, a netCDF file of
any type, to the output file bar.nc:
\code
nccopy -d1 foo.nc bar.nc
\endcode
If foo.nc was a classic or 64-bit offset netCDF file, bar.nc will be a
netCDF-4 classic model netCDF file, because the classic and 64-bit
offset format variants don't support compression. If foo.nc was a
netCDF-4 file with some variables compressed using various deflation
levels, the output will also be a netCDF-4 file of the same type, but
all the variables, including any uncompressed variables in the input,
will now use deflation level 1.
@subsection rechunk Rechunk Data for Faster Access
Assume the input data includes gridded variables that use time, lat,
lon dimensions, with 1000 times by 1000 latitudes by 1000 longitudes,
and that the time dimension varies most slowly. Also assume that
users want quick access to data at all times for a small set of
lat-lon points. Accessing data for 1000 times would typically require
accessing 1000 disk blocks, which may be slow.
Reorganizing the data into chunks on disk that have all the time in
each chunk for a few lat and lon coordinates would greatly speed up
such access. To chunk the data in the input file slow.nc, a netCDF
file of any type, to the output file fast.nc, you could use;
\code
nccopy -c time/1000,lat/40,lon/40 slow.nc fast.nc
\endcode
to specify data chunks of 1000 times, 40 latitudes, and 40 longitudes.
If you had enough memory to contain the output file, you could speed
up the rechunking operation significantly by creating the output in
memory before writing it to disk on close:
\code
nccopy -w -c time/1000,lat/40,lon/40 slow.nc fast.nc
\endcode
@section see_also SEE ALSO
netcdf(3), ncgen(1), netcdf(3)
*/
int
main(int argc, char**argv)
{
char* inputfile = NULL;
char* outputfile = NULL;
int c;
/* table of formats for legal -k values */
struct Kvalues {
char* name;
int kind;
} legalkinds[] = {
{"1", NC_FORMAT_CLASSIC},
{"classic", NC_FORMAT_CLASSIC},
/* The 64-bit offset kind (2) */
{"2", NC_FORMAT_64BIT},
{"64-bit-offset", NC_FORMAT_64BIT},
{"64-bit offset", NC_FORMAT_64BIT},
/* NetCDF-4 HDF5 format */
{"3", NC_FORMAT_NETCDF4},
{"hdf5", NC_FORMAT_NETCDF4},
{"netCDF-4", NC_FORMAT_NETCDF4},
{"netCDF4", NC_FORMAT_NETCDF4},
{"enhanced", NC_FORMAT_NETCDF4},
/* NetCDF-4 HDF5 format, but using only nc3 data model */
{"4", NC_FORMAT_NETCDF4_CLASSIC},
{"hdf5-nc3", NC_FORMAT_NETCDF4_CLASSIC},
{"netCDF-4 classic model", NC_FORMAT_NETCDF4_CLASSIC},
{"netCDF4_classic", NC_FORMAT_NETCDF4_CLASSIC},
{"enhanced-nc3", NC_FORMAT_NETCDF4_CLASSIC},
/* null terminate*/
{NULL,0}
};
opterr = 1;
progname = argv[0];
if (argc <= 1)
{
usage();
}
while ((c = getopt(argc, argv, "k:d:sum:c:h:e:rwx")) != -1) {
switch(c) {
case 'k': /* for specifying variant of netCDF format to be generated
Possible values are:
1 (=> classic 32 bit)
2 (=> classic 64 bit offsets)
3 (=> netCDF-4/HDF5)
4 (=> classic, but stored in netCDF-4/HDF5 format)
Also allow string versions of above
"classic"
"64-bit-offset"
"64-bit offset"
"enhanced" | "hdf5" | "netCDF-4"
"enhanced-nc3" | "hdf5-nc3" | "netCDF-4 classic model"
*/
{
struct Kvalues* kvalue;
char *kind_name = (char *) emalloc(strlen(optarg)+1);
(void)strcpy(kind_name, optarg);
for(kvalue=legalkinds;kvalue->name;kvalue++) {
if(strcmp(kind_name,kvalue->name) == 0) {
option_kind = kvalue->kind;
break;
}
}
if(kvalue->name == NULL) {
error("invalid format: %s", kind_name);
}
}
break;
case 'd': /* non-default compression level specified */
option_deflate_level = strtol(optarg, NULL, 10);
if(option_deflate_level < 0 || option_deflate_level > 9) {
error("invalid deflation level: %d", option_deflate_level);
}
break;
case 's': /* shuffling, may improve compression */
option_shuffle_vars = NC_SHUFFLE;
break;
case 'u': /* convert unlimited dimensions to fixed size */
option_fix_unlimdims = 1;
break;
case 'm': /* non-default size of data copy buffer */
{
double dval;
char *suffix = 0; /* "K" for kilobytes. "M" for megabytes, ... */
dval = strtod(optarg, &suffix);
if(*suffix) {
switch (*suffix) {
case 'k': case 'K':
dval *= 1000;
break;
case 'm': case 'M':
dval *= 1000000;
break;
case 'g': case 'G':
dval *= 1000000000;
break;
case 't': case 'T':
dval *= 1.0e12;
break;
default:
error("If suffix used for '-m' option value, it must be K, M, G, or T: %c",
*suffix);
}
}
option_copy_buffer_size = dval;
break;
}
case 'h': /* non-default size of chunk cache */
{
double dval;
char *suffix = 0; /* "K" for kilobytes, "M" for megabytes, ... */
dval = strtod(optarg, &suffix);
if(*suffix) {
switch (*suffix) {
case 'k': case 'K':
dval *= 1000;
break;
case 'm': case 'M':
dval *= 1000000;
break;
case 'g': case 'G':
dval *= 1000000000;
break;
case 't': case 'T':
dval *= 1.0e12;
break;
default:
error("If suffix used for '-h' option value, it must be K, M, G, or T: %c",
*suffix);
}
}
option_chunk_cache_size = dval;
break;
}
case 'e': /* number of elements chunk cache can hold */
option_chunk_cache_nelems = strtol(optarg, NULL, 10);
if(option_chunk_cache_nelems <= 0) {
error("invalid value for number of chunk cache elements: %d", option_chunk_cache_nelems);
}
break;
case 'r':
option_read_diskless = 1; /* read into memory on open */
break;
case 'w':
option_write_diskless = 1; /* write to memory, persist on close */
break;
case 'x': /* use experimental variable-specific chunk caches */
option_compute_chunkcaches = 1;
break;
case 'c': /* optional chunking spec for each dimension in list */
{
/* save chunkspec string for parsing later, once we know input ncid */
option_chunkspec = strdup(optarg);
break;
}
default:
usage();
}
}
argc -= optind;
argv += optind;
if (argc != 2) {
error("one input file and one output file required");
}
inputfile = argv[0];
outputfile = argv[1];
if(strcmp(inputfile, outputfile) == 0) {
error("output would overwrite input");
}
if(copy(inputfile, outputfile) != NC_NOERR)
exit(1);
return 0;
}
END_OF_MAIN();
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