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Fixed bug NCF-211 with nccopy. Minor updates to top-level README.
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Russ Rew
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README
39
README
@ -1,4 +1,4 @@
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Unidata NetCDF
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Unidata NetCDF
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The Unidata network Common Data Form (netCDF) is an interface for
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scientific data access and a freely-distributed software library that
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@ -34,43 +34,36 @@ For more information about netCDF, see the netCDF Web page at
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http://www.unidata.ucar.edu/netcdf/
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You can obtain a copy of the latest released version of netCDF software
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using a WWW browser or anonymous FTP from
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from
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ftp://ftp.unidata.ucar.edu/pub/netcdf/
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http://www.unidata.ucar.edu/downloads/netcdf
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Included in this distribution are: the C source for the netCDF data
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access library, sources for the FORTRAN and C++ interfaces,
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documentation for the netCDF library and utilities in the form of a
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netCDF User's Guide, source for the netCDF utilities ncdump, ncgen,
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and nccopy, and test programs to verify the correct implementation of
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the netCDF library.
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Copyright and licensing information can be found here, as well as in
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the COPYRIGHT file accompanying the software
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Copyright and licensing information can be found in the file
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COPYRIGHT.
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http://www.unidata.ucar.edu/software/netcdf/copyright.html
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To install this package, please see the file INSTALL in the
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distribution, or the (possibly more up-to-date) document:
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http://www.unidata.ucar.edu/netcdf/docs/netcdf-install
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http://www.unidata.ucar.edu/netcdf/docs/building.html
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The netCDF-3 C and FORTRAN-77 interfaces are documented in man(1)
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pages in the distribution in files netcdf.3 and netcdf.3f,
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respectively, or at
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pages at
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http://www.unidata.ucar.edu/software/netcdf/docs
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http://www.unidata.ucar.edu/netcdf/docs/netcdf-man-3.html
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http://www.unidata.ucar.edu/netcdf/docs/netcdf-man-3f.html
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User's Guides for C, FORTRAN, and FORTRAN-90 are also available in
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several forms from the same location.
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User's Guides are also available in several forms from the same
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location.
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A mailing list, netcdfgroup@unidata.ucar.edu, exists for discussion of
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the netCDF interface and announcements about netCDF bugs, fixes, and
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enhancements. For information about how to subscribe, see the URL
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http://www.unidata.ucar.edu/software/netcdf/mailing-lists.html
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An archive of past postings to the netcdfgroup mailing list is available
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for searching from the netCDF home page.
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http://www.unidata.ucar.edu/netcdf/mailing-lists.html
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We appreciate feedback from users of this package. Please send
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comments, suggestions, and bug reports to <support@unidata.ucar.edu>.
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Please identify the version of the package (file VERSION).
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comments, suggestions, and bug reports to
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<support-netcdf@unidata.ucar.edu>. Please identify the version of the
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package (file VERSION).
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140
ncdump/nccopy.c
140
ncdump/nccopy.c
@ -33,7 +33,7 @@ int optind;
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#define COPY_BUFFER_SIZE (5000000)
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#define COPY_CHUNKCACHE_PREEMPTION (1.0f) /* for copying, can eject fully read chunks */
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#define SAME_AS_INPUT (-1) /* default, if kind not specified */
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#define CHUNK_THRESHOLD (1024) /* variables with fewer bytes don't get chunked */
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#define CHUNK_THRESHOLD (8192) /* variables with fewer bytes don't get chunked */
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#ifndef USE_NETCDF4
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#define NC_CLASSIC_MODEL 0x0100 /* Enforce classic model if netCDF-4 not available. */
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@ -49,10 +49,13 @@ static char* option_chunkspec = 0; /* default, no chunk specification */
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static size_t option_copy_buffer_size = COPY_BUFFER_SIZE;
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static size_t option_chunk_cache_size = CHUNK_CACHE_SIZE; /* default from config.h */
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static size_t option_chunk_cache_nelems = CHUNK_CACHE_NELEMS; /* default from config.h */
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static int option_compute_chunkcaches = 0; /* default, don't try still flaky estimate of
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* chunk cache for each variable */
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static int option_read_diskless = 0; /* default, don't read input into memory on open */
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static int option_write_diskless = 0; /* default, don't write output to diskless file */
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static int option_min_chunk_bytes = CHUNK_THRESHOLD; /* default, don't chunk variable if prod of
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* chunksizes of its dimensions is smaller
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* than this */
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static int option_compute_chunkcaches = 0; /* default, don't try still flaky estimate of
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* chunk cache for each variable */
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/* get group id in output corresponding to group igrp in input,
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* given parent group id (or root group id) parid in output. */
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@ -79,6 +82,15 @@ get_grpid(int igrp, int parid, int *ogrpp) {
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return stat;
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}
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/* Return size in bytes of a variable value */
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static size_t
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val_size(int grpid, int varid) {
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nc_type vartype;
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size_t value_size;
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NC_CHECK(nc_inq_vartype(grpid, varid, &vartype));
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NC_CHECK(nc_inq_type(grpid, vartype, NULL, &value_size));
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return value_size;
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}
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#ifdef USE_NETCDF4
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/* Get parent id needed to define a new group from its full name in an
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@ -383,29 +395,31 @@ copy_groups(int iroot, int oroot)
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/* get total number of groups and their ids, including all descendants */
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NC_CHECK(nc_inq_grps_full(iroot, &numgrps, NULL));
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grpids = emalloc(numgrps * sizeof(int));
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NC_CHECK(nc_inq_grps_full(iroot, NULL, grpids));
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/* create corresponding new groups in ogrp, except for root group */
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for(i = 1; i < numgrps; i++) {
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char *grpname_full;
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char grpname[NC_MAX_NAME];
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size_t len_name;
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int ogid, oparid;
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/* get full group name of input group */
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NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, NULL));
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grpname_full = emalloc(len_name + 1);
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NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, grpname_full));
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/* get id of parent group of corresponding group in output.
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* Note that this exists, because nc_inq_groups returned
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* grpids in preorder, so parents are always copied before
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* their subgroups */
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NC_CHECK(nc_inq_parid(oroot, grpname_full, &oparid));
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NC_CHECK(nc_inq_grpname(grpids[i], grpname));
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/* define corresponding group in output */
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NC_CHECK(nc_def_grp(oparid, grpname, &ogid));
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free(grpname_full);
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if(numgrps > 1) { /* there's always 1 root group */
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grpids = emalloc(numgrps * sizeof(int));
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NC_CHECK(nc_inq_grps_full(iroot, NULL, grpids));
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/* create corresponding new groups in ogrp, except for root group */
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for(i = 1; i < numgrps; i++) {
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char *grpname_full;
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char grpname[NC_MAX_NAME];
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size_t len_name;
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int ogid, oparid;
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/* get full group name of input group */
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NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, NULL));
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grpname_full = emalloc(len_name + 1);
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NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, grpname_full));
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/* get id of parent group of corresponding group in output.
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* Note that this exists, because nc_inq_groups returned
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* grpids in preorder, so parents are always copied before
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* their subgroups */
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NC_CHECK(nc_inq_parid(oroot, grpname_full, &oparid));
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NC_CHECK(nc_inq_grpname(grpids[i], grpname));
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/* define corresponding group in output */
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NC_CHECK(nc_def_grp(oparid, grpname, &ogid));
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free(grpname_full);
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}
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free(grpids);
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}
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free(grpids);
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return stat;
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}
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@ -463,27 +477,36 @@ copy_var_specials(int igrp, int varid, int ogrp, int o_varid)
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NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
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if (ndims > 0) { /* no chunking for scalar variables */
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int contig = 0;
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NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, NULL));
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if(contig == 1) {
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size_t *chunkp = (size_t *) emalloc(ndims * sizeof(size_t));
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int *dimids = (int *) emalloc(ndims * sizeof(int));
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int idim;
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/* size of a chunk: product of dimension chunksizes and size of value */
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size_t csprod = val_size(ogrp, o_varid);
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int is_unlimited = 0;
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NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, chunkp));
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NC_CHECK(nc_inq_vardimid(igrp, varid, dimids));
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for(idim = 0; idim < ndims; idim++) {
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int idimid = dimids[idim];
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int odimid = dimmap_odimid(idimid);
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size_t chunksize = chunkspec_size(idimid);
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if(chunksize > 0) { /* found in chunkspec */
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chunkp[idim] = chunksize;
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}
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csprod *= chunkp[idim];
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if(dimmap_ounlim(odimid))
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is_unlimited = 1;
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}
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/* Explicitly set chunking, even if default */
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/* If product of chunksizes is too small and no unlimited
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* dimensions used, don't chunk */
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if ((csprod < option_min_chunk_bytes && !is_unlimited) || contig == 1) {
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NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CONTIGUOUS, NULL));
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} else {
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size_t *chunkp = (size_t *) emalloc(ndims * sizeof(size_t));
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int *dimids = (int *) emalloc(ndims * sizeof(int));
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int idim;
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NC_CHECK(nc_inq_var_chunking(igrp, varid, NULL, chunkp));
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NC_CHECK(nc_inq_vardimid(igrp, varid, dimids));
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for(idim = 0; idim < ndims; idim++) {
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int dimid = dimids[idim];
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size_t chunksize = chunkspec_size(dimid);
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if(chunkspec_size(dimid) > 0) { /* found in chunkspec */
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chunkp[idim] = chunksize;
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}
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}
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/* explicitly set chunking, even if default */
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NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CHUNKED, chunkp));
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free(dimids);
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free(chunkp);
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}
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free(dimids);
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free(chunkp);
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}
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}
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{ /* handle compression parameters, copying from input, overriding
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@ -904,8 +927,7 @@ copy_var_data(int igrp, int varid, int ogrp) {
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NC_CHECK(nc_inq_varname(igrp, varid, varname));
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NC_CHECK(nc_inq_varid(ogrp, varname, &ovarid));
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NC_CHECK(nc_inq_vartype(igrp, varid, &vartype));
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/* from type, get size in memory needed for each value */
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NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
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value_size = val_size(igrp, varid);
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if(value_size > option_copy_buffer_size) {
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option_copy_buffer_size = value_size;
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do_realloc = 1;
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@ -1035,23 +1057,24 @@ copy_data(int igrp, int ogrp)
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return stat;
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}
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/* Count total number of dimensions in ncid and all its subgroups */
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/* Count total number of dimensions in ncid and all its descendant subgroups */
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int
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count_dims(ncid) {
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int numgrps;
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int *grpids;
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int igrp;
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int ndims=0;
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/* get total number of groups and their ids, including all descendants */
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NC_CHECK(nc_inq_grps_full(ncid, &numgrps, NULL));
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grpids = emalloc(numgrps * sizeof(int));
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NC_CHECK(nc_inq_grps_full(ncid, NULL, grpids));
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for(igrp = 0; igrp < numgrps; igrp++) {
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int ndims_local;
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nc_inq_ndims(grpids[igrp], &ndims_local);
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ndims += ndims_local;
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int ndims;
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NC_CHECK(nc_inq_ndims(ncid, &ndims));
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#ifdef USE_NETCDF4
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NC_CHECK(nc_inq_grps(ncid, &numgrps, NULL));
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if(numgrps > 0) {
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int igrp;
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int *grpids = emalloc(numgrps * sizeof(int));
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NC_CHECK(nc_inq_grps(ncid, &numgrps, grpids));
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for(igrp = 0; igrp < numgrps; igrp++) {
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ndims += count_dims(grpids[igrp]);
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}
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free(grpids);
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}
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free(grpids);
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#endif /* USE_NETCDF4 */
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return ndims;
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}
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@ -1186,8 +1209,7 @@ copy_record_data(int ncid, int ogrp, size_t nrec_vars, int *rec_varids) {
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start[ivar] = (size_t *) emalloc(ndims * sizeof(size_t));
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count[ivar] = (size_t *) emalloc(ndims * sizeof(size_t));
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NC_CHECK(nc_inq_vardimid (ncid, varid, dimids));
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NC_CHECK(nc_inq_vartype(ncid, varid, &vartype));
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NC_CHECK(nc_inq_type(ncid, vartype, NULL, &value_size));
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value_size = val_size(ncid, varid);
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nvals = 1;
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for(ii = 1; ii < ndims; ii++) { /* for rec size, don't include first record dimension */
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size_t dimlen;
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