mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-11-27 07:30:33 +08:00
751300ec59
This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
571 lines
19 KiB
C
571 lines
19 KiB
C
/*********************************************************************
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* Copyright 1993, UCAR/Unidata
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
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* $Header: /upc/share/CVS/netcdf-3/ncgen/genbin.c,v 1.4 2010/05/27 21:34:17 dmh Exp $
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*********************************************************************/
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#include "includes.h"
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#include <ctype.h> /* for isprint() */
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#include "netcdf_aux.h"
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#ifdef ENABLE_BINARY
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#undef TRACE
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/* Forward*/
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static int genbin_defineattr(Symbol* asym);
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static int genbin_definevardata(Symbol* vsym);
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static int genbin_write(Generator*,Symbol*,Bytebuffer*,int,size_t*,size_t*);
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static int genbin_writevar(Generator*,Symbol*,Bytebuffer*,int,size_t*,size_t*);
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static int genbin_writeattr(Generator*,Symbol*,Bytebuffer*,int,size_t*,size_t*);
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#ifdef USE_NETCDF4
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static int genbin_deftype(Symbol* tsym);
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static int genbin_definespecialattributes(Symbol* var);
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#endif
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/*
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* Generate C code for creating netCDF from in-memory structure.
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*/
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void
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genbin_netcdf(void)
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{
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int stat, ncid;
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int idim, ivar, iatt;
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int ndims, nvars, natts, ngatts;
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const char* filename = rootgroup->file.filename;
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#ifdef USE_NETCDF4
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int ntyps, ngrps, igrp;
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#endif
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ndims = listlength(dimdefs);
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nvars = listlength(vardefs);
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natts = listlength(attdefs);
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ngatts = listlength(gattdefs);
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#ifdef USE_NETCDF4
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ntyps = listlength(typdefs);
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ngrps = listlength(grpdefs);
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#endif /*USE_NETCDF4*/
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/* Turn on logging */
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#ifdef LOGGING
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nc_set_log_level(ncloglevel);
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#endif
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/* create netCDF file, uses NC_CLOBBER mode */
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cmode_modifier |= NC_CLOBBER;
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#ifdef USE_NETCDF4
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if(!usingclassic)
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cmode_modifier |= NC_NETCDF4;
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#endif
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stat = nc_create(filename, cmode_modifier, &ncid);
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check_err(stat,__LINE__,__FILE__);
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/* ncid created above is also root group*/
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rootgroup->nc_id = ncid;
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#ifdef USE_NETCDF4
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/* Define the group structure */
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/* walking grdefs list will do a preorder walk of all defined groups*/
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for(igrp=0;igrp<ngrps;igrp++) {
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Symbol* gsym = (Symbol*)listget(grpdefs,igrp);
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if(gsym == rootgroup) continue; /* ignore root group*/
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stat = nc_def_grp(gsym->container->nc_id,gsym->name,&gsym->nc_id);
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check_err(stat,__LINE__,__FILE__);
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}
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#endif
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#ifdef USE_NETCDF4
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/* Define the types*/
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if (ntyps > 0) {
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int ityp;
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for(ityp = 0; ityp < ntyps; ityp++) {
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Symbol* tsym = (Symbol*)listget(typdefs,ityp);
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genbin_deftype(tsym);
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}
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}
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#endif
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/* define dimensions from info in dims array */
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if (ndims > 0) {
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for(idim = 0; idim < ndims; idim++) {
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Symbol* dsym = (Symbol*)listget(dimdefs,idim);
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stat = nc_def_dim(dsym->container->nc_id,
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dsym->name,
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(dsym->dim.isunlimited?NC_UNLIMITED:dsym->dim.declsize),
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&dsym->nc_id);
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check_err(stat,__LINE__,__FILE__);
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}
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}
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/* define variables from info in vars array */
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if (nvars > 0) {
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for(ivar = 0; ivar < nvars; ivar++) {
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Symbol* vsym = (Symbol*)listget(vardefs,ivar);
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if (vsym->typ.dimset.ndims > 0) { /* a dimensioned variable */
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/* construct a vector of dimension ids*/
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int dimids[NC_MAX_VAR_DIMS];
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for(idim=0;idim<vsym->typ.dimset.ndims;idim++)
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dimids[idim] = vsym->typ.dimset.dimsyms[idim]->nc_id;
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stat = nc_def_var(vsym->container->nc_id,
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vsym->name,
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vsym->typ.basetype->nc_id,
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vsym->typ.dimset.ndims,
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dimids,
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&vsym->nc_id);
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} else { /* a scalar */
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stat = nc_def_var(vsym->container->nc_id,
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vsym->name,
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vsym->typ.basetype->nc_id,
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vsym->typ.dimset.ndims,
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NULL,
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&vsym->nc_id);
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}
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check_err(stat,__LINE__,__FILE__);
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}
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}
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#ifdef USE_NETCDF4
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/* define special variable properties */
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if(nvars > 0) {
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for(ivar = 0; ivar < nvars; ivar++) {
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Symbol* var = (Symbol*)listget(vardefs,ivar);
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genbin_definespecialattributes(var);
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}
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}
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#endif /*USE_NETCDF4*/
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/* define global attributes */
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if(ngatts > 0) {
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for(iatt = 0; iatt < ngatts; iatt++) {
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Symbol* gasym = (Symbol*)listget(gattdefs,iatt);
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genbin_defineattr(gasym);
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}
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}
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/* define per-variable attributes */
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if(natts > 0) {
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for(iatt = 0; iatt < natts; iatt++) {
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Symbol* asym = (Symbol*)listget(attdefs,iatt);
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genbin_defineattr(asym);
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}
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}
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if (nofill_flag) {
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stat = nc_set_fill(rootgroup->nc_id, NC_NOFILL, 0);
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check_err(stat,__LINE__,__FILE__);
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}
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/* leave define mode */
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stat = nc_enddef(rootgroup->nc_id);
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check_err(stat,__LINE__,__FILE__);
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if(!header_only) {
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/* Load values into those variables with defined data */
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if(nvars > 0) {
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for(ivar = 0; ivar < nvars; ivar++) {
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Symbol* vsym = (Symbol*)listget(vardefs,ivar);
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if(vsym->data != NULL) {
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genbin_definevardata(vsym);
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}
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}
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}
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}
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}
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#ifdef USE_NETCDF4
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#if 0
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Turn off for now.
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static void
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genbin_defineglobalspecials(void)
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{
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int stat = NC_NOERR;
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const char* format = NULL;
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if(usingclassic) return;
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if(!/*Main.*/format_attribute) return;
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/* Watch out, this is a global Attribute */
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format = kind_string(/*Main.*/format_flag);
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stat = nc_put_att_text(rootgroup->nc_id,NC_GLOBAL,"_Format",strlen(format),format);
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check_err(stat,__LINE__,__FILE__);
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}
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#endif /*0*/
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static int
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genbin_definespecialattributes(Symbol* var)
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{
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int stat = NC_NOERR;
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Specialdata* special = var->var.special;
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if(special->flags & _STORAGE_FLAG) {
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if(special->_Storage == NC_CONTIGUOUS) {
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stat = nc_def_var_chunking(var->container->nc_id, var->nc_id, NC_CONTIGUOUS, NULL);
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} else { /* chunked */
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if(special->nchunks == 0 || special->_ChunkSizes == NULL)
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derror("NC_CHUNKED requested, but no chunksizes specified");
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stat = nc_def_var_chunking(var->container->nc_id, var->nc_id, NC_CHUNKED, special->_ChunkSizes);
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}
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check_err(stat,__LINE__,__FILE__);
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}
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if(special->flags & _FLETCHER32_FLAG) {
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stat = nc_def_var_fletcher32(var->container->nc_id,
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var->nc_id,
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special->_Fletcher32);
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check_err(stat,__LINE__,__FILE__);
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}
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if(special->flags & (_DEFLATE_FLAG | _SHUFFLE_FLAG)) {
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stat = nc_def_var_deflate(var->container->nc_id,
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var->nc_id,
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(special->_Shuffle == 1?1:0),
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(special->_DeflateLevel >= 0?1:0),
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(special->_DeflateLevel >= 0?special->_DeflateLevel
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:0));
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check_err(stat,__LINE__,__FILE__);
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}
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if(special->flags & _ENDIAN_FLAG) {
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stat = nc_def_var_endian(var->container->nc_id,
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var->nc_id,
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(special->_Endianness == NC_ENDIAN_LITTLE?
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NC_ENDIAN_LITTLE
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:NC_ENDIAN_BIG));
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check_err(stat,__LINE__,__FILE__);
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}
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if(special->flags & _NOFILL_FLAG) {
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stat = nc_def_var_fill(var->container->nc_id,
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var->nc_id,
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(special->_Fill?NC_FILL:NC_NOFILL),
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NULL);
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check_err(stat,__LINE__,__FILE__);
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}
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if(special->flags & _FILTER_FLAG) {
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/* Special check for alternate way to specify _Deflate */
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if(special->_FilterID == ZIP_ID) {
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unsigned int level;
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if(special->nparams == 0 || special->_FilterParams == NULL)
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level = 9; /* default */
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else
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level = special->_FilterParams[0];
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if(level > 9)
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derror("Illegal deflate level");
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else {
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stat = nc_def_var_deflate(var->container->nc_id,
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var->nc_id,
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(special->_Shuffle == 1?1:0),
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(level > 0?1:0),
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level);
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}
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} else {
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stat = nc_def_var_filter(var->container->nc_id,
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var->nc_id,
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special->_FilterID,
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special->nparams,
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special->_FilterParams
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);
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}
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check_err(stat,__LINE__,__FILE__);
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}
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return stat;
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}
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#endif /*USE_NETCDF4*/
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void
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genbin_close(void)
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{
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int stat;
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stat = nc_close(rootgroup->nc_id);
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check_err(stat,__LINE__,__FILE__);
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}
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#ifdef USE_NETCDF4
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/*
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Generate type definitions
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*/
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static int
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genbin_deftype(Symbol* tsym)
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{
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unsigned long i;
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int stat;
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ASSERT(tsym->objectclass == NC_TYPE);
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switch (tsym->subclass) {
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case NC_PRIM: break; /* these are already taken care of*/
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case NC_OPAQUE:
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stat = nc_def_opaque(tsym->container->nc_id,
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tsym->typ.size,
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tsym->name,
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&tsym->nc_id);
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check_err(stat,__LINE__,__FILE__);
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break;
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case NC_ENUM:
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{
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Bytebuffer* datum;
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stat = nc_def_enum(tsym->container->nc_id,
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tsym->typ.basetype->nc_id,
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tsym->name,
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&tsym->nc_id);
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check_err(stat,__LINE__,__FILE__);
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datum = bbNew();
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for(i=0;i<listlength(tsym->subnodes);i++) {
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Symbol* econst = (Symbol*)listget(tsym->subnodes,i);
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ASSERT(econst->subclass == NC_ECONST);
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generator_reset(bin_generator,NULL);
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bbClear(datum);
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generate_basetype(econst->typ.basetype,econst->typ.econst,datum,NULL,bin_generator);
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stat = nc_insert_enum(tsym->container->nc_id,
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tsym->nc_id,
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econst->name,
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bbContents(datum));
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check_err(stat,__LINE__,__FILE__);
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}
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bbFree(datum);
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}
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break;
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case NC_VLEN:
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stat = nc_def_vlen(tsym->container->nc_id,
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tsym->name,
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tsym->typ.basetype->nc_id,
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&tsym->nc_id);
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check_err(stat,__LINE__,__FILE__);
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break;
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case NC_COMPOUND:
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stat = nc_def_compound(tsym->container->nc_id,
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tsym->typ.size,
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tsym->name,
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&tsym->nc_id);
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check_err(stat,__LINE__,__FILE__);
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for(i=0;i<listlength(tsym->subnodes);i++) {
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Symbol* efield = (Symbol*)listget(tsym->subnodes,i);
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ASSERT(efield->subclass == NC_FIELD);
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if(efield->typ.dimset.ndims == 0){
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stat = nc_insert_compound(
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tsym->container->nc_id,
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tsym->nc_id,
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efield->name,
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efield->typ.offset,
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efield->typ.basetype->nc_id);
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} else {
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int j;
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int dimsizes[NC_MAX_VAR_DIMS]; /* int because inside compound */
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/* Generate the field dimension constants*/
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for(j=0;j<efield->typ.dimset.ndims;j++) {
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unsigned int size = efield->typ.dimset.dimsyms[j]->dim.declsize;
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dimsizes[j] = size;
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}
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stat = nc_insert_array_compound(
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tsym->container->nc_id,
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tsym->nc_id,
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efield->name,
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efield->typ.offset,
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efield->typ.basetype->nc_id,
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efield->typ.dimset.ndims,
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dimsizes);
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}
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check_err(stat,__LINE__,__FILE__);
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}
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break;
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default: panic("definectype: unexpected type subclass");
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}
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return stat;
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}
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#endif /*USE_NETCDF4*/
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static int
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genbin_defineattr(Symbol* asym)
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{
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int stat = NC_NOERR;
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Bytebuffer* databuf = bbNew();
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generator_reset(bin_generator,NULL);
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generate_attrdata(asym,bin_generator,(Writer)genbin_write,databuf);
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if((stat = ncaux_reclaim_data(asym->container->nc_id,asym->typ.basetype->nc_id,bbContents(databuf),datalistlen(asym->data))))
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goto done;
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done:
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bbFree(databuf);
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return stat;
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}
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/* Following is patterned after the walk functions in semantics.c */
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static int
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genbin_definevardata(Symbol* vsym)
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{
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int stat = NC_NOERR;
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Bytebuffer* databuf = NULL;
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if(vsym->data == NULL) goto done;
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databuf = bbNew();
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generator_reset(bin_generator,NULL);
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generate_vardata(vsym,bin_generator,(Writer)genbin_write,databuf);
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ncaux_reclaim_data(vsym->container->nc_id,vsym->typ.basetype->nc_id,bbContents(databuf),datalistlen(vsym->data));
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done:
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bbFree(databuf);
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return stat;
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}
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static int
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genbin_write(Generator* generator, Symbol* sym, Bytebuffer* memory,
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int rank, size_t* start, size_t* count)
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{
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if(sym->objectclass == NC_ATT)
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return genbin_writeattr(generator,sym,memory,rank,start,count);
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else if(sym->objectclass == NC_VAR)
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return genbin_writevar(generator,sym,memory,rank,start,count);
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else
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PANIC("illegal symbol for genbin_write");
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return NC_EINVAL;
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}
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static int
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genbin_writevar(Generator* generator, Symbol* vsym, Bytebuffer* memory,
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int rank, size_t* start, size_t* count)
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{
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int stat = NC_NOERR;
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int i;
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char* data = bbContents(memory);
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size_t nelems;
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/* Compute total number of elements */
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for(nelems=1,i=0;i<rank;i++) nelems *= count[i];
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#ifdef GENDEBUG
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{
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int i;
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fprintf(stderr,"startset = [");
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for(i=0;i<rank;i++)
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fprintf(stderr,"%s%lu",(i>0?", ":""),(unsigned long)start[i]);
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fprintf(stderr,"] ");
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fprintf(stderr,"countset = [");
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for(i=0;i<rank;i++)
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fprintf(stderr,"%s%lu",(i>0?", ":""),(unsigned long)count[i]);
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fprintf(stderr,"]\n");
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fflush(stderr);
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}
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#endif
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if(rank == 0) {
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size_t count[1] = {1};
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stat = nc_put_var1(vsym->container->nc_id, vsym->nc_id, count, data);
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} else {
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stat = nc_put_vara(vsym->container->nc_id, vsym->nc_id, start, count, data);
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}
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check_err(stat,__LINE__,__FILE__);
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// /* Reclaim the data */
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// stat = ncaux_reclaim_data(vsym->container->nc_id, vsym->typ.basetype->nc_id, data, nelems);
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// check_err(stat,__LINE__,__FILE__);
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// bbClear(memory); /* reclaim top-level memory */
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return stat;
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}
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static int
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genbin_writeattr(Generator* generator, Symbol* asym, Bytebuffer* databuf,
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int rank, size_t* start, size_t* count)
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{
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int stat = NC_NOERR;
|
|
size_t len;
|
|
Datalist* list;
|
|
int varid, grpid, typid;
|
|
Symbol* basetype = asym->typ.basetype;
|
|
|
|
grpid = asym->container->nc_id;
|
|
varid = (asym->att.var == NULL?NC_GLOBAL : asym->att.var->nc_id);
|
|
typid = basetype->nc_id;
|
|
|
|
list = asym->data;
|
|
len = list->length;
|
|
|
|
/* Use the specialized put_att_XX routines if possible*/
|
|
if(isprim(basetype->typ.typecode)) {
|
|
switch (basetype->typ.typecode) {
|
|
case NC_BYTE: {
|
|
signed char* data = (signed char*)bbContents(databuf);
|
|
stat = nc_put_att_schar(grpid,varid,asym->name,typid,len,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_CHAR: {
|
|
char* data = (char*)bbContents(databuf);
|
|
size_t slen = bbLength(databuf);
|
|
/* Revise length if slen == 0 */
|
|
if(slen == 0) {
|
|
bbAppend(databuf,'\0');
|
|
/* bbAppend frees the memory pointed to by char* data,
|
|
so re-assign. See Coverity issue: 1265731.*/
|
|
data = (char*)bbContents(databuf);
|
|
slen++;
|
|
}
|
|
stat = nc_put_att_text(grpid,varid,asym->name,slen,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_SHORT: {
|
|
short* data = (short*)bbContents(databuf);
|
|
stat = nc_put_att_short(grpid,varid,asym->name,typid,len,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_INT: {
|
|
int* data = (int*)bbContents(databuf);
|
|
stat = nc_put_att_int(grpid,varid,asym->name,typid,len,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_FLOAT: {
|
|
float* data = (float*)bbContents(databuf);
|
|
stat = nc_put_att_float(grpid,varid,asym->name,typid,len,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_DOUBLE: {
|
|
double* data = (double*)bbContents(databuf);
|
|
stat = nc_put_att_double(grpid,varid,asym->name,typid,len,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_STRING: {
|
|
const char** data;
|
|
data = (const char**)bbContents(databuf);
|
|
stat = nc_put_att_string(grpid,varid,asym->name,
|
|
bbLength(databuf)/sizeof(char*),
|
|
data);
|
|
} break;
|
|
case NC_UBYTE: {
|
|
unsigned char* data = (unsigned char*)bbContents(databuf);
|
|
stat = nc_put_att_uchar(grpid,varid,asym->name,typid,len,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_USHORT: {
|
|
unsigned short* data = (unsigned short*)bbContents(databuf);
|
|
stat = nc_put_att_ushort(grpid,varid,asym->name,typid,len,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_UINT: {
|
|
unsigned int* data = (unsigned int*)bbContents(databuf);
|
|
stat = nc_put_att_uint(grpid,varid,asym->name,typid,len,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_INT64: {
|
|
long long* data = (long long*)bbContents(databuf);
|
|
stat = nc_put_att_longlong(grpid,varid,asym->name,typid,len,data);
|
|
check_err2(stat,asym->lineno,__LINE__,__FILE__);
|
|
} break;
|
|
case NC_UINT64: {
|
|
unsigned long long* data = (unsigned long long*)bbContents(databuf);
|
|
stat = nc_put_att_ulonglong(grpid,varid,asym->name,typid,len,data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
} break;
|
|
default: PANIC1("genbin_defineattr: unexpected basetype: %d",basetype->typ.typecode);
|
|
}
|
|
} else { /* use the generic put_attribute for user defined types*/
|
|
const char* data;
|
|
data = (const char*)bbContents(databuf);
|
|
stat = nc_put_att(grpid,varid,asym->name,typid,
|
|
len,(void*)data);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
#ifdef GENDEBUG
|
|
{
|
|
char out[4096];
|
|
memset(out,0x77,sizeof(out));
|
|
stat = nc_get_att(grpid,varid,asym->name,&out);
|
|
check_err(stat,__LINE__,__FILE__);
|
|
}
|
|
#endif
|
|
}
|
|
return stat;
|
|
}
|
|
|
|
#endif /*ENABLE_BINARY*/
|