mirror of
https://github.com/Unidata/netcdf-c.git
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fb40a72b45
re: Issue https://github.com/Unidata/netcdf-c/issues/2685 re: PR https://github.com/Unidata/netcdf-c/pull/2179 As noted in PR https://github.com/Unidata/netcdf-c/pull/2179, the old code did not allow for reclaiming instances of types, nor for properly copying them. That PR provided new functions capable of reclaiming/copying instances of arbitrary types. However, as noted by Issue https://github.com/Unidata/netcdf-c/issues/2685, using these most general functions resulted in a significant performance degradation, even for common cases. This PR attempts to mitigate the cost of using the general reclaim/copy functions in two ways. First, the previous functions operating at the top level by using ncid and typeid arguments. These functions were augmented with equivalent versions that used the netcdf-c library internal data structures to allow direct access to needed information. These new functions are used internally to the library. The second mitigation involves optimizing the internal functions by providing early tests for common cases. This avoids unnecessary recursive function calls. The overall result is a significant improvement in speed by a factor of roughly twenty -- your mileage may vary. These optimized functions are still not as fast as the original (more limited) functions, but they are getting close. Additional optimizations are possible. But the cost is a significant "uglification" of the code that I deemed a step too far, at least for now. ## Misc. Changes 1. Added a test case to check the proper reclamation/copy of complex types. 2. Found and fixed some places where nc_reclaim/copy should have been used. 3. Replaced, in the netcdf-c library, (almost all) occurrences of nc_reclaim_copy with calls to NC_reclaim/copy. This plus the optimizations is the primary speed-up mechanism. 4. In DAP4, the metadata is held in a substrate in-memory file; this required some changes so that the reclaim/copy code accessed that substrate dispatcher rather than the DAP4 dispatcher. 5. Re-factored and isolated the code that computes if a type is (transitively) variable-sized or not. 6. Clean up the reclamation code in ncgen; adding the use of nc_reclaim exposed some memory problems.
346 lines
9.1 KiB
C
346 lines
9.1 KiB
C
/*********************************************************************
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* Copyright 2018, UCAR/Unidata
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
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*********************************************************************/
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/**
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Test the various type walker functions:
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nc_reclaim_data => NC_reclaim_data
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nc_reclaim_data_all => NC_reclaim_data_all => NC_reclaim_data
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nc_copy_data => NC_copy_data
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nc_copy_data_all => NC_copy_data_all => NC_copy_data
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nc_dump_data => NC_dump_data
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See the file "reclaim_tests.cdl" to see the input file semantics.
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*/
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#include "config.h"
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#include <stdlib.h>
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#include <stdio.h>
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#include <string.h>
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#include <assert.h>
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#include "netcdf.h"
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#include "netcdf_aux.h"
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#define NCCATCH
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#include "nclog.h"
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#ifdef HAVE_GETOPT_H
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#include <getopt.h>
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#endif
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#if defined(_WIN32) && !defined(__MINGW32__)
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#include "XGetopt.h"
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#endif
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#define DEBUG
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#define FILE "reclaim_tests.nc"
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#define MAXOBJECTS 1024
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struct Options {
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int debug;
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} dumpoptions;
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struct Type {
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char name[NC_MAX_NAME];
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int tid;
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size_t size;
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};
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struct Dim {
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char name[NC_MAX_NAME];
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int did;
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size_t size;
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};
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struct Var {
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char name[NC_MAX_NAME];
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int vid;
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int tid;
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size_t dimprod;
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void* data;
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};
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struct Metadata {
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int ncid;
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/* type ids */
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struct Type vint_t;
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struct Type vstr_t;
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struct Type vvint_t;
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struct Type vvstr_t;
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struct Type cmpd_atomic_t;
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struct Type cmpd_str_t;
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struct Type cmpd_vlen_t;
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struct Type cmpd_cmpd_t;
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struct Type vcmpd_atomic_t;
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struct Type vcmpd_str_t;
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struct Type vcmpd_vlen_t;
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struct Type vcmpd_cmpd_t;
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/* dim ids */
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struct Dim d1;
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struct Dim d2;
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struct Dim d4;
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/* var ids */
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struct Var intvar;
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struct Var strvar;
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struct Var vintvar;
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struct Var vstrvar;
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struct Var vvintvar;
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struct Var vvstrvar;
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struct Var catomvar;
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struct Var cstrvar;
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struct Var cvlenvar;
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struct Var ccmpdvar;
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struct Var vcatomvar;
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struct Var vcstrvar;
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struct Var vcvlenvar;
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struct Var vccmpdvar;
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} metadata;
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/* atomic Types */
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static struct Type atomics[NC_MAX_ATOMIC_TYPE+1];
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/* Track the metadata objects */
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static struct Type* typemap[MAXOBJECTS];
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static struct Dim* dimmap[MAXOBJECTS];
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static struct Var* varmap[MAXOBJECTS];
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#define CHECK(code) do {stat = check(code,__func__,__LINE__); if(stat) {goto done;}} while(0)
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static int
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check(int code, const char* fcn, int line)
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{
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if(code == NC_NOERR) return code;
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fprintf(stderr,"***fail: (%d) %s @ %s:%d\n",code,nc_strerror(code),fcn,line);
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#ifdef debug
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abort();
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#endif
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exit(1);
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}
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static int
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initialize(void)
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{
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int i,stat = NC_NOERR;
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memset(atomics,0,sizeof(atomics));
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memset(typemap,0,sizeof(typemap));
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memset(dimmap,0,sizeof(dimmap));
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memset(varmap,0,sizeof(varmap));
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for(i=1;i<=NC_MAX_ATOMIC_TYPE;i++) {
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struct Type* t = &atomics[i];
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t->tid = i;
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if((stat=ncaux_inq_any_type(0,i,t->name,&t->size,NULL,NULL,NULL))) return NCTHROW(stat);
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typemap[i] = t;
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}
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return NCTHROW(stat);
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}
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static void
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cleanup(void)
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{
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int i;
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for(i=0;i<MAXOBJECTS;i++) {
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if(varmap[i] == NULL) break;
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if(varmap[i]->data != NULL) free(varmap[i]->data);
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}
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}
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static int
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setuptype(int ncid, const char* name, struct Type* t)
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{
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int stat = NC_NOERR;
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strcpy(t->name,name);
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if((stat=nc_inq_typeid(ncid,name,&t->tid))) return NCTHROW(stat);
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if((stat=ncaux_inq_any_type(ncid,t->tid,NULL,&t->size,NULL,NULL,NULL))) return NCTHROW(stat);
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typemap[t->tid] = t;
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return NCTHROW(stat);
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}
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static int
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setupdim(int ncid, const char* name, struct Dim* dim)
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{
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int stat = NC_NOERR;
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strcpy(dim->name,name);
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if((stat = nc_inq_dimid(ncid,name,&dim->did))) return NCTHROW(stat);
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if((nc_inq_dimlen(ncid,dim->did,&dim->size))) return NCTHROW(stat);
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dimmap[dim->did] = dim;
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return NCTHROW(stat);
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}
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static int
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setupvar(int ncid, const char* name, struct Var* var)
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{
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int stat = NC_NOERR;
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int i,ndims;
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int dimids[NC_MAX_VAR_DIMS];
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size_t product,dimsizes[NC_MAX_VAR_DIMS];
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strcpy(var->name,name);
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if((stat=nc_inq_varid(ncid,name,&var->vid))) return NCTHROW(stat);
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if((stat=nc_inq_vartype(ncid,var->vid,&var->tid))) return NCTHROW(stat);
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if((stat=nc_inq_varndims(ncid,var->vid,&ndims))) return NCTHROW(stat);
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if((stat=nc_inq_vardimid(ncid,var->vid,dimids))) return NCTHROW(stat);
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for(product=1,i=0;i<ndims;i++) {
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if((stat=nc_inq_dimlen(ncid,dimids[i],&dimsizes[i]))) return NCTHROW(stat);
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product *= dimsizes[i];
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}
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var->dimprod = product;
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varmap[var->vid] = var;
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return NCTHROW(stat);
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}
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static void
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setup(struct Metadata* md)
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{
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int stat = NC_NOERR;
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CHECK(nc_open(FILE,NC_NETCDF4,&md->ncid));
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CHECK(setupdim(md->ncid,"d1",&md->d1));
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CHECK(setupdim(md->ncid,"d2",&md->d2));
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CHECK(setupdim(md->ncid,"d4",&md->d4));
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CHECK(setuptype(md->ncid,"vint_t",&md->vint_t));
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CHECK(setuptype(md->ncid,"vstr_t",&md->vstr_t));
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CHECK(setuptype(md->ncid,"vvint_t",&md->vvint_t));
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CHECK(setuptype(md->ncid,"vvstr_t",&md->vvstr_t));
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CHECK(setuptype(md->ncid,"cmpd_atomic_t",&md->cmpd_atomic_t));
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CHECK(setuptype(md->ncid,"cmpd_str_t",&md->cmpd_str_t));
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CHECK(setuptype(md->ncid,"cmpd_vlen_t",&md->cmpd_vlen_t));
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CHECK(setuptype(md->ncid,"cmpd_cmpd_t",&md->cmpd_cmpd_t));
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CHECK(setuptype(md->ncid,"vcmpd_atomic_t",&md->vcmpd_atomic_t));
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CHECK(setuptype(md->ncid,"vcmpd_str_t",&md->vcmpd_str_t));
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CHECK(setuptype(md->ncid,"vcmpd_vlen_t",&md->vcmpd_vlen_t));
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CHECK(setuptype(md->ncid,"vcmpd_cmpd_t",&md->vcmpd_cmpd_t));
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CHECK(setupvar(md->ncid,"intvar",&md->intvar));
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CHECK(setupvar(md->ncid,"strvar",&md->strvar));
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CHECK(setupvar(md->ncid,"vintvar",&md->vintvar));
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CHECK(setupvar(md->ncid,"vstrvar",&md->vstrvar));
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CHECK(setupvar(md->ncid,"vvintvar",&md->vvintvar));
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CHECK(setupvar(md->ncid,"vvstrvar",&md->vvstrvar));
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CHECK(setupvar(md->ncid,"catomvar",&md->catomvar));
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CHECK(setupvar(md->ncid,"cstrvar",&md->cstrvar));
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CHECK(setupvar(md->ncid,"cvlenvar",&md->cvlenvar));
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CHECK(setupvar(md->ncid,"ccmpdvar",&md->ccmpdvar));
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CHECK(setupvar(md->ncid,"vcatomvar",&md->vcatomvar));
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CHECK(setupvar(md->ncid,"vcstrvar",&md->vcstrvar));
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CHECK(setupvar(md->ncid,"vcvlenvar",&md->vcvlenvar));
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CHECK(setupvar(md->ncid,"vccmpdvar",&md->vccmpdvar));
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done:
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assert(stat == NC_NOERR);
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}
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static int
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readvar(int ncid, struct Var* v)
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{
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int stat = NC_NOERR;
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size_t size;
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struct Type* basetype = typemap[v->tid];
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size = (basetype->size * v->dimprod);
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v->data = calloc(1,size);
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if((stat=nc_get_var(ncid,v->vid,v->data)))
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return NCTHROW(stat);
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return NCTHROW(stat);
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}
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static int
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dumpvar(int ncid, struct Var* v, void* data, char** bufp)
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{
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int stat = NC_NOERR;
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if((stat=ncaux_dump_data(ncid,v->tid,data,v->dimprod,bufp))) return NCTHROW(stat);
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return NCTHROW(stat);
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}
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static int
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testvar(int ncid, struct Var* v)
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{
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int stat = NC_NOERR;
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char* buforig = NULL;
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char* bufcopy = NULL;
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void* copy = NULL;
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if((stat=readvar(ncid,v))) return NCTHROW(stat);
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if((stat=dumpvar(ncid,v,v->data,&buforig))) return NCTHROW(stat);
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printf("(o) %s: %s\n",v->name,buforig);
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// Test copying
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if((stat=nc_copy_data_all(ncid,v->tid,v->data,v->dimprod,©))) return NCTHROW(stat);
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// Print copy
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if((stat=dumpvar(ncid,v,copy,&bufcopy))) return NCTHROW(stat);
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printf("(c) %s: %s\n",v->name,bufcopy);
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/* Compare */
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if(strcmp(buforig,bufcopy) != 0)
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fprintf(stderr,"*** orig != copy\n");
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if(buforig) free(buforig);
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if(bufcopy) free(bufcopy);
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// reclaim original
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if((stat=nc_reclaim_data_all(ncid,v->tid,v->data,v->dimprod))) return NCTHROW(stat);
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// reclaim copy
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if((stat=nc_reclaim_data_all(ncid,v->tid,copy,v->dimprod))) return NCTHROW(stat);
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v->data = NULL;
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return NCTHROW(stat);
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}
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static void
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test(struct Metadata* md)
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{
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int stat = NC_NOERR;
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CHECK(testvar(md->ncid,&md->intvar));
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CHECK(testvar(md->ncid,&md->strvar));
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CHECK(testvar(md->ncid,&md->vintvar));
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CHECK(testvar(md->ncid,&md->vstrvar));
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CHECK(testvar(md->ncid,&md->vvintvar));
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CHECK(testvar(md->ncid,&md->vvstrvar));
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CHECK(testvar(md->ncid,&md->catomvar));
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CHECK(testvar(md->ncid,&md->cstrvar));
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CHECK(testvar(md->ncid,&md->cvlenvar));
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CHECK(testvar(md->ncid,&md->ccmpdvar));
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CHECK(testvar(md->ncid,&md->vcatomvar));
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CHECK(testvar(md->ncid,&md->vcstrvar));
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CHECK(testvar(md->ncid,&md->vcvlenvar));
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CHECK(testvar(md->ncid,&md->vccmpdvar));
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done:
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return;
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}
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int
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main(int argc, char** argv)
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{
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int c,stat = NC_NOERR;
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CHECK(nc_initialize());
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CHECK(initialize());
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/* Init options */
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memset((void*)&dumpoptions,0,sizeof(dumpoptions));
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while ((c = getopt(argc, argv, "dhk:tu:")) != EOF) {
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switch(c) {
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case 'd':
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dumpoptions.debug = 1;
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break;
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case '?':
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fprintf(stderr,"unknown option\n");
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stat = NC_EINVAL;
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goto done;
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}
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}
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setup(&metadata);
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test(&metadata);
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done:
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cleanup();
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if(metadata.ncid) nc_close(metadata.ncid);
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(void)nc_finalize();
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exit(stat?1:0);
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}
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