mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-12-21 08:39:46 +08:00
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.
574 lines
18 KiB
C
574 lines
18 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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* $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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#include "netcdf_filter.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(int ncid, Symbol* asym);
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static int genbin_definevardata(int ncid, 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);
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/* ncid created above is also root group*/
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rootgroup->nc_id = ncid;
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if (nofill_flag) {
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stat = nc_set_fill(ncid, NC_NOFILL, 0);
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CHECK_ERR(stat);
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}
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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);
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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);
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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);
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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(ncid,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(ncid,asym);
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}
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}
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if (nofill_flag) {
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stat = nc_set_fill(ncid, NC_NOFILL, 0);
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CHECK_ERR(stat);
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}
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/* leave define mode */
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stat = nc_enddef(ncid);
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CHECK_ERR(stat);
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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(ncid,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);
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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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|| special->_Storage == NC_COMPACT) {
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stat = nc_def_var_chunking(var->container->nc_id, var->nc_id, special->_Storage, 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);
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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);
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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);
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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);
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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);
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}
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if(special->flags & _FILTER_FLAG) {
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int k;
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for(k=0;k<special->nfilters;k++) {
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NC_H5_Filterspec* nfs = special->_Filters[k];
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/* See if the filter is available */
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stat = nc_inq_filter_avail(var->container->nc_id, nfs->filterid);
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switch (stat) {
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case NC_NOERR: break;
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case NC_ENOFILTER:
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derror("Filter id=%u; filter not available",nfs->filterid);
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/* fall thru */
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default: CHECK_ERR(stat); break;
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}
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stat = nc_def_var_filter(var->container->nc_id,
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var->nc_id,
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nfs->filterid,
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nfs->nparams,
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nfs->params
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);
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}
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CHECK_ERR(stat);
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}
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if(special->flags & (_QUANTIZEBG_FLAG | _QUANTIZEGBR_FLAG | _QUANTIZEBR_FLAG)) {
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stat = nc_def_var_quantize(var->container->nc_id,
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var->nc_id, special->_Quantizer, special->_NSD);
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CHECK_ERR(stat);
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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);
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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 = 0;
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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);
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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);
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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,rootgroup);
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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);
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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);
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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);
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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);
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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(int ncid, 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,rootgroup);
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generate_attrdata(asym,bin_generator,(Writer)genbin_write,databuf);
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stat = nc_reclaim_data(ncid,asym->typ.basetype->nc_id,bbContents(databuf),datalistlen(asym->data));
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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(int ncid, 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,rootgroup);
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generate_vardata(vsym,bin_generator,(Writer)genbin_write,databuf);
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stat = nc_reclaim_data(ncid,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);
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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,
|
|
int rank, size_t* start, size_t* count)
|
|
{
|
|
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(typid)) {
|
|
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);
|
|
} 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);
|
|
} break;
|
|
case NC_SHORT: {
|
|
short* data = (short*)bbContents(databuf);
|
|
stat = nc_put_att_short(grpid,varid,asym->name,typid,len,data);
|
|
CHECK_ERR(stat);
|
|
} break;
|
|
case NC_INT: {
|
|
int* data = (int*)bbContents(databuf);
|
|
stat = nc_put_att_int(grpid,varid,asym->name,typid,len,data);
|
|
CHECK_ERR(stat);
|
|
} break;
|
|
case NC_FLOAT: {
|
|
float* data = (float*)bbContents(databuf);
|
|
stat = nc_put_att_float(grpid,varid,asym->name,typid,len,data);
|
|
CHECK_ERR(stat);
|
|
} break;
|
|
case NC_DOUBLE: {
|
|
double* data = (double*)bbContents(databuf);
|
|
stat = nc_put_att_double(grpid,varid,asym->name,typid,len,data);
|
|
CHECK_ERR(stat);
|
|
} 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);
|
|
} 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);
|
|
} 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);
|
|
} 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);
|
|
} 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);
|
|
} 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);
|
|
#ifdef GENDEBUG
|
|
{
|
|
char out[4096];
|
|
memset(out,0x77,sizeof(out));
|
|
stat = nc_get_att(grpid,varid,asym->name,&out);
|
|
CHECK_ERR(stat);
|
|
}
|
|
#endif
|
|
}
|
|
CHECK_ERR(stat);
|
|
return stat;
|
|
}
|
|
|
|
#endif /*ENABLE_BINARY*/
|