netcdf-c/libdap2/cache.c

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/*********************************************************************
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* Copyright 2018, UCAR/Unidata
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
Primary change: add dap4 support Specific changes: 1. Add dap4 code: libdap4 and dap4_test. Note that until the d4ts server problem is solved, dap4 is turned off. 2. Modify various files to support dap4 flags: configure.ac, Makefile.am, CMakeLists.txt, etc. 3. Add nc_test/test_common.sh. This centralizes the handling of the locations of various things in the build tree: e.g. where is ncgen.exe located. See nc_test/test_common.sh for details. 4. Modify .sh files to use test_common.sh 5. Obsolete separate oc2 by moving it to be part of netcdf-c. This means replacing code with netcdf-c equivalents. 5. Add --with-testserver to configure.ac to allow override of the servers to be used for --enable-dap-remote-tests. 6. There were multiple versions of nctypealignment code. Try to centralize in libdispatch/doffset.c and include/ncoffsets.h 7. Add a unit test for the ncuri code because of its complexity. 8. Move the findserver code out of libdispatch and into a separate, self contained program in ncdap_test and dap4_test. 9. Move the dispatch header files (nc{3,4}dispatch.h) to .../include because they are now shared by modules. 10. Revamp the handling of TOPSRCDIR and TOPBUILDDIR for shell scripts. 11. Make use of MREMAP if available 12. Misc. minor changes e.g. - #include <config.h> -> #include "config.h" - Add some no-install headers to /include - extern -> EXTERNL and vice versa as needed - misc header cleanup - clean up checking for misc. unix vs microsoft functions 13. Change copyright decls in some files to point to LICENSE file. 14. Add notes to RELEASENOTES.md
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#include "dapincludes.h"
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#include "dapdump.h"
/*
Grads servers always require a constraint,
which does not necessarily happen during prefetch.
So this flag controls this. By default, it is on.
*/
#define GRADS_PREFETCH
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static int iscacheableconstraint(DCEconstraint* con);
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/* Return 1 if we can reuse cached data to address
the current get_vara request; return 0 otherwise.
Target is in the constrained tree space.
Currently, if the target matches a cache that is not
a whole variable, then match is false.
*/
int
iscached(NCDAPCOMMON* nccomm, CDFnode* target, NCcachenode** cachenodep)
{
int i,j,found,index;
NCcache* cache;
NCcachenode* cachenode;
found = 0;
if(target == NULL) goto done;
/* Match the target variable against the prefetch, if any */
/* Note that prefetches are always whole variable */
cache = nccomm->cdf.cache;
cachenode = cache->prefetch;
if(cachenode!= NULL) {
for(found=0,i=0;i<nclistlength(cachenode->vars);i++) {
CDFnode* var = (CDFnode*)nclistget(cachenode->vars,i);
if(var == target) {
if(cachenodep) *cachenodep = cachenode;
found=1;
goto done;
}
}
}
/*search other cache nodes starting at latest first */
index = 0;
for(i=nclistlength(cache->nodes)-1;i>=0;i--) {
cachenode = (NCcachenode*)nclistget(cache->nodes,i);
/* We currently do not try to match constraints;
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If the cachenode is constrained by more than
simple wholevariable projections, then skip it.
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*/
if(!cachenode->wholevariable) continue;
for(found=0,j=0;j<nclistlength(cachenode->vars);j++) {
CDFnode* var = (CDFnode*)nclistget(cachenode->vars,j);
if(var == target) {found=1;index=i;break;}
}
if(found) break;
}
if(found) {
ASSERT((cachenode != NULL));
if(nclistlength(cache->nodes) > 1) {
/* Manage the cache nodes as LRU */
nclistremove(cache->nodes,index);
nclistpush(cache->nodes,(void*)cachenode);
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}
if(cachenodep) *cachenodep = cachenode;
}
done:
#ifdef DEBUG
fprintf(stderr,"iscached: search: %s\n",makecdfpathstring(target,"."));
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if(found)
fprintf(stderr,"iscached: found: %s\n",dumpcachenode(cachenode));
else
fprintf(stderr,"iscached: notfound\n");
#endif
return found;
}
/* Compute the set of prefetched data.
Notes:
1. All prefetches are whole variable fetches.
2. If the data set is unconstrainable, we
will prefetch the whole thing
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*/
NCerror
prefetchdata(NCDAPCOMMON* nccomm)
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{
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int i;
NCFLAGS flags;
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NCerror ncstat = NC_NOERR;
NClist* allvars = nccomm->cdf.ddsroot->tree->varnodes;
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DCEconstraint* urlconstraint = nccomm->oc.dapconstraint;
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NClist* vars = nclistnew();
NCcachenode* cache = NULL;
DCEconstraint* newconstraint = NULL;
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if(FLAGSET(nccomm->controls,NCF_UNCONSTRAINABLE)) {
/* If we cannot constrain and caching is enabled,
then pull in everything */
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if(FLAGSET(nccomm->controls,NCF_CACHE)) {
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for(i=0;i<nclistlength(allvars);i++) {
nclistpush(vars,nclistget(allvars,i));
}
} else { /* do no prefetching */
nccomm->cdf.cache->prefetch = NULL;
goto done;
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}
} else {
/* pull in those variables previously marked as prefetchable */
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for(i=0;i<nclistlength(allvars);i++) {
CDFnode* var = (CDFnode*)nclistget(allvars,i);
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/* Most of the important testing was already done */
if(!var->basenode->prefetchable)
continue;
/* Do not attempt to prefetch any variables in the
nc_open url's projection list
*/
if(nclistcontains(nccomm->cdf.projectedvars,(void*)var))
continue;
/* Should be prefetchable */
nclistpush(vars,(void*)var);
if(SHOWFETCH) {
nclog(NCLOGDBG,"prefetch: %s",var->ncfullname);
}
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}
}
/* If there are no vars, then do nothing */
if(nclistlength(vars) == 0) {
nccomm->cdf.cache->prefetch = NULL;
goto done;
}
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/* Create a single constraint consisting of the projections for the variables;
each projection is whole variable. The selections are passed on as is.
Conditionally, The exception is if we are prefetching everything.
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*/
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newconstraint = (DCEconstraint*)dcecreate(CES_CONSTRAINT);
newconstraint->projections = nclistnew();
newconstraint->selections = dceclonelist(urlconstraint->selections);
for(i=0;i<nclistlength(vars);i++) {
DCEprojection* varprojection;
CDFnode* var = (CDFnode*)nclistget(vars,i);
/* Ignore invisible vars */
if(var->invisible) continue;
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/* convert var to a projection */
ncstat = dapvar2projection(var,&varprojection);
if(ncstat != NC_NOERR) {THROWCHK(ncstat); goto done;}
nclistpush(newconstraint->projections,(void*)varprojection);
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}
if(SHOWFETCH) {
char* s = dumpprojections(newconstraint->projections);
LOG1(NCLOGNOTE,"prefetch.final: %s",s);
nullfree(s);
}
flags = NCF_PREFETCH;
#ifndef GRADS_PREFETCH
if(nclistlength(allvars) == nclistlength(vars)) flags |= NCF_PREFETCH_ALL;
#endif
ncstat = buildcachenode(nccomm,newconstraint,vars,&cache,flags);
newconstraint = NULL; /* buildcachenodetakes control of newconstraint */
if(ncstat != OC_NOERR) goto done;
else if(cache == NULL) goto done;
else
cache->wholevariable = 1; /* All prefetches are whole variable */
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/* Make cache node be the prefetch node */
nccomm->cdf.cache->prefetch = cache;
if(SHOWFETCH) {
LOG0(NCLOGNOTE,"prefetch.complete");
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}
if(SHOWFETCH) {
char* s = NULL;
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/* Log the set of prefetch variables */
NCbytes* buf = ncbytesnew();
ncbytescat(buf,"prefetch.vars: ");
for(i=0;i<nclistlength(vars);i++) {
CDFnode* var = (CDFnode*)nclistget(vars,i);
ncbytescat(buf," ");
s = makecdfpathstring(var,".");
ncbytescat(buf,s);
nullfree(s);
}
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ncbytescat(buf,"\n");
nclog(NCLOGNOTE,"%s",ncbytescontents(buf));
ncbytesfree(buf);
}
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done:
nclistfree(vars);
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dcefree((DCEnode*)newconstraint);
if(ncstat && cache != NULL) freenccachenode(nccomm,cache);
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return THROW(ncstat);
}
NCerror
buildcachenode(NCDAPCOMMON* nccomm,
DCEconstraint* constraint,
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NClist* varlist,
NCcachenode** cachep,
NCFLAGS flags)
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{
NCerror ncstat = NC_NOERR;
OCerror ocstat = OC_NOERR;
OClink conn = nccomm->oc.conn;
OCddsnode ocroot = NULL;
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CDFnode* dxdroot = NULL;
NCcachenode* cachenode = NULL;
char* ce = NULL;
int isprefetch = 0;
if((flags & NCF_PREFETCH) != 0)
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isprefetch = 1;
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#ifndef GRADS_PREFETCH
if((flags & NCF_PREFETCH_ALL) == 0)
#endif
ce = dcebuildconstraintstring(constraint);
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ncstat = dap_fetch(nccomm,conn,ce,OCDATADDS,&ocroot);
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nullfree(ce);
if(ncstat != NC_NOERR) {THROWCHK(ncstat); goto done;}
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ncstat = buildcdftree(nccomm,ocroot,OCDATA,&dxdroot);
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if(ncstat) {THROWCHK(ncstat); goto done;}
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/* re-struct*/
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if(!FLAGSET(nccomm->controls,NCF_UNCONSTRAINABLE)) {
ncstat = restruct(nccomm,dxdroot,nccomm->cdf.fullddsroot,
constraint->projections);
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if(ncstat) {THROWCHK(ncstat); goto done;}
}
/* create the cache node */
cachenode = createnccachenode();
cachenode->isprefetch = isprefetch;
This PR adds EXPERIMENTAL support for accessing data in the cloud using a variant of the Zarr protocol and storage format. This enhancement is generically referred to as "NCZarr". The data model supported by NCZarr is netcdf-4 minus the user-defined types and the String type. In this sense it is similar to the CDF-5 data model. More detailed information about enabling and using NCZarr is described in the document NUG/nczarr.md and in a [Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in). WARNING: this code has had limited testing, so do use this version for production work. Also, performance improvements are ongoing. Note especially the following platform matrix of successful tests: Platform | Build System | S3 support ------------------------------------ Linux+gcc | Automake | yes Linux+gcc | CMake | yes Visual Studio | CMake | no Additionally, and as a consequence of the addition of NCZarr, major changes have been made to the Filter API. NOTE: NCZarr does not yet support filters, but these changes are enablers for that support in the future. Note that it is possible (probable?) that there will be some accidental reversions if the changes here did not correctly mimic the existing filter testing. In any case, previously filter ids and parameters were of type unsigned int. In order to support the more general zarr filter model, this was all converted to char*. The old HDF5-specific, unsigned int operations are still supported but they are wrappers around the new, char* based nc_filterx_XXX functions. This entailed at least the following changes: 1. Added the files libdispatch/dfilterx.c and include/ncfilter.h 2. Some filterx utilities have been moved to libdispatch/daux.c 3. A new entry, "filter_actions" was added to the NCDispatch table and the version bumped. 4. An overly complex set of structs was created to support funnelling all of the filterx operations thru a single dispatch "filter_actions" entry. 5. Move common code to from libhdf5 to libsrc4 so that it is accessible to nczarr. Changes directly related to Zarr: 1. Modified CMakeList.txt and configure.ac to support both C and C++ -- this is in support of S3 support via the awd-sdk libraries. 2. Define a size64_t type to support nczarr. 3. More reworking of libdispatch/dinfermodel.c to support zarr and to regularize the structure of the fragments section of a URL. Changes not directly related to Zarr: 1. Make client-side filter registration be conditional, with default off. 2. Hack include/nc4internal.h to make some flags added by Ed be unique: e.g. NC_CREAT, NC_INDEF, etc. 3. cleanup include/nchttp.h and libdispatch/dhttp.c. 4. Misc. changes to support compiling under Visual Studio including: * Better testing under windows for dirent.h and opendir and closedir. 5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags and to centralize error reporting. 6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them. 7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible. Changes Left TO-DO: 1. fix provenance code, it is too HDF5 specific.
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cachenode->vars = nclistclone(varlist,0);
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cachenode->datadds = dxdroot;
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/* Give the constraint over to the cachenode */
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cachenode->constraint = constraint;
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constraint = NULL;
cachenode->wholevariable = iscacheableconstraint(cachenode->constraint);
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/* save the root content*/
cachenode->ocroot = ocroot;
ocstat = oc_data_getroot(conn,ocroot,&cachenode->content);
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if(ocstat) {THROWCHK(ocerrtoncerr(ocstat)); goto done;}
/* capture the packet size */
ocstat = oc_raw_xdrsize(conn,ocroot,&cachenode->xdrsize);
if(ocstat) {THROWCHK(ocerrtoncerr(ocstat)); goto done;}
#ifdef DEBUG
fprintf(stderr,"buildcachenode: new cache node: %s\n",
dumpcachenode(cachenode));
#endif
/* Insert into the cache. If not caching, then
remove any previous cache node
*/
if(!isprefetch) {
NCcache* cache = nccomm->cdf.cache;
if(cache->nodes == NULL) cache->nodes = nclistnew();
/* remove cache nodes to get below the max cache size */
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while(cache->cachesize + cachenode->xdrsize > cache->cachelimit
&& nclistlength(cache->nodes) > 0) {
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NCcachenode* node = (NCcachenode*)nclistremove(cache->nodes,0);
#ifdef DEBUG
fprintf(stderr,"buildcachenode: purge cache node: %s\n",
dumpcachenode(cachenode));
#endif
cache->cachesize -= node->xdrsize;
freenccachenode(nccomm,node);
}
/* Remove cache nodes to get below the max cache count */
/* If not caching, then cachecount should be 0 */
while(nclistlength(cache->nodes) > cache->cachecount) {
NCcachenode* node = (NCcachenode*)nclistremove(cache->nodes,0);
#ifdef DEBUG
fprintf(stderr,"buildcachenode: count purge cache node: %s\n",
dumpcachenode(node));
#endif
cache->cachesize -= node->xdrsize;
freenccachenode(nccomm,node);
}
nclistpush(nccomm->cdf.cache->nodes,(void*)cachenode);
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cache->cachesize += cachenode->xdrsize;
}
#ifdef DEBUG
fprintf(stderr,"buildcachenode: %s\n",dumpcachenode(cachenode));
#endif
done:
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if(constraint != NULL) dcefree((DCEnode*)constraint);
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if(cachep) *cachep = cachenode;
if(ocstat != OC_NOERR) ncstat = ocerrtoncerr(ocstat);
if(ncstat != OC_NOERR) {
freecdfroot(dxdroot);
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freenccachenode(nccomm,cachenode);
if(cachep) *cachep = NULL;
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}
return THROW(ncstat);
}
NCcachenode*
createnccachenode(void)
{
NCcachenode* mem = (NCcachenode*)calloc(1,sizeof(NCcachenode));
return mem;
}
void
freenccachenode(NCDAPCOMMON* nccomm, NCcachenode* node)
{
if(node == NULL) return;
#ifdef DEBUG
fprintf(stderr,"freecachenode: %s\n",
dumpcachenode(node));
#endif
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oc_data_free(nccomm->oc.conn,node->content);
dcefree((DCEnode*)node->constraint);
freecdfroot(node->datadds);
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nclistfree(node->vars);
nullfree(node);
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}
void
freenccache(NCDAPCOMMON* nccomm, NCcache* cache)
{
int i;
if(cache == NULL) return;
freenccachenode(nccomm,cache->prefetch);
for(i=0;i<nclistlength(cache->nodes);i++) {
freenccachenode(nccomm,(NCcachenode*)nclistget(cache->nodes,i));
}
nclistfree(cache->nodes);
nullfree(cache);
}
NCcache*
createnccache(void)
{
NCcache* c = (NCcache*)calloc(1,sizeof(NCcache));
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if(c == NULL)
return NULL;
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c->cachelimit = DFALTCACHELIMIT;
c->cachesize = 0;
c->nodes = nclistnew();
c->cachecount = DFALTCACHECOUNT;
return c;
}
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static int
iscacheableprojection(DCEprojection* proj)
{
int i,cacheable;
if(proj->discrim != CES_VAR) return 0;
cacheable = 1; /* assume so */
for(i=0;i<nclistlength(proj->var->segments);i++) {
DCEsegment* segment = (DCEsegment*)nclistget(proj->var->segments,i);
if(!dapiswholesegment(segment)) {cacheable = 0; break;}
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}
return cacheable;
}
static int
iscacheableconstraint(DCEconstraint* con)
{
int i;
if(con == NULL) return 1;
if(con->selections != NULL && nclistlength(con->selections) > 0)
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return 0; /* can't deal with selections */
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for(i=0;i<nclistlength(con->projections);i++) {
if(!iscacheableprojection((DCEprojection*)nclistget(con->projections,i)))
return 0;
}
return 1;
}
/*
A variable is prefetchable if
1. it is atomic
2. it's size is sufficiently small
3. it is not contained in sequence or a dimensioned structure.
*/
NCerror
markprefetch(NCDAPCOMMON* nccomm)
{
int i,j;
NClist* allvars = nccomm->cdf.fullddsroot->tree->varnodes;
assert(allvars != NULL);
/* mark those variables of sufficiently small size */
for(i=0;i<nclistlength(allvars);i++) {
CDFnode* var = (CDFnode*)nclistget(allvars,i);
size_t nelems;
/* If var is not atomic, then it is not prefetchable */
if(var->nctype != NC_Atomic)
continue;
/* if var is under a sequence, then never prefetch */
if(dapinsequence(var))
continue;
/* Compute the # of elements in the variable */
for(nelems=1,j=0;j<nclistlength(var->array.dimsettrans);j++) {
CDFnode* dim = (CDFnode*)nclistget(var->array.dimsettrans,j);
nelems *= dim->dim.declsize;
}
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if(nelems <= nccomm->cdf.smallsizelimit
&& FLAGSET(nccomm->controls,NCF_PREFETCH)) {
var->prefetchable = 1;
if(SHOWFETCH)
{
extern char* ocfqn(OCddsnode);
char *tmp = ocfqn(var->ocnode);
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nclog(NCLOGDBG,"prefetchable: %s=%lu",
tmp,(unsigned long)nelems);
free(tmp);
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}
}
}
return NC_NOERR;
}