mirror of
https://github.com/Unidata/netcdf-c.git
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df3636b959
This PR started as an attempt to add unlimited dimensions to NCZarr. It did that, but this exposed significant problems with test interference. So this PR is mostly about fixing -- well mitigating anyway -- test interference. The problem of test interference is now documented in the document docs/internal.md. The solutions implemented here are also describe in that document. The solution is somewhat fragile but multiple cleanup mechanisms are provided. Note that this feature requires that the AWS command line utility must be installed. ## Unlimited Dimensions. The existing NCZarr extensions to Zarr are modified to support unlimited dimensions. NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group". Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2. * Form 1: An integer representing the size of the dimension, which is used for simple named dimensions. * Form 2: A dictionary with the following keys and values" - "size" with an integer value representing the (current) size of the dimension. - "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension. For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases. That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension. This is the standard semantics for unlimited dimensions. Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following. * Did a partial refactor of the slice handling code in zwalk.c to clean it up. * Added a number of tests for unlimited dimensions derived from the same test in nc_test4. * Added several NCZarr specific unlimited tests; more are needed. * Add test of endianness. ## Misc. Other Changes * Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the AWS Transfer Utility mechanism. This is controlled by the ```#define TRANSFER```` command in that file. It defaults to being disabled. * Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE). * Fixed an obscure memory leak in ncdump. * Removed some obsolete unit testing code and test cases. * Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c. * Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4. * Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects. * Modify the semantics of zodom to properly handle stride > 1. * Add a truncate operation to the libnczarr zmap code.
439 lines
13 KiB
C
439 lines
13 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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#include "dapincludes.h"
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#include "dapdump.h"
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/*
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Grads servers always require a constraint,
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which does not necessarily happen during prefetch.
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So this flag controls this. By default, it is on.
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*/
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#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
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the current get_vara request; return 0 otherwise.
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Target is in the constrained tree space.
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Currently, if the target matches a cache that is not
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a whole variable, then match is false.
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*/
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int
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iscached(NCDAPCOMMON* nccomm, CDFnode* target, NCcachenode** cachenodep)
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{
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int i,j,found,index;
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NCcache* cache;
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NCcachenode* cachenode;
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found = 0;
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if(target == NULL) goto done;
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/* Match the target variable against the prefetch, if any */
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/* Note that prefetches are always whole variable */
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cache = nccomm->cdf.cache;
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cachenode = cache->prefetch;
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if(cachenode!= NULL) {
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for(found=0,i=0;i<nclistlength(cachenode->vars);i++) {
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CDFnode* var = (CDFnode*)nclistget(cachenode->vars,i);
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if(var == target) {
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if(cachenodep) *cachenodep = cachenode;
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found=1;
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goto done;
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}
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}
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}
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/*search other cache nodes starting at latest first */
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index = 0;
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for(i=nclistlength(cache->nodes)-1;i>=0;i--) {
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cachenode = (NCcachenode*)nclistget(cache->nodes,i);
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/* We currently do not try to match constraints;
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If the cachenode is constrained by more than
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simple wholevariable projections, then skip it.
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*/
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if(!cachenode->wholevariable) continue;
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for(found=0,j=0;j<nclistlength(cachenode->vars);j++) {
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CDFnode* var = (CDFnode*)nclistget(cachenode->vars,j);
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if(var == target) {found=1;index=i;break;}
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}
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if(found) break;
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}
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if(found) {
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ASSERT((cachenode != NULL));
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if(nclistlength(cache->nodes) > 1) {
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/* Manage the cache nodes as LRU */
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nclistremove(cache->nodes,index);
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nclistpush(cache->nodes,(void*)cachenode);
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}
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if(cachenodep) *cachenodep = cachenode;
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}
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done:
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#ifdef DEBUG
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fprintf(stderr,"iscached: search: %s\n",makecdfpathstring(target,"."));
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if(found)
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fprintf(stderr,"iscached: found: %s\n",dumpcachenode(cachenode));
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else
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fprintf(stderr,"iscached: notfound\n");
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#endif
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return found;
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}
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/* Compute the set of prefetched data.
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Notes:
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1. All prefetches are whole variable fetches.
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2. If the data set is unconstrainable, we
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will prefetch the whole thing
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*/
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NCerror
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prefetchdata(NCDAPCOMMON* nccomm)
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{
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int i;
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NCFLAGS flags;
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NCerror ncstat = NC_NOERR;
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NClist* allvars = nccomm->cdf.ddsroot->tree->varnodes;
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DCEconstraint* urlconstraint = nccomm->oc.dapconstraint;
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NClist* vars = nclistnew();
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NCcachenode* cache = NULL;
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DCEconstraint* newconstraint = NULL;
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if(FLAGSET(nccomm->controls,NCF_UNCONSTRAINABLE)) {
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/* If we cannot constrain and caching is enabled,
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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++) {
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nclistpush(vars,nclistget(allvars,i));
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}
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} else { /* do no prefetching */
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nccomm->cdf.cache->prefetch = NULL;
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goto done;
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}
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} else {
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/* pull in those variables previously marked as prefetchable */
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for(i=0;i<nclistlength(allvars);i++) {
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CDFnode* var = (CDFnode*)nclistget(allvars,i);
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/* Most of the important testing was already done */
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if(!var->basenode->prefetchable)
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continue;
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/* Do not attempt to prefetch any variables in the
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nc_open url's projection list
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*/
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if(nclistcontains(nccomm->cdf.projectedvars,(void*)var))
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continue;
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/* Should be prefetchable */
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nclistpush(vars,(void*)var);
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if(SHOWFETCH) {
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nclog(NCLOGDEBUG,"prefetch: %s",var->ncfullname);
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}
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}
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}
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/* If there are no vars, then do nothing */
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if(nclistlength(vars) == 0) {
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nccomm->cdf.cache->prefetch = NULL;
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goto done;
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}
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/* Create a single constraint consisting of the projections for the variables;
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each projection is whole variable. The selections are passed on as is.
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Conditionally, The exception is if we are prefetching everything.
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*/
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newconstraint = (DCEconstraint*)dcecreate(CES_CONSTRAINT);
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newconstraint->projections = nclistnew();
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newconstraint->selections = dceclonelist(urlconstraint->selections);
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for(i=0;i<nclistlength(vars);i++) {
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DCEprojection* varprojection;
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CDFnode* var = (CDFnode*)nclistget(vars,i);
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/* Ignore invisible vars */
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if(var->invisible) continue;
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/* convert var to a projection */
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ncstat = dapvar2projection(var,&varprojection);
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if(ncstat != NC_NOERR) {THROWCHK(ncstat); goto done;}
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nclistpush(newconstraint->projections,(void*)varprojection);
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}
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if(SHOWFETCH) {
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char* s = dumpprojections(newconstraint->projections);
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LOG1(NCLOGNOTE,"prefetch.final: %s",s);
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nullfree(s);
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}
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flags = NCF_PREFETCH;
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#ifndef GRADS_PREFETCH
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if(nclistlength(allvars) == nclistlength(vars)) flags |= NCF_PREFETCH_ALL;
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#endif
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ncstat = buildcachenode(nccomm,newconstraint,vars,&cache,flags);
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newconstraint = NULL; /* buildcachenodetakes control of newconstraint */
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if(ncstat != OC_NOERR) goto done;
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else if(cache == NULL) goto done;
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else
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cache->wholevariable = 1; /* All prefetches are whole variable */
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/* Make cache node be the prefetch node */
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nccomm->cdf.cache->prefetch = cache;
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if(SHOWFETCH) {
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LOG0(NCLOGNOTE,"prefetch.complete");
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}
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if(SHOWFETCH) {
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char* s = NULL;
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/* Log the set of prefetch variables */
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NCbytes* buf = ncbytesnew();
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ncbytescat(buf,"prefetch.vars: ");
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for(i=0;i<nclistlength(vars);i++) {
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CDFnode* var = (CDFnode*)nclistget(vars,i);
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ncbytescat(buf," ");
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s = makecdfpathstring(var,".");
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ncbytescat(buf,s);
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nullfree(s);
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}
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ncbytescat(buf,"\n");
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nclog(NCLOGNOTE,"%s",ncbytescontents(buf));
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ncbytesfree(buf);
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}
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done:
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nclistfree(vars);
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dcefree((DCEnode*)newconstraint);
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if(ncstat && cache != NULL) freenccachenode(nccomm,cache);
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return THROW(ncstat);
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}
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NCerror
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buildcachenode(NCDAPCOMMON* nccomm,
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DCEconstraint* constraint,
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NClist* varlist,
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NCcachenode** cachep,
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NCFLAGS flags)
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{
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NCerror ncstat = NC_NOERR;
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OCerror ocstat = OC_NOERR;
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OClink conn = nccomm->oc.conn;
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OCddsnode ocroot = NULL;
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CDFnode* dxdroot = NULL;
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NCcachenode* cachenode = NULL;
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char* ce = NULL;
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int isprefetch = 0;
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if((flags & NCF_PREFETCH) != 0)
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isprefetch = 1;
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#ifndef GRADS_PREFETCH
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if((flags & NCF_PREFETCH_ALL) == 0)
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#endif
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ce = dcebuildconstraintstring(constraint);
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ncstat = dap_fetch(nccomm,conn,ce,OCDATADDS,&ocroot);
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nullfree(ce);
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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)) {
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ncstat = restruct(nccomm,dxdroot,nccomm->cdf.fullddsroot,
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constraint->projections);
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if(ncstat) {THROWCHK(ncstat); goto done;}
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}
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/* create the cache node */
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cachenode = createnccachenode();
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cachenode->isprefetch = isprefetch;
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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;
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cachenode->wholevariable = iscacheableconstraint(cachenode->constraint);
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/* save the root content*/
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cachenode->ocroot = ocroot;
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ocstat = oc_data_getroot(conn,ocroot,&cachenode->content);
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if(ocstat) {THROWCHK(ocerrtoncerr(ocstat)); goto done;}
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/* capture the packet size */
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ocstat = oc_raw_xdrsize(conn,ocroot,&cachenode->xdrsize);
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if(ocstat) {THROWCHK(ocerrtoncerr(ocstat)); goto done;}
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#ifdef DEBUG
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fprintf(stderr,"buildcachenode: new cache node: %s\n",
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dumpcachenode(cachenode));
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#endif
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/* Insert into the cache. If not caching, then
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remove any previous cache node
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*/
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if(!isprefetch) {
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NCcache* cache = nccomm->cdf.cache;
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if(cache->nodes == NULL) cache->nodes = nclistnew();
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/* remove cache nodes to get below the max cache size */
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while(cache->cachesize + cachenode->xdrsize > cache->cachelimit
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&& nclistlength(cache->nodes) > 0) {
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NCcachenode* node = (NCcachenode*)nclistremove(cache->nodes,0);
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#ifdef DEBUG
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fprintf(stderr,"buildcachenode: purge cache node: %s\n",
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dumpcachenode(cachenode));
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#endif
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cache->cachesize -= node->xdrsize;
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freenccachenode(nccomm,node);
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}
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/* Remove cache nodes to get below the max cache count */
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/* If not caching, then cachecount should be 0 */
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while(nclistlength(cache->nodes) > cache->cachecount) {
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NCcachenode* node = (NCcachenode*)nclistremove(cache->nodes,0);
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#ifdef DEBUG
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fprintf(stderr,"buildcachenode: count purge cache node: %s\n",
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dumpcachenode(node));
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#endif
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cache->cachesize -= node->xdrsize;
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freenccachenode(nccomm,node);
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}
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nclistpush(nccomm->cdf.cache->nodes,(void*)cachenode);
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cache->cachesize += cachenode->xdrsize;
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}
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#ifdef DEBUG
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fprintf(stderr,"buildcachenode: %s\n",dumpcachenode(cachenode));
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#endif
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done:
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if(constraint != NULL) dcefree((DCEnode*)constraint);
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if(cachep) *cachep = cachenode;
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if(ocstat != OC_NOERR) ncstat = ocerrtoncerr(ocstat);
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if(ncstat != OC_NOERR) {
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freecdfroot(dxdroot);
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freenccachenode(nccomm,cachenode);
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if(cachep) *cachep = NULL;
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}
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return THROW(ncstat);
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}
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NCcachenode*
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createnccachenode(void)
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{
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NCcachenode* mem = (NCcachenode*)calloc(1,sizeof(NCcachenode));
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return mem;
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}
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void
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freenccachenode(NCDAPCOMMON* nccomm, NCcachenode* node)
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{
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if(node == NULL) return;
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#ifdef DEBUG
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fprintf(stderr,"freecachenode: %s\n",
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dumpcachenode(node));
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#endif
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oc_data_free(nccomm->oc.conn,node->content);
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dcefree((DCEnode*)node->constraint);
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freecdfroot(node->datadds);
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nclistfree(node->vars);
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nullfree(node);
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}
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void
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freenccache(NCDAPCOMMON* nccomm, NCcache* cache)
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{
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int i;
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if(cache == NULL) return;
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freenccachenode(nccomm,cache->prefetch);
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for(i=0;i<nclistlength(cache->nodes);i++) {
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freenccachenode(nccomm,(NCcachenode*)nclistget(cache->nodes,i));
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}
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nclistfree(cache->nodes);
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nullfree(cache);
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}
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NCcache*
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createnccache(void)
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{
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NCcache* c = (NCcache*)calloc(1,sizeof(NCcache));
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if(c == NULL)
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return NULL;
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c->cachelimit = DFALTCACHELIMIT;
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c->cachesize = 0;
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c->nodes = nclistnew();
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c->cachecount = DFALTCACHECOUNT;
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return c;
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}
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static int
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iscacheableprojection(DCEprojection* proj)
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{
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int i,cacheable;
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if(proj->discrim != CES_VAR) return 0;
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cacheable = 1; /* assume so */
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for(i=0;i<nclistlength(proj->var->segments);i++) {
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DCEsegment* segment = (DCEsegment*)nclistget(proj->var->segments,i);
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if(!dapiswholesegment(segment)) {cacheable = 0; break;}
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}
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return cacheable;
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}
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static int
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iscacheableconstraint(DCEconstraint* con)
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{
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int i;
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if(con == NULL) return 1;
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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++) {
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if(!iscacheableprojection((DCEprojection*)nclistget(con->projections,i)))
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return 0;
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}
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return 1;
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}
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/*
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A variable is prefetchable if
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1. it is atomic
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2. it's size is sufficiently small
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3. it is not contained in sequence or a dimensioned structure.
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*/
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NCerror
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markprefetch(NCDAPCOMMON* nccomm)
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{
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int i,j;
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NClist* allvars = nccomm->cdf.fullddsroot->tree->varnodes;
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assert(allvars != NULL);
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/* mark those variables of sufficiently small size */
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for(i=0;i<nclistlength(allvars);i++) {
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CDFnode* var = (CDFnode*)nclistget(allvars,i);
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size_t nelems;
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/* If var is not atomic, then it is not prefetchable */
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if(var->nctype != NC_Atomic)
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continue;
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/* if var is under a sequence, then never prefetch */
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if(dapinsequence(var))
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continue;
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/* Compute the # of elements in the variable */
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for(nelems=1,j=0;j<nclistlength(var->array.dimsettrans);j++) {
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CDFnode* dim = (CDFnode*)nclistget(var->array.dimsettrans,j);
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nelems *= dim->dim.declsize;
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}
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if(nelems <= nccomm->cdf.smallsizelimit
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&& FLAGSET(nccomm->controls,NCF_PREFETCH)) {
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var->prefetchable = 1;
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if(SHOWFETCH)
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{
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extern char* ocfqn(OCddsnode);
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char *tmp = ocfqn(var->ocnode);
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nclog(NCLOGDEBUG,"prefetchable: %s=%lu",
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tmp,(unsigned long)nelems);
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free(tmp);
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}
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}
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}
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return NC_NOERR;
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}
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