netcdf-c/libnczarr/zcache.c

/* Copyright 2018, University Corporation for Atmospheric
 * Research. See COPYRIGHT file for copying and redistribution
 * conditions. */

/**
 * @file @internal The functions which control NCZ
 * caching. These caching controls allow the user to change the cache
 * sizes of ZARR before opening files.
 *
 * @author Dennis Heimbigner, Ed Hartnett
 */

#include "zincludes.h"
#include "zcache.h"

#undef DEBUG

#undef FILLONREAD

#undef FLUSH

/* Forward */
static int get_chunk(NCZChunkCache* cache, const char* key, NCZCacheEntry* entry);
static int put_chunk(NCZChunkCache* cache, const char* key, const NCZCacheEntry*);
static int create_chunk(NCZChunkCache* cache, const char* key, NCZCacheEntry* entry);
static int buildchunkkey(size_t R, const size64_t* chunkindices, char** keyp);
static int makeroom(NCZChunkCache* cache);

/**************************************************/
/* Dispatch table per-var cache functions */

/**
 * @internal Set chunk cache size for a variable. This is the internal
 * function called by nc_set_var_chunk_cache().
 *
 * @param ncid File ID.
 * @param varid Variable ID.
 * @param size Size in bytes to set cache.
 * @param nelems # of entries in cache
 * @param preemption Controls cache swapping.
 *
 * @returns ::NC_NOERR No error.
 * @returns ::NC_EBADID Bad ncid.
 * @returns ::NC_ENOTVAR Invalid variable ID.
 * @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict
 * nc3 netcdf-4 file.
 * @returns ::NC_EINVAL Invalid input.
 * @returns ::NC_EHDFERR HDF5 error.
 * @author Ed Hartnett
 */
int
NCZ_set_var_chunk_cache(int ncid, int varid, size_t cachesize, size_t nelems, float preemption)
{
    NC_GRP_INFO_T *grp;
    NC_FILE_INFO_T *h5;
    NC_VAR_INFO_T *var;
    NCZ_VAR_INFO_T *zvar;
    int retval;

    /* Check input for validity. */
    if (preemption < 0 || preemption > 1)
        return NC_EINVAL;

    /* Find info for this file and group, and set pointer to each. */
    if ((retval = nc4_find_nc_grp_h5(ncid, NULL, &grp, &h5)))
        return retval;
    assert(grp && h5);

    /* Find the var. */
    if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid)))
        return NC_ENOTVAR;
    assert(var && var->hdr.id == varid);

    zvar = (NCZ_VAR_INFO_T*)var->format_var_info;
    assert(zvar != NULL && zvar->cache != NULL);

    /* Set the values. */
    var->chunk_cache_size = cachesize;
    var->chunk_cache_nelems = nelems;
    var->chunk_cache_preemption = preemption;

#ifdef LOOK
    /* Reopen the dataset to bring new settings into effect. */
    if ((retval = nc4_reopen_dataset(grp, var)))
        return retval;
#endif
    return NC_NOERR;
}

/**
 * @internal Adjust the chunk cache of a var for better
 * performance.
 *
 * @note For contiguous and compact storage vars, or when parallel I/O
 * is in use, this function will do nothing and return ::NC_NOERR;
 *
 * @param grp Pointer to group info struct.
 * @param var Pointer to var info struct.
 *
 * @return ::NC_NOERR No error.
 * @author Ed Hartnett
 */
int
NCZ_adjust_var_cache(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
    return NC_NOERR;
}

/**************************************************/

/**
 * Create a chunk cache object
 *
 * @param var containing var
 * @param entrysize Size in bytes of an entry
 * @param cachep return cache pointer
 *
 * @return ::NC_NOERR No error.
 * @return ::NC_EINVAL Bad preemption.
 * @author Dennis Heimbigner, Ed Hartnett
 */
int
NCZ_create_chunk_cache(NC_VAR_INFO_T* var, size64_t chunksize, NCZChunkCache** cachep)
{
    int stat = NC_NOERR;
    NCZChunkCache* cache = NULL;
    void* fill = NULL;
    size_t nelems, cachesize;
	
    if(chunksize == 0) return NC_EINVAL;

    if((cache = calloc(1,sizeof(NCZChunkCache))) == NULL)
	{stat = NC_ENOMEM; goto done;}
    cache->var = var;
    cache->chunksize = chunksize;
    assert(cache->fillchunk == NULL);
    cache->fillchunk = NULL;

    /* Figure out the actual cache size */
    cachesize = var->chunk_cache_size;
    nelems = (cachesize / chunksize);
    if(nelems == 0) nelems = 1;
    /* Make consistent */
    cachesize = nelems * chunksize;
    cache->maxentries = nelems;
#ifdef FLUSH
    cache->maxentries = 1;
#endif

#ifdef DEBUG
    fprintf(stderr,"%s.cache: nelems=%ld size=%ld\n",
        var->hdr.name,(unsigned long)cache->maxentries,(unsigned long)(cache->maxentries*cache->chunksize));
#endif
    if((cache->entries = nclistnew()) == NULL)
	{stat = NC_ENOMEM; goto done;}
    nclistsetalloc(cache->entries,cache->maxentries);
    if(cachep) {*cachep = cache; cache = NULL;}
done:
    nullfree(fill);
    nullfree(cache);
    return THROW(stat);
}

void
NCZ_free_chunk_cache(NCZChunkCache* cache)
{
    if(cache == NULL) return;
    /* Iterate over the entries */
    while(nclistlength(cache->entries) > 0) {
        NCZCacheEntry* entry = nclistremove(cache->entries,0);
	nullfree(entry->data); nullfree(entry->key); nullfree(entry);
    }
#ifdef DEBUG
fprintf(stderr,"|cache.free|=%ld\n",nclistlength(cache->entries));
#endif
    nclistfree(cache->entries);
    cache->entries = NULL;
    nullfree(cache->fillchunk);
    nullfree(cache);
}

size64_t
NCZ_cache_entrysize(NCZChunkCache* cache)
{
    assert(cache);
    return cache->chunksize;
}

/* Return number of active entries in cache */
size64_t
NCZ_cache_size(NCZChunkCache* cache)
{
    assert(cache);
    return nclistlength(cache->entries);
}

int
NCZ_read_cache_chunk(NCZChunkCache* cache, const size64_t* indices, void** datap)
{
    int stat = NC_NOERR;
    char* key = NULL;
    int rank = cache->var->ndims;
    NC_FILE_INFO_T* file = cache->var->container->nc4_info;
    NCZCacheEntry* entry = NULL;
    int i;
	
    /* Create the key for this cache */
    if((stat = NCZ_buildchunkpath(cache,indices,&key))) goto done;

    /* See if already in cache try MRU */
    for(i=nclistlength(cache->entries)-1;i>=0;i--) {
	entry = (NCZCacheEntry*)nclistget(cache->entries,i);
	if(strcmp(key,entry->key)==0) {
            if(datap) *datap = entry->data;
	    /* Move to keep MRU at end */
	    nclistremove(cache->entries,i);	    
	    break;
        } else entry = NULL;
    }
    if(entry == NULL) { /*!found*/
	/* Make room in the cache */
	if((stat=makeroom(cache))) goto done;
	/* Create a new entry */
	if((entry = calloc(1,sizeof(NCZCacheEntry)))==NULL)
	    {stat = NC_ENOMEM; goto done;}
	memcpy(entry->indices,indices,rank*sizeof(size64_t));
	/* Create the local copy space */
	if((entry->data = calloc(1,cache->chunksize)) == NULL)
	    {stat = NC_ENOMEM; goto done;}
	entry->key= key; key = NULL;
	/* Try to read the object in toto */
	stat=get_chunk(cache,entry->key,entry);
	switch (stat) {
	case NC_NOERR: break;
	case NC_EEMPTY:
	case NC_ENOTFOUND: /*signals the chunk needs to be created */
	    /* If the file is read-only, then fake the chunk */
	    entry->modified = (!file->no_write);
	    if(!file->no_write) {
                if((stat = create_chunk(cache,entry->key,entry))) goto done;
	    }
#ifdef FILLONREAD
	    /* apply fill value */
	    memcpy(entry->data,cache->fillchunk,cache->chunksize);
#else
	    memset(entry->data,0,cache->chunksize);
#endif
	    break;
	default: goto done;
	}
    }
    nclistpush(cache->entries,entry);
#ifdef DEBUG
fprintf(stderr,"|cache.read.lru|=%ld\n",nclistlength(cache->entries));
#endif
    if(datap) *datap = entry->data;
    entry = NULL;

done:
    if(entry) {nullfree(entry->data); nullfree(entry->key);}
    nullfree(entry);
    nullfree(key);
    return THROW(stat);
}

int
NCZ_write_cache_chunk(NCZChunkCache* cache, const size64_t* indices, void** datap)
{
    int stat = NC_NOERR;
    char* key = NULL;
    int i,rank = cache->var->ndims;
    NCZCacheEntry* entry = NULL;
    
    /* Create the key for this cache */
    if((stat = NCZ_buildchunkpath(cache,indices,&key))) goto done;

    /* See if already in cache try MRU */
    for(i=nclistlength(cache->entries)-1;i>=0;i--) {
	entry = (NCZCacheEntry*)nclistget(cache->entries,i);
	if(strcmp(key,entry->key)==0) {
            if(datap) *datap = entry->data;
	    /* Move to keep MRU at end */
	    nclistremove(cache->entries,i);	    
	    break;
        } else entry = NULL;
    }
    if(entry == NULL) { /*!found*/
	if((stat=makeroom(cache))) goto done;
	/* Create a new entry */
	if((entry = calloc(1,sizeof(NCZCacheEntry)))==NULL)
	    {stat = NC_ENOMEM; goto done;}
	memcpy(entry->indices,indices,rank*sizeof(size64_t));
	/* Create the local copy space */
	if((entry->data = calloc(1,cache->chunksize)) == NULL)
	    {stat = NC_ENOMEM; goto done;}
	entry->key= key; key = NULL;
    }
    entry->modified = 1;
    nclistpush(cache->entries,entry); /* MRU order */
#ifdef DEBUG
fprintf(stderr,"|cache.write|=%ld\n",nclistlength(cache->entries));
#endif
    entry = NULL;

done:
    if(entry) {nullfree(entry->data); nullfree(entry->key);}
    nullfree(entry);
    nullfree(key);
    return THROW(stat);
}

static int
makeroom(NCZChunkCache* cache)
{
    int stat = NC_NOERR;
    /* Flush from LRU end if we are at capacity */
    while(nclistlength(cache->entries) >= cache->maxentries) {
	NCZCacheEntry* e = nclistremove(cache->entries,0);
	assert(e != NULL);
	if(e->modified) /* flush to file */
	    stat=put_chunk(cache,e->key,e);
	/* reclaim */
        nullfree(e->data); nullfree(e->key); nullfree(e);
    }
#ifdef DEBUG
fprintf(stderr,"|cache.makeroom|=%ld\n",nclistlength(cache->entries));
#endif
    return stat;
}

int
NCZ_flush_chunk_cache(NCZChunkCache* cache)
{
    int stat = NC_NOERR;
    size_t i;

    if(NCZ_cache_size(cache) == 0) goto done;
    
    /* Iterate over the entries in hashmap */
    for(i=0;i<nclistlength(cache->entries);i++) {
        NCZCacheEntry* entry = nclistget(cache->entries,i);
        if(entry->modified) {
	    /* Write out this chunk in toto*/
  	    if((stat=put_chunk(cache,entry->key,entry)))
	        goto done;
	}
        entry->modified = 0;
    }

done:
    return THROW(stat);
}

#if 0
int
NCZ_chunk_cache_modified(NCZChunkCache* cache, const size64_t* indices)
{
    int stat = NC_NOERR;
    char* key = NULL;
    NCZCacheEntry* entry = NULL;
    int rank = cache->var->ndims;

    /* Create the key for this cache */
    if((stat=buildchunkkey(rank, indices, &key))) goto done;

    /* See if already in cache */
    if(NC_hashmapget(cache->entries, key, strlen(key), (uintptr_t*)entry)) { /* found */
	entry->modified = 1;
    }

done:
    nullfree(key);
    return THROW(stat);
}
#endif

/**************************************************/
/*
From Zarr V2 Specification:
"The compressed sequence of bytes for each chunk is stored under
a key formed from the index of the chunk within the grid of
chunks representing the array.  To form a string key for a
chunk, the indices are converted to strings and concatenated
with the period character (".") separating each index. For
example, given an array with shape (10000, 10000) and chunk
shape (1000, 1000) there will be 100 chunks laid out in a 10 by
10 grid. The chunk with indices (0, 0) provides data for rows
0-1000 and columns 0-1000 and is stored under the key "0.0"; the
chunk with indices (2, 4) provides data for rows 2000-3000 and
columns 4000-5000 and is stored under the key "2.4"; etc."
*/

/**
 * @param R Rank
 * @param chunkindices The chunk indices
 * @param keyp Return the chunk key string
 */
static int
buildchunkkey(size_t R, const size64_t* chunkindices, char** keyp)
{
    int stat = NC_NOERR;
    int r;
    NCbytes* key = ncbytesnew();

    if(keyp) *keyp = NULL;
    
    for(r=0;r<R;r++) {
	char sindex[64];
        if(r > 0) ncbytescat(key,".");
	/* Print as decimal with no leading zeros */
	snprintf(sindex,sizeof(sindex),"%lu",(unsigned long)chunkindices[r]);	
	ncbytescat(key,sindex);
    }
    ncbytesnull(key);
    if(keyp) *keyp = ncbytesextract(key);

    ncbytesfree(key);
    return THROW(stat);
}

/**
 * @internal Push data to chunk of a file.
 * If chunk does not exist, create it
 *
 * @param file Pointer to file info struct.
 * @param proj Chunk projection
 * @param datalen size of data
 * @param data Buffer containing the chunk data to write
 *
 * @return ::NC_NOERR No error.
 * @author Dennis Heimbigner
 */
static int
put_chunk(NCZChunkCache* cache, const char* key, const NCZCacheEntry* entry)
{
    int stat = NC_NOERR;
    NCZ_FILE_INFO_T* zfile = NULL;
    NCZMAP* map = NULL;

    LOG((3, "%s: var: %p", __func__, cache->var));

    zfile = ((cache->var->container)->nc4_info)->format_file_info;
    map = zfile->map;

    stat = nczmap_write(map,key,0,cache->chunksize,entry->data);
    switch(stat) {
    case NC_NOERR: break;
    case NC_EEMPTY:
	/* Create the chunk */
	if((stat = nczmap_defineobj(map,key))) goto done;
	/* write again */
	if((stat = nczmap_write(map,key,0,cache->chunksize,entry->data)))
	    goto done;
	break;
    default: goto done;
    }
done:
    return THROW(stat);
}

/**
 * @internal Push data from memory to file.
 *
 * @param cache Pointer to parent cache
 * @param key chunk key
 * @param entry cache entry to read into
 *
 * @return ::NC_NOERR No error.
 * @author Dennis Heimbigner
 */
static int
get_chunk(NCZChunkCache* cache, const char* key, NCZCacheEntry* entry)
{
    int stat = NC_NOERR;
    NCZMAP* map = NULL;
    NC_FILE_INFO_T* file = NULL;
    NCZ_FILE_INFO_T* zfile = NULL;

    LOG((3, "%s: file: %p", __func__, file));

    file = (cache->var->container)->nc4_info;
    zfile = file->format_file_info;
    map = zfile->map;
    assert(map && entry->data);

    stat = nczmap_read(map,key,0,cache->chunksize,(char*)entry->data);

    return THROW(stat);
}

static int
create_chunk(NCZChunkCache* cache, const char* key, NCZCacheEntry* entry)
{
    int stat = NC_NOERR;
    NC_FILE_INFO_T* file = NULL;
    NCZ_FILE_INFO_T* zfile = NULL;
    NCZMAP* map = NULL;

    file = (cache->var->container)->nc4_info;
    zfile = file->format_file_info;
    map = zfile->map;

    /* Create the chunk */
    if((stat = nczmap_defineobj(map,key))) goto done;
    entry->modified = 1; /* mark as modified */
    /* let higher function decide on fill */

done:
    return THROW(stat);
}

int
NCZ_buildchunkpath(NCZChunkCache* cache, const size64_t* chunkindices, char** keyp)
{
    int stat = NC_NOERR;
    char* chunkname = NULL;
    char* varkey = NULL;
    char* key = NULL;

    /* Get the chunk object name */
    if((stat = buildchunkkey(cache->var->ndims, chunkindices, &chunkname))) goto done;
    /* Get the var object key */
    if((stat = NCZ_varkey(cache->var,&varkey))) goto done;
    /* Prefix the path to the containing variable object */
    if((stat=nczm_concat(varkey,chunkname,&key))) goto done;
    if(keyp) {*keyp = key; key = NULL;}

done:
    nullfree(chunkname);
    nullfree(varkey);
    nullfree(key);
    return THROW(stat);
}