/* Copyright 2003-2018, University Corporation for Atmospheric * Research. See the COPYRIGHT file for copying and redistribution * conditions. */ /** * @file @internal Internal netcdf-4 functions for filters * * This file contains functions internal to the netcdf4 library. None of * the functions in this file are exposed in the exetnal API. These * functions all relate to the manipulation of netcdf-4 filters * * @author Dennis Heimbigner */ #include "config.h" #include #include #include "hdf5internal.h" #include "hdf5debug.h" #include "netcdf.h" #include "netcdf_filter.h" #ifdef ENABLE_BLOSC #include #endif #undef TFILTERS /* Forward */ static int NC4_hdf5_filter_free(struct NC_HDF5_Filter* spec); /**************************************************/ /* Filter registration support */ #ifdef ENABLE_CLIENTSIDE_FILTERS /* Mnemonic */ #define FILTERACTIVE 1 /* WARNING: GLOBAL VARIABLE */ /* Define list of registered filters */ static NClist* NC4_registeredfilters = NULL; /** List */ /**************************************************/ /* Filter registration support */ static int clientfilterlookup(unsigned int id) { int i; if(NC4_registeredfilters == NULL) NC4_registeredfilters = nclistnew(); for(i=0;iid == id) { return i; /* return position */ } } return -1; } static void reclaiminfo(NC_FILTER_CLIENT_HDF5* info) { nullfree(info); } static int filterremove(int pos) { NC_FILTER_CLIENT_HDF5* info = NULL; if(NC4_registeredfilters == NULL) return THROW(NC_EINVAL); if(pos < 0 || pos >= nclistlength(NC4_registeredfilters)) return THROW(NC_EINVAL); info = nclistget(NC4_registeredfilters,pos); reclaiminfo(info); nclistremove(NC4_registeredfilters,pos); return NC_NOERR; } static NC_FILTER_CLIENT_HDF5* dupfilterinfo(NC_FILTER_CLIENT_HDF5* info) { NC_FILTER_CLIENT_HDF5* dup = NULL; if(info == NULL) goto fail; if((dup = calloc(1,sizeof(NC_FILTER_CLIENT_HDF5))) == NULL) goto fail; *dup = *info; return dup; fail: reclaiminfo(dup); return NULL; } int nc4_global_filter_action(int op, unsigned int id, NC_FILTER_OBJ_HDF5* infop) { int stat = NC_NOERR; H5Z_class2_t* h5filterinfo = NULL; herr_t herr; int pos = -1; NC_FILTER_CLIENT_HDF5* dup = NULL; NC_FILTER_CLIENT_HDF5* elem = NULL; NC_FILTER_CLIENT_HDF5 ncf; NC_UNUSED(format); switch (op) { case NCFILTER_CLIENT_REG: /* Ignore id argument */ if(infop == NULL) {stat = NC_EINVAL; goto done;} assert(NC_FILTER_FORMAT_HDF5 == infop->hdr.format); assert(NC_FILTER_SORT_CLIENT == infop->sort); elem = (NC_FILTER_CLIENT_HDF5*)&infop->u.client; h5filterinfo = elem->info; /* Another sanity check */ if(id != h5filterinfo->id) {stat = NC_EINVAL; goto done;} /* See if this filter is already defined */ if((pos = clientfilterlookup(id)) >= 0) {stat = NC_ENAMEINUSE; goto done;} /* Already defined */ if((herr = H5Zregister(h5filterinfo)) < 0) {stat = NC_EFILTER; goto done;} /* Save a copy of the passed in info */ ncf.id = id; ncf.info = elem->info; if((dup=dupfilterinfo(&ncf)) == NULL) {stat = NC_ENOMEM; goto done;} nclistpush(NC4_registeredfilters,dup); break; case NCFILTER_CLIENT_UNREG: if(id <= 0) {stat = NC_ENOTNC4; goto done;} /* See if this filter is already defined */ if((pos = clientfilterlookup(id)) < 0) {stat = NC_ENOFILTER; goto done;} /* Not defined */ if((herr = H5Zunregister(id)) < 0) {stat = NC_EFILTER; goto done;} if((stat=filterremove(pos))) goto done; break; case NCFILTER_CLIENT_INQ: if(infop == NULL) goto done; /* Look up the id in our local table */ if((pos = clientfilterlookup(id)) < 0) {stat = NC_ENOFILTER; goto done;} /* Not defined */ elem = (NC_FILTER_CLIENT_HDF5*)nclistget(NC4_registeredfilters,pos); if(elem == NULL) {stat = NC_EINTERNAL; goto done;} if(infop != NULL) { infop->u.client = *elem; } break; default: {stat = NC_EINTERNAL; goto done;} } done: return THROW(stat); } #endif /*ENABLE_CLIENTSIDE_FILTERS*/ /**************************************************/ /**************************************************/ /** * @file * @internal * Internal netcdf hdf5 filter functions. * * This file contains functions internal to the libhdf5 library. * None of the functions in this file are exposed in the exetnal API. These * functions all relate to the manipulation of netcdf-4's var->filters list. * * @author Dennis Heimbigner */ #ifdef TFILTERS static void printfilter1(struct NC_HDF5_Filter* nfs) { int i; if(nfs == NULL) { fprintf(stderr,"{null}"); return; } fprintf(stderr,"{%u,(%u)",nfs->filterid,(int)nfs->nparams); for(i=0;inparams;i++) { fprintf(stderr," %s",nfs->params[i]); } fprintf(stderr,"}"); } static void printfilter(struct NC_HDF5_Filter* nfs, const char* tag, int line) { fprintf(stderr,"%s: line=%d: ",tag,line); printfilter1(nfs); fprintf(stderr,"\n"); } static void printfilterlist(NC_VAR_INFO_T* var, const char* tag, int line) { int i; const char* name; if(var == NULL) name = "null"; else if(var->hdr.name == NULL) name = "?"; else name = var->hdr.name; fprintf(stderr,"%s: line=%d: var=%s filters=",tag,line,name); if(var != NULL) { NClist* filters = (NClist*)var->filters; for(i=0;ifilters; if(filters == NULL) goto done; PRINTFILTERLIST(var,"free: before"); /* Free the filter list backward */ for(i=nclistlength(filters)-1;i>=0;i--) { struct NC_HDF5_Filter* spec = (struct NC_HDF5_Filter*)nclistremove(filters,i); if(spec->nparams > 0) nullfree(spec->params); nullfree(spec); } PRINTFILTERLIST(var,"free: after"); nclistfree(filters); var->filters = NULL; done: return stat; } static int NC4_hdf5_filter_free(struct NC_HDF5_Filter* spec) { if(spec == NULL) goto done; PRINTFILTER(spec,"free"); if(spec->nparams > 0) nullfree(spec->params) free(spec); done: return NC_NOERR; } int NC4_hdf5_addfilter(NC_VAR_INFO_T* var, unsigned int id, size_t nparams, const unsigned int* params, int flags) { int stat = NC_NOERR; struct NC_HDF5_Filter* fi = NULL; int olddef = 0; /* 1=>already defined */ NClist* flist = (NClist*)var->filters; if(nparams > 0 && params == NULL) {stat = NC_EINVAL; goto done;} if((stat=NC4_hdf5_filter_lookup(var,id,&fi))==NC_NOERR) { assert(fi != NULL); /* already exists */ olddef = 1; } else { stat = NC_NOERR; if((fi = calloc(1,sizeof(struct NC_HDF5_Filter))) == NULL) {stat = NC_ENOMEM; goto done;} fi->filterid = id; olddef = 0; } fi->nparams = nparams; if(fi->params != NULL) { nullfree(fi->params); fi->params = NULL; } assert(fi->params == NULL); if(fi->nparams > 0) { if((fi->params = (unsigned int*)malloc(sizeof(unsigned int)*fi->nparams)) == NULL) {stat = NC_ENOMEM; goto done;} memcpy(fi->params,params,sizeof(unsigned int)*fi->nparams); } fi->flags = flags; if(!olddef) { size_t pos = nclistlength(flist); /* Need to be careful about where we insert fletcher32 and shuffle */ if(nclistlength(flist) > 0) { if(id == H5Z_FILTER_FLETCHER32) pos = 0; /* alway first filter */ else if(id == H5Z_FILTER_SHUFFLE) { /* See if first filter is fletcher32 */ struct NC_HDF5_Filter* f0 = (struct NC_HDF5_Filter*)nclistget(flist,0); if(f0->filterid == H5Z_FILTER_FLETCHER32) pos = 1; else pos = 0; } } nclistinsert(flist,pos,fi); PRINTFILTERLIST(var,"add"); } fi = NULL; /* either way,its in the var->filters list */ done: if(fi) NC4_hdf5_filter_free(fi); return THROW(stat); } int NC4_hdf5_filter_remove(NC_VAR_INFO_T* var, unsigned int id) { int k; NClist* flist = (NClist*)var->filters; /* Walk backwards */ for(k=nclistlength(flist)-1;k>=0;k--) { struct NC_HDF5_Filter* f = (struct NC_HDF5_Filter*)nclistget(flist,k); if(f->filterid == id) { /* Remove from variable */ nclistremove(flist,k); #ifdef TFILTERS PRINTFILTERLIST(var,"remove"); fprintf(stderr,"\tid=%s\n",id); #endif /* Reclaim */ NC4_hdf5_filter_free(f); return NC_NOERR; } } return NC_ENOFILTER; } int NC4_hdf5_filter_lookup(NC_VAR_INFO_T* var, unsigned int id, struct NC_HDF5_Filter** specp) { size_t i; NClist* flist = (NClist*)var->filters; if(flist == NULL) { if((flist = nclistnew())==NULL) return NC_ENOMEM; var->filters = (void*)flist; } for(i=0;ifilterid) { if(specp) *specp = spec; return NC_NOERR; } } return NC_ENOFILTER; } int NC4_hdf5_def_var_filter(int ncid, int varid, unsigned int id, size_t nparams, const unsigned int* params) { int stat = NC_NOERR; NC *nc; NC_FILE_INFO_T* h5 = NULL; NC_GRP_INFO_T* grp = NULL; NC_VAR_INFO_T* var = NULL; struct NC_HDF5_Filter* oldspec = NULL; int flags = 0; htri_t avail = -1; int havedeflate = 0; int haveszip = 0; LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid)); if((stat = NC_check_id(ncid,&nc))) return stat; assert(nc); /* Find info for this file and group and var, and set pointer to each. */ if ((stat = nc4_hdf5_find_grp_h5_var(ncid, varid, &h5, &grp, &var))) {stat = THROW(stat); goto done;} assert(h5 && var && var->hdr.id == varid); /* If the HDF5 dataset has already been created, then it is too * late to set all the extra stuff. */ if (!(h5->flags & NC_INDEF)) {stat = THROW(NC_EINDEFINE); goto done;} if (!var->ndims) {stat = NC_EINVAL; goto done;} /* For scalars, complain */ if (var->created) {stat = THROW(NC_ELATEDEF); goto done;} /* Can't turn on parallel and szip before HDF5 1.10.2. */ #ifdef USE_PARALLEL #ifndef HDF5_SUPPORTS_PAR_FILTERS if (h5->parallel == NC_TRUE) {stat = THROW(NC_EINVAL); goto done;} #endif /* HDF5_SUPPORTS_PAR_FILTERS */ #endif /* USE_PARALLEL */ /* See if this filter is missing or not */ if((avail = H5Zfilter_avail(id)) < 0) {stat = NC_EHDFERR; goto done;} /* Something in HDF5 went wrong */ if(avail == 0) {stat = NC_ENOFILTER; goto done;} /* filter not available */ /* Lookup incoming id to see if already defined for this variable*/ switch((stat=NC4_hdf5_filter_lookup(var,id,&oldspec))) { case NC_NOERR: break; /* already defined */ case NC_ENOFILTER: break; /*not defined*/ default: goto done; } stat = NC_NOERR; /* reset */ /* See if deflate &/or szip is defined */ switch ((stat = NC4_hdf5_filter_lookup(var,H5Z_FILTER_DEFLATE,NULL))) { case NC_NOERR: havedeflate = 1; break; case NC_ENOFILTER: havedeflate = 0; break; default: goto done; } switch ((stat = NC4_hdf5_filter_lookup(var,H5Z_FILTER_SZIP,NULL))) { case NC_NOERR: haveszip = 1; break; case NC_ENOFILTER: haveszip = 0; break; default: goto done; } stat = NC_NOERR; /* reset */ if(!avail) { NC_HDF5_VAR_INFO_T* hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info; flags |= NC_HDF5_FILTER_MISSING; /* mark variable as unreadable */ hdf5_var->flags |= NC_HDF5_VAR_FILTER_MISSING; } /* If incoming filter not already defined, then check for conflicts */ if(oldspec == NULL) { if(id == H5Z_FILTER_DEFLATE) { int level; if(nparams != 1) {stat = THROW(NC_EFILTER); goto done;}/* incorrect no. of parameters */ level = (int)params[0]; if (level < NC_MIN_DEFLATE_LEVEL || level > NC_MAX_DEFLATE_LEVEL) {stat = THROW(NC_EINVAL); goto done;} /* If szip compression is already applied, return error. */ if(haveszip) {stat = THROW(NC_EINVAL); goto done;} } if(id == H5Z_FILTER_SZIP) { /* Do error checking */ if(nparams != 2) {stat = THROW(NC_EFILTER); goto done;}/* incorrect no. of parameters */ /* Pixels per block must be an even number, <= 32. */ if (params[1] % 2 || params[1] > NC_MAX_PIXELS_PER_BLOCK) {stat = THROW(NC_EINVAL); goto done;} /* If zlib compression is already applied, return error. */ if(havedeflate) {stat = THROW(NC_EINVAL); goto done;} } /* Filter => chunking */ var->storage = NC_CHUNKED; /* Determine default chunksizes for this variable unless already specified */ if(var->chunksizes && !var->chunksizes[0]) { /* Should this throw error? */ if((stat = nc4_find_default_chunksizes2(grp, var))) goto done; /* Adjust the cache. */ if ((stat = nc4_adjust_var_cache(grp, var))) goto done; } } /* More error checking */ if(id == H5Z_FILTER_SZIP) { /* szip X chunking error checking */ /* For szip, the pixels_per_block parameter must not be greater * than the number of elements in a chunk of data. */ size_t num_elem = 1; int d; for (d = 0; d < var->ndims; d++) if (var->dim[d]->len) num_elem *= var->dim[d]->len; /* Pixels per block must be <= number of elements. */ if (params[1] > num_elem) {stat = THROW(NC_EINVAL); goto done;} } /* addfilter can handle case where filter is already defined, and will just replace parameters */ if((stat = NC4_hdf5_addfilter(var,id,nparams,params,flags))) goto done; #ifdef USE_PARALLEL #ifdef HDF5_SUPPORTS_PAR_FILTERS /* Switch to collective access. HDF5 requires collevtive access * for filter use with parallel I/O. */ if (h5->parallel) var->parallel_access = NC_COLLECTIVE; #else if (h5->parallel) {stat = THROW(NC_EINVAL); goto done;} #endif /* HDF5_SUPPORTS_PAR_FILTERS */ #endif /* USE_PARALLEL */ done: return stat; } int NC4_hdf5_inq_var_filter_ids(int ncid, int varid, size_t* nfiltersp, unsigned int* ids) { int stat = NC_NOERR; NC *nc; NC_FILE_INFO_T* h5 = NULL; NC_GRP_INFO_T* grp = NULL; NC_VAR_INFO_T* var = NULL; NClist* flist = NULL; size_t nfilters; LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid)); if((stat = NC_check_id(ncid,&nc))) return stat; assert(nc); /* Find info for this file and group and var, and set pointer to each. */ if ((stat = nc4_hdf5_find_grp_h5_var(ncid, varid, &h5, &grp, &var))) {stat = THROW(stat); goto done;} assert(h5 && var && var->hdr.id == varid); flist = var->filters; nfilters = nclistlength(flist); if(nfilters > 0 && ids != NULL) { size_t k; for(k=0;kfilterid; } } if(nfiltersp) *nfiltersp = nfilters; done: return stat; } int NC4_hdf5_inq_var_filter_info(int ncid, int varid, unsigned int id, size_t* nparamsp, unsigned int* params) { int stat = NC_NOERR; NC *nc; NC_FILE_INFO_T* h5 = NULL; NC_GRP_INFO_T* grp = NULL; NC_VAR_INFO_T* var = NULL; struct NC_HDF5_Filter* spec = NULL; LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid)); if((stat = NC_check_id(ncid,&nc))) return stat; assert(nc); /* Find info for this file and group and var, and set pointer to each. */ if ((stat = nc4_hdf5_find_grp_h5_var(ncid, varid, &h5, &grp, &var))) {stat = THROW(stat); goto done;} assert(h5 && var && var->hdr.id == varid); if((stat = NC4_hdf5_filter_lookup(var,id,&spec))) goto done; if(nparamsp) *nparamsp = spec->nparams; if(params && spec->nparams > 0) { memcpy(params,spec->params,sizeof(unsigned int)*spec->nparams); } done: return stat; } /* Return ID for the first missing filter; 0 if no missing filters */ int NC4_hdf5_find_missing_filter(NC_VAR_INFO_T* var, unsigned int* idp) { size_t i; int stat = NC_NOERR; NClist* flist = (NClist*)var->filters; int id = 0; for(i=0;iflags & NC_HDF5_FILTER_MISSING) {id = spec->filterid; break;} } if(idp) *idp = id; return stat; } int NC4_hdf5_filter_initialize(void) { return NC_NOERR; } int NC4_hdf5_filter_finalize(void) { return NC_NOERR; } /* Test if filter available */ int NC4_hdf5_inq_filter_avail(int ncid, unsigned id) { int stat = NC_NOERR; htri_t avail = -1; NC_UNUSED(ncid); /* See if this filter is available or not */ if((avail = H5Zfilter_avail(id)) < 0) {stat = NC_EHDFERR; goto done;} /* Something in HDF5 went wrong */ if(avail == 0) stat = NC_ENOFILTER; done: return stat; }