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25f062528b
The file docs/indexing.dox tries to provide design information for the refactoring. The primary change is to replace all walking of linked lists with the use of the NCindex data structure. Ncindex is a combination of a hash table (for name-based lookup) and a vector (for walking the elements in the index). Additionally, global vectors are added to NC_HDF5_FILE_INFO_T to support direct mapping of an e.g. dimid to the NC_DIM_INFO_T object. These global vectors exist for dimensions, types, and groups because they have globally unique id numbers. WARNING: 1. since libsrc4 and libsrchdf4 share code, there are also changes in libsrchdf4. 2. Any outstanding pull requests that change libsrc4 or libhdf4 are likely to cause conflicts with this code. 3. The original reason for doing this was for performance improvements, but as noted elsewhere, this may not be significant because the meta-data read performance apparently is being dominated by the hdf5 library because we do bulk meta-data reading rather than lazy reading.
297 lines
7.2 KiB
C
297 lines
7.2 KiB
C
/*
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Report from Ansely Manke:
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I've attached a file with a short c program that
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demonstrates what I'm seeing. I don't know that we'd call
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this a constraint, so that was a misleading description.
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The thing I'm mimicking is a sequence where I read the 2-D
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coordinate variables, make some decisions about the size of
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a subset region, and then define index ranges and strides
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for reading other variables. Reading the full variable
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happens correctly, but the read with strides winds up
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messing up the data. Here it shows up returning some valid
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data and some zero's, but in other sequences of events it
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seems to be actually mis-ordered.
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I notice that the results are correct if the initial read of
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the variable uses counts that are size-1. So that might be a
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clue. And the read is correct if I either close and reopen
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the dataset after reading the original full variable, or if
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I don't do that step of first reading the whole grid. It's
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also fine with NetCDF 4.2.1.1.
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-Ansley
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Problem was two-fold:
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1. struct Getvara has the dsttype field as OC_Type rather than nc_type
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2. the dap odometer code dapnew_segment was incorrectly
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handling strides > 1: specifically, the stop position was incorrect.
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*/
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/* vars_whoi_test */
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/* acm 4/2013 */
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/* ansley.b.manke@noaa.gov */
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/* test nc_get_vars_float with calls similar to Ferret calls */
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/*linked with:
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cc vars_whoi_test.c -g -o vars_whoi_test_4211 /usr/local/netcdf_4211/lib/libnetcdf.a /usr/local/hdf5_189/lib/libhdf5_hl.a /usr/local/hdf5_189/lib/libhdf5.a /usr/local/lib/libz.a -L/usr/lib64 -lc -lm -lcurl
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cc vars_whoi_test.c -g -o vars_whoi_test /home/users/ansley/local/x86_nc43/lib/libnetcdf.a /usr/local/hdf5_189/lib/libhdf5_hl.a /usr/local/hdf5_189/lib/libhdf5.a /usr/local/lib/libz.a -L/usr/lib64 -lc -lm -lcurl
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Closing and reopening the dataset between the two reads fixes the
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incorrect data return
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Setting the count to one less in the full data read also fixes the
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incorrect data return
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*/
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#include<stdlib.h>
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#include<stdio.h>
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#include<string.h>
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#include "netcdf.h"
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#include "ncdispatch.h"
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#include "nctestserver.h"
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#define VERBOSE 1
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/*
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2014-07-01: (DMH) Changed the URL to use one from remotetest server.
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to remove dependence on an external server.
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*/
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/*
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static char* URL="http://geoport.whoi.edu/thredds/dodsC/coawst_4/use/fmrc/coawst_4_use_best.ncd";
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Float64 lon_rho[eta_rho = 336][xi_rho = 896];
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Float64 lat_rho[eta_rho = 336][xi_rho = 896];
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*/
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#define URL "%s/dodsC/testdods/rtofs.nc"
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#define VAR1 "Latitude"
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#define VAR2 "Longitude"
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#define XSIZE 850
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#define YSIZE 712
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static char url[1024];
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int
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main()
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{
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int ncid;
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int varid;
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int i;
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int ncstatus;
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size_t start[5], count[5];
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ptrdiff_t stride[5];
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int pass = 1;
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int nelems = XSIZE*YSIZE;
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int idim, ndim;
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float *dat = (float*)malloc(sizeof(float)*nelems);
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float sdat[10];
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char* svc;
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/* Find Test Server */
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svc = nc_findtestserver("thredds",0,REMOTETESTSERVERS);
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if(svc == NULL) {
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fprintf(stderr,"Cannot locate test server\n");
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exit(0);
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}
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snprintf(url,sizeof(url),URL,svc);
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for (idim=0; idim<5; idim++) {
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start[idim] = 0;
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count[idim] = 1;
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stride[idim] = 1;
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}
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ndim=2;
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printf(" \n");
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printf("********************\n");
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printf("open URL %s\n",url);
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printf(" \n");
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ncstatus = nc_open(url, NC_NOWRITE, &ncid);
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if(ncstatus != NC_NOERR) {
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fprintf(stderr,"Could not open: %s; server may be down; test ignored\n",url);
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exit(0);
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}
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ncstatus = nc_inq_varid(ncid, VAR1, &varid);
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ndim=2;
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#ifdef VERBOSE
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printf(" \n");
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printf("********************\n");
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printf("Read %s data w/o strides\n",VAR1);
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printf(" \n");
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#endif
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start[0] = 0;
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start[1] = 0;
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start[2] = 0;
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start[3] = 0;
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count[0] = XSIZE;
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count[1] = YSIZE;
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stride[0] = 1;
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stride[1] = 1;
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#ifdef VERBOSE
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for (idim=0; idim<ndim; idim++)
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printf("start[%1d]=%3lu count[%1d]=%3lu stride[%1d]=%3lu\n",
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idim,(unsigned long)start[idim],idim,(unsigned long)count[idim],idim,(unsigned long)stride[idim]);
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#endif
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ncstatus = nc_get_vars_float (ncid, varid, start, count, stride, (float*) dat);
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#ifdef VERBOSE
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printf(" \n");
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printf("********************\n");
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printf("Print some of %s\n",VAR1);
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printf(" \n");
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for (i=0; i<10; i++)
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printf("%s[%d] = %f\n",VAR1,i,dat[i]);
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printf(" \n");
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for (i=(nelems-11); i<(nelems-1); i++)
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printf("%s[%d] = %f\n",VAR1,i,dat[i]);
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printf(" \n");
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#endif
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memset((void*)dat,0,sizeof(dat));
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/* Read a second variable */
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ncstatus = nc_inq_varid(ncid, VAR2, &varid);
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ndim=2;
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#ifdef VERBOSE
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printf(" \n");
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printf("********************\n");
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printf("Read %s data w/o strides\n",VAR2);
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printf(" \n");
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#endif
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start[0] = 0;
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start[1] = 0;
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start[2] = 0;
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start[3] = 0;
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count[0] = XSIZE;
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count[1] = YSIZE;
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stride[0] = 1;
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stride[1] = 1;
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#ifdef VERBOSE
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for (idim=0; idim<ndim; idim++)
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printf("start[%d]=%3lu count[%d]=%3lu stride[%d]=%3lu\n",
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idim, (unsigned long)start[idim], idim, (unsigned long)count[idim], idim, (unsigned long)stride[idim]);
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#endif
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ncstatus = nc_get_vars_float (ncid, varid, start, count, stride, (float*) dat);
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#ifdef VERBOSE
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printf(" \n");
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printf("********************\n");
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printf("Print some of %s\n",VAR2);
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printf(" \n");
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for (i=0; i<10; i++)
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printf("%s[%d] = %f\n",VAR2,i,dat[i]);
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printf(" \n");
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printf(" \n");
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for (i=(nelems-11); i<(nelems-1); i++)
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printf("%s[%d] = %f\n",VAR2,i,dat[i]);
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printf(" \n");
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#endif
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memset((void*)dat,0,sizeof(dat));
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/* close and reopen the dataset, then the below read is correct */
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#ifdef VERBOSE
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printf(" \n");
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printf("********************\n");
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printf("Close and reopen the dataset\n");
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#endif
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ncstatus = nc_close (ncid);
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ncstatus = nc_open(url, NC_NOWRITE, &ncid);
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/* ----------------------------------------------------- */
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/* Read a subset of the data with strides */
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ncstatus = nc_inq_varid(ncid, VAR1, &varid);
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#ifdef VERBOSE
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printf(" \n");
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printf("********************\n");
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printf("Read a subset of %s data with strides\n",VAR1);
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printf(" \n");
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#endif
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start[0] = 250;
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start[1] = 704;
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count[0] = 5;
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count[1] = 2;
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stride[0] = 2;
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stride[1] = 4;
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#ifdef VERBOSE
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for (idim=0; idim<ndim; idim++)
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printf("start[%1d]=%3lu count[%1d]=%3lu stride[%1d]=%3lu\n",
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idim,(unsigned long)start[idim],idim,(unsigned long)count[idim],idim,(unsigned long)stride[idim]);
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#endif
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memset((void*)sdat,0,sizeof(sdat));
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ncstatus = nc_get_vars_float (ncid, varid, start, count, stride, (float*) sdat);
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printf("status = %d\n", ncstatus);
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/* Verify that all read values are 50 <= n < 51 */
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for (i=0; i<10; i++) {
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if(sdat[i] <= 50.0 || sdat[i] > 51.0) {
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printf("Out of range: %s[%d] = %f\n",VAR1, i,sdat[i]);
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pass = 0;
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}
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}
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#ifdef VERBOSE
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printf(" \n");
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printf("********************\n");
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printf("Print values read. They should all be 50.xxxx \n");
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printf(" \n");
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for (i=0; i<10; i++)
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printf("%s[%d] = %f\n",VAR1,i,sdat[i]);
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#endif
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ncstatus = nc_close (ncid);
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if(!pass) {
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printf("*** FAIL: %s value out of range.\n",VAR1);
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exit(1);
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}
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printf("*** PASS\n");
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free(dat);
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exit(0);
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}
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