Fix jira NCF-249

libdap2/common34.c

@@ -433,17 +433,25 @@ buildcdftree34r(NCDAPCOMMON* nccomm, OCddsnode ocnode, CDFnode* container,
 {
     size_t i,ocrank,ocnsubnodes;
     OCtype octype;
+    OCtype ocatomtype;
     char* ocname = NULL;
     NCerror ncerr = NC_NOERR;
     CDFnode* cdfnode;
 
     oc_dds_class(nccomm->oc.conn,ocnode,&octype);
+    if(octype == OC_Atomic)
+	oc_dds_atomictype(nccomm->oc.conn,ocnode,&ocatomtype);
+    else
+	ocatomtype = OC_NAT;
     oc_dds_name(nccomm->oc.conn,ocnode,&ocname);
     oc_dds_rank(nccomm->oc.conn,ocnode,&ocrank);
     oc_dds_nsubnodes(nccomm->oc.conn,ocnode,&ocnsubnodes);
 
 #ifdef DEBUG1
-    fprintf(stderr,"buildcdftree: connect: %s %s\n",oc_typetostring(octype),ocname);
+    if(ocatomtype == OC_NAT)
+	fprintf(stderr,"buildcdftree: connect: %s %s\n",oc_typetostring(octype),ocname);
+    else
+	fprintf(stderr,"buildcdftree: connect: %s %s\n",oc_typetostring(ocatomtype),ocname);
 #endif
 
     switch (octype) {

libdap2/dapdebug.h

@@ -7,7 +7,7 @@
 #define DEBUG_H
 
 
-#if 0
+#if 1
 #define DAPDEBUG 1
 #define OCDEBUG
 #endif

libdap2/dapodom.c

@@ -12,25 +12,27 @@
 
 /* Build an odometer covering slices startslice upto, but not including, stopslice */
 Dapodometer*
-dapodom_fromsegment(DCEsegment* segment, size_t startslice, size_t stopslice)
+dapodom_fromsegment(DCEsegment* segment, size_t startindex, size_t stopindex)
 {
     int i;
     Dapodometer* odom;
 
-    assert(stopslice > startslice);
-    assert((stopslice - startslice) <= NC_MAX_VAR_DIMS);
+    assert(stopindex > startindex);
+    assert((stopindex - startindex) <= NC_MAX_VAR_DIMS);
     odom = (Dapodometer*)calloc(1,sizeof(Dapodometer));
     MEMCHECK(odom,NULL);
-    odom->rank = (stopslice - startslice);
+    odom->rank = (stopindex - startindex);
     for(i=0;i<odom->rank;i++) {
-	odom->start[i] = segment->slices[i+startslice].first;
-	odom->count[i] = segment->slices[i+startslice].count;
-	odom->stride[i] = segment->slices[i+startslice].stride;
-	odom->declsize[i] = segment->slices[i+startslice].declsize;
-	odom->stop[i] = odom->start[i] + odom->count[i];
+	odom->start[i] = segment->slices[i+startindex].first;
+	odom->stride[i] = segment->slices[i+startindex].stride;
+	odom->stop[i] = (segment->slices[i+startindex].last + 1);
 	/* should the above line be instead?
  	odom->stop[i] = odom->start[i] + (odom->count[i]*odom->stride[i]);
 	*/
+#if 0
+	odom->count[i] = segment->slices[i+startindex].count;
+#endif
+	odom->declsize[i] = segment->slices[i+startindex].declsize;
 	odom->index[i] = odom->start[i];
     }    
     return odom;
@@ -47,13 +49,17 @@ dapodom_new(size_t rank,
     odom->rank = rank;
     assert(odom->rank <= NC_MAX_VAR_DIMS);
     for(i=0;i<odom->rank;i++) {
-	odom->start[i] = (start != NULL ? start[i] : 0);
-	odom->count[i] = (count != NULL ? count[i]
-                                        : (size != NULL ? size[i] : 1));
-	odom->stride[i] = (size_t)(stride != NULL ? stride[i] : 1);
-	odom->declsize[i] = (size != NULL ? size[i]
-				      : (odom->start[i]+odom->count[i]));
-	odom->stop[i] = odom->start[i] + odom->count[i];
+	size_t istart,icount,istop,ideclsize;
+	ptrdiff_t istride;
+	istart = (start != NULL ? start[i] : 0);
+	icount = (count != NULL ? count[i] : (size != NULL ? size[i] : 1));
+	istride = (size_t)(stride != NULL ? stride[i] : 1);
+	istop = istart + icount*istride;
+	ideclsize = (size != NULL ? size[i]: (istop - istart));
+	odom->start[i] = istart;
+	odom->stop[i] = istop;
+	odom->stride[i] = istride;
+	odom->declsize[i] = ideclsize;
 	odom->index[i] = odom->start[i];
     }    
     return odom;

libdap2/dapodom.h

@@ -11,7 +11,9 @@ typedef struct Dapodometer {
     int            rank;
     size_t         index[NC_MAX_VAR_DIMS];
     size_t         start[NC_MAX_VAR_DIMS];
+#if 0
     size_t         count[NC_MAX_VAR_DIMS];
+#endif
     size_t         stride[NC_MAX_VAR_DIMS];
     size_t         stop[NC_MAX_VAR_DIMS];
     size_t         declsize[NC_MAX_VAR_DIMS];

libdap2/dceconstraints.c

@@ -65,12 +65,12 @@ fprintf(stderr,"constraint: %s",dcetostring((DCEnode*)dapconstraint));
 
 #ifdef DEBUG1
 static void
-dumpslice(const char* prefix, DCEslice* s)
+slicedump(const char* prefix, DCEslice* s)
 {
 #if 1
     int v = dceverbose;
     dceverbose = 1;
-    fprintf(stderr,"%s: %s\n",prefix,dcetostring(s));
+    fprintf(stderr,"%s: %s\n",prefix,dcetostring((DCEnode*)s));
     dceverbose = v;
 #else
     size_t last = (s->first+s->length)-1;
@@ -199,8 +199,8 @@ dceslicecompose(DCEslice* s1, DCEslice* s2, DCEslice* result)
     size_t lastx = 0;
     DCEslice sr; /* For back compatability so s1 and result can be same object */
 #ifdef DEBUG1
-dumpslice("compose: s1",s1);
-dumpslice("compose: s2",s2);
+slicedump("compose: s1",s1);
+slicedump("compose: s2",s2);
 #endif
     sr.node.sort = CES_SLICE;
     sr.stride    = s1->stride * s2->stride;
@@ -213,10 +213,10 @@ dumpslice("compose: s2",s2);
     sr.declsize = XMAX(s1->declsize,s2->declsize); /* use max declsize */
     /* fill in other fields */
     sr.count = (sr.length + (sr.stride - 1))/sr.stride;
-#ifdef DEBUG1
-dumpslice("compose: result",sr);
-#endif
     *result = sr;
+#ifdef DEBUG1
+slicedump("compose: result",result);
+#endif
     return err;
 }
 

libdap2/getvara.h

@@ -31,8 +31,8 @@ typedef struct Getvara {
     void* memory; /* where result is put*/
     struct NCcachenode* cache;
     struct DCEprojection* varaprojection;
-    /* associated variable*/
-    OCtype dsttype;
+    /* associated nc variable*/
+    nc_type dsttype;
     CDFnode* target;
     int wholevariable;
 } Getvara;

libdap2/getvara3.c

@@ -158,7 +158,7 @@ nc3d_getvarx(int ncid, int varid,
 int i;
 fprintf(stderr,"getvarx: %s",cdfvar->ncfullname);
 for(i=0;i<ncrank;i++)
-  fprintf(stderr,"[%ld:%ld:%ld]",
+  fprintf(stderr,"(%ld:%ld:%ld)",
 	(long)startp[i],
 	(long)countp[i],
 	(long)stridep[i]
@@ -199,7 +199,7 @@ NClist* dims = cdfvar->array.dimsetall;
 fprintf(stderr,"getvarx: %s",cdfvar->ncfullname);
 if(nclistlength(dims) > 0) {int i;
 for(i=0;i<nclistlength(dims);i++) 
-fprintf(stderr,"[%lu:%lu:%lu]",(unsigned long)startp[i],(unsigned long)countp[i],(unsigned long)stridep[i]);
+fprintf(stderr,"(%lu:%lu:%lu)",(unsigned long)startp[i],(unsigned long)countp[i],(unsigned long)stridep[i]);
 fprintf(stderr," -> ");
 for(i=0;i<nclistlength(dims);i++) 
 if(stridep[i]==1)

ncdap_test/Makefile.am

@@ -36,14 +36,17 @@ test_vara_SOURCES = test_vara.c
 test_partvar_SOURCES = test_partvar.c
 test_varm3_SOURCES = test_varm3.c
 t_dap3a_SOURCES = t_dap3a.c
+test_nstride_cached_SOURCE = test_nstride_cached.c
 
 TESTS += t_dap3a test_cvt3 test_vara test_partvar
 TESTS += test_varm3
 TESTS += t_dap3a
+TESTS += test_nstride_cached
 
 check_PROGRAMS += t_dap3a test_cvt3 test_vara test_partvar
 check_PROGRAMS += test_varm3
 check_PROGRAMS += t_dap3a
+check_PROGRAMS += test_nstride_cached
 
 endif #ENABLE_DAP_REMOTE_TESTS
 
@@ -80,7 +83,7 @@ EXTRA_DIST = tst_ncdap3.sh tst_ncdap4.sh \
              tst_ncdap.sh tst_ncdap_shared.sh tst_remote.sh \
 	     t_dap.c CMakeLists.txt
 
-CLEANFILES = test_varm3 test_cvt3 results/*.dmp results/*.das results/*.dds datadds* t_dap3a
+CLEANFILES = test_varm3 test_cvt3 results/*.dmp results/*.das results/*.dds datadds* t_dap3a test_nstride_cached
 
 if USE_NETCDF4
 CLEANFILES += test_cvt4 t_dap4

ncdap_test/test_nstride_cached.c

@@ -0,0 +1,233 @@
+/*
+Report from Ansely Manke:
+I've attached a file with a short c program that
+demonstrates what I'm seeing. I don't know that we'd call
+this a constraint, so that was a misleading description.
+
+The thing I'm mimicking is a sequence where I read the 2-D
+coordinate variables, make some decisions about the size of
+a subset region, and then define index ranges and strides
+for reading other variables.  Reading the full variable
+happens correctly, but the read with strides winds up
+messing up the data.  Here it shows up returning some valid
+data and some zero's, but in other sequences of events it
+seems to be actually mis-ordered.
+
+I notice that the results are correct if the initial read of
+the variable uses counts that are size-1. So that might be a
+clue.  And the read is correct if I either close and reopen
+the dataset after reading the original full variable, or if
+I don't do that step of first reading the whole grid. It's
+also fine with NetCDF 4.2.1.1.
+
+-Ansley
+
+Problem was two-fold:
+1. struct Getvara has the dsttype field as OC_Type rather than nc_type
+2. the dap odometer code dapnew_segment was incorrectly
+   handling strides > 1: specifically, the stop position was incorrect.
+
+*/
+
+/* vars_whoi_test */
+/* acm 4/2013 */
+/* ansley.b.manke@noaa.gov */
+/*
+/* test nc_get_vars_float with calls similar to Ferret calls */
+
+
+/*linked with:
+
+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
+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
+
+*/
+
+/* Closing and reopening the dataset between the two reads fixes the
+incorrect data return */
+
+/* Setting the count to one less in the full data read also fixes the
+incorrect data return */
+
+#include<stdlib.h>
+#include<stdio.h>
+#include<string.h>
+#include "netcdf.h"
+
+static int coords = 0;
+
+static char* URL="[noprefetch]http://geoport.whoi.edu/thredds/dodsC/coawst_4/use/fmrc/coawst_4_use_best.ncd";
+
+int
+main()
+{
+
+    int ncid;
+    int varid;
+    int i;
+    int ncstatus;
+    size_t start[5], count[5];
+    ptrdiff_t stride[5], tmp_ptrdiff_t;
+
+    int idim, ndim;
+    float dat[301060];
+    float sdat[10];
+
+    for (idim=0; idim<5; idim++) {
+        start[idim] = 0;
+        count[idim] = 1;
+        stride[idim] = 1;
+    }
+
+    ndim=2;
+
+    printf(" \n");
+    printf("********************\n");
+    printf("open URL %s\n",URL);
+    printf(" \n");
+
+    ncstatus = nc_open(URL, NC_NOWRITE, &ncid);
+
+    ncstatus = nc_inq_varid(ncid, "lon_rho", &varid);
+
+    printf("varid = %d\n", varid);
+    printf("ncid = %d\n", ncid);
+
+    ndim=2;
+
+
+    printf(" \n");
+    printf("********************\n");
+    printf("Read lon_rho data w/o strides\n");
+    printf(" \n");
+
+    start[0] = 0;
+    start[1] = 0;
+    start[2] = 0;
+    start[3] = 0;
+
+    count[0] =  336;
+    count[1] =  896;
+
+    stride[0] = 1;
+    stride[1] = 1;
+
+    for (idim=0; idim<ndim; idim++)
+	printf("start[%1d]=%3d count[%1d]=%3d stride[%1d]=%3d\n",
+		idim,start[idim],idim,count[idim],idim,stride[idim]);
+
+    ncstatus = nc_get_vars_float (ncid, varid, start, count, stride, (float*) dat);
+
+if(coords) {
+    printf(" \n");
+    printf("********************\n");
+    printf("Print some of lon_rho\n");
+    printf(" \n");
+
+    for (i=0; i<10; i++)
+        printf("lon_rho[%d] = %f\n",i,dat[i]);
+    printf(" \n");
+
+    for (i=301045; i<301055; i++)
+        printf("lon_rho[%d] = %f\n",i,dat[i]);
+    printf(" \n");
+}
+
+    memset((void*)dat,0,sizeof(dat));
+
+    /* Read a second variable */
+
+    ncstatus = nc_inq_varid(ncid, "lat_rho", &varid);
+
+    printf("varid = %d\n", varid);
+    printf("ncid = %d\n", ncid);
+
+    ndim=2;
+
+    printf(" \n");
+    printf("********************\n");
+    printf("Read lat_rho data w/o strides\n");
+    printf(" \n");
+
+    start[0] = 0;
+    start[1] = 0;
+    start[2] = 0;
+    start[3] = 0;
+
+    count[0] =  336;
+    count[1] =  896;
+
+    stride[0] = 1;
+    stride[1] = 1;
+
+    for (idim=0; idim<ndim; idim++)
+        printf("start[%d]=%3d count[%d]=%3d stride[%d]=%3d\n",
+		idim, start[idim], idim, count[idim], idim, stride[idim]);
+
+    ncstatus = nc_get_vars_float (ncid, varid, start, count, stride, (float*) dat);
+
+if(coords) {
+    printf(" \n");
+    printf("********************\n");
+    printf("Print some of lat_rho\n");
+    printf(" \n");
+    for (i=0; i<10; i++)
+        printf("lat_rho[%d] = %f\n",i,dat[i]);
+    printf(" \n");
+
+    printf(" \n");
+    for (i=301045; i<301055; i++)
+        printf("lon_rho[%d] = %f\n",i,dat[i]);
+    printf(" \n");
+}
+
+    memset((void*)dat,0,sizeof(dat));
+
+    /* close and reopen the dataset, then the below read is correct
+
+    printf(" \n");
+    printf("********************\n");
+    printf("Close and reopen the dataset\n");
+
+    ncstatus = nc_close (ncid);
+    ncstatus = nc_open(URL, NC_NOWRITE, &ncid);
+
+    /*  ----------------------------------------------------- */
+    /* Read a subset of the data with strides */
+
+    ncstatus = nc_inq_varid(ncid, "lon_rho", &varid);
+
+    printf(" \n");
+    printf("********************\n");
+    printf("Read a subset of lon_rho data with strides\n");
+    printf(" \n");
+
+    start[0] = 250;
+    start[1] = 704;
+
+    count[0] =  5;
+    count[1] =  2;
+
+    stride[0] = 2;
+    stride[1] = 4;
+
+    for (idim=0; idim<ndim; idim++)
+	printf("start[%1d]=%3d count[%1d]=%3d stride[%1d]=%3d\n",
+		idim,start[idim],idim,count[idim],idim,stride[idim]);
+
+    memset((void*)sdat,0,sizeof(sdat));
+    ncstatus = nc_get_vars_float (ncid, varid, start, count, stride,  (float*) sdat);
+
+    printf("status = %d\n", ncstatus);
+
+    printf(" \n");
+    printf("********************\n");
+    printf("Print  values read. They should all be -67.xxxx \n");
+    printf(" \n");
+
+    for (i=0; i<10; i++)
+        printf("lon_rho[%d] = %f\n",i,sdat[i]);
+
+    ncstatus = nc_close (ncid);
+
+}