Merge branch 'master' into fix-warnings

CMakeLists.txt

@@ -750,7 +750,7 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
     SET(H5_USE_16_API 0)
   ENDIF()
 
-  FIND_PATH(HAVE_HDF5_H hdf5.h)
+  FIND_PATH(HAVE_HDF5_H hdf5.h PATHS ${HDF5_INCLUDE_DIR})
   IF(NOT HAVE_HDF5_H)
     MESSAGE(FATAL_ERROR "Compiling a test with hdf5 failed. Either hdf5.h cannot be found, or the log messages should be checked for another reason.")
   ELSE(NOT HAVE_HDF5_H)

examples/C/parallel_vara.c

@@ -4,7 +4,6 @@
  *  See COPYRIGHT notice in top-level directory.
  *
  *********************************************************************/
-
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * This example shows how to use nc_put_vara_int() to write a 2D 4-byte integer
  * array in parallel and read it back using the same array partitioning pattern.
@@ -81,7 +80,7 @@ int main(int argc, char** argv)
 {
     extern int optind;
     char filename[128];
-    int i, j, rank, nprocs, verbose=1, err;
+    int i, j, rank, nprocs, err;
     int ncid, cmode, omode, varid, dimid[2], buf[NY][NX];
     char str_att[128];
     float float_att[100];
@@ -94,8 +93,7 @@ int main(int argc, char** argv)
     /* get command-line arguments */
     while ((i = getopt(argc, argv, "hq")) != EOF)
         switch(i) {
-            case 'q': verbose = 0;
-                      break;
+            case 'q': break;
             case 'h':
             default:  if (rank==0) usage(argv[0]);
                       MPI_Finalize();

include/hdf5internal.h

@@ -104,7 +104,7 @@ int hdf5_set_log_level();
 /* These functions deal with HDF5 dimension scales. */
 int rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
 int rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
-int delete_existing_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim);
+int delete_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim);
 
 /* Write metadata. */
 int nc4_rec_write_metadata(NC_GRP_INFO_T *grp, nc_bool_t bad_coord_order);

libdap2/cache.c

@@ -151,8 +151,10 @@ nclog(NCLOGDBG,"prefetch: %s",var->ncfullname);
     newconstraint->selections = dceclonelist(urlconstraint->selections);
 
     for(i=0;i<nclistlength(vars);i++) {
-        CDFnode* var = (CDFnode*)nclistget(vars,i);
 	DCEprojection* varprojection;
+        CDFnode* var = (CDFnode*)nclistget(vars,i);
+	/* Ignore invisible vars */
+	if(var->invisible) continue; 
 	/* convert var to a projection */
 	ncstat = dapvar2projection(var,&varprojection);
 	if(ncstat != NC_NOERR) {THROWCHK(ncstat); goto done;}

libhdf5/hdf5attr.c

@@ -153,7 +153,6 @@ nc4_get_att_special(NC_FILE_INFO_T* h5, const char* name,
 int
 NC4_HDF5_rename_att(int ncid, int varid, const char *name, const char *newname)
 {
-   NC *nc;
    NC_GRP_INFO_T *grp;
    NC_FILE_INFO_T *h5;
    NC_VAR_INFO_T *var = NULL;
@@ -174,9 +173,9 @@ NC4_HDF5_rename_att(int ncid, int varid, const char *name, const char *newname)
       return NC_EMAXNAME;
 
    /* Find info for this file, group, and h5 info. */
-   if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
+   if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
       return retval;
-   assert(h5 && grp && h5);
+   assert(h5 && grp);
 
    /* If the file is read-only, return an error. */
    if (h5->no_write)

libhdf5/hdf5dim.c

@@ -206,7 +206,6 @@ NC4_inq_dim(int ncid, int dimid, char *name, size_t *lenp)
 int
 NC4_rename_dim(int ncid, int dimid, const char *name)
 {
-   NC *nc;
    NC_GRP_INFO_T *grp;
    NC_DIM_INFO_T *dim;
    NC_HDF5_DIM_INFO_T *hdf5_dim;
@@ -222,9 +221,9 @@ NC4_rename_dim(int ncid, int dimid, const char *name)
         dimid, name));
 
    /* Find info for this file and group, and set pointer to each. */
-   if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
+   if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
       return retval;
-   assert(nc && h5 && grp);
+   assert(h5 && grp);
 
    /* Trying to write to a read-only file? No way, Jose! */
    if (h5->no_write)
@@ -251,7 +250,7 @@ NC4_rename_dim(int ncid, int dimid, const char *name)
       LOG((3, "dim %s is a dim without variable", dim->hdr.name));
 
       /* Delete the dimscale-only dataset. */
-      if ((retval = delete_existing_dimscale_dataset(grp, dimid, dim)))
+      if ((retval = delete_dimscale_dataset(grp, dimid, dim)))
          return retval;
    }
 
@@ -262,8 +261,9 @@ NC4_rename_dim(int ncid, int dimid, const char *name)
    if (!(dim->hdr.name = strdup(norm_name)))
       return NC_ENOMEM;
    LOG((3, "dim is now named %s", dim->hdr.name));
-   dim->hdr.hashkey = NC_hashmapkey(dim->hdr.name,strlen(dim->hdr.name)); /* Fix hash key */
 
+   /* Fix hash key and rebuild index. */
+   dim->hdr.hashkey = NC_hashmapkey(dim->hdr.name,strlen(dim->hdr.name));
    if (!ncindexrebuild(grp->dim))
       return NC_EINTERNAL;
 

libhdf5/hdf5file.c

@@ -539,7 +539,7 @@ NC4_enddef(int ncid)
    LOG((1, "%s: ncid 0x%x", __func__, ncid));
 
    /* Find pointer to group and nc4_info. */
-   if ((retval = nc4_find_nc_grp_h5(ncid, NULL, &grp, &nc4_info)))
+   if ((retval = nc4_find_grp_h5(ncid, &grp, &nc4_info)))
       return retval;
 
    /* When exiting define mode, mark all variable written. */
@@ -650,7 +650,6 @@ int
 NC4_close(int ncid, void* params)
 {
    NC_GRP_INFO_T *grp;
-   NC *nc;
    NC_FILE_INFO_T *h5;
    int retval;
    int inmemory;
@@ -659,10 +658,10 @@ NC4_close(int ncid, void* params)
    LOG((1, "%s: ncid 0x%x", __func__, ncid));
 
    /* Find our metadata for this file. */
-   if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
+   if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
       return retval;
 
-   assert(nc && h5 && grp);
+   assert(h5 && grp);
 
    /* This must be the root group. */
    if (grp->parent)

libhdf5/hdf5internal.c

@@ -346,8 +346,7 @@ nc4_break_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var,
  * @author Ed Hartnett
  */
 int
-delete_existing_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid,
-                                 NC_DIM_INFO_T *dim)
+delete_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim)
 {
    NC_HDF5_DIM_INFO_T *hdf5_dim;
    NC_HDF5_GRP_INFO_T *hdf5_grp;

libhdf5/hdf5open.c

@@ -337,6 +337,8 @@ dimscale_visitor(hid_t did, unsigned dim, hid_t dsid,
 {
    H5G_stat_t statbuf;
 
+   LOG((4, "%s", __func__));
+
    /* Get more info on the dimscale object.*/
    if (H5Gget_objinfo(dsid, ".", 1, &statbuf) < 0)
       return -1;
@@ -1070,31 +1072,40 @@ get_attached_info(NC_VAR_INFO_T *var, NC_HDF5_VAR_INFO_T *hdf5_var, int ndims,
    int d;
    int num_scales = 0;
 
+   LOG((4, "%s ndims %d datasetid %ld", __func__, ndims, datasetid));
+
    /* Find out how many scales are attached to this
     * dataset. H5DSget_num_scales returns an error if there are no
     * scales, so convert a negative return value to zero. */
    num_scales = H5DSget_num_scales(datasetid, 0);
    if (num_scales < 0)
       num_scales = 0;
+   LOG((4, "num_scales %d", num_scales));
 
-   if (num_scales && ndims)
+   /* If an enddef has already been called, the dimscales will already
+    * be taken care of. */
+   if (num_scales && ndims && !var->dimscale_attached)
    {
       /* Allocate space to remember whether the dimscale has been
-       * attached for each dimension. */
+       * attached for each dimension, and the HDF5 object IDs of the
+       * scale(s). */
+      assert(!hdf5_var->dimscale_hdf5_objids);
       if (!(var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
          return NC_ENOMEM;
-
-      /* Store id information allowing us to match hdf5
-       * dimscales to netcdf dimensions. */
       if (!(hdf5_var->dimscale_hdf5_objids = malloc(ndims *
                                                     sizeof(struct hdf5_objid))))
          return NC_ENOMEM;
+
+      /* Store id information allowing us to match hdf5 dimscales to
+       * netcdf dimensions. */
       for (d = 0; d < var->ndims; d++)
       {
+         LOG((4, "about to iterate scales for dim %d", d));
          if (H5DSiterate_scales(hdf5_var->hdf_datasetid, d, NULL, dimscale_visitor,
                                 &(hdf5_var->dimscale_hdf5_objids[d])) < 0)
             return NC_EHDFERR;
          var->dimscale_attached[d] = NC_TRUE;
+         LOG((4, "dimscale attached"));
       }
    }
 
@@ -1131,13 +1142,17 @@ get_scale_info(NC_GRP_INFO_T *grp, NC_DIM_INFO_T *dim, NC_VAR_INFO_T *var,
    {
       assert(ndims);
       var->dimscale = NC_TRUE;
+
+      /* If this is a multi-dimensional coordinate var, then the
+       * dimids must be stored in the hidden coordinates attribute. */
       if (var->ndims > 1)
       {
          if ((retval = read_coord_dimids(grp, var)))
             return retval;
       }
       else
       {
+         /* This is a 1-dimensional coordinate var. */
          assert(!strcmp(var->hdr.name, dim->hdr.name));
          var->dimids[0] = dim->hdr.id;
          var->dim[0] = dim;
@@ -1176,7 +1191,7 @@ nc4_get_var_meta(NC_VAR_INFO_T *var)
    int retval = NC_NOERR;
 
    assert(var && var->format_var_info);
-   LOG((3, "%s: var %s", var->hdr.name));
+   LOG((3, "%s: var %s", __func__, var->hdr.name));
 
    /* Have we already read the var metadata? */
    if (var->meta_read)

libhdf5/hdf5type.c

@@ -52,20 +52,17 @@ NC4_inq_type_equal(int ncid1, nc_type typeid1, int ncid2,
    if ((typeid1 <= NC_STRING && typeid2 > NC_STRING) ||
        (typeid2 <= NC_STRING && typeid1 > NC_STRING))
    {
-      if (equalp) *equalp = 0;
+      *equalp = 0;
       return NC_NOERR;
    }
 
    /* If both are atomic types, the answer is easy. */
    if (typeid1 <= NUM_ATOMIC_TYPES)
    {
-      if (equalp)
-      {
-         if (typeid1 == typeid2)
-            *equalp = 1;
-         else
-            *equalp = 0;
-      }
+      if (typeid1 == typeid2)
+         *equalp = 1;
+      else
+         *equalp = 0;
       return NC_NOERR;
    }
 
@@ -80,7 +77,6 @@ NC4_inq_type_equal(int ncid1, nc_type typeid1, int ncid2,
       return NC_EBADTYPE;
 
    /* Are the two types equal? */
-   if (equalp)
    {
       hid_t hid1, hid2;
 

libhdf5/hdf5var.c

@@ -1034,23 +1034,21 @@ NC4_def_var_filter(int ncid, int varid, unsigned int id, size_t nparams,
 int
 NC4_rename_var(int ncid, int varid, const char *name)
 {
-   NC *nc;
    NC_GRP_INFO_T *grp;
    NC_HDF5_GRP_INFO_T *hdf5_grp;
    NC_FILE_INFO_T *h5;
-   NC_VAR_INFO_T *var, *tmpvar;
+   NC_VAR_INFO_T *var;
    int retval = NC_NOERR;
 
    if (!name)
       return NC_EINVAL;
 
-   LOG((2, "%s: ncid 0x%x varid %d name %s", __func__, ncid, varid,
-        name));
+   LOG((2, "%s: ncid 0x%x varid %d name %s", __func__, ncid, varid, name));
 
    /* Find info for this file and group, and set pointer to each. */
-   if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
+   if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
       return retval;
-   assert(h5 && grp && grp->format_grp_info && h5);
+   assert(h5 && grp && grp->format_grp_info);
 
    /* Get HDF5-specific group info. */
    hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
@@ -1069,14 +1067,12 @@ NC4_rename_var(int ncid, int varid, const char *name)
       return retval;
 
    /* Get the variable wrt varid */
-   var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
-   if (!var)
+   if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid)))
       return NC_ENOTVAR;
 
    /* Check if new name is in use; note that renaming to same name is still an error
       according to the nc_test/test_write.c code. Why?*/
-   tmpvar = (NC_VAR_INFO_T*)ncindexlookup(grp->vars,name);
-   if(tmpvar != NULL)
+   if (ncindexlookup(grp->vars, name))
       return NC_ENAMEINUSE;
 
    /* If we're not in define mode, new name must be of equal or
@@ -1103,8 +1099,8 @@ NC4_rename_var(int ncid, int varid, const char *name)
           * so, it must be deleted. */
          if (hdf5_d0->hdf_dimscaleid)
          {
-            if ((retval = delete_existing_dimscale_dataset(grp, var->dim[0]->hdr.id,
-                                                           var->dim[0])))
+            if ((retval = delete_dimscale_dataset(grp, var->dim[0]->hdr.id,
+                                                  var->dim[0])))
                return retval;
          }
       }
@@ -1119,37 +1115,40 @@ NC4_rename_var(int ncid, int varid, const char *name)
    if (!(var->hdr.name = strdup(name)))
       return NC_ENOMEM;
    LOG((3, "var is now %s", var->hdr.name));
-   var->hdr.hashkey = NC_hashmapkey(var->hdr.name,strlen(var->hdr.name)); /* Fix hash key */
 
-   if(!ncindexrebuild(grp->vars))
+   /* Fix hash key and rebuild index. */
+   var->hdr.hashkey = NC_hashmapkey(var->hdr.name, strlen(var->hdr.name));
+   if (!ncindexrebuild(grp->vars))
       return NC_EINTERNAL;
 
-   /* Check if this was a coordinate variable previously, but names are different now */
+   /* Check if this was a coordinate variable previously, but names
+    * are different now */
    if (var->dimscale && strcmp(var->hdr.name, var->dim[0]->hdr.name))
    {
       /* Break up the coordinate variable */
       if ((retval = nc4_break_coord_var(grp, var, var->dim[0])))
          return retval;
    }
 
-   /* Check if this should become a coordinate variable */
+   /* Check if this should become a coordinate variable. */
    if (!var->dimscale)
    {
-      /* Only variables with >0 dimensions can become coordinate variables */
+      /* Only variables with >0 dimensions can become coordinate
+       * variables. */
       if (var->ndims)
       {
          NC_GRP_INFO_T *dim_grp;
          NC_DIM_INFO_T *dim;
 
-         /* Check to see if this is became a coordinate variable.  If so, it
-          * will have the same name as dimension index 0. If it is a
-          * coordinate var, is it a coordinate var in the same group as the dim?
-          */
+         /* Check to see if this is became a coordinate variable.  If
+          * so, it will have the same name as dimension index 0. If it
+          * is a coordinate var, is it a coordinate var in the same
+          * group as the dim? */
          if ((retval = nc4_find_dim(grp, var->dimids[0], &dim, &dim_grp)))
             return retval;
          if (!strcmp(dim->hdr.name, name) && dim_grp == grp)
          {
-            /* Reform the coordinate variable */
+            /* Reform the coordinate variable. */
             if ((retval = nc4_reform_coord_var(grp, var, dim)))
                return retval;
             var->became_coord_var = NC_TRUE;