EXODUS: Fixing group usage

Author: gdsjaar

packages/seacas/libraries/exodus/src/ex_copy.c

@@ -176,6 +176,7 @@ int ex_copy_transient(int in_exoid, int out_exoid)
 static int cpy_variable_data(int in_exoid, int out_exoid, int in_large, int mesh_only)
 {
   int nvars; /* number of variables */
+  /* NOTE: This is incorrect for files containing groups */
   EXCHECKI(nc_inq(in_exoid, NULL, &nvars, NULL, NULL));
   for (int varid = 0; varid < nvars; varid++) {
     bool         is_filtered;
@@ -216,6 +217,7 @@ static int cpy_variables(int in_exoid, int out_exoid, int in_large, int mesh_onl
 {
   int recdimid; /* id of unlimited dimension */
   int nvars;    /* number of variables */
+  /* NOTE: This is incorrect for files containing groups */
   EXCHECKI(nc_inq(in_exoid, NULL, &nvars, NULL, &recdimid));
   for (int varid = 0; varid < nvars; varid++) {
     struct ncvar var; /* variable */
@@ -259,6 +261,7 @@ static int cpy_dimension(int in_exoid, int out_exoid, int mesh_only)
 
   int ndims;    /* number of dimensions */
   int recdimid; /* id of unlimited dimension */
+  /* NOTE: This is incorrect for files containing groups */
   EXCHECKI(nc_inq(in_exoid, &ndims, NULL, NULL, &recdimid));
   for (int dimid = 0; dimid < ndims; dimid++) {
 
@@ -344,6 +347,7 @@ static int cpy_global_att(int in_exoid, int out_exoid)
   struct ncatt att; /* attribute */
 
   int ngatts;
+  /* NOTE: This is incorrect for files containing groups */
   EXCHECKI(nc_inq(in_exoid, NULL, NULL, &ngatts, NULL));
 
   /* copy global attributes */

packages/seacas/libraries/exodus/src/ex_get_group_id.c

@@ -40,17 +40,20 @@ int ex_get_group_id(int parent_id, const char *group_name, int *group_id)
                "group in file id %d",
                group_name, parent_id);
       ex_err_fn(parent_id, __func__, errmsg, status);
+      *group_id = 0;
       EX_FUNC_LEAVE(EX_FATAL);
     }
   }
   else {
     /* Full path name */
-    int status = nc_inq_grp_full_ncid(parent_id, group_name, group_id);
+    int rootid = parent_id & EX_FILE_ID_MASK;
+    int status = nc_inq_grp_full_ncid(rootid, group_name, group_id);
     if (status != NC_NOERR) {
       snprintf(errmsg, MAX_ERR_LENGTH,
                "ERROR: Failed to locate group with full path name %s in file id %d", group_name,
                parent_id);
       ex_err_fn(parent_id, __func__, errmsg, status);
+      *group_id = 0;
       EX_FUNC_LEAVE(EX_FATAL);
     }
   }
@@ -64,6 +67,7 @@ int ex_get_group_id(int parent_id, const char *group_name, int *group_id)
            "ERROR: Group capabilities are not available in this netcdf "
            "version--not netcdf4");
   ex_err_fn(parent_id, __func__, errmsg, NC_ENOTNC4);
+  *group_id = 0;
   EX_FUNC_LEAVE(EX_FATAL);
 #endif
 }

packages/seacas/libraries/exodus/src/ex_get_init_ext.c

@@ -26,13 +26,16 @@
 
 static void exi_get_entity_count(int exoid, ex_init_params *info)
 {
-  int ndims;
-  int include_parent_group = 1;
+  int include_parent_group = 0; // Only want dims in current group
+  int ndims                = 0;
   nc_inq_dimids(exoid, &ndims, NULL, include_parent_group);
+  int *dimids = calloc(ndims, sizeof(int));
+  nc_inq_dimids(exoid, &ndims, dimids, include_parent_group);
+
   for (int dimid = 0; dimid < ndims; dimid++) {
     char   dim_nm[NC_MAX_NAME + 1] = {'\0'};
     size_t dim_sz;
-    nc_inq_dim(exoid, dimid, dim_nm, &dim_sz);
+    nc_inq_dim(exoid, dimids[dimid], dim_nm, &dim_sz);
     /* For assemblies, we check for a dim starting with "num_entity_assembly" */
     if (strncmp(dim_nm, "num_entity_assembly", 19) == 0) {
       info->num_assembly++;
@@ -41,6 +44,7 @@ static void exi_get_entity_count(int exoid, ex_init_params *info)
       info->num_blob++;
     }
   }
+  free(dimids);
 }
 
 /* Used to reduce repeated code below */

packages/seacas/libraries/ioss/src/main/io_shell.C

@@ -260,11 +260,12 @@ namespace {
       }
 
       if (!interFace.groupName.empty()) {
-        bool success = dbi->open_group(interFace.groupName);
+	std::string group_path = "/" + interFace.groupName;
+        bool success = dbi->open_group(group_path);
         if (!success) {
           if (rank == 0) {
             fmt::print(stderr, "ERROR: Unable to open group '{}' in file '{}'\n",
-                       interFace.groupName, inpfile);
+                       group_path, inpfile);
           }
           return;
         }