Merge pull request #298 from scottaiton/feature-patch-threshold-api-n…

…ew-semantic

Add patch threshold to api and add user option

src/patches/clawpatch/fclaw2d_clawpatch_options.c

@@ -103,6 +103,11 @@ clawpatch_register(fclaw2d_clawpatch_options_t *clawpatch_options,
                          &clawpatch_options->save_aux,0,
                          "Save aux variables when re-taking a time step [F]");
 
+    /* ---------------------- vtk options -------------------------- */
+    sc_options_add_int(opt, 0, "vtk-patch-threshold", 
+                       &clawpatch_options->vtk_patch_threshold, 0,
+                       "Number of patches to buffer before each write in vtk output. 0 means buffer all patches before writing [0]");
+
     /* Set verbosity level for reporting timing */
     sc_keyvalue_t *kv = clawpatch_options->kv_refinement_criteria = kv_refinement_criterea_new();
     sc_options_add_keyvalue (opt, 0, "refinement-criteria", 
@@ -159,6 +164,13 @@ clawpatch_check(fclaw2d_clawpatch_options_t *clawpatch_opt)
         return FCLAW_EXIT_ERROR;            
     }
 
+    if (clawpatch_opt->vtk_patch_threshold < 0)
+    {
+        fclaw_global_essentialf("Clawpatch error : vtk-patch-threshold must be " \
+                                "non-negative.\n");
+        return FCLAW_EXIT_ERROR;            
+    }
+
     return FCLAW_NOEXIT;
 }
 

src/patches/clawpatch/fclaw2d_clawpatch_options.h

@@ -86,6 +86,8 @@ struct fclaw2d_clawpatch_options
     int save_aux;             /**< Save the aux array when retaking a time step */
 
 
+    int vtk_patch_threshold; /**< The buffer threshold for vtk output */
+
     int is_registered; /**< true if options have been registered */
 
 };

src/patches/clawpatch/fclaw2d_clawpatch_output_vtk.c

@@ -223,7 +223,7 @@ fclaw2d_vtk_write_header (fclaw2d_domain_t * domain, fclaw2d_vtk_state_t * s)
  *
  * This function assumes that the buffer consists of patch data of the size
  * \b psize_field. This means it must hold
- * \b s->sink->buffer_bytes % \b s->sink->buffer_bytes == 0.
+ * \b s->sink->buffer_bytes % \b psize_field == 0.
  *
  * \param [in,out]  s               The VTK state.
  * \param [in]      psize_field     The number of bytes, which are intended to
@@ -232,7 +232,7 @@ fclaw2d_vtk_write_header (fclaw2d_domain_t * domain, fclaw2d_vtk_state_t * s)
  *                                  stored in the buffer + 1 is greater than
  *                                  \b threshold, the buffer is flushed to disk.
  *                                  Then the new patch is added to the buffer.
- *                                  -1 means that there is no threshold and
+ *                                  0 means that there is no threshold and
  *                                  the data just added to \b s->sink.
  */
 static void
@@ -723,10 +723,13 @@ fclaw2d_vtk_write_file (fclaw2d_global_t * glob, const char *basename,
                         int meqn,
                         double vtkspace, int vtkwrite,
                         fclaw2d_vtk_patch_data_t coordinate_cb,
-                        fclaw2d_vtk_patch_data_t value_cb)
+                        fclaw2d_vtk_patch_data_t value_cb,
+                        int patch_threshold)
 {
     fclaw2d_domain_t *domain = glob->domain;
 
+    FCLAW_ASSERT (patch_threshold >= 0);
+
     int retval, gretval;
     int mpiret;
     fclaw2d_vtk_state_t ps, *s = &ps;
@@ -788,10 +791,8 @@ fclaw2d_vtk_write_file (fclaw2d_global_t * glob, const char *basename,
 
     s->buf = NULL;
     s->sink = NULL;
-    /* The threshold may be adjusted; see the documentation of
-     * fclaw2d_vtk_state_t for further information.
-     */
-    s->patch_threshold = 0;
+    /* See the documentation of fclaw2d_vtk_state_t for further information. */
+    s->patch_threshold = patch_threshold;
     s->num_buffered_patches = 0;
 
     /* write header meta data and check for error */
@@ -1018,6 +1019,9 @@ void fclaw2d_clawpatch_output_vtk (fclaw2d_global_t * glob, int iframe)
     char basename[BUFSIZ];
     snprintf (basename, BUFSIZ, "%s_frame_%04d", fclaw_opt->prefix, iframe);
 
+    /* The last parameter of the call of fclaw2d_vtk_write_file can be replaced
+     * by a value from flcaw_opt or clawpatch_opt.
+     */
     (void) fclaw2d_vtk_write_file (glob, basename,
                                    clawpatch_opt->mx, clawpatch_opt->my,
 #if PATCH_DIM == 3
@@ -1026,7 +1030,7 @@ void fclaw2d_clawpatch_output_vtk (fclaw2d_global_t * glob, int iframe)
                                    clawpatch_opt->meqn,
                                    fclaw_opt->vtkspace, 0,
                                    fclaw2d_output_vtk_coordinate_cb,
-                                   fclaw2d_output_vtk_value_cb);
+                                   fclaw2d_output_vtk_value_cb, clawpatch_opt->vtk_patch_threshold);
 }
 
 

src/patches/clawpatch/fclaw2d_clawpatch_output_vtk.h

@@ -73,6 +73,9 @@ typedef void (*fclaw2d_vtk_patch_data_t) (struct fclaw2d_global * glob,
  *                         1 for MPI_File_write (less memory usage).
  * @param[in] coordniate_cb the callback to write a patch's coordinate binary data
  * @param[in] value_cb the callback to write a patch's value binary data
+ * @param[in] patch_threshold The maximal number of buffered patches.
+ *                            0 means that an unlimited number of patches is
+ *                            buffered and flushed to disk at the end.
  * @return          0 if successful, negative otherwise.
  *                  Collective with identical value on all ranks.
  */
@@ -85,7 +88,8 @@ fclaw2d_vtk_write_file (struct fclaw2d_global * glob, const char *basename,
                         int meqn,
                         double vtkspace, int vtkwrite,
                         fclaw2d_vtk_patch_data_t coordinate_cb,
-                        fclaw2d_vtk_patch_data_t value_cb);
+                        fclaw2d_vtk_patch_data_t value_cb,
+                        int patch_threshold);
 
 /**
  * @brief Output vtu file

src/patches/clawpatch/fclaw3dx_clawpatch_options.h

@@ -86,6 +86,8 @@ struct fclaw3dx_clawpatch_options
     int ghost_patch_pack_aux; /**< True if aux equations should be packed */
     int save_aux;             /**< Save the aux array when retaking a time step */
 
+    int vtk_patch_threshold; /**< The buffer threshold for vtk output */
+
     int is_registered; /**< true if options have been registered */
 
 };

src/patches/clawpatch/fclaw3dx_clawpatch_output_vtk.h

@@ -73,6 +73,9 @@ typedef void (*fclaw3dx_vtk_patch_data_t) (struct fclaw2d_global * glob,
  *                         1 for MPI_File_write (less memory usage).
  * @param[in] coordniate_cb the callback to write a patch's coordinate binary data
  * @param[in] value_cb the callback to write a patch's value binary data
+ * @param[in] patch_threshold The maximal number of buffered patches.
+ *                            0 means that an unlimited number of patches is
+ *                            buffered and flushed to disk at the end.
  * @return          0 if successful, negative otherwise.
  *                  Collective with identical value on all ranks.
  */
@@ -82,7 +85,8 @@ fclaw3dx_vtk_write_file (struct fclaw2d_global * glob, const char *basename,
                         int meqn,
                         double vtkspace, int vtkwrite,
                         fclaw3dx_vtk_patch_data_t coordinate_cb,
-                        fclaw3dx_vtk_patch_data_t value_cb);
+                        fclaw3dx_vtk_patch_data_t value_cb,
+                        int patch_threshold);
 
 /**
  * @brief Output vtu file