fix #26, update ex7 ex8 (#28)

Update ex7 ex8
---------

Co-authored-by: JAuriac <[email protected]>

Author: jmorice91

README.md

@@ -340,60 +340,76 @@ then triggers an event and finally does all the reclaim in reverse order.
   diff ex6.log <(grep Trace-plugin ex6.result.log)
 ```
 
-
 ### Ex7. Writing a selection
 
 In this exercise, you will only write a selection of the 2D array in memory
 excluding ghosts to the HDF5 file.
 Once again, you only need to modify the YAML file in this exercise, no need to
 touch the C file.
 
+\remark This exercise will run with 4 MPI processes.
+
 * Examine the YAML file and compile the code.
 
 As you can notice, now the dataset is independently described in the file.
 
 * Restrict the selection to the non-ghost part of the array in memory (excluding
   one element on each side).
-  You should be able to match the expected output described in `ex7.h5dump`.
-  You can easily check if the files are the same by running:
+
+You can achieve this by using the `memory_selection` directive in ex7.yml that 
+specifies the selection of data from memory to write.
+
+You should be able to match the expected output described in `ex7.h5dump`. 
+You can easily check if the files are the same by running:
 ```bash
   diff ex7.h5dump <(h5dump ex7*.h5)
 ```
-
-You can achieve this by using the `memory_selection` directive that specifies
-the selection of data from memory to write.
+To see your `h5` file in readable file format, 
+you can check the section [Comparison with the `h5dump` command](#h5comparison).
 
 ![graphical representation](PDI_hdf5_selection.jpg)
 
-
 ### Ex8. Selecting on the dataset size
 
 In this exercise, you will once again change the YAML file to handle a selection
 in the dataset in addition to the selection in memory from the previous
 exercise.
-You will write the 2D array from the previous exercise as a slice of 3D dataset
-including a dimension for time.
+In this exercise, you don't want to get one output file per iteration.
+You will write the 2D array from the previous exercise as a slice of a 3D dataset
+including a time dimension for iterations 1 to 3 (inclusive).
+
 Once again, you only need to modify the YAML file in this exercise, no need to
 touch the C file.
 
 * Examine the YAML file and compile the code.
 
-Notice how the dataset is now extended with an additional dimension for three
-time-steps.
+Notice how the dataset is extended with an additional dimension 
+```yaml
+      datasets:
+        #*** add one dimention to main_field datasets to represent the time step
+        main_field: { type: array, subtype: double, size: [..., '$dsize[0]-2', '$dsize[1]-2' ] }
+```
+
+* replace `...` in previous line by the number of iteration time, we want to save
+  in this exercise.
+
+* Change the `when` directive to write the `main_field` at iterations 1 to 3 inclusive.
 
 * Write the 2D selection from `main_field` at iterations 1 to 3 inclusive into
-  slices at coordinate 0 to 2 of first dimension of the 3D dataset.
-  Match the expected output described in `ex8.h5dump`. You can easily check if
-  the files are the same by running:
-```bash
-  diff ex8.h5dump <(h5dump ex8*.h5)
-```
+  slices at coordinate 0 to 2 of the first dimension of the 3D dataset.
 
 You can achieve this by using the `dataset_selection` directive that specifies
 the selection where to write in the file dataset.
 
-![graphical representation](PDI_hdf5_selection_advanced.jpg)
+You should be able to match the expected output described in `ex8.h5dump`.
+You can easily check if the files are the same by running:
+```bash
+  diff ex8.h5dump <(h5dump ex8*.h5)
+```
+To see your `h5` file in readable file format, you can check the section
+[Comparison with the `h5dump` command](#h5comparison).
 
+![graphical representation](PDI_hdf5_selection_advanced.jpg)
 
 ## parallel Decl'HDF5
 

ex7.c

@@ -44,13 +44,32 @@ int pcoord[2];
 /// the alpha coefficient used in the computation
 double alpha;
 
+double L=1.0;
+double source1[4]={0.4, 0.4, 0.2, 100};
+double source2[4]={0.7, 0.8, 0.1, 200};
+
 /** Initialize the data all to 0 except for the left border (XX==0) initialized to 1 million
  * \param[out] dat the local data to initialize
  */
 void init(double dat[dsize[0]][dsize[1]])
 {
 	for (int yy=0; yy<dsize[0]; ++yy)  for (int xx=0; xx<dsize[1]; ++xx)  dat[yy][xx] = 0;
-	if ( pcoord[1] == 0 ) for (int yy=0; yy<dsize[0]; ++yy)  dat[yy][0] = 1000000;
+	double dy = L / ((dsize[0]-2) *psize[0]) ;
+	double dx = L / ((dsize[1]-2) *psize[1]) ;
+
+	double cpos_x,cpos_y;
+	for(int yy=0; yy<dsize[0];++yy) {
+		cpos_y=(yy+pcoord[0]*(dsize[0]-2))*dy-0.5*dy;
+		for(int xx=0; xx<dsize[1];++xx) {
+			cpos_x=(xx+pcoord[1]*(dsize[1]-2))*dx-0.5*dx;
+			if((cpos_y-source1[0])*(cpos_y-source1[0]) + (cpos_x-source1[1])*(cpos_x-source1[1]) <= source1[2]*source1[2]) {
+				dat[yy][xx] = source1[3];
+			}
+			if((cpos_y-source2[0])*(cpos_y-source2[0]) + (cpos_x-source2[1])*(cpos_x-source2[1]) <= source2[2]*source2[2]) {
+				dat[yy][xx] = source2[3];
+			}
+		}
+	}
 }
 
 /** Compute the values at the next time-step based on the values at the current time-step
@@ -60,21 +79,15 @@ void init(double dat[dsize[0]][dsize[1]])
 void iter(double cur[dsize[0]][dsize[1]], double next[dsize[0]][dsize[1]])
 {
 	int xx, yy;
-	for (xx=0; xx<dsize[1]; ++xx) next[0][xx] = cur[0][xx];
 	for (yy=1; yy<dsize[0]-1; ++yy) {
-		next[yy][0] = cur[yy][0];
 		for (xx=1; xx<dsize[1]-1; ++xx) {
-			next[yy][xx] =
-					  (1.-4.*alpha) * cur[yy][xx]
-					+        alpha  * (   cur[yy][xx-1]
-					                    + cur[yy][xx+1]
-					                    + cur[yy-1][xx]
-					                    + cur[yy+1][xx]
-					                  ); 
+			next[yy][xx] = (1.-4.*alpha) * cur[yy][xx]
+					             +alpha  * ( cur[yy][xx-1]
+					                       + cur[yy][xx+1]
+					                       + cur[yy-1][xx]
+					                       + cur[yy+1][xx]); 
 		}
-		next[yy][dsize[1]-1] = cur[yy][dsize[1]-1];
 	}
-	for (xx=0; xx<dsize[1]; ++xx) next[dsize[0]-1][xx] = cur[dsize[0]-1][xx];
 }
 
 /** Exchanges ghost values with neighbours
@@ -162,7 +175,7 @@ int main( int argc, char* argv[] )
 	dsize[1] = global_size[1]/psize[1] + 2;
 
 	// create a 2D Cartesian MPI communicator & get our coordinate (rank) in it
-	int cart_period[2] = { 0, 0 };
+	int cart_period[2] = { 1, 1 };
 	MPI_Comm cart_comm; MPI_Cart_create(main_comm, 2, psize, cart_period, 1, &cart_comm);
 	MPI_Cart_coords(cart_comm, pcoord_1d, 2, pcoord);
 
@@ -178,11 +191,9 @@ int main( int argc, char* argv[] )
 	int ii=0;
 
 	// share useful configuration bits with PDI
-	PDI_expose("ii",         &ii,    PDI_OUT);
 	PDI_expose("pcoord",     pcoord, PDI_OUT);
 	PDI_expose("dsize",      dsize,  PDI_OUT);
 	PDI_expose("psize",      psize,  PDI_OUT);
-	PDI_expose("main_field", cur,    PDI_OUT);
 
 	// the main loop
 	for (; ii<10; ++ii) {

ex7.h5dump

@@ -1,69 +1,159 @@
-HDF5 "ex7-data0x0.h5" {
+HDF5 "ex7-data-0x0_iter_1.h5" {
 GROUP "/" {
    DATASET "main_field" {
       DATATYPE  H5T_IEEE_F64LE
-      DATASPACE  SIMPLE { ( 60, 12 ) / ( 60, 12 ) }
+      DATASPACE  SIMPLE { ( 30, 6 ) / ( 30, 6 ) }
       DATA {
-      (0,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (1,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (2,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (3,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (4,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (5,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (6,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (7,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (8,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (9,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (10,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (11,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (12,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (13,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (14,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (15,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (16,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (17,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (18,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (19,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (20,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (21,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (22,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (23,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (24,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (25,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (26,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (27,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (28,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (29,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (30,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (31,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (32,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (33,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (34,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (35,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (36,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (37,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (38,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (39,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (40,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (41,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (42,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (43,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (44,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (45,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (46,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (47,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (48,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (49,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (50,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (51,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (52,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (53,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (54,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (55,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (56,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (57,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (58,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      (59,0): 125000, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
+      (0,0): 0, 0, 0, 0, 0, 0,
+      (1,0): 0, 0, 0, 0, 0, 0,
+      (2,0): 0, 0, 0, 0, 0, 0,
+      (3,0): 0, 0, 0, 0, 0, 0,
+      (4,0): 0, 0, 0, 0, 0, 0,
+      (5,0): 0, 0, 0, 0, 0, 0,
+      (6,0): 0, 0, 0, 0, 0, 0,
+      (7,0): 0, 0, 0, 0, 0, 0,
+      (8,0): 0, 0, 0, 0, 0, 0,
+      (9,0): 0, 0, 0, 0, 0, 0,
+      (10,0): 0, 0, 0, 0, 0, 0,
+      (11,0): 0, 0, 0, 0, 12.5, 0,
+      (12,0): 0, 0, 0, 12.5, 62.5, 25,
+      (13,0): 0, 0, 0, 25, 87.5, 75,
+      (14,0): 0, 0, 12.5, 75, 100, 87.5,
+      (15,0): 0, 0, 12.5, 87.5, 100, 87.5,
+      (16,0): 0, 0, 12.5, 87.5, 100, 100,
+      (17,0): 0, 0, 12.5, 87.5, 100, 100,
+      (18,0): 0, 0, 12.5, 87.5, 100, 100,
+      (19,0): 0, 0, 12.5, 87.5, 100, 100,
+      (20,0): 0, 0, 25, 87.5, 100, 100,
+      (21,0): 0, 12.5, 75, 100, 100, 100,
+      (22,0): 0, 12.5, 87.5, 100, 100, 100,
+      (23,0): 0, 12.5, 87.5, 100, 100, 100,
+      (24,0): 0, 12.5, 87.5, 100, 100, 100,
+      (25,0): 0, 12.5, 87.5, 100, 100, 100,
+      (26,0): 0, 12.5, 75, 100, 100, 100,
+      (27,0): 0, 0, 25, 87.5, 100, 100,
+      (28,0): 0, 0, 12.5, 87.5, 100, 100,
+      (29,0): 0, 0, 12.5, 87.5, 100, 100
+      }
+   }
+}
+}
+HDF5 "ex7-data-0x1_iter_1.h5" {
+GROUP "/" {
+   DATASET "main_field" {
+      DATATYPE  H5T_IEEE_F64LE
+      DATASPACE  SIMPLE { ( 30, 6 ) / ( 30, 6 ) }
+      DATA {
+      (0,0): 0, 0, 0, 0, 0, 0,
+      (1,0): 0, 0, 0, 0, 0, 0,
+      (2,0): 0, 0, 0, 0, 0, 0,
+      (3,0): 0, 0, 0, 0, 0, 0,
+      (4,0): 0, 0, 0, 0, 0, 0,
+      (5,0): 0, 0, 0, 0, 0, 0,
+      (6,0): 0, 0, 0, 0, 0, 0,
+      (7,0): 0, 0, 0, 0, 0, 0,
+      (8,0): 0, 0, 0, 0, 0, 0,
+      (9,0): 0, 0, 0, 0, 0, 0,
+      (10,0): 0, 0, 0, 0, 0, 0,
+      (11,0): 0, 0, 0, 0, 0, 0,
+      (12,0): 0, 0, 0, 0, 0, 0,
+      (13,0): 12.5, 0, 0, 0, 0, 0,
+      (14,0): 12.5, 0, 0, 0, 0, 0,
+      (15,0): 25, 0, 0, 0, 0, 0,
+      (16,0): 75, 12.5, 0, 0, 0, 0,
+      (17,0): 87.5, 12.5, 0, 0, 0, 0,
+      (18,0): 87.5, 12.5, 0, 0, 0, 0,
+      (19,0): 87.5, 12.5, 0, 0, 0, 0,
+      (20,0): 87.5, 12.5, 0, 0, 0, 0,
+      (21,0): 87.5, 12.5, 0, 0, 0, 0,
+      (22,0): 87.5, 12.5, 0, 0, 0, 0,
+      (23,0): 87.5, 12.5, 0, 0, 0, 0,
+      (24,0): 87.5, 12.5, 0, 0, 0, 0,
+      (25,0): 87.5, 12.5, 0, 0, 0, 0,
+      (26,0): 87.5, 12.5, 0, 0, 0, 0,
+      (27,0): 87.5, 12.5, 0, 0, 0, 0,
+      (28,0): 87.5, 12.5, 0, 0, 0, 0,
+      (29,0): 87.5, 12.5, 0, 0, 0, 0
+      }
+   }
+}
+}
+HDF5 "ex7-data-1x0_iter_1.h5" {
+GROUP "/" {
+   DATASET "main_field" {
+      DATATYPE  H5T_IEEE_F64LE
+      DATASPACE  SIMPLE { ( 30, 6 ) / ( 30, 6 ) }
+      DATA {
+      (0,0): 0, 0, 12.5, 87.5, 100, 100,
+      (1,0): 0, 0, 12.5, 87.5, 100, 100,
+      (2,0): 0, 0, 12.5, 87.5, 100, 87.5,
+      (3,0): 0, 0, 12.5, 75, 100, 87.5,
+      (4,0): 0, 0, 0, 25, 87.5, 75,
+      (5,0): 0, 0, 0, 12.5, 62.5, 25,
+      (6,0): 0, 0, 0, 0, 12.5, 0,
+      (7,0): 0, 0, 0, 0, 0, 0,
+      (8,0): 0, 0, 0, 0, 0, 0,
+      (9,0): 0, 0, 0, 0, 0, 0,
+      (10,0): 0, 0, 0, 0, 0, 0,
+      (11,0): 0, 0, 0, 0, 0, 0,
+      (12,0): 0, 0, 0, 0, 0, 0,
+      (13,0): 0, 0, 0, 0, 0, 0,
+      (14,0): 0, 0, 0, 0, 0, 0,
+      (15,0): 0, 0, 0, 0, 0, 0,
+      (16,0): 0, 0, 0, 0, 0, 0,
+      (17,0): 0, 0, 0, 0, 0, 0,
+      (18,0): 0, 0, 0, 0, 0, 0,
+      (19,0): 0, 0, 0, 0, 0, 0,
+      (20,0): 0, 0, 0, 0, 0, 0,
+      (21,0): 0, 0, 0, 0, 0, 0,
+      (22,0): 0, 0, 0, 0, 0, 0,
+      (23,0): 0, 0, 0, 0, 0, 0,
+      (24,0): 0, 0, 0, 0, 0, 0,
+      (25,0): 0, 0, 0, 0, 0, 0,
+      (26,0): 0, 0, 0, 0, 0, 0,
+      (27,0): 0, 0, 0, 0, 0, 0,
+      (28,0): 0, 0, 0, 0, 0, 0,
+      (29,0): 0, 0, 0, 0, 0, 0
+      }
+   }
+}
+}
+HDF5 "ex7-data-1x1_iter_1.h5" {
+GROUP "/" {
+   DATASET "main_field" {
+      DATATYPE  H5T_IEEE_F64LE
+      DATASPACE  SIMPLE { ( 30, 6 ) / ( 30, 6 ) }
+      DATA {
+      (0,0): 87.5, 12.5, 0, 0, 0, 0,
+      (1,0): 75, 12.5, 0, 0, 0, 0,
+      (2,0): 25, 0, 0, 0, 0, 0,
+      (3,0): 12.5, 0, 0, 0, 0, 0,
+      (4,0): 12.5, 0, 0, 0, 0, 0,
+      (5,0): 0, 0, 0, 25, 0, 0,
+      (6,0): 0, 0, 25, 125, 25, 0,
+      (7,0): 0, 0, 25, 150, 50, 0,
+      (8,0): 0, 0, 25, 175, 150, 25,
+      (9,0): 0, 0, 50, 175, 175, 25,
+      (10,0): 0, 25, 150, 200, 175, 25,
+      (11,0): 0, 25, 175, 200, 175, 25,
+      (12,0): 0, 25, 175, 200, 175, 25,
+      (13,0): 0, 25, 150, 200, 175, 25,
+      (14,0): 0, 0, 50, 175, 175, 25,
+      (15,0): 0, 0, 25, 175, 150, 25,
+      (16,0): 0, 0, 25, 150, 50, 0,
+      (17,0): 0, 0, 25, 125, 25, 0,
+      (18,0): 0, 0, 0, 25, 0, 0,
+      (19,0): 0, 0, 0, 0, 0, 0,
+      (20,0): 0, 0, 0, 0, 0, 0,
+      (21,0): 0, 0, 0, 0, 0, 0,
+      (22,0): 0, 0, 0, 0, 0, 0,
+      (23,0): 0, 0, 0, 0, 0, 0,
+      (24,0): 0, 0, 0, 0, 0, 0,
+      (25,0): 0, 0, 0, 0, 0, 0,
+      (26,0): 0, 0, 0, 0, 0, 0,
+      (27,0): 0, 0, 0, 0, 0, 0,
+      (28,0): 0, 0, 0, 0, 0, 0,
+      (29,0): 0, 0, 0, 0, 0, 0
       }
    }
 }