fix #19, update ex10

README.md

@@ -379,42 +379,55 @@ of processes used. You can easily check if the files are the same by running:
 
 ### Ex10. Post-processing the data in python
 
+\attention 
+You need to have a version %PDI with the \ref pycall_plugin "Pycall plugin" to do this exercise.
+
 In this exercise, you will once again modify the YAML file only and use python
 to post-process the data in situ before writing it to HDF5.
 Here, you will write the square root of the raw data to HDF5 instead of the
 data itself.
 
 * Examine the YAML file and compile the code.
 
+* Load the \ref pycall_plugin "Pycall plugin" and enable this plugin when the `loop` event is triggered.
+
+Some variables of the python script inside `ex10.yml` are not defined. 
+The `with` directive of this plugin allows to specify input variables (parameters) to pass to Python as a set of "$-expressions". 
+These parameters can be given as multiple blocks. 
+
+* Add a `with` block with the missing parameter to let the Python code process
+  the data exposed in `main_field` for event `loop`.
+
+* Use the keyword `exec` of \ref pycall_plugin "Pycall plugin" and decomment the python script.
+
 Notice that the Decl'HDF5 configuration was simplified, no memory selection is
-applied, the when condition disappeared.
+applied, the `when` condition disappeared because it is done in the python script:
+```python
+  if 0 < iter_id < 4: 
+    transformed_field = np.sqrt(source_field[1:-1,1:-1])
+    pdi.expose('transformed_field', transformed_field, pdi.OUT) 
+```
+The last line of the python script allows to expose the transformed field to %PDI. Moreover, this data is known to %PDI in this call.
+
+* Modify the Decl'HDF5 configuration to write the new data `transformed_field` exposed from Python.
+
+\attention
 The dataset name is however explicitly specified now because it does not match
 the %PDI variable name anymore, you will instead write a new variable exposed
 from python.
 
-The `pycall` section has been added to load the 
-\ref pycall_plugin "Pycall plugin".
-It executes the provided code when the "loop" event is triggered.
-The `with` section specifies the variables (parameters) to pass to Python as a
-set of "$-expressions".
-The provided code again exposes its result to %PDI and multiple blocks can be
-chained this way.
-
-* Add the missing parameter to the `with` block to let the Python code process
-  the data exposed in `main_field`.
-
-* Modify the Decl'HDF5 configuration to write the new data exposed from Python.
-
-* Match the output from `ex10.h5dump`. You can easily check if the files are the
-  same by running:
+You should be able to match the expected output described in `ex10.h5dump`. You can easily check if the files are the same by running:
 ```bash
   diff ex10.h5dump <(h5dump ex10*.h5)
 ```
+To see your `h5` file in readable file format, you can check the section [Comparison with the `h5dump` command](#h5comparison).
+
+\warning
+If you relaunch the executable, remember to delete your old `ex10.h5` file before, otherwise the data will not be changed.
 
 \attention
 In a more realistic setup, one would typically not write much code in the YAML
-file directly, but would instead call functions specified in a `.py` file on
-the side.
+file directly, but would instead call functions specified in a `.py` file on the side.
 
 ## What next ?
 

ex10.c

@@ -29,7 +29,6 @@
 #include <time.h>
 
 #include <paraconf.h>
-// load the PDI header
 #include <pdi.h>
 
 /// size of the local data as [HEIGHT, WIDTH] including ghosts & boundary constants
@@ -44,13 +43,32 @@ 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 +78,15 @@ 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
@@ -87,7 +99,7 @@ void exchange(MPI_Comm cart_comm, double cur[dsize[0]][dsize[1]])
 	int rank_source, rank_dest;
 	static MPI_Datatype column, row;
 	static int initialized = 0;
-	
+
 	if ( !initialized ) {
 		MPI_Type_vector(dsize[0]-2, 1, dsize[1], MPI_DOUBLE, &column);
 		MPI_Type_commit(&column);
@@ -104,8 +116,8 @@ void exchange(MPI_Comm cart_comm, double cur[dsize[0]][dsize[1]])
 
 	// send up
 	MPI_Cart_shift(cart_comm, 0, -1, &rank_source, &rank_dest);
-	MPI_Sendrecv(&cur[1][1],          1, row, rank_dest,   100, // send column after ghost
-	             &cur[dsize[0]-1][1], 1, row, rank_source, 100, // receive last column (ghost)
+	MPI_Sendrecv(&cur[1][1],          1, row, rank_dest,   100, // send row after ghost
+	             &cur[dsize[0]-1][1], 1, row, rank_source, 100, // receive last row (ghost)
 	             cart_comm, &status);
 
 	// send to the right
@@ -162,7 +174,7 @@ 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 +190,9 @@ 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) {
@@ -197,14 +207,14 @@ int main( int argc, char* argv[] )
 
 		// exchange data with the neighbours
 		exchange(cart_comm, next);
-		
+
 		// swap the current and next values
 		double (*tmp)[dsize[1]] = cur; cur = next; next = tmp;
 	}
 	// finally share the main field as well as the loop counter after the loop
 	PDI_multi_expose("finalization",
-	        "main_field", cur, PDI_OUT,
 	        "ii",         &ii, PDI_OUT,
+	        "main_field", cur, PDI_OUT,
 	        NULL);
 
 	// finalize PDI

ex10.yml

@@ -21,17 +21,20 @@ pdi:
       datasets:
         main_field: { type: array, subtype: double, size: [ 3, '$psize[0]*($dsize[0]-2)', '$psize[1]*($dsize[1]-2)' ] }
       write:
-        TODO: # the name of the PDI data to write
-          dataset: main_field
-          dataset_selection:
-            size: [1, '$dsize[0]-2', '$dsize[1]-2']
-            start: ['$ii-1', '$pcoord[0]*($dsize[0]-2)', '$pcoord[1]*($dsize[1]-2)']
-    pycall:
-      on_event:
-        loop:
-          with: { iter_id: $ii, ... }
-          exec: |
-            import numpy as np
-            if 0 < iter_id < 4:
-                transformed_field = np.sqrt(source_field[1:-1,1:-1])
-                pdi.expose('transformed_field', transformed_field, pdi.OUT)
+        #*** the name of the PDI variable to write.
+        #...
+        dataset: main_field  # name of the dataset in "ex10.h5"
+        dataset_selection:
+          size: [1, '$dsize[0]-2', '$dsize[1]-2']
+          start: ['$ii-1', '$pcoord[0]*($dsize[0]-2)', '$pcoord[1]*($dsize[1]-2)']
+    #*** load the pycall plugin and enable this plugin for event loop.
+    #...
+    #*** Specifies the input parameters (variables) to pass to Python as a set of "$-expressions" (expressions must be defined in .yml script)
+    #...
+    #*** add exec keyword of pycall plugin. Decomment and the following python script 
+    #...
+#            import numpy as np
+#            if 0 < iter_id < 4: # iter_id: time iteration
+#              transformed_field = np.sqrt(source_field[1:-1,1:-1])
+#              pdi.expose('transformed_field', transformed_field, pdi.OUT)
+## Comment: The last line allows to expose transformed field to PDI. Hence, the data is known by PDI in this call.

solutions/ex10.yml

@@ -18,14 +18,16 @@ pdi:
     decl_hdf5:
       file: ex10.h5
       communicator: $MPI_COMM_WORLD
-      datasets:
+      datasets: # List the name of the dataset in the file ex10.h5
         main_field: { type: array, subtype: double, size: [ 3, '$psize[0]*($dsize[0]-2)', '$psize[1]*($dsize[1]-2)' ] }
       write:
+        #*** the name of the PDI data to write
         transformed_field:
-          dataset: main_field
+          dataset: main_field  # name of the dataset in the h5 file (defined in the directive datasets) that we want to fill
           dataset_selection:
             size: [1, '$dsize[0]-2', '$dsize[1]-2']
             start: ['$ii-1', '$pcoord[0]*($dsize[0]-2)', '$pcoord[1]*($dsize[1]-2)']
+    #*** load the pycall plugin
     pycall:
       on_event:
         loop:
@@ -34,4 +36,5 @@ pdi:
             import numpy as np
             if 0 < iter_id < 4:
                 transformed_field = np.sqrt(source_field[1:-1,1:-1])
-                pdi.expose('transformed_field', transformed_field, pdi.OUT)
+                pdi.expose('transformed_field', transformed_field, pdi.OUT) 
+# The last line allows to expose transformed field to PDI. Hence, the data is known by PDI in this call.