update ex1 and ex2, fix #12 (#13)

* Update ex1 and ex2
---------
Co-authored-by: JAuriac <[email protected]>

Author: jmorice91

README.md

@@ -58,6 +58,8 @@ pdirun mpirun -n 4 ./ex?
 Where `?` is the number of the exercise and 4 represents the number of MPI
 processes to use.
 
+#### Execution with storage of the log
+
 To store the logs for later comparison, you can use the following command (for
 example for ex2.):
 ```bash
@@ -109,25 +111,48 @@ read this file.
 * Set values in `ex1.yml` to be able to run the code with 4 MPI processes.
 
 ```bash
-srun -n 4 ./ex1
+mpirun -np 4 ./ex1
 ```
 
 
 ## PDI core & trace plugin
 
 ### Ex2. Now with some PDI
 
-Ex2. is the same code as that of ex1. with %PDI calls added in `main` function.
-In our YAML file (`ex2.yml`), a new sub-tree has been added under the `pdi` key.
-This sub-tree is the %PDI specification tree passed to %PDI at initialization.
-Here, the %PDI \ref trace_plugin "Trace plugin" is used to trace %PDI calls.
+Ex2. C code is similar to ex1. C code with %PDI calls added in `main` function.
+This exercise will be run sequentially.
 
 * Examine the source code, compile it and run it.
 
-* Add the required `::PDI_share` and `::PDI_reclaim` calls to match the output
-  of `ex2.log` file (only the lines matching `[Trace-plugin]` have been kept).
-  You only need to change the `ex2.c` file. You can easily check if the files
-  are the same by running the command:
+In our YAML file (`ex2.yml`), the `pdi` key is added. The sub-tree, defined
+after this key, is the %PDI specification tree passed to %PDI at initialization.
+
+* To observe %PDI calls on the standard output, add \ref trace_plugin
+ "Trace plugin" (`trace`) plugin of %PDI in our YAML file (`ex2.yml`).
+
+* In the C file (`ex2.c`), add `::PDI_share` and `::PDI_reclaim` call to share
+  some data with %PDI.
+  The shared data are defined in the line that starts with "//***" in `ex2.c`.
+
+Here, the objective is to match the output of `ex2.log` file.
+In this file, only the line corresponding to `[Trace-plugin]` have been kept.
+Moreover, the time are given for each %PDI calls.
+To compare, we need to remove this information from the log.
+It is done by adding this line in the sub-tree of the trace plugin.
+
+```yaml
+  logging: { pattern: '[PDI][%n-plugin] *** %l: %v' }
+```
+Additionally, we run sequentially to facilitate the comparison between logs
+(in parallel each rank send a `trace` message and the order of writing can be
+different).
+
+* Add the previous line in the sub-tree of \ref trace_plugin "Trace plugin"
+(don't forget to indent this line correctly).
+Using the previous section [Execution with storage of the log](#execution-with-storage-of-the-log),
+run this exercise and save the output log in the file `ex2.result.log`.
+After that you can easily check if the files are the same by running the command:
+
 ```bash
   diff ex2.log <(grep Trace-plugin ex2.result.log)
 ```
@@ -138,6 +163,9 @@ interlaced.
 Is one better than the other?
 If you do not know the answer to this question, just wait until ex5. :)
 
+\attention
+In this exercise, the shared variable and the reclaimed variable are not defined
+in the YAML file (see ex3. and further for this).
 
 ## Decl'HDF5 plugin
 

ex1.c

@@ -29,26 +29,59 @@
 #include <time.h>
 
 #include <paraconf.h>
+#include <pdi.h>
 
-/// size of the local data as [HEIGHT, WIDTH] including ghosts & boundary constants
+// size of the local data as [HEIGHT, WIDTH] including the number of ghost layers
+// for communications or boundary conditions
 int dsize[2];
 
-/// 2D size of the process grid as [HEIGHT, WIDTH]
+// 2D size of the process grid as [HEIGHT, WIDTH]
 int psize[2];
 
-/// 2D rank of the local process in the process grid as [YY, XX]
+// 2D rank of the local process in the process grid as [YY, XX]
 int pcoord[2];
 
-/// the alpha coefficient used in the computation
+// the alpha coefficient used in the computation
 double alpha;
 
-/** Initialize the data all to 0 except for the left border (XX==0) initialized to 1 million
+double L=1.0;
+// definition of the source
+// the source corresponds to a disk of an uniform value
+// source1: center=(0.4,0.4), radius=0.2 and value=100
+double source1[4]={0.4, 0.4, 0.2, 100};
+// source2: center=(0.8,0.7), radius=0.1 and value=200
+double source2[4]={0.7, 0.8, 0.1, 200};
+// the order of the coordinates of the center (XX,YY) is inverted in the vector
+
+/** Initialize all the data to 0, with the exception of a given cell
+ *  whose center (cpos_x,cpos_y) is inside of the disks
+ *  defined by source1 or source2
  * \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;
+	double square_dist1, square_dist2;
+	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;
+			square_dist1 = ( cpos_y-source1[0] ) * ( cpos_y-source1[0] )
+				     + ( cpos_x-source1[1] ) * ( cpos_x-source1[1] );
+			if (square_dist1 <= source1[2] * source1[2]) {
+				dat[yy][xx] = source1[3];
+			}
+			square_dist2 = ( cpos_y-source2[0] ) * ( cpos_y-source2[0] )
+				     + ( cpos_x-source2[1] ) * ( cpos_x-source2[1] );
+			if (square_dist2 <= 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
@@ -58,24 +91,18 @@ 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
+/** Exchange ghost values with neighbours
  * \param[in] cart_comm the MPI communicator with all processes organized in a 2D Cartesian grid
  * \param[in] cur the local data at the current time-step whose ghosts need exchanging
  */
@@ -102,8 +129,8 @@ 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
@@ -114,7 +141,7 @@ void exchange(MPI_Comm cart_comm, double cur[dsize[0]][dsize[1]])
 
 	// send to the left
 	MPI_Cart_shift(cart_comm, 1, -1, &rank_source, &rank_dest);
-	MPI_Sendrecv(&cur[1][1], 1, column, rank_dest,   100, // send column after ghost
+	MPI_Sendrecv(&cur[1][1],          1, column, rank_dest,   100, // send column after ghost
 	             &cur[1][dsize[1]-1], 1, column, rank_source, 100, // receive last column (ghost)
 	             cart_comm, &status);
 }
@@ -138,8 +165,9 @@ int main( int argc, char* argv[] )
 	// load the alpha parameter
 	PC_double(PC_get(conf, ".alpha"), &alpha);
 
-	// load the global data-size
 	int global_size[2];
+	// load the global data-size
+	// you can use paraconf to read some parameters from the yml config file
 	PC_int(PC_get(conf, ".global_size.height"), &longval); global_size[0] = longval;
 	PC_int(PC_get(conf, ".global_size.width"), &longval); global_size[1] = longval;
 
@@ -152,12 +180,12 @@ int main( int argc, char* argv[] )
 	assert(global_size[1]%psize[1]==0);
 	assert(psize[1]*psize[0] == psize_1d);
 
-	// compute the local data-size with space for ghosts and boundary constants
+	// compute the local data-size (the number of ghost layers is 2 for each coordinate)
 	dsize[0] = global_size[0]/psize[0] + 2;
 	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);
 
@@ -173,6 +201,7 @@ int main( int argc, char* argv[] )
 
 	// the main loop
 	for (; ii<10; ++ii) {
+
 		// compute the values for the next iteration
 		iter(cur, next);
 

ex1.yml

@@ -1,6 +1,6 @@
 # the alpha parameter
 alpha: 0.125
-# global data-size (excluding spacer for boundary conditions or ghosts)
+# global data-size (excluding the number of ghost layers for boundary conditions)
 global_size: { height: 60, width: 12 }
 # degree of parallelism (number of blocks in each dimension)
-parallelism: { height: 1, width: 1 }
+parallelism: { height: 1, width: 1 }