fix #25, update ex6 (#29)

* fix #25, update ex6

* Update README.md

Co-authored-by: [email protected]

* small fix

* change the filename output

* fix typo + indent

* homogenization

---------

Co-authored-by: [email protected] and [email protected]

Author: jmorice91

README.md

@@ -336,6 +336,7 @@ in two distinct groups `iter1` and `iter2`.
 ```bash
   diff ex5.h5dump <(h5dump ex5-data-*.h5)
 ```
+
   To see your `h5` file in readable file format, you can check the section
   [Comparison with the `h5dump` command](#h5comparison).
 
@@ -346,10 +347,13 @@ As you can notice, the %PDI code is quite redundant.
 In this exercise, you will use `::PDI_expose` and `::PDI_multi_expose` to
 simplify the code while keeping the exact same behaviour.
 For once, there is no need to modify the YAML file here, you only need to modify
-the C file in this exercise.
+the C file. Moreover, this exercise will be launched sequentially to facilitate
+the comparison between logs.
 
 * Examine the source code, compile it and run it.
 
+\remark At the end of the iteration loop, a new event `finalization` is added.
+
 There are lots of matched `::PDI_share`/`::PDI_reclaim` in the code.
 
 * Replace these by `::PDI_expose` that is the exact equivalent of a
@@ -362,12 +366,22 @@ then triggers an event and finally does all the reclaim in reverse order.
 
 * Replace the remaining `::PDI_share`/`::PDI_reclaim` by `::PDI_expose`s and
   `::PDI_multi_expose`s and ensure that your code keeps the exact same behaviour
-  by comparing its trace to `ex6.log` (only the lines matching `[Trace-plugin]`
-  have been kept). You can easily check if the files are the same by running:
+  as in previous exercise by comparing its trace to `ex6.log` (only the lines matching
+  `[Trace-plugin]` have been kept). Using the previous section
+  [Execution with storage of the log](#execution-with-storage-of-the-log),
+  run  this exercise in saving the output log in the `ex6.result.log`.
+  After that you can easily check if the files are the same by running:
 ```bash
   diff ex6.log <(grep Trace-plugin ex6.result.log)
 ```
 
+In summary:
+
+1. `::PDI_expose` is equivalent to `::PDI_share` + `::PDI_reclaim`.
+
+2. `::PDI_multi_expose` is equivalent to `::PDI_share` + `::PDI_event` + `::PDI_reclaim`.
+
+
 ### Ex7. Writing a selection
 
 In this exercise, you will only write a selection of the 2D array in memory

ex6.c

@@ -32,25 +32,57 @@
 // load the PDI header
 #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
@@ -60,24 +92,18 @@ 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
  */
@@ -104,8 +130,8 @@ 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
@@ -116,7 +142,7 @@ 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);
 }
@@ -157,12 +183,12 @@ 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);
 
@@ -178,20 +204,20 @@ int main( int argc, char* argv[] )
 	int ii=0;
 
 	// share useful configuration bits with PDI
-	PDI_share("ii",         &ii,    PDI_OUT);
-	PDI_reclaim("ii");
+	//*** use PDI_expose to replace PDI_share + reclaim
+	//...
 	PDI_share("pcoord",     pcoord, PDI_OUT);
 	PDI_reclaim("pcoord");
 	PDI_share("dsize",      dsize,  PDI_OUT);
 	PDI_reclaim("dsize");
 	PDI_share("psize",      psize,  PDI_OUT);
 	PDI_reclaim("psize");
-	PDI_share("main_field", cur,    PDI_OUT);
-	PDI_reclaim("main_field");
 
 	// the main loop
-	for (; ii<10; ++ii) {
+	for (; ii<4; ++ii) {
 		// share the loop counter & main field at each iteration
+		//*** use PDI_multi_expose to replace PDI_share + event + reclaim
+		//...
 		PDI_share("ii",         &ii, PDI_OUT);
 		PDI_share("main_field", cur, PDI_OUT);
 		PDI_event("loop");
@@ -208,11 +234,13 @@ int main( int argc, char* argv[] )
 		double (*tmp)[dsize[1]] = cur; cur = next; next = tmp;
 	}
 	// finally share the main field as well as the loop counter after the loop
-	PDI_share("main_field", cur, PDI_OUT);
+	//*** use PDI_multi_expose to replace PDI_share + event + reclaim
+	//...
 	PDI_share("ii",         &ii, PDI_OUT);
+	PDI_share("main_field", cur, PDI_OUT);
 	PDI_event("finalization");
-	PDI_reclaim("ii");
 	PDI_reclaim("main_field");
+	PDI_reclaim("ii");
 
 	// finalize PDI
 	PDI_finalize();
@@ -230,3 +258,4 @@ int main( int argc, char* argv[] )
 	fprintf(stderr, "[%d] SUCCESS\n", pcoord_1d);
 	return EXIT_SUCCESS;
 }
+

ex6.log

@@ -1,15 +1,16 @@
 [PDI][Trace-plugin] *** info: Welcome!
 [PDI][Trace-plugin] *** info: !!!                            named event: initialization
-[PDI][Trace-plugin] *** info: =>>   data becoming available in the store: ii
-[PDI][Trace-plugin] *** info: <<= data stop being available in the store: ii
 [PDI][Trace-plugin] *** info: =>>   data becoming available in the store: pcoord
 [PDI][Trace-plugin] *** info: <<= data stop being available in the store: pcoord
 [PDI][Trace-plugin] *** info: =>>   data becoming available in the store: dsize
 [PDI][Trace-plugin] *** info: <<= data stop being available in the store: dsize
 [PDI][Trace-plugin] *** info: =>>   data becoming available in the store: psize
 [PDI][Trace-plugin] *** info: <<= data stop being available in the store: psize
+[PDI][Trace-plugin] *** info: =>>   data becoming available in the store: ii
 [PDI][Trace-plugin] *** info: =>>   data becoming available in the store: main_field
+[PDI][Trace-plugin] *** info: !!!                            named event: loop
 [PDI][Trace-plugin] *** info: <<= data stop being available in the store: main_field
+[PDI][Trace-plugin] *** info: <<= data stop being available in the store: ii
 [PDI][Trace-plugin] *** info: =>>   data becoming available in the store: ii
 [PDI][Trace-plugin] *** info: =>>   data becoming available in the store: main_field
 [PDI][Trace-plugin] *** info: !!!                            named event: loop

ex6.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 }
@@ -16,3 +16,14 @@ pdi:
   plugins:
     trace:
       logging: { pattern: '[PDI][%n-plugin] *** %l: %v' }
+    decl_hdf5:
+      - file: ex6-meta-${pcoord[0]}x${pcoord[1]}.h5
+        write: [ dsize, psize ]
+      - file: ex6-data-${pcoord[0]}x${pcoord[1]}.h5
+        on_event: loop
+        when: '$ii>0 & $ii<3' 
+        write:
+          ii:
+            dataset: 'iter${ii}/ii' 
+          main_field:
+            dataset: 'iter${ii}/main_field'

solutions/ex6.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
@@ -104,8 +117,8 @@ 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
@@ -116,7 +129,7 @@ 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);
 }
@@ -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);
 
@@ -178,15 +191,15 @@ int main( int argc, char* argv[] )
 	int ii=0;
 
 	// share useful configuration bits with PDI
-	PDI_expose("ii",         &ii,    PDI_OUT);
+	//*** use PDI_expose to replace PDI_share + reclaim
 	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<3; ++ii) {
+	for (; ii<4; ++ii) {
 		// share the loop counter & main field at each iteration
+		//*** use PDI_multi_expose to replace PDI_share + event + reclaim
 		PDI_multi_expose("loop",
 				"ii",         &ii, PDI_OUT,
 				"main_field", cur, PDI_OUT,
@@ -202,6 +215,7 @@ int main( int argc, char* argv[] )
 		double (*tmp)[dsize[1]] = cur; cur = next; next = tmp;
 	}
 	// finally share the main field as well as the loop counter after the loop
+	//*** use PDI_multi_expose to replace PDI_share + event + reclaim
 	PDI_multi_expose("finalization",
 	        "main_field", cur, PDI_OUT,
 	        "ii",         &ii, PDI_OUT,