Timing study

cuda-global/src/game.cu

@@ -1,11 +1,12 @@
 #include "game.cuh"
 
+// Count the number of life neighbors a cell has
 __device__ int neighbors(struct GAME game, int x, int y) {
   int n = 0;
 
   for (int dy = -1; dy <= 1; dy++) {
     for (int dx = -1; dx <= 1; dx++) {
-      if (!(dx == 0 && dy == 0) && (x+dx) >= 0 && (y+dy) >= 0 && (x+dx) < game.width+(game.padding*2) && (y+dy) < game.height+(game.padding*2)) {
+      if (!(dx == 0 && dy == 0) && (x+dx) > 0 && (y+dy) > 0 && (x+dx) < game.width+(game.padding*2) && (y+dy) < game.height+(game.padding*2)) {
         if (game.grid[(y+dy) * (game.width+game.padding*2) + (x+dx)]) {
           n++;
         }
@@ -15,11 +16,14 @@ __device__ int neighbors(struct GAME game, int x, int y) {
   return n;
 }
 
+// Compute the next iteration of a board
+// We have to give it the newGrid as a parameter otherwise 
+// each block will be computing its own version of the next grid
 __global__ void next(struct GAME game, unsigned char* newGrid) {
   int idy = blockDim.y * blockIdx.y + threadIdx.y;
   int idx = blockDim.x * blockIdx.x + threadIdx.x;
 
-  if (idy <= game.height+game.padding*2 && idx <= game.width+game.padding*2) {
+  if (idy < game.height+game.padding*2 && idx < game.width+game.padding*2) {
     int my_neighbors = neighbors(game, idx, idy);
     int my_coord = idy * (game.width+game.padding*2) + idx;
     newGrid[my_coord] = 0; // It's possible that there are artifacts from the last iteration
@@ -37,6 +41,7 @@ __global__ void next(struct GAME game, unsigned char* newGrid) {
   }
 }
 
+// Randomly assign life value to each cell
 void randomize(struct GAME* game) {
   for (int y = game->padding; y < game->height+game->padding; y++) {
     for (int x = game->padding; x < game->width+game->padding; x++) {

cuda-global/src/main.cu

@@ -18,7 +18,7 @@
  */
 #define BLOCK 32
 #define PADDING 10
-#define VERBOSE 1
+//#define VERBOSE 1
 #define SEED 100
 
 // gpuErrchk source: https://stackoverflow.com/questions/14038589/what-is-the-canonical-way-to-check-for-errors-using-the-cuda-runtime-api
@@ -33,14 +33,16 @@ true) {
   }
 }
 
+// Do the simulation
 void simulate(int argc, char** argv) {
   srand(SEED);
-  clock_t totalStart = clock();
+  clock_t global_start = clock();
   char* filename;
   struct GAME game;
   game.padding = PADDING;
   int iterations, log_each_step;
   if (argc == 7) {
+    // Parse the arguments
     filename = argv[2];
     game.width = atoi(argv[3]);
     game.height = atoi(argv[4]);
@@ -60,6 +62,7 @@ void simulate(int argc, char** argv) {
   game.grid = (unsigned char*)malloc(size);
   memset(game.grid, 0, size);
 
+  // Choose where to read initial position
   if (strcmp(filename, "random") == 0) {
     randomize(&game);
   } else {
@@ -68,43 +71,53 @@ void simulate(int argc, char** argv) {
 
   char iteration_file[1024];
 
+  // Allocate device memory
   unsigned char* grid_d;
   unsigned char* newGrid;
   gpuErrchk(cudaMalloc(&grid_d, size));
-  gpuErrchk(cudaMemcpy(grid_d, game.grid, size, cudaMemcpyHostToDevice));
   gpuErrchk(cudaMalloc(&newGrid, size));
+  gpuErrchk(cudaMemcpy(grid_d, game.grid, size, cudaMemcpyHostToDevice)); // Copy the initial grid to the device
+  free(game.grid);
+  game.grid = grid_d; // Use the device copy
 
+  // The grid that we will copy results 
   unsigned char* grid_h = (unsigned char*)malloc(size);
   unsigned char* temp;
 
-  game.grid = grid_d;
-
-  int grid_num = (int)ceil((game.width+(2*game.padding))/(float)BLOCK);
-  dim3 dim_grid(grid_num, grid_num, 1);
+  // Calculate grid width for kernel
+  int grid_width = (int)ceil((game.width+(2*game.padding))/(float)BLOCK);
+  int grid_height = (int)ceil((game.height+(2*game.padding))/(float)BLOCK);
+  dim3 dim_grid(grid_width, grid_height, 1);
   dim3 dim_block(BLOCK, BLOCK, 1);
 
-  cudaEvent_t startLife, stopLife;
-  cudaEventCreate(&startLife);
-  cudaEventCreate(&stopLife);
-  double timeComputingLife = 0;
-  float localTime = 0;
+  // Timing
+  cudaEvent_t start, end;
+  cudaEventCreate(&start);
+  cudaEventCreate(&end);
+  double time_computing_life = 0;
+  float local_time = 0;
 
   for (int i = 0; i <= iterations; i++) {
+    // Iteration 0 will just be the initial grid
     if (i > 0) {
-      cudaEventRecord(startLife);
+      cudaEventRecord(start);
+      // Compute the next grid
       next<<<dim_grid, dim_block>>>(game, newGrid);
-      cudaEventRecord(stopLife);
-      cudaEventSynchronize(stopLife);
-      cudaEventElapsedTime(&localTime, startLife, stopLife);
-      timeComputingLife += localTime/1000;
+      cudaEventRecord(end);
+      cudaEventSynchronize(end);
+      cudaEventElapsedTime(&local_time, start, end);
+      time_computing_life += local_time/1000;
 
+      // Swap game.grid and newGrid
       temp = game.grid;
       game.grid = newGrid;
       newGrid = temp;
     }
     if (log_each_step) {
+      // If we are logging each step, perform IO operations
       gpuErrchk(cudaMemcpy(grid_h, game.grid, size, cudaMemcpyDeviceToHost));
       #ifdef VERBOSE
+        // Print the board without the padding elements
         printf("\n===Iteration %i===\n", i);
         for (int y = game.padding; y < game.height+game.padding; y++) {
           for (int x = game.padding; x < game.width+game.padding; x++) {
@@ -114,6 +127,7 @@ void simulate(int argc, char** argv) {
         }
         printf("===End iteration %i===\n", i);
       #endif
+      // Save to a file
       sprintf(iteration_file, "output/iteration-%07d.bin", i);
       temp = game.grid;
       game.grid = grid_h;
@@ -122,13 +136,7 @@ void simulate(int argc, char** argv) {
     }
   }
 
-  clock_t totalEnd = clock();
-  printf("\n===Timing===\nTime computing life: %f\nClock time: %f\n", timeComputingLife, ((double)totalEnd - (double)totalStart)/CLOCKS_PER_SEC);
-
-  cudaFree(&newGrid);
-  cudaFree(&grid_d);
-  cudaFree(&game.grid);
-  free(grid_h);
+  printf("\n===Timing===\nTime computing life: %f\nClock time: %f\n", time_computing_life, ((double)clock() - (double)global_start)/CLOCKS_PER_SEC);
 }
 
 int main(int argc, char** argv) {

cuda-global/timing-study/output--1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.169687
+Clock time: 1.560000

cuda-global/timing-study/output--1000-1250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.254989
+Clock time: 2.240000

cuda-global/timing-study/output--1000-1500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.354361
+Clock time: 3.050000

cuda-global/timing-study/output--1000-1750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.480174
+Clock time: 4.070000

cuda-global/timing-study/output--1000-2000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.619636
+Clock time: 5.220000

cuda-global/timing-study/output--1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.029867
+Clock time: 0.330000

cuda-global/timing-study/output--1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.059907
+Clock time: 0.540000

cuda-global/timing-study/output--1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.110954
+Clock time: 1.000000

cuda-global/timing-study/timing_study.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --time=0:30:00 # walltime, abbreviated by -t
+#SBATCH --nodes=1      # number of cluster nodes, abbreviated by -N
+#SBATCH -o slurm-%j.out-%N # name of the stdout, using the job number (%j) and the first node (%N)
+#SBATCH -e slurm-%j.err-%N # name of the stderr, using job and first node values
+#SBATCH --ntasks=1    # number of MPI tasks, abbreviated by -n
+# additional information for allocated clusters
+#SBATCH --account=notchpeak-shared-short     # account - abbreviated by -A
+#SBATCH --partition=notchpeak-shared-short  # partition, abbreviated by -p
+#SBATCH --gres=gpu:k80:1
+
+cd $HOME/gol/cuda-global
+
+iterations=1000
+for size in 250 500 750 1000 1250 1500 1750 2000
+do
+  srun ./gol simulate random $size $size $iterations 1 > timing-study/output-$cores-$iterations-$size.txt
+done

mpi/src/main.c

@@ -15,10 +15,12 @@
   Any live cell with more than three live neighbors dies (overpopulation).
   Any dead cell with exactly three live neighbors becomes a live cell (reproduction).
  */
-#define PADDING 16
+#define PADDING 10
 //#define VERBOSE 1
 #define SEED 100
 
+// A structure to keep the global arguments because each process
+// will use its own GAME structure
 struct Args {
   int process_count;
   int iterations;
@@ -30,6 +32,7 @@ struct Args {
   int data_per_proc;
 };
 
+// Make a datatype out of an Args struct
 void broadcast_and_receive_input(MPI_Comm comm, struct Args* args) {
   int blocks[8] = {1,1,1,1,1,1,1,1};
   MPI_Aint displacements[8];
@@ -50,6 +53,7 @@ void broadcast_and_receive_input(MPI_Comm comm, struct Args* args) {
   MPI_Bcast(args, 1, arg_t, 0, comm);
 }
 
+// Scatter the grid among nodes
 void scatter_data(MPI_Comm comm, struct Args* args, unsigned char* local_data, int rank, int* data_counts, int* displacements, char* filename) {
   unsigned char* data;
 
@@ -63,12 +67,14 @@ void scatter_data(MPI_Comm comm, struct Args* args, unsigned char* local_data, i
     data = malloc(size);
     memset(data, 0, size); 
     game.grid = data;
+    // Choose where to read initial position
     if (strcmp(filename, "random") == 0) {
       randomize(&game);
     } else {
       read_in(filename, &game);
     }
   }
+  // Do the scatter (some nodes may work on more rows)
   MPI_Scatterv(data, data_counts, displacements, MPI_UNSIGNED_CHAR, local_data, data_counts[rank], MPI_UNSIGNED_CHAR, 0, comm);
 
   if (rank == 0) {
@@ -77,12 +83,13 @@ void scatter_data(MPI_Comm comm, struct Args* args, unsigned char* local_data, i
 }
 
 
+// Do the simulation
 void simulate(int argc, char** argv) {
   srand(SEED);
-  double totalStart = MPI_Wtime();
   struct Args args;
   args.padding = PADDING;
 
+  // Initialize MPI stuff
   int rank, process_count;
   MPI_Comm comm;
   MPI_Init(&argc, &argv);
@@ -91,7 +98,9 @@ void simulate(int argc, char** argv) {
   MPI_Comm_size(comm, &args.process_count);
 
   char* filename;
+  double global_start;
   if (rank == 0) {
+    // Parse the arguments
     if (argc == 7) {
       filename = argv[2];
       args.width = atoi(argv[3]);
@@ -99,7 +108,7 @@ void simulate(int argc, char** argv) {
       args.iterations = atoi(argv[5]);
       args.log_each_step = atoi(argv[6]);
     } else {
-      printf("Usage: ./gol simulate <filename | random> <width> <height> <iterations> <log-each-step?1:0> <block-size>\n");
+      printf("Usage: ./gol simulate <filename | random> <width> <height> <iterations> <log-each-step?1:0>\n");
       filename = "random";
       args.height = 5;
       args.width = 5;
@@ -107,12 +116,17 @@ void simulate(int argc, char** argv) {
       args.log_each_step = 0;
     }
 
+    global_start = MPI_Wtime();
+
+    // Figure out how much work the average node will be doing
     args.rows_per_proc = (args.height + args.padding*2)/args.process_count;
     args.data_per_proc = args.rows_per_proc * (args.width + args.padding*2);
   }
 
   broadcast_and_receive_input(comm, &args);
 
+  // Calculate the exact work each thread will do and arguments for
+  // the Scatterv to scatter the grid
   int grid_size = ((args.width + args.padding*2)*(args.height + args.padding*2));
   int* data_counts = malloc(sizeof(int) * args.process_count);
   int* displacements = malloc(sizeof(int) * args.process_count);
@@ -123,19 +137,20 @@ void simulate(int argc, char** argv) {
   data_counts[args.process_count-1] += grid_size % (args.data_per_proc * args.process_count);
   unsigned char* local_data = malloc(data_counts[rank]*sizeof(unsigned char));
   memset(local_data, 0, sizeof(unsigned char) * data_counts[rank]); 
+
+  // Scatter the data among nodes
   scatter_data(comm, &args, local_data, rank, data_counts, displacements, filename);
  
-  // Allocate space for current grid (1 byte per tile)
   char iteration_file[1024];
 
-  double timeComputingLife = 0;
-  float localTime = 0;
-
+  // Local_game is our current job
   struct GAME local_game;
   local_game.grid = local_data;
   local_game.width = args.width;
   local_game.height = data_counts[rank] / (args.width + args.padding*2);
   local_game.padding = args.padding;
+
+  // Assign halo elements to send to be received from above and below nodes
   unsigned char* halo_above = NULL;
   unsigned char* halo_below = NULL;
   if (rank > 0) {
@@ -148,32 +163,46 @@ void simulate(int argc, char** argv) {
   }
 
   unsigned char* global_data;
+  if (rank == 0) {
+    global_data = malloc(sizeof(unsigned char) * grid_size);
+    memset(global_data, 0, sizeof(unsigned char) * grid_size); 
+  }
+
+  // Timing code
+  double time_computing_life = 0;
+  double start,end;
 
   for (int i = 0; i <= args.iterations; i++) {
+    // Iteration 0 will just be the initial grid
     if (i > 0) {
       int total_width = args.width + args.padding*2;
+
+      MPI_Status status;
       if (rank < args.process_count - 1) {
         MPI_Send(&local_game.grid[(local_game.height-1) * total_width], total_width, MPI_UNSIGNED_CHAR, rank+1, 1, comm); 
       }
       if (rank > 0) {
-        MPI_Recv(halo_above, total_width, MPI_UNSIGNED_CHAR, rank-1, 1, comm, NULL);
+        MPI_Recv(halo_above, total_width, MPI_UNSIGNED_CHAR, rank-1, 1, comm, &status);
         MPI_Send(&local_game.grid[0], total_width, MPI_UNSIGNED_CHAR, rank-1, 0, comm); 
       }
       if (rank < args.process_count - 1) {
-        MPI_Recv(halo_below, total_width, MPI_UNSIGNED_CHAR, rank+1, 0, comm, NULL);
+        MPI_Recv(halo_below, total_width, MPI_UNSIGNED_CHAR, rank+1, 0, comm, &status);
       }
       MPI_Barrier(comm);
+      start = MPI_Wtime();
+      // Compute the next grid 
       next(&local_game, halo_above, halo_below);
+      end = MPI_Wtime();
+      time_computing_life += end-start;
     }
     if (args.log_each_step) {
-      if (rank == 0) {
-        global_data = malloc(sizeof(unsigned char) * grid_size);
-        memset(global_data, 0, sizeof(unsigned char) * grid_size); 
-      }
+      // If we are logging each step, perform IO operations
+      // Gather all of the local grids into global_data
       MPI_Gatherv(local_game.grid, data_counts[rank], MPI_UNSIGNED_CHAR, global_data, data_counts, displacements, MPI_UNSIGNED_CHAR, 0, comm);
       if (rank == 0) {
-        #ifdef VERBOSE
+        #if VERBOSE == 1
           printf("\n===Iteration %i===\n", i);
+          // Print the baord without the padding elements
           for (int y = args.padding; y < args.height+args.padding; y++) {
             for (int x = args.padding; x < args.width+args.padding; x++) {
               printf("%s ", global_data[y*(args.width+2*args.padding) + x] ? "X" : " ");
@@ -183,6 +212,7 @@ void simulate(int argc, char** argv) {
           printf("===End iteration %i===\n", i);
         #endif
 
+        // Save to a file
         struct GAME global_game;
         global_game.grid = global_data;
         global_game.width = args.width;
@@ -194,12 +224,15 @@ void simulate(int argc, char** argv) {
     }
   }
 
-  double totalEnd = MPI_Wtime();
-  MPI_Finalize();
+  double total_end = MPI_Wtime();
   if (rank == 0) {
-    printf("\n===Timing===\nTime computing life: %f\nClock time: %f\n", timeComputingLife, (totalEnd - totalStart));
+    printf("\n===Timing===\nTime computing life: %f\nClock time: %f\n", time_computing_life, (total_end - global_start));
+    free(local_game.grid);
+    free(data_counts);
+    free(halo_above);
+    free(halo_below);
   } 
-
+  MPI_Finalize();
 }
 
 int main(int argc, char** argv) {

mpi/timing-study/output-1-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 33.832562
+Clock time: 37.939663

mpi/timing-study/output-1-1000-1250.txt

@@ -0,0 +1,11 @@
+
+===================================================================================
+=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
+=   PID 21716 RUNNING AT kp013
+=   EXIT CODE: 11
+=   CLEANING UP REMAINING PROCESSES
+=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
+===================================================================================
+YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
+This typically refers to a problem with your application.
+Please see the FAQ page for debugging suggestions

mpi/timing-study/output-1-1000-1500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 75.141736
+Clock time: 83.149478

mpi/timing-study/output-1-1000-1750.txt

@@ -0,0 +1,11 @@
+
+===================================================================================
+=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
+=   PID 21837 RUNNING AT kp013
+=   EXIT CODE: 11
+=   CLEANING UP REMAINING PROCESSES
+=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
+===================================================================================
+YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
+This typically refers to a problem with your application.
+Please see the FAQ page for debugging suggestions

mpi/timing-study/output-1-1000-2000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 132.636661
+Clock time: 145.001708

mpi/timing-study/output-1-1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 2.383001
+Clock time: 4.113476

mpi/timing-study/output-1-1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 8.793952
+Clock time: 9.832794

mpi/timing-study/output-1-1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 19.270078
+Clock time: 21.813069

mpi/timing-study/output-12-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 2.833550
+Clock time: 6.323680

mpi/timing-study/output-12-1000-1250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 4.347700
+Clock time: 9.178630

mpi/timing-study/output-12-1000-1500.txt

@@ -0,0 +1,11 @@
+
+===================================================================================
+=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
+=   PID 23209 RUNNING AT kp013
+=   EXIT CODE: 11
+=   CLEANING UP REMAINING PROCESSES
+=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
+===================================================================================
+YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
+This typically refers to a problem with your application.
+Please see the FAQ page for debugging suggestions

mpi/timing-study/output-12-1000-1750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 8.483342
+Clock time: 17.330302

mpi/timing-study/output-12-1000-2000.txt

@@ -0,0 +1,11 @@
+
+===================================================================================
+=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
+=   PID 23290 RUNNING AT kp013
+=   EXIT CODE: 11
+=   CLEANING UP REMAINING PROCESSES
+=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
+===================================================================================
+YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
+This typically refers to a problem with your application.
+Please see the FAQ page for debugging suggestions

mpi/timing-study/output-12-1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.198089
+Clock time: 2.217166

mpi/timing-study/output-12-1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.735509
+Clock time: 2.513034

mpi/timing-study/output-12-1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 1.617002
+Clock time: 4.091923

mpi/timing-study/output-16-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 2.106571
+Clock time: 7.500836

mpi/timing-study/output-16-1000-1250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 3.445883
+Clock time: 11.167682

mpi/timing-study/output-16-1000-1500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 4.741983
+Clock time: 16.777514

mpi/timing-study/output-16-1000-1750.txt

@@ -0,0 +1,8 @@
+
+===================================================================================
+=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
+=   PID 34784 RUNNING AT kp160
+=   EXIT CODE: 11
+=   CLEANING UP REMAINING PROCESSES
+=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
+===================================================================================

mpi/timing-study/output-16-1000-2000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 8.301682
+Clock time: 28.791425

mpi/timing-study/output-16-1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.145483
+Clock time: 2.572587

mpi/timing-study/output-16-1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.570992
+Clock time: 3.899400

mpi/timing-study/output-16-1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 1.215016
+Clock time: 5.047125

mpi/timing-study/output-24-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 1.414322
+Clock time: 9.439315

mpi/timing-study/output-24-1000-1250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 2.171989
+Clock time: 13.927639

mpi/timing-study/output-24-1000-1500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 3.133675
+Clock time: 19.271850

mpi/timing-study/output-24-1000-1750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 4.398371
+Clock time: 25.650748

mpi/timing-study/output-24-1000-2000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 5.639865
+Clock time: 33.529967

mpi/timing-study/output-24-1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.100765
+Clock time: 2.412458

mpi/timing-study/output-24-1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.465147
+Clock time: 3.942927

mpi/timing-study/output-24-1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.815429
+Clock time: 5.642879

mpi/timing-study/output-4-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 8.467197
+Clock time: 11.707533

mpi/timing-study/output-4-1000-1250.txt

@@ -0,0 +1,11 @@
+
+===================================================================================
+=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
+=   PID 22126 RUNNING AT kp013
+=   EXIT CODE: 11
+=   CLEANING UP REMAINING PROCESSES
+=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
+===================================================================================
+YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
+This typically refers to a problem with your application.
+Please see the FAQ page for debugging suggestions

mpi/timing-study/output-4-1000-1500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 18.823087
+Clock time: 26.449810

mpi/timing-study/output-4-1000-1750.txt

@@ -0,0 +1,11 @@
+
+===================================================================================
+=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
+=   PID 22197 RUNNING AT kp013
+=   EXIT CODE: 11
+=   CLEANING UP REMAINING PROCESSES
+=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
+===================================================================================
+YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
+This typically refers to a problem with your application.
+Please see the FAQ page for debugging suggestions

mpi/timing-study/output-4-1000-2000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 33.274214
+Clock time: 45.841294

mpi/timing-study/output-4-1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.599813
+Clock time: 2.807879

mpi/timing-study/output-4-1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 2.212790
+Clock time: 4.133439

mpi/timing-study/output-4-1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 4.830949
+Clock time: 6.854574

mpi/timing-study/output-8-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 4.226861
+Clock time: 7.517444

mpi/timing-study/output-8-1000-1250.txt

@@ -0,0 +1,11 @@
+
+===================================================================================
+=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
+=   PID 22852 RUNNING AT kp013
+=   EXIT CODE: 11
+=   CLEANING UP REMAINING PROCESSES
+=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
+===================================================================================
+YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
+This typically refers to a problem with your application.
+Please see the FAQ page for debugging suggestions

mpi/timing-study/output-8-1000-1500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 9.416485
+Clock time: 16.706325

mpi/timing-study/output-8-1000-1750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 12.741221
+Clock time: 22.281683

mpi/timing-study/output-8-1000-2000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 16.578412
+Clock time: 26.921717

mpi/timing-study/output-8-1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.296146
+Clock time: 2.211905

mpi/timing-study/output-8-1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 1.111486
+Clock time: 2.710176

mpi/timing-study/output-8-1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 2.419305
+Clock time: 4.675962

mpi/timing-study/slurm-10870703.err-kp013

@@ -0,0 +1,11 @@
+mkdir: cannot create directory ‘timing-study’: File exists
+[proxy:0:0@kp013] HYD_pmcd_pmip_control_cmd_cb (../../../../../../srcdir/mpich/3.2.1/src/pm/hydra/pm/pmiserv/pmip_cb.c:887): assert (!closed) failed
+[proxy:0:0@kp013] HYDT_dmxu_poll_wait_for_event (../../../../../../srcdir/mpich/3.2.1/src/pm/hydra/tools/demux/demux_poll.c:76): callback returned error status
+[proxy:0:0@kp013] main (../../../../../../srcdir/mpich/3.2.1/src/pm/hydra/pm/pmiserv/pmip.c:202): demux engine error waiting for event
+srun: error: kp013: task 0: Exited with exit code 7
+[mpiexec@kp013] HYDT_bscu_wait_for_completion (../../../../../../srcdir/mpich/3.2.1/src/pm/hydra/tools/bootstrap/utils/bscu_wait.c:76): one of the processes terminated badly; aborting
+[mpiexec@kp013] HYDT_bsci_wait_for_completion (../../../../../../srcdir/mpich/3.2.1/src/pm/hydra/tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for completion
+[mpiexec@kp013] HYD_pmci_wait_for_completion (../../../../../../srcdir/mpich/3.2.1/src/pm/hydra/pm/pmiserv/pmiserv_pmci.c:218): launcher returned error waiting for completion
+[mpiexec@kp013] main (../../../../../../srcdir/mpich/3.2.1/src/pm/hydra/ui/mpich/mpiexec.c:340): process manager error waiting for completion
+srun: error: Unable to create step for job 10870703: Job/step already completing or completed
+slurmstepd: error: *** JOB 10870703 ON kp013 CANCELLED AT 2021-12-08T01:29:02 DUE TO TIME LIMIT ***

mpi/timing-study/timing_study.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+#SBATCH --time=0:10:00 # walltime, abbreviated by -t
+#SBATCH --nodes=2     # number of cluster nodes, abbreviated by -N
+#SBATCH -o slurm-%j.out-%N # name of the stdout, using the job number (%j) and the first node (%N)
+#SBATCH -e slurm-%j.err-%N # name of the stderr, using job and first node values
+#SBATCH --ntasks=24   # number of MPI tasks, abbreviated by -n
+# additional information for allocated clusters
+#SBATCH --account=usucs5030     # account - abbreviated by -A
+#SBATCH --partition=kingspeak  # partition, abbreviated by -p
+
+cd $HOME/gol/mpi
+mkdir timing-study
+
+module load intel mpich 
+
+iterations=1000
+
+for cores in 1 4 8 12 16 20 #24
+do
+  for size in 250 500 750 1000 1250 1500 1750 2000
+  do
+    mpirun -np $cores ./gol simulate random $size $size $iterations 1 > timing-study/output-$cores-$iterations-$size.txt
+  done
+done

openmp/src/create_grid.c

@@ -1,5 +1,6 @@
 #include "create_grid.h"
 
+// Print entirety of a grid to verify input 
 void print_grid(struct GAME* game) {
   printf("\n===GRID===\n");
   for (int y = 0; y < game->height; y++) {
@@ -10,6 +11,7 @@ void print_grid(struct GAME* game) {
   }
 }
 
+// Go through user input
 void create_grid(int argc, char** argv) {
   char* filename;
   struct GAME game;

openmp/src/file.c

@@ -1,5 +1,6 @@
 #include "file.h"
 
+// Read a grid from a binary file into the space without padding
 void read_in(char* filename, struct GAME* game) {
   FILE* file = fopen(filename, "rb");
   for (int i = game->padding; i < game->height+game->padding; i++) {
@@ -8,6 +9,7 @@ void read_in(char* filename, struct GAME* game) {
   fclose(file);
 }
 
+// Write a grid to a binary file into the space without padding
 void write_out(char* filename, struct GAME* game) {
   FILE* file = fopen(filename, "w+");
   for (int i = game->padding; i < game->height+game->padding; i++) {

openmp/src/game.c

@@ -1,5 +1,6 @@
 #include "game.h"
 
+// Calculate the number of live neighbors a cell has
 int neighbors(struct GAME* game, int x, int y) {
   int n = 0;
   for (int dy = -1; dy <= 1; dy++) {
@@ -15,6 +16,7 @@ int neighbors(struct GAME* game, int x, int y) {
   return n;
 }
 
+// Compute the next iteration of a board
 void next(struct GAME* game, int threads) {
   unsigned char** newGrid = malloc(sizeof(unsigned char*) * (game->height+(game->padding*2)));
   int y,x,i,size;
@@ -30,10 +32,12 @@ void next(struct GAME* game, int threads) {
 
 #pragma omp parallel num_threads(threads) shared(per_thread, threads, total_width, total_height, newGrid, game) private(y,x,i)
   {
+    // Each thread gets a number of cells to compute
     int me = omp_get_thread_num();
     int thread_start = per_thread * me;
     int thread_end = thread_start + per_thread + (me == threads-1 ? (total_width*total_height) % per_thread : 0);
     for (i = thread_start; i < thread_end; i++) {
+      // Iterate through each cell assigned for this thread
       y = i / total_width;
       x = i % total_width;
       int my_neighbors = neighbors(game, x, y);
@@ -55,6 +59,7 @@ void next(struct GAME* game, int threads) {
   game->grid = newGrid;
 }
 
+//Rnadomly assign life value to each cell
 void randomize(struct GAME* game) {
   for (int y = game->padding; y < game->height+game->padding; y++) {
     for (int x = game->padding; x < game->width+game->padding; x++) {

openmp/src/main.c

@@ -19,6 +19,7 @@
 //#define VERBOSE 1
 #define SEED 100
 
+// Do the simulation
 void simulate(int argc, char** argv) {
   srand(SEED);
   char* filename;
@@ -26,6 +27,7 @@ void simulate(int argc, char** argv) {
   game.padding = PADDING;
   int iterations, log_each_step, threads;
   if (argc == 8) {
+    // Parse the arguments
     filename = argv[2];
     game.width = atoi(argv[3]);
     game.height = atoi(argv[4]);
@@ -51,6 +53,7 @@ void simulate(int argc, char** argv) {
     memset(game.grid[i], 0, game.width+(2*game.padding));
   }
 
+  // Choose where to read initial position
   if (strcmp(filename, "random") == 0) {
     randomize(&game);
   } else {
@@ -62,16 +65,19 @@ void simulate(int argc, char** argv) {
   double start, end;
 
   for (int i = 0; i <= iterations; i++) {
+    // Iteration 0 will just be the initial grid
     if (i > 0) {
-      // Iteration 0 is just the input board
       start = omp_get_wtime();
+      // Compute the next grid with threads
       next(&game, threads);
       end = omp_get_wtime();
       time_computing_life += ((double) (end - start));
     }
     if (log_each_step) {
+      // If we are logging each step, perform IO operations
       #if VERBOSE == 1
       printf("\n===Iteration %i===\n", i);
+      // Print the board without the padding elements
       for (int y = game.padding; y < game.height+game.padding; y++) {
         for (int x = game.padding; x < game.width+game.padding; x++) {
           printf("%s ", game.grid[y][x] ? "X" : " ");
@@ -80,6 +86,7 @@ void simulate(int argc, char** argv) {
       }
       printf("===End iteration %i===\n", i);
       #endif
+      // Save to a file
       sprintf(iteration_file, "output/iteration-%07d.bin", i);
       write_out(iteration_file, &game);
     }

openmp/timing-study/output-1-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 73.312715
+Clock time: 77.450210

openmp/timing-study/output-1-1000-1250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 113.646203
+Clock time: 118.646829

openmp/timing-study/output-1-1000-1500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 163.034248
+Clock time: 171.017339

openmp/timing-study/output-1-1000-1750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 220.656360
+Clock time: 231.050593

openmp/timing-study/output-1-1000-2000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 287.698970
+Clock time: 300.176503

openmp/timing-study/output-1-1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 5.088550
+Clock time: 5.963468

openmp/timing-study/output-1-1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 18.956314
+Clock time: 20.440567

openmp/timing-study/output-1-1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 41.660313
+Clock time: 44.581177

openmp/timing-study/output-12-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 7.026118
+Clock time: 10.251363

openmp/timing-study/output-12-1000-1250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 10.801676
+Clock time: 15.900482

openmp/timing-study/output-12-1000-1500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 25.918769
+Clock time: 34.562182

openmp/timing-study/output-12-1000-1750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 25.862278
+Clock time: 34.828966

openmp/timing-study/output-12-1000-2000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 30.705054
+Clock time: 43.042410

openmp/timing-study/output-12-1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.860293
+Clock time: 3.331446

openmp/timing-study/output-12-1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 2.097878
+Clock time: 3.643646

openmp/timing-study/output-12-1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 4.321400
+Clock time: 6.663178

openmp/timing-study/output-16-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 9.131005
+Clock time: 12.449032

openmp/timing-study/output-16-1000-1250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 13.434282
+Clock time: 18.116181

openmp/timing-study/output-16-1000-1500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 16.706991
+Clock time: 24.712374

openmp/timing-study/output-16-1000-1750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 23.733395
+Clock time: 33.306681

openmp/timing-study/output-16-1000-2000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 30.429469
+Clock time: 42.369926

openmp/timing-study/output-16-1000-250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 0.738930
+Clock time: 3.383995

openmp/timing-study/output-16-1000-500.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 2.352756
+Clock time: 3.601057

openmp/timing-study/output-16-1000-750.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 5.147589
+Clock time: 7.427564

openmp/timing-study/output-20-1000-1000.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 7.390921
+Clock time: 11.239737

openmp/timing-study/output-20-1000-1250.txt

@@ -0,0 +1,4 @@
+
+===Timing===
+Time computing life: 11.254777
+Clock time: 16.136264