Merge pull request #2478 from devitocodes/restore_mpi

ci: Restore MPI notebook testing
devitocodes · Nov 5, 2024 · d9a4c7a · d9a4c7a
2 parents 337f2e1 + 36ef7a8
commit d9a4c7a
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Showing 2 changed files with 39 additions and 59 deletions.
diff --git a/.github/workflows/examples-mpi.yml b/.github/workflows/examples-mpi.yml
@@ -65,12 +65,11 @@ jobs:
         python3 scripts/clear_devito_cache.py
 
     - name: Test mpi notebooks
-      continue-on-error: true
       run : |
         ./scripts/create_ipyparallel_mpi_profile.sh
         ipcluster start --profile=mpi --engines=mpi -n 4 --daemonize
         # A few seconds to ensure workers are ready
-        sleep 20
+        sleep 10
         py.test --nbval examples/mpi
         ipcluster stop --profile=mpi
 

diff --git a/examples/mpi/overview.ipynb b/examples/mpi/overview.ipynb
@@ -245,17 +245,7 @@
      "output_type": "stream",
      "text": [
       "[stderr:0] \n",
-      "Operator `Kernel` ran in 0.01 s\n",
-      "INFO:Devito:Operator `Kernel` ran in 0.01 s\n",
-      "[stderr:1] \n",
-      "Operator `Kernel` ran in 0.01 s\n",
-      "INFO:Devito:Operator `Kernel` ran in 0.01 s\n",
-      "[stderr:2] \n",
-      "Operator `Kernel` ran in 0.01 s\n",
-      "INFO:Devito:Operator `Kernel` ran in 0.01 s\n",
-      "[stderr:3] \n",
-      "Operator `Kernel` ran in 0.01 s\n",
-      "INFO:Devito:Operator `Kernel` ran in 0.01 s\n"
+      "Operator `Kernel` ran in 0.01 s\n"
      ]
     }
    ],
@@ -447,10 +437,10 @@
        "  double section0;\n",
        "} ;\n",
        "\n",
-       "static void gather0(float *restrict buf_vec, int bx_size, int by_size, struct dataobj *restrict u_vec, const int otime, const int ox, const int oy);\n",
-       "static void scatter0(float *restrict buf_vec, int bx_size, int by_size, struct dataobj *restrict u_vec, const int otime, const int ox, const int oy);\n",
        "static void sendrecv0(struct dataobj *restrict u_vec, const int x_size, const int y_size, int ogtime, int ogx, int ogy, int ostime, int osx, int osy, int fromrank, int torank, MPI_Comm comm);\n",
        "static void haloupdate0(struct dataobj *restrict u_vec, MPI_Comm comm, struct neighborhood * nb, int otime);\n",
+       "static void gather0(float *restrict buf_vec, int bx_size, int by_size, struct dataobj *restrict u_vec, const int otime, const int ox, const int oy);\n",
+       "static void scatter0(float *restrict buf_vec, int bx_size, int by_size, struct dataobj *restrict u_vec, const int otime, const int ox, const int oy);\n",
        "\n",
        "int Kernel(struct dataobj *restrict u_vec, const float h_x, const int time_M, const int time_m, const int x_M, const int x_m, const int y_M, const int y_m, MPI_Comm comm, struct neighborhood * nb, struct profiler * timers)\n",
        "{\n",
@@ -471,7 +461,7 @@
        "      #pragma omp simd aligned(u:64)\n",
        "      for (int y = y_m; y <= y_M; y += 1)\n",
        "      {\n",
-       "        u[t1][x + 2][y + 2] = r0*(-u[t0][x + 2][y + 2]) + r0*u[t0][x + 3][y + 2] + 1;\n",
+       "        u[t1][x + 2][y + 2] = -r0*u[t0][x + 2][y + 2] + r0*u[t0][x + 3][y + 2] + 1;\n",
        "      }\n",
        "    }\n",
        "    STOP(section0,timers)\n",
@@ -480,6 +470,38 @@
        "  return 0;\n",
        "}\n",
        "\n",
+       "static void sendrecv0(struct dataobj *restrict u_vec, const int x_size, const int y_size, int ogtime, int ogx, int ogy, int ostime, int osx, int osy, int fromrank, int torank, MPI_Comm comm)\n",
+       "{\n",
+       "  MPI_Request rrecv;\n",
+       "  MPI_Request rsend;\n",
+       "\n",
+       "  float *restrict bufg_vec __attribute__ ((aligned (64)));\n",
+       "  posix_memalign((void**)(&bufg_vec),64,x_size*y_size*sizeof(float));\n",
+       "  float *restrict bufs_vec __attribute__ ((aligned (64)));\n",
+       "  posix_memalign((void**)(&bufs_vec),64,x_size*y_size*sizeof(float));\n",
+       "\n",
+       "  MPI_Irecv(bufs_vec,x_size*y_size,MPI_FLOAT,fromrank,13,comm,&(rrecv));\n",
+       "  if (torank != MPI_PROC_NULL)\n",
+       "  {\n",
+       "    gather0(bufg_vec,x_size,y_size,u_vec,ogtime,ogx,ogy);\n",
+       "  }\n",
+       "  MPI_Isend(bufg_vec,x_size*y_size,MPI_FLOAT,torank,13,comm,&(rsend));\n",
+       "  MPI_Wait(&(rsend),MPI_STATUS_IGNORE);\n",
+       "  MPI_Wait(&(rrecv),MPI_STATUS_IGNORE);\n",
+       "  if (fromrank != MPI_PROC_NULL)\n",
+       "  {\n",
+       "    scatter0(bufs_vec,x_size,y_size,u_vec,ostime,osx,osy);\n",
+       "  }\n",
+       "\n",
+       "  free(bufg_vec);\n",
+       "  free(bufs_vec);\n",
+       "}\n",
+       "\n",
+       "static void haloupdate0(struct dataobj *restrict u_vec, MPI_Comm comm, struct neighborhood * nb, int otime)\n",
+       "{\n",
+       "  sendrecv0(u_vec,u_vec->hsize[3],u_vec->npsize[2],otime,u_vec->oofs[2],u_vec->hofs[4],otime,u_vec->hofs[3],u_vec->hofs[4],nb->rc,nb->lc,comm);\n",
+       "}\n",
+       "\n",
        "static void gather0(float *restrict buf_vec, int bx_size, int by_size, struct dataobj *restrict u_vec, const int otime, const int ox, const int oy)\n",
        "{\n",
        "  float (*restrict buf)[bx_size][by_size] __attribute__ ((aligned (64))) = (float (*)[bx_size][by_size]) buf_vec;\n",
@@ -489,6 +511,7 @@
        "  const int y_m = 0;\n",
        "  const int x_M = bx_size - 1;\n",
        "  const int y_M = by_size - 1;\n",
+       "\n",
        "  for (int x = x_m; x <= x_M; x += 1)\n",
        "  {\n",
        "    #pragma omp simd aligned(u:64)\n",
@@ -518,38 +541,6 @@
        "    }\n",
        "  }\n",
        "}\n",
-       "\n",
-       "static void sendrecv0(struct dataobj *restrict u_vec, const int x_size, const int y_size, int ogtime, int ogx, int ogy, int ostime, int osx, int osy, int fromrank, int torank, MPI_Comm comm)\n",
-       "{\n",
-       "  float *restrict bufg_vec __attribute__ ((aligned (64)));\n",
-       "  posix_memalign((void**)(&bufg_vec),64,x_size*y_size*sizeof(float));\n",
-       "  float *restrict bufs_vec __attribute__ ((aligned (64)));\n",
-       "  posix_memalign((void**)(&bufs_vec),64,x_size*y_size*sizeof(float));\n",
-       "\n",
-       "  MPI_Request rrecv;\n",
-       "  MPI_Request rsend;\n",
-       "\n",
-       "  MPI_Irecv(bufs_vec,x_size*y_size,MPI_FLOAT,fromrank,13,comm,&(rrecv));\n",
-       "  if (torank != MPI_PROC_NULL)\n",
-       "  {\n",
-       "    gather0(bufg_vec,x_size,y_size,u_vec,ogtime,ogx,ogy);\n",
-       "  }\n",
-       "  MPI_Isend(bufg_vec,x_size*y_size,MPI_FLOAT,torank,13,comm,&(rsend));\n",
-       "  MPI_Wait(&(rsend),MPI_STATUS_IGNORE);\n",
-       "  MPI_Wait(&(rrecv),MPI_STATUS_IGNORE);\n",
-       "  if (fromrank != MPI_PROC_NULL)\n",
-       "  {\n",
-       "    scatter0(bufs_vec,x_size,y_size,u_vec,ostime,osx,osy);\n",
-       "  }\n",
-       "\n",
-       "  free(bufg_vec);\n",
-       "  free(bufs_vec);\n",
-       "}\n",
-       "\n",
-       "static void haloupdate0(struct dataobj *restrict u_vec, MPI_Comm comm, struct neighborhood * nb, int otime)\n",
-       "{\n",
-       "  sendrecv0(u_vec,u_vec->hsize[3],u_vec->npsize[2],otime,u_vec->oofs[2],u_vec->hofs[4],otime,u_vec->hofs[3],u_vec->hofs[4],nb->rc,nb->lc,comm);\n",
-       "}\n",
        "\n"
       ]
      },
@@ -789,17 +780,7 @@
      "output_type": "stream",
      "text": [
       "[stderr:0] \n",
-      "Operator `Kernel` ran in 0.01 s\n",
-      "INFO:Devito:Operator `Kernel` ran in 0.01 s\n",
-      "[stderr:1] \n",
-      "Operator `Kernel` ran in 0.01 s\n",
-      "INFO:Devito:Operator `Kernel` ran in 0.01 s\n",
-      "[stderr:2] \n",
-      "Operator `Kernel` ran in 0.01 s\n",
-      "INFO:Devito:Operator `Kernel` ran in 0.01 s\n",
-      "[stderr:3] \n",
-      "Operator `Kernel` ran in 0.01 s\n",
-      "INFO:Devito:Operator `Kernel` ran in 0.01 s\n"
+      "Operator `Kernel` ran in 0.01 s\n"
      ]
     }
    ],