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ci: Restore MPI notebook testing
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@georgebisbas
georgebisbas committed Nov 5, 2024
1 parent 337f2e1 commit 36ef7a8
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Showing 2 changed files with 39 additions and 59 deletions.
3 changes: 1 addition & 2 deletions .github/workflows/examples-mpi.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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95 changes: 38 additions & 57 deletions examples/mpi/overview.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
]
}
],
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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"
]
},
Expand Down Expand Up @@ -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"
]
}
],
Expand Down

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