Actual source code: ex5.c

  1: static char help[] = "Demonstrate HDF5 parallel load-save-reload cycle\n\n";

  3: #include <petscdmplex.h>
  4: #include <petscviewerhdf5.h>
  5: #define EX "ex5.c"

  7: typedef struct {
  8:   char              infile[PETSC_MAX_PATH_LEN];  /* Input mesh filename */
  9:   char              outfile[PETSC_MAX_PATH_LEN]; /* Dump/reload mesh filename */
 10:   PetscViewerFormat informat;                    /* Input mesh format */
 11:   PetscViewerFormat outformat;                   /* Dump/reload mesh format */
 12:   PetscBool         heterogeneous;               /* Test save on N / load on M */
 13:   PetscInt          ntimes;                      /* How many times do the cycle */
 14: } AppCtx;

 16: static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
 17: {
 18:   PetscBool flg;

 20:   PetscFunctionBeginUser;
 21:   options->infile[0]     = '\0';
 22:   options->outfile[0]    = '\0';
 23:   options->informat      = PETSC_VIEWER_HDF5_XDMF;
 24:   options->outformat     = PETSC_VIEWER_HDF5_XDMF;
 25:   options->heterogeneous = PETSC_FALSE;
 26:   options->ntimes        = 2;
 27:   PetscOptionsBegin(comm, "", "Meshing Problem Options", "DMPLEX");
 28:   PetscCall(PetscOptionsString("-infile", "The input mesh file", EX, options->infile, options->infile, sizeof(options->infile), &flg));
 29:   PetscCheck(flg, comm, PETSC_ERR_USER_INPUT, "-infile needs to be specified");
 30:   PetscCall(PetscOptionsString("-outfile", "The output mesh file (by default it's the same as infile)", EX, options->outfile, options->outfile, sizeof(options->outfile), &flg));
 31:   PetscCheck(flg, comm, PETSC_ERR_USER_INPUT, "-outfile needs to be specified");
 32:   PetscCall(PetscOptionsEnum("-informat", "Input mesh format", EX, PetscViewerFormats, (PetscEnum)options->informat, (PetscEnum *)&options->informat, NULL));
 33:   PetscCall(PetscOptionsEnum("-outformat", "Dump/reload mesh format", EX, PetscViewerFormats, (PetscEnum)options->outformat, (PetscEnum *)&options->outformat, NULL));
 34:   PetscCall(PetscOptionsBool("-heterogeneous", "Test save on N / load on M", EX, options->heterogeneous, &options->heterogeneous, NULL));
 35:   PetscCall(PetscOptionsInt("-ntimes", "How many times do the cycle", EX, options->ntimes, &options->ntimes, NULL));
 36:   PetscOptionsEnd();
 37:   PetscFunctionReturn(PETSC_SUCCESS);
 38: }

 40: //TODO test DMLabel I/O (not yet working for PETSC_VIEWER_HDF5_XDMF)
 41: int main(int argc, char **argv)
 42: {
 43:   AppCtx            user;
 44:   MPI_Comm          comm;
 45:   PetscMPIInt       gsize, grank, mycolor;
 46:   PetscInt          i;
 47:   PetscBool         flg;
 48:   const char        exampleDMPlexName[] = "DMPlex Object";
 49:   const char       *infilename;
 50:   PetscViewerFormat informat;

 52:   PetscFunctionBeginUser;
 53:   PetscCall(PetscInitialize(&argc, &argv, NULL, help));
 54:   PetscCall(ProcessOptions(PETSC_COMM_WORLD, &user));
 55:   PetscCallMPI(MPI_Comm_size(PETSC_COMM_WORLD, &gsize));
 56:   PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &grank));

 58:   for (i = 0; i < user.ntimes; i++) {
 59:     if (i == 0) {
 60:       /* Use infile/informat for the initial load */
 61:       infilename = user.infile;
 62:       informat   = user.informat;
 63:     } else {
 64:       /* Use outfile/outformat for all I/O except the very initial load */
 65:       infilename = user.outfile;
 66:       informat   = user.outformat;
 67:     }

 69:     if (user.heterogeneous) {
 70:       mycolor = (PetscMPIInt)(grank > user.ntimes - i);
 71:     } else {
 72:       mycolor = (PetscMPIInt)0;
 73:     }
 74:     PetscCallMPI(MPI_Comm_split(PETSC_COMM_WORLD, mycolor, grank, &comm));

 76:     if (mycolor == 0) {
 77:       /* Load/Save only on processes with mycolor == 0 */
 78:       DM          dm;
 79:       PetscViewer v;

 81:       PetscCall(PetscPrintf(comm, "Begin cycle %" PetscInt_FMT "\n", i));

 83:       /* Load data from XDMF into dm in parallel */
 84:       /* We could also use
 85:           PetscCall(DMPlexCreateFromFile(PETSC_COMM_WORLD, user.filename, "ex5_plex", PETSC_TRUE, &dm));
 86:         This currently support a few more formats than DMLoad().
 87:       */
 88:       PetscCall(PetscViewerHDF5Open(comm, infilename, FILE_MODE_READ, &v));
 89:       PetscCall(PetscViewerPushFormat(v, informat));
 90:       PetscCall(DMCreate(comm, &dm));
 91:       PetscCall(DMSetType(dm, DMPLEX));
 92:       PetscCall(PetscObjectSetName((PetscObject)dm, exampleDMPlexName));
 93:       PetscCall(DMSetOptionsPrefix(dm, "loaded_"));
 94:       PetscCall(DMLoad(dm, v));
 95:       PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE));
 96:       PetscCall(DMSetFromOptions(dm));
 97:       PetscCall(DMViewFromOptions(dm, NULL, "-dm_view"));
 98:       PetscCall(PetscViewerPopFormat(v));
 99:       PetscCall(PetscViewerDestroy(&v));

101:       /* We just test/demonstrate DM is indeed distributed - unneeded in the application code */
102:       PetscCall(DMPlexIsDistributed(dm, &flg));
103:       PetscCall(PetscPrintf(comm, "Loaded mesh distributed? %s\n", PetscBools[flg]));

105:       /* Interpolate */
106:       PetscCall(DMSetOptionsPrefix(dm, "interpolated_"));
107:       PetscCall(DMSetFromOptions(dm));
108:       PetscCall(DMViewFromOptions(dm, NULL, "-dm_view"));

110:       /* Redistribute */
111:       PetscCall(DMSetOptionsPrefix(dm, "redistributed_"));
112:       PetscCall(DMSetFromOptions(dm));
113:       PetscCall(DMViewFromOptions(dm, NULL, "-dm_view"));

115:       /* Save redistributed dm to XDMF in parallel and destroy it */
116:       PetscCall(PetscViewerHDF5Open(comm, user.outfile, FILE_MODE_WRITE, &v));
117:       PetscCall(PetscViewerPushFormat(v, user.outformat));
118:       PetscCall(PetscObjectSetName((PetscObject)dm, exampleDMPlexName));
119:       PetscCall(DMView(dm, v));
120:       PetscCall(PetscViewerPopFormat(v));
121:       PetscCall(PetscViewerDestroy(&v));
122:       PetscCall(DMDestroy(&dm));

124:       PetscCall(PetscPrintf(comm, "End   cycle %" PetscInt_FMT "\n--------\n", i));
125:     }
126:     PetscCallMPI(MPI_Comm_free(&comm));
127:     PetscCallMPI(MPI_Barrier(PETSC_COMM_WORLD));
128:   }

130:   /* Final clean-up */
131:   PetscCall(PetscFinalize());
132:   return 0;
133: }

135: /*TEST
136:   build:
137:     requires: hdf5
138:   testset:
139:     suffix: 0
140:     requires: !complex
141:     nsize: 4
142:     args: -infile ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.h5 -informat hdf5_xdmf
143:     args: -outfile ex5_dump.h5 -outformat {{hdf5_xdmf hdf5_petsc}separate output}
144:     args: -ntimes 3 -interpolated_dm_plex_interpolate_pre -redistributed_dm_distribute
145:     args: -loaded_dm_view -interpolated_dm_view -redistributed_dm_view
146:     test:
147:       # this partitioner should not shuffle anything, it should yield the same partitioning as the XDMF reader - added just for testing
148:       suffix: simple
149:       args: -petscpartitioner_type simple
150:     test:
151:       suffix: parmetis
152:       requires: parmetis
153:       args: -petscpartitioner_type parmetis
154:     test:
155:       suffix: ptscotch
156:       requires: ptscotch
157:       args: -petscpartitioner_type ptscotch

159:   testset:
160:     suffix: 1
161:     requires: !complex
162:     nsize: 4
163:     args: -infile ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.h5 -informat hdf5_xdmf
164:     args: -outfile ex5_dump.h5 -outformat {{hdf5_xdmf hdf5_petsc}separate output}
165:     args: -ntimes 3 -interpolated_dm_plex_interpolate_pre -redistributed_dm_distribute
166:     args: -heterogeneous True
167:     args: -loaded_dm_view -interpolated_dm_view -redistributed_dm_view
168:     test:
169:       suffix: simple
170:       args: -petscpartitioner_type simple
171:     test:
172:       suffix: parmetis
173:       requires: parmetis
174:       args: -petscpartitioner_type parmetis
175:     test:
176:       suffix: ptscotch
177:       requires: ptscotch
178:       args: -petscpartitioner_type ptscotch

180: TEST*/