Actual source code: ex5.c
petsc-3.15.0 2021-03-30
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      1: static char help[] = "Demonstrate HDF5/XDMF 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         redistribute;                /* Redistribute the mesh */
     13:   PetscBool         heterogeneous;               /* Test save on N / load on M */
     14:   PetscInt          ntimes;                      /* How many times do the cycle */
     15: } AppCtx;

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

     23:   options->infile[0]     = '\0';
     24:   options->outfile[0]    = '\0';
     25:   options->informat      = PETSC_VIEWER_HDF5_XDMF;
     26:   options->outformat     = PETSC_VIEWER_HDF5_XDMF;
     27:   options->redistribute  = PETSC_TRUE;
     28:   options->heterogeneous = PETSC_FALSE;
     29:   options->ntimes        = 2;
     30:   PetscOptionsBegin(comm, "", "Meshing Problem Options", "DMPLEX");
     31:   PetscOptionsString("-infile", "The input mesh file", EX, options->infile, options->infile, sizeof(options->infile), &flg);
     32:   if (!flg) SETERRQ(comm, PETSC_ERR_USER_INPUT, "-infile needs to be specified");
     33:   PetscOptionsString("-outfile", "The output mesh file (by default it's the same as infile)", EX, options->outfile, options->outfile, sizeof(options->outfile), &flg);
     34:   if (!flg) SETERRQ(comm, PETSC_ERR_USER_INPUT, "-outfile needs to be specified");
     35:   PetscOptionsEnum("-informat", "Input mesh format", EX, PetscViewerFormats, (PetscEnum)options->informat, (PetscEnum*)&options->informat, NULL);
     36:   PetscOptionsEnum("-outformat", "Dump/reload mesh format", EX, PetscViewerFormats, (PetscEnum)options->outformat, (PetscEnum*)&options->outformat, NULL);
     37:   PetscOptionsBool("-redistribute", "Redistribute the mesh", EX, options->redistribute, &options->redistribute, NULL);
     38:   PetscOptionsBool("-heterogeneous", "Test save on N / load on M", EX, options->heterogeneous, &options->heterogeneous, NULL);
     39:   PetscOptionsInt("-ntimes", "How many times do the cycle", EX, options->ntimes, &options->ntimes, NULL);
     40:   PetscOptionsEnd();
     41:   return(0);
     42: };

     44: //TODO test DMLabel I/O (not yet working for PETSC_VIEWER_HDF5_XDMF)
     45: int main(int argc, char **argv)
     46: {
     47:   AppCtx            user;
     48:   MPI_Comm          comm;
     49:   PetscMPIInt       gsize, grank, mycolor;
     50:   PetscInt          i;
     51:   PetscBool         flg;
     52:   PetscErrorCode    ierr;
     53:   const char        *infilename;
     54:   PetscViewerFormat informat;

     56:   PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
     57:   ProcessOptions(PETSC_COMM_WORLD, &user);
     58:   MPI_Comm_size(PETSC_COMM_WORLD,&gsize);
     59:   MPI_Comm_rank(PETSC_COMM_WORLD,&grank);

     61:   for (i=0; i<user.ntimes; i++) {
     62:     if (i==0) {
     63:       /* Use infile/informat for the initial load */
     64:       infilename = user.infile;
     65:       informat   = user.informat;
     66:     } else {
     67:       /* Use outfile/outformat for all I/O except the very initial load */
     68:       infilename = user.outfile;
     69:       informat   = user.outformat;
     70:     }

     72:     if (user.heterogeneous) {
     73:       mycolor = (PetscMPIInt)(grank > user.ntimes-i);
     74:     } else {
     75:       mycolor = (PetscMPIInt)0;
     76:       /* comm = PETSC_COMM_WORLD; */
     77:     }
     78:     MPI_Comm_split(PETSC_COMM_WORLD,mycolor,grank,&comm);

     80:     if (mycolor == 0) {
     81:       /* Load/Save only on processes with mycolor == 0 */
     82:       DM                dm;
     83:       PetscPartitioner  part;
     84:       PetscViewer       v;

     86:       PetscPrintf(comm, "Begin cycle %D\n",i);

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

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

    109:       /* Interpolate */
    110:       //TODO we want to be able to do this from options in DMSetFromOptions() probably
    111:       //TODO we want to be able to do this in-place
    112:       {
    113:         DM idm;

    115:         DMPlexInterpolate(dm, &idm);
    116:         DMDestroy(&dm);
    117:         dm   = idm;
    118:           DMSetOptionsPrefix(dm,"interpolated_");
    119:           DMSetFromOptions(dm);
    120:           DMViewFromOptions(dm, NULL, "-dm_view");
    121:       }

    123:       /* Redistribute */
    124:       //TODO we want to be able to do this from options in DMSetFromOptions() probably
    125:       if (user.redistribute) {
    126:         DM dmdist;

    128:         DMPlexGetPartitioner(dm, &part);
    129:         PetscPartitionerSetFromOptions(part);
    130:         DMPlexDistribute(dm, 0, NULL, &dmdist);
    131:         //TODO we want to be able to do this in-place
    132:         if (dmdist) {
    133:           DMDestroy(&dm);
    134:           dm   = dmdist;
    135:           DMSetOptionsPrefix(dm,"redistributed_");
    136:           DMSetFromOptions(dm);
    137:           DMViewFromOptions(dm, NULL, "-dm_view");
    138:         }
    139:       }

    141:       /* Save redistributed dm to XDMF in parallel and destroy it */
    142:       PetscViewerHDF5Open(comm, user.outfile, FILE_MODE_WRITE, &v);
    143:       PetscViewerPushFormat(v, user.outformat);
    144:       DMView(dm, v);
    145:       PetscViewerPopFormat(v);
    146:       PetscViewerDestroy(&v);
    147:       DMDestroy(&dm);

    149:       PetscPrintf(comm, "End   cycle %D\n--------\n",i);
    150:     }
    151:     MPI_Comm_free(&comm);
    152:     MPI_Barrier(PETSC_COMM_WORLD);
    153:   }

    155:   /* Final clean-up */
    156:   PetscFinalize();
    157:   return ierr;
    158: }

    160: /*TEST
    161:   build:
    162:     requires: hdf5
    163:   testset:
    164:     suffix: 0
    165:     requires: !complex
    166:     nsize: 4
    167:     args: -infile ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.h5 -informat hdf5_xdmf
    168:     args: -outfile ex5_dump.h5 -outformat {{hdf5_xdmf hdf5_petsc}separate output}
    169:     args: -ntimes 3
    170:     args: -loaded_dm_view -interpolated_dm_view -redistributed_dm_view
    171:     test:
    172:       # this partitioner should not shuffle anything, it should yield the same partititioning as the XDMF reader - added just for testing
    173:       suffix: simple
    174:       args: -petscpartitioner_type simple
    175:     test:
    176:       suffix: parmetis
    177:       requires: parmetis
    178:       args: -petscpartitioner_type parmetis
    179:     test:
    180:       suffix: ptscotch
    181:       requires: ptscotch
    182:       args: -petscpartitioner_type ptscotch

    184:   testset:
    185:     suffix: 1
    186:     requires: !complex
    187:     nsize: 4
    188:     args: -infile ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.h5 -informat hdf5_xdmf
    189:     args: -outfile ex5_dump.h5 -outformat {{hdf5_xdmf hdf5_petsc}separate output}
    190:     args: -ntimes 3
    191:     args: -heterogeneous True
    192:     args: -loaded_dm_view -interpolated_dm_view -redistributed_dm_view
    193:     test:
    194:       suffix: simple
    195:       args: -petscpartitioner_type simple
    196:     test:
    197:       suffix: parmetis
    198:       requires: parmetis
    199:       args: -petscpartitioner_type parmetis
    200:     test:
    201:       suffix: ptscotch
    202:       requires: ptscotch
    203:       args: -petscpartitioner_type ptscotch

    205: TEST*/