xref: /petsc/src/dm/impls/plex/tests/ex55.c (revision 2c71b3e237ead271e4f3aa1505f92bf476e3413d) 
1 static char help[] = "Load and save the mesh and fields to HDF5 and ExodusII\n\n";
2 
3 #include <petscdmplex.h>
4 #include <petscviewerhdf5.h>
5 #include <petscsf.h>
6 
7 typedef struct {
8   PetscBool compare;                      /* Compare the meshes using DMPlexEqual() */
9   PetscBool compare_labels;               /* Compare labels in the meshes using DMCompareLabels() */
10   PetscBool distribute;                   /* Distribute the mesh */
11   PetscBool interpolate;                  /* Generate intermediate mesh elements */
12   char      filename[PETSC_MAX_PATH_LEN]; /* Mesh filename */
13   char      meshname[PETSC_MAX_PATH_LEN]; /* Mesh name */
14   PetscViewerFormat format;               /* Format to write and read */
15   PetscBool second_write_read;            /* Write and read for the 2nd time */
16   PetscBool use_low_level_functions;      /* Use low level functions for viewing and loading */
17 } AppCtx;
18 
19 static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
20 {
21   PetscErrorCode ierr;
22 
23   PetscFunctionBeginUser;
24   options->compare = PETSC_FALSE;
25   options->compare_labels = PETSC_FALSE;
26   options->distribute = PETSC_TRUE;
27   options->interpolate = PETSC_FALSE;
28   options->filename[0] = '\0';
29   options->meshname[0] = '\0';
30   options->format = PETSC_VIEWER_DEFAULT;
31   options->second_write_read = PETSC_FALSE;
32   options->use_low_level_functions = PETSC_FALSE;
33 
34   ierr = PetscOptionsBegin(comm, "", "Meshing Problem Options", "DMPLEX");CHKERRQ(ierr);
35   ierr = PetscOptionsBool("-compare", "Compare the meshes using DMPlexEqual()", "ex55.c", options->compare, &options->compare, NULL);CHKERRQ(ierr);
36   ierr = PetscOptionsBool("-compare_labels", "Compare labels in the meshes using DMCompareLabels()", "ex55.c", options->compare_labels, &options->compare_labels, NULL);CHKERRQ(ierr);
37   ierr = PetscOptionsBool("-distribute", "Distribute the mesh", "ex55.c", options->distribute, &options->distribute, NULL);CHKERRQ(ierr);
38   ierr = PetscOptionsBool("-interpolate", "Generate intermediate mesh elements", "ex55.c", options->interpolate, &options->interpolate, NULL);CHKERRQ(ierr);
39   ierr = PetscOptionsString("-filename", "The mesh file", "ex55.c", options->filename, options->filename, sizeof(options->filename), NULL);CHKERRQ(ierr);
40   ierr = PetscOptionsString("-meshname", "The mesh file", "ex55.c", options->meshname, options->meshname, sizeof(options->meshname), NULL);CHKERRQ(ierr);
41   ierr = PetscOptionsEnum("-format", "Format to write and read", "ex55.c", PetscViewerFormats, (PetscEnum)options->format, (PetscEnum*)&options->format, NULL);CHKERRQ(ierr);
42   ierr = PetscOptionsBool("-second_write_read", "Write and read for the 2nd time", "ex55.c", options->second_write_read, &options->second_write_read, NULL);CHKERRQ(ierr);
43   ierr = PetscOptionsBool("-use_low_level_functions", "Use low level functions for viewing and loading", "ex55.c", options->use_low_level_functions, &options->use_low_level_functions, NULL);CHKERRQ(ierr);
44   ierr = PetscOptionsEnd();CHKERRQ(ierr);
45   PetscFunctionReturn(0);
46 };
47 
48 static PetscErrorCode DMPlexWriteAndReadHDF5(DM dm, const char filename[], const char prefix[], AppCtx user, DM *dm_new)
49 {
50   DM             dmnew;
51   const char     savedName[]  = "Mesh";
52   const char     loadedName[] = "Mesh_new";
53   PetscViewer    v;
54   PetscErrorCode ierr;
55 
56   PetscFunctionBeginUser;
57   ierr = PetscViewerHDF5Open(PetscObjectComm((PetscObject) dm), filename, FILE_MODE_WRITE, &v);CHKERRQ(ierr);
58   ierr = PetscViewerPushFormat(v, user.format);CHKERRQ(ierr);
59   ierr = PetscObjectSetName((PetscObject) dm, savedName);CHKERRQ(ierr);
60   if (user.use_low_level_functions) {
61     ierr = DMPlexTopologyView(dm, v);CHKERRQ(ierr);
62     ierr = DMPlexCoordinatesView(dm, v);CHKERRQ(ierr);
63     ierr = DMPlexLabelsView(dm, v);CHKERRQ(ierr);
64   } else {
65     ierr = DMView(dm, v);CHKERRQ(ierr);
66   }
67 
68   ierr = PetscViewerFileSetMode(v, FILE_MODE_READ);CHKERRQ(ierr);
69   ierr = DMCreate(PETSC_COMM_WORLD, &dmnew);CHKERRQ(ierr);
70   ierr = DMSetType(dmnew, DMPLEX);CHKERRQ(ierr);
71   ierr = PetscObjectSetName((PetscObject) dmnew, savedName);CHKERRQ(ierr);
72   ierr = DMSetOptionsPrefix(dmnew, prefix);CHKERRQ(ierr);
73   if (user.use_low_level_functions) {
74     PetscSF  sfXC;
75 
76     ierr = DMPlexTopologyLoad(dmnew, v, &sfXC);CHKERRQ(ierr);
77     ierr = DMPlexCoordinatesLoad(dmnew, v, sfXC);CHKERRQ(ierr);
78     ierr = DMPlexLabelsLoad(dmnew, v, sfXC);CHKERRQ(ierr);
79     ierr = PetscSFDestroy(&sfXC);CHKERRQ(ierr);
80   } else {
81     ierr = DMLoad(dmnew, v);CHKERRQ(ierr);
82   }
83   ierr = PetscObjectSetName((PetscObject)dmnew,loadedName);CHKERRQ(ierr);
84 
85   ierr = PetscViewerPopFormat(v);CHKERRQ(ierr);
86   ierr = PetscViewerDestroy(&v);CHKERRQ(ierr);
87   *dm_new = dmnew;
88   PetscFunctionReturn(0);
89 }
90 
91 int main(int argc, char **argv)
92 {
93   DM             dm, dmnew;
94   PetscPartitioner part;
95   AppCtx         user;
96   PetscBool      flg;
97   PetscErrorCode ierr;
98 
99   ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
100   ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
101   ierr = DMPlexCreateFromFile(PETSC_COMM_WORLD, user.filename, user.meshname, user.interpolate, &dm);CHKERRQ(ierr);
102   ierr = DMSetOptionsPrefix(dm,"orig_");CHKERRQ(ierr);
103   ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
104 
105   if (user.distribute) {
106     DM dmdist;
107 
108     ierr = DMPlexGetPartitioner(dm, &part);CHKERRQ(ierr);
109     ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
110     ierr = DMPlexDistribute(dm, 0, NULL, &dmdist);CHKERRQ(ierr);
111     if (dmdist) {
112       ierr = DMDestroy(&dm);CHKERRQ(ierr);
113       dm   = dmdist;
114     }
115   }
116 
117   ierr = DMSetOptionsPrefix(dm,NULL);CHKERRQ(ierr);
118   ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
119   ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
120 
121   ierr = DMPlexWriteAndReadHDF5(dm, "dmdist.h5", "new_", user, &dmnew);CHKERRQ(ierr);
122 
123   if (user.second_write_read) {
124     ierr = DMDestroy(&dm);CHKERRQ(ierr);
125     dm = dmnew;
126     ierr = DMPlexWriteAndReadHDF5(dm, "dmdist.h5", "new_", user, &dmnew);CHKERRQ(ierr);
127   }
128 
129   ierr = DMViewFromOptions(dmnew, NULL, "-dm_view");CHKERRQ(ierr);
130   /* TODO: Is it still true? */
131   /* The NATIVE format for coordiante viewing is killing parallel output, since we have a local vector. Map it to global, and it will work. */
132 
133   /* This currently makes sense only for sequential meshes. */
134   if (user.compare) {
135     ierr = DMPlexEqual(dmnew, dm, &flg);CHKERRQ(ierr);
136     PetscCheckFalse(!flg,PETSC_COMM_WORLD, PETSC_ERR_ARG_INCOMP, "DMs are not equal");
137     ierr = PetscPrintf(PETSC_COMM_WORLD,"DMs equal\n");CHKERRQ(ierr);
138   }
139   if (user.compare_labels) {
140     ierr = DMCompareLabels(dmnew, dm, NULL, NULL);CHKERRQ(ierr);
141     ierr = PetscPrintf(PETSC_COMM_WORLD,"DMLabels equal\n");CHKERRQ(ierr);
142   }
143 
144   ierr = DMDestroy(&dm);CHKERRQ(ierr);
145   ierr = DMDestroy(&dmnew);CHKERRQ(ierr);
146   ierr = PetscFinalize();
147   return ierr;
148 }
149 
150 /*TEST
151   build:
152     requires: hdf5
153   # Idempotence of saving/loading
154   #   Have to replace Exodus file, which is creating uninterpolated edges
155   test:
156     suffix: 0
157     TODO: broken
158     requires: exodusii
159     args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail
160     args: -format hdf5_petsc -compare
161   test:
162     suffix: 1
163     TODO: broken
164     requires: exodusii parmetis !defined(PETSC_USE_64BIT_INDICES)
165     nsize: 2
166     args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail
167     args: -petscpartitioner_type parmetis
168     args: -format hdf5_petsc -new_dm_view ascii::ascii_info_detail
169   testset:
170     requires: exodusii
171     args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo
172     args: -petscpartitioner_type simple
173     args: -dm_view ascii::ascii_info_detail
174     args: -new_dm_view ascii::ascii_info_detail
175     test:
176       suffix: 2
177       nsize: {{1 2 4 8}separate output}
178       args: -format {{default hdf5_petsc}separate output}
179       args: -interpolate {{0 1}separate output}
180     test:
181       suffix: 2a
182       nsize: {{1 2 4 8}separate output}
183       args: -format {{hdf5_xdmf hdf5_viz}separate output}
184   test:
185     suffix: 3
186     requires: exodusii
187     args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo -compare -compare_labels
188 
189   # Load HDF5 file in XDMF format in parallel, write, read dm1, write, read dm2, and compare dm1 and dm2
190   testset:
191     suffix: 4
192     requires: !complex
193     args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.h5 -dm_plex_create_from_hdf5_xdmf
194     args: -distribute 0 -second_write_read -compare
195     test:
196       suffix: hdf5_petsc
197       nsize: {{1 2}}
198       args: -format hdf5_petsc -compare_labels
199     test:
200       suffix: hdf5_xdmf
201       nsize: {{1 3 8}}
202       args: -format hdf5_xdmf
203 
204   # Use low level functions, DMPlexTopologyView()/Load(), DMPlexCoordinatesView()/Load(), and DMPlexLabelsView()/Load()
205   # Output must be the same as ex55_2_nsize-2_format-hdf5_petsc_interpolate-0.out
206   test:
207     suffix: 5
208     requires: exodusii
209     nsize: 2
210     args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo
211     args: -petscpartitioner_type simple
212     args: -dm_view ascii::ascii_info_detail
213     args: -new_dm_view ascii::ascii_info_detail
214     args: -format hdf5_petsc -use_low_level_functions
215 
216   testset:
217     suffix: 6
218     requires: hdf5 !complex datafilespath
219     nsize: {{1 3}}
220     args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry
221     args: -filename ${DATAFILESPATH}/meshes/cube-hexahedra-refined.h5 -dm_plex_create_from_hdf5_xdmf -dm_plex_hdf5_topology_path /cells -dm_plex_hdf5_geometry_path /coordinates
222     args: -format hdf5_petsc -second_write_read -compare -compare_labels
223     args: -interpolate {{0 1}} -distribute {{0 1}} -petscpartitioner_type simple
224 
225   testset:
226     # the same data and settings as dm_impls_plex_tests-ex18_9%
227     suffix: 9
228     requires: hdf5 !complex datafilespath
229     nsize: {{1 2 4}}
230     args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry
231     args: -filename ${DATAFILESPATH}/meshes/cube-hexahedra-refined.h5 -dm_plex_create_from_hdf5_xdmf -dm_plex_hdf5_topology_path /cells -dm_plex_hdf5_geometry_path /coordinates
232     args: -format hdf5_xdmf -second_write_read -compare
233     test:
234       suffix: hdf5_seqload
235       args: -distribute -petscpartitioner_type simple
236       args: -interpolate {{0 1}}
237       args: -dm_plex_hdf5_force_sequential
238     test:
239       suffix: hdf5_seqload_metis
240       requires: parmetis
241       args: -distribute -petscpartitioner_type parmetis
242       args: -interpolate 1
243       args: -dm_plex_hdf5_force_sequential
244     test:
245       suffix: hdf5
246       args: -interpolate 1 -petscpartitioner_type simple
247     test:
248       suffix: hdf5_repart
249       requires: parmetis
250       args: -distribute -petscpartitioner_type parmetis
251       args: -interpolate 1
252     test:
253       TODO: Parallel partitioning of uninterpolated meshes not supported
254       suffix: hdf5_repart_ppu
255       requires: parmetis
256       args: -distribute -petscpartitioner_type parmetis
257       args: -interpolate 0
258 
259   # reproduce PetscSFView() crash - fixed, left as regression test
260   test:
261     suffix: new_dm_view
262     requires: exodusii
263     nsize: 2
264     args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/TwoQuads.exo -new_dm_view ascii:ex5_new_dm_view.log:ascii_info_detail
265 
266   # test backward compatibility of petsc_hdf5 format
267   testset:
268     suffix: 10-v3.16.0-v1.0.0
269     requires: hdf5 !complex datafilespath
270     args: -dm_plex_check_all -compare -compare_labels
271     args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0}} -use_low_level_functions {{0 1}}
272     test:
273       suffix: a
274       args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/annulus-20.h5
275     test:
276       suffix: b
277       TODO: broken
278       args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/barycentricallyrefinedcube.h5
279     test:
280       suffix: c
281       args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/blockcylinder-50.h5
282     test:
283       suffix: d
284       args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/cube-hexahedra-refined.h5
285     test:
286       suffix: e
287       args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/hybrid_hexwedge.h5
288     test:
289       suffix: f
290       args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/square.h5
291 
292 TEST*/
293