1import petsc4py 2from petsc4py import PETSc 3import unittest 4import os 5import filecmp 6import numpy as np 7 8# -------------------------------------------------------------------- 9 10ERR_SUP = 56 11 12class BaseTestPlex(object): 13 14 COMM = PETSc.COMM_WORLD 15 DIM = 1 16 CELLS = [[0, 1], [1, 2]] 17 COORDS = [[0.], [0.5], [1.]] 18 COMP = 1 19 DOFS = [1, 0] 20 21 def setUp(self): 22 self.plex = PETSc.DMPlex().createFromCellList(self.DIM, 23 self.CELLS, 24 self.COORDS, 25 comm=self.COMM) 26 27 def tearDown(self): 28 self.plex.destroy() 29 self.plex = None 30 31 def testTopology(self): 32 rank = self.COMM.rank 33 dim = self.plex.getDimension() 34 pStart, pEnd = self.plex.getChart() 35 cStart, cEnd = self.plex.getHeightStratum(0) 36 vStart, vEnd = self.plex.getDepthStratum(0) 37 numDepths = self.plex.getLabelSize("depth") 38 coords_raw = self.plex.getCoordinates().getArray() 39 coords = np.reshape(coords_raw, (vEnd - vStart, dim)) 40 self.assertEqual(dim, self.DIM) 41 self.assertEqual(numDepths, self.DIM+1) 42 if rank == 0 and self.CELLS is not None: 43 self.assertEqual(cEnd-cStart, len(self.CELLS)) 44 if rank == 0 and self.COORDS is not None: 45 self.assertEqual(vEnd-vStart, len(self.COORDS)) 46 self.assertTrue((coords == self.COORDS).all()) 47 48 def testClosure(self): 49 pStart, pEnd = self.plex.getChart() 50 for p in range(pStart, pEnd): 51 closure = self.plex.getTransitiveClosure(p)[0] 52 for c in closure: 53 cone = self.plex.getCone(c) 54 self.assertEqual(self.plex.getConeSize(c), len(cone)) 55 for i in cone: 56 self.assertIn(i, closure) 57 star = self.plex.getTransitiveClosure(p, useCone=False)[0] 58 for s in star: 59 support = self.plex.getSupport(s) 60 self.assertEqual(self.plex.getSupportSize(s), len(support)) 61 for i in support: 62 self.assertIn(i, star) 63 64 def testAdjacency(self): 65 PETSc.DMPlex.setAdjacencyUseAnchors(self.plex, False) 66 flag = PETSc.DMPlex.getAdjacencyUseAnchors(self.plex) 67 self.assertFalse(flag) 68 PETSc.DMPlex.setAdjacencyUseAnchors(self.plex, True) 69 flag = PETSc.DMPlex.getAdjacencyUseAnchors(self.plex) 70 self.assertTrue(flag) 71 PETSc.DMPlex.setBasicAdjacency(self.plex, False, False) 72 flagA, flagB = PETSc.DMPlex.getBasicAdjacency(self.plex) 73 self.assertFalse(flagA) 74 self.assertFalse(flagB) 75 PETSc.DMPlex.setBasicAdjacency(self.plex, True, True) 76 flagA, flagB = PETSc.DMPlex.getBasicAdjacency(self.plex) 77 self.assertTrue(flagA) 78 self.assertTrue(flagB) 79 pStart, pEnd = self.plex.getChart() 80 for p in range(pStart, pEnd): 81 adjacency = self.plex.getAdjacency(p) 82 self.assertTrue(p in adjacency) 83 self.assertTrue(len(adjacency) > 1) 84 85 def testSectionDofs(self): 86 self.plex.setNumFields(1) 87 section = self.plex.createSection([self.COMP], [self.DOFS]) 88 size = section.getStorageSize() 89 entity_dofs = [self.plex.getStratumSize("depth", d) * 90 self.DOFS[d] for d in range(self.DIM+1)] 91 self.assertEqual(sum(entity_dofs), size) 92 93 def testSectionClosure(self): 94 section = self.plex.createSection([self.COMP], [self.DOFS]) 95 self.plex.setSection(section) 96 vec = self.plex.createLocalVec() 97 pStart, pEnd = self.plex.getChart() 98 for p in range(pStart, pEnd): 99 for i in range(section.getDof(p)): 100 off = section.getOffset(p) 101 vec.setValue(off+i, p) 102 103 for p in range(pStart, pEnd): 104 point_closure = self.plex.getTransitiveClosure(p)[0] 105 dof_closure = self.plex.vecGetClosure(section, vec, p) 106 for p in dof_closure: 107 self.assertIn(p, point_closure) 108 109 def testBoundaryLabel(self): 110 pStart, pEnd = self.plex.getChart() 111 if (pEnd - pStart == 0): return 112 113 self.assertFalse(self.plex.hasLabel("boundary")) 114 self.plex.markBoundaryFaces("boundary") 115 self.assertTrue(self.plex.hasLabel("boundary")) 116 117 faces = self.plex.getStratumIS("boundary", 1) 118 for f in faces.getIndices(): 119 points, orient = self.plex.getTransitiveClosure(f, useCone=True) 120 for p in points: 121 self.plex.setLabelValue("boundary", p, 1) 122 123 for p in range(pStart, pEnd): 124 if self.plex.getLabelValue("boundary", p) != 1: 125 self.plex.setLabelValue("boundary", p, 2) 126 127 numBoundary = self.plex.getStratumSize("boundary", 1) 128 numInterior = self.plex.getStratumSize("boundary", 2) 129 self.assertNotEqual(numBoundary, pEnd - pStart) 130 self.assertNotEqual(numInterior, pEnd - pStart) 131 self.assertEqual(numBoundary + numInterior, pEnd - pStart) 132 133 def testMetric(self): 134 if self.DIM == 1: return 135 self.plex.distribute() 136 if self.CELLS is None and not self.plex.isSimplex(): return 137 138 h_min = 1.0e-30 139 h_max = 1.0e+30 140 a_max = 1.0e+10 141 target = 10.0 142 p = 1.0 143 self.plex.metricSetIsotropic(False) 144 self.plex.metricSetRestrictAnisotropyFirst(False) 145 self.plex.metricSetMinimumMagnitude(h_min) 146 self.plex.metricSetMaximumMagnitude(h_max) 147 self.plex.metricSetMaximumAnisotropy(a_max) 148 self.plex.metricSetTargetComplexity(target) 149 self.plex.metricSetNormalizationOrder(p) 150 151 self.assertFalse(self.plex.metricIsIsotropic()) 152 self.assertFalse(self.plex.metricRestrictAnisotropyFirst()) 153 assert np.isclose(self.plex.metricGetMinimumMagnitude(), h_min) 154 assert np.isclose(self.plex.metricGetMaximumMagnitude(), h_max) 155 assert np.isclose(self.plex.metricGetMaximumAnisotropy(), a_max) 156 assert np.isclose(self.plex.metricGetTargetComplexity(), target) 157 assert np.isclose(self.plex.metricGetNormalizationOrder(), p) 158 159 metric1 = self.plex.metricCreateUniform(1.0) 160 metric2 = self.plex.metricCreateUniform(2.0) 161 metric = self.plex.metricAverage2(metric1, metric2) 162 metric2.array[:] *= 0.75 163 assert np.allclose(metric.array, metric2.array) 164 metric = self.plex.metricIntersection2(metric1, metric2) 165 assert np.allclose(metric.array, metric1.array) 166 self.plex.metricEnforceSPD(metric) 167 assert np.allclose(metric.array, metric1.array) 168 169 def testAdapt(self): 170 if self.DIM == 1: return 171 self.plex.distribute() 172 if self.CELLS is None and not self.plex.isSimplex(): return 173 if sum(self.DOFS) > 1: return 174 metric = self.plex.metricCreateUniform(9.0) 175 try: 176 newplex = self.plex.adaptMetric(metric,"") 177 except PETSc.Error as exc: 178 if exc.ierr != ERR_SUP: raise 179 180 181# -------------------------------------------------------------------- 182 183class BaseTestPlex_2D(BaseTestPlex): 184 DIM = 2 185 CELLS = [[0, 1, 3], [1, 3, 4], [1, 2, 4], [2, 4, 5], 186 [3, 4, 6], [4, 6, 7], [4, 5, 7], [5, 7, 8]] 187 COORDS = [[0.0, 0.0], [0.5, 0.0], [1.0, 0.0], 188 [0.0, 0.5], [0.5, 0.5], [1.0, 0.5], 189 [0.0, 1.0], [0.5, 1.0], [1.0, 1.0]] 190 DOFS = [1, 0, 0] 191 192class BaseTestPlex_3D(BaseTestPlex): 193 DIM = 3 194 CELLS = [[0, 2, 3, 7], [0, 2, 6, 7], [0, 4, 6, 7], 195 [0, 1, 3, 7], [0, 1, 5, 7], [0, 4, 5, 7]] 196 COORDS = [[0., 0., 0.], [1., 0., 0.], [0., 1., 0.], [1., 1., 0.], 197 [0., 0., 1.], [1., 0., 1.], [0., 1., 1.], [1., 1., 1.]] 198 DOFS = [1, 0, 0, 0] 199 200# -------------------------------------------------------------------- 201 202class TestPlex_1D(BaseTestPlex, unittest.TestCase): 203 pass 204 205class TestPlex_2D(BaseTestPlex_2D, unittest.TestCase): 206 pass 207 208class TestPlex_3D(BaseTestPlex_3D, unittest.TestCase): 209 pass 210 211class TestPlex_2D_P3(BaseTestPlex_2D, unittest.TestCase): 212 DOFS = [1, 2, 1] 213 214class TestPlex_3D_P3(BaseTestPlex_3D, unittest.TestCase): 215 DOFS = [1, 2, 1, 0] 216 217class TestPlex_3D_P4(BaseTestPlex_3D, unittest.TestCase): 218 DOFS = [1, 3, 3, 1] 219 220class TestPlex_2D_BoxTensor(BaseTestPlex_2D, unittest.TestCase): 221 CELLS = None 222 COORDS = None 223 def setUp(self): 224 self.plex = PETSc.DMPlex().createBoxMesh([3,3], simplex=False) 225 226class TestPlex_3D_BoxTensor(BaseTestPlex_3D, unittest.TestCase): 227 CELLS = None 228 COORDS = None 229 def setUp(self): 230 self.plex = PETSc.DMPlex().createBoxMesh([3,3,3], simplex=False) 231 232try: 233 raise PETSc.Error 234 PETSc.DMPlex().createBoxMesh([2,2], simplex=True, comm=PETSc.COMM_SELF).destroy() 235except PETSc.Error: 236 pass 237else: 238 class TestPlex_2D_Box(BaseTestPlex_2D, unittest.TestCase): 239 CELLS = None 240 COORDS = None 241 def setUp(self): 242 self.plex = PETSc.DMPlex().createBoxMesh([1,1], simplex=True) 243 244 class TestPlex_2D_Boundary(BaseTestPlex_2D, unittest.TestCase): 245 CELLS = None 246 COORDS = None 247 def setUp(self): 248 boundary = PETSc.DMPlex().create(self.COMM) 249 boundary.createSquareBoundary([0., 0.], [1., 1.], [2, 2]) 250 boundary.setDimension(self.DIM-1) 251 self.plex = PETSc.DMPlex().generate(boundary) 252 253 class TestPlex_3D_Box(BaseTestPlex_3D, unittest.TestCase): 254 CELLS = None 255 COORDS = None 256 def setUp(self): 257 self.plex = PETSc.DMPlex().createBoxMesh([1,1,1], simplex=True) 258 259 class TestPlex_3D_Boundary(BaseTestPlex_3D, unittest.TestCase): 260 CELLS = None 261 COORDS = None 262 def setUp(self): 263 boundary = PETSc.DMPlex().create(self.COMM) 264 boundary.createCubeBoundary([0., 0., 0.], [1., 1., 1.], [1, 1, 1]) 265 boundary.setDimension(self.DIM-1) 266 self.plex = PETSc.DMPlex().generate(boundary) 267 268# -------------------------------------------------------------------- 269 270PETSC_DIR = petsc4py.get_config()['PETSC_DIR'] 271 272def check_dtype(method): 273 def wrapper(self, *args, **kwargs): 274 if PETSc.ScalarType is PETSc.ComplexType: 275 return 276 else: 277 return method(self, *args, **kwargs) 278 return wrapper 279 280def check_package(method): 281 def wrapper(self, *args, **kwargs): 282 if not PETSc.Sys.hasExternalPackage("hdf5"): 283 return 284 elif self.PARTITIONERTYPE != "simple" and \ 285 not PETSc.Sys.hasExternalPackage(self.PARTITIONERTYPE): 286 return 287 else: 288 return method(self, *args, **kwargs) 289 return wrapper 290 291def check_nsize(method): 292 def wrapper(self, *args, **kwargs): 293 if PETSc.COMM_WORLD.size != self.NSIZE: 294 return 295 else: 296 return method(self, *args, **kwargs) 297 return wrapper 298 299class BaseTestPlexHDF5(object): 300 NSIZE = 4 301 NTIMES = 3 302 303 def setUp(self): 304 self.txtvwr = PETSc.Viewer() 305 306 def tearDown(self): 307 if not PETSc.COMM_WORLD.rank: 308 if os.path.exists(self.outfile()): 309 os.remove(self.outfile()) 310 if os.path.exists(self.tmp_output_file()): 311 os.remove(self.tmp_output_file()) 312 self.txtvwr = None 313 314 def _name(self): 315 return "%s_outformat-%s_%s" % (self.SUFFIX, 316 self.OUTFORMAT, 317 self.PARTITIONERTYPE) 318 319 def infile(self): 320 return os.path.join(PETSC_DIR, "share/petsc/datafiles/", 321 "meshes/blockcylinder-50.h5") 322 323 def outfile(self): 324 return os.path.join("./temp_test_dmplex_%s.h5" % self._name()) 325 326 def informat(self): 327 return PETSc.Viewer.Format.HDF5_XDMF 328 329 def outformat(self): 330 d = {"hdf5_petsc": PETSc.Viewer.Format.HDF5_PETSC, 331 "hdf5_xdmf": PETSc.Viewer.Format.HDF5_XDMF} 332 return d[self.OUTFORMAT] 333 334 def partitionerType(self): 335 d = {"simple": PETSc.Partitioner.Type.SIMPLE, 336 "ptscotch": PETSc.Partitioner.Type.PTSCOTCH, 337 "parmetis": PETSc.Partitioner.Type.PARMETIS} 338 return d[self.PARTITIONERTYPE] 339 340 def ref_output_file(self): 341 return os.path.join(PETSC_DIR, "src/dm/impls/plex/tutorials/", 342 "output/ex5_%s.out" % self._name()) 343 344 def tmp_output_file(self): 345 return os.path.join("./temp_test_dmplex_%s.out" % self._name()) 346 347 def outputText(self, msg, comm): 348 if not comm.rank: 349 with open(self.tmp_output_file(), 'a') as f: 350 f.write(msg) 351 352 def outputPlex(self, plex): 353 self.txtvwr.createASCII(self.tmp_output_file(), 354 mode='a', comm=plex.comm) 355 plex.view(viewer=self.txtvwr) 356 self.txtvwr.destroy() 357 358 @check_dtype 359 @check_package 360 @check_nsize 361 def testViewLoadCycle(self): 362 grank = PETSc.COMM_WORLD.rank 363 for i in range(self.NTIMES): 364 if i == 0: 365 infname = self.infile() 366 informt = self.informat() 367 else: 368 infname = self.outfile() 369 informt = self.outformat() 370 if self.HETEROGENEOUS: 371 mycolor = (grank > self.NTIMES - i) 372 else: 373 mycolor = 0 374 try: 375 import mpi4py 376 except ImportError: 377 self.skipTest('mpi4py') # throws special exception to signal test skip 378 mpicomm = PETSc.COMM_WORLD.tompi4py() 379 comm = PETSc.Comm(comm=mpicomm.Split(color=mycolor, key=grank)) 380 if mycolor == 0: 381 self.outputText("Begin cycle %d\n" % i, comm) 382 plex = PETSc.DMPlex() 383 vwr = PETSc.ViewerHDF5() 384 # Create plex 385 plex.create(comm=comm) 386 plex.setName("DMPlex Object") 387 # Load data from XDMF into dm in parallel 388 vwr.create(infname, mode='r', comm=comm) 389 vwr.pushFormat(format=informt) 390 plex.load(viewer=vwr) 391 plex.setOptionsPrefix("loaded_") 392 plex.setFromOptions() 393 vwr.popFormat() 394 vwr.destroy() 395 self.outputPlex(plex) 396 # Test DM is indeed distributed 397 flg = plex.isDistributed() 398 self.outputText("Loaded mesh distributed? %s\n" % 399 str(flg).upper(), comm) 400 # Interpolate 401 plex.interpolate() 402 plex.setOptionsPrefix("interpolated_") 403 plex.setFromOptions() 404 self.outputPlex(plex) 405 # Redistribute 406 part = plex.getPartitioner() 407 part.setType(self.partitionerType()) 408 _ = plex.distribute(overlap=0) 409 plex.setOptionsPrefix("redistributed_") 410 plex.setFromOptions() 411 self.outputPlex(plex) 412 # Save redistributed dm to XDMF in parallel 413 vwr.create(self.outfile(), mode='w', comm=comm) 414 vwr.pushFormat(format=self.outformat()) 415 plex.setName("DMPlex Object") 416 plex.view(viewer=vwr) 417 vwr.popFormat() 418 vwr.destroy() 419 # Destroy plex 420 plex.destroy() 421 self.outputText("End cycle %d\n--------\n" % i, comm) 422 PETSc.COMM_WORLD.Barrier() 423 # Check that the output is identical to that of plex/tutorial/ex5.c. 424 self.assertTrue(filecmp.cmp(self.tmp_output_file(), 425 self.ref_output_file(), shallow=False), 426 'Contents of the files not the same.') 427 PETSc.COMM_WORLD.Barrier() 428 429class BaseTestPlexHDF5Homogeneous(BaseTestPlexHDF5): 430 """Test save on N / load on N.""" 431 SUFFIX = 0 432 HETEROGENEOUS = False 433 434class BaseTestPlexHDF5Heterogeneous(BaseTestPlexHDF5): 435 """Test save on N / load on M.""" 436 SUFFIX = 1 437 HETEROGENEOUS = True 438 439class TestPlexHDF5PETSCSimpleHomogeneous(BaseTestPlexHDF5Homogeneous, 440 unittest.TestCase): 441 OUTFORMAT = "hdf5_petsc" 442 PARTITIONERTYPE = "simple" 443 444""" 445Skipping. PTScotch produces different distributions when run 446in a sequence in a single session. 447 448class TestPlexHDF5PETSCPTScotchHomogeneous(BaseTestPlexHDF5Homogeneous, 449 unittest.TestCase): 450 OUTFORMAT = "hdf5_petsc" 451 PARTITIONERTYPE = "ptscotch" 452""" 453 454class TestPlexHDF5PETSCParmetisHomogeneous(BaseTestPlexHDF5Homogeneous, 455 unittest.TestCase): 456 OUTFORMAT = "hdf5_petsc" 457 PARTITIONERTYPE = "parmetis" 458 459class TestPlexHDF5XDMFSimpleHomogeneous(BaseTestPlexHDF5Homogeneous, 460 unittest.TestCase): 461 OUTFORMAT = "hdf5_xdmf" 462 PARTITIONERTYPE = "simple" 463 464""" 465Skipping. PTScotch produces different distributions when run 466in a sequence in a single session. 467 468class TestPlexHDF5XDMFPTScotchHomogeneous(BaseTestPlexHDF5Homogeneous, 469 unittest.TestCase): 470 OUTFORMAT = "hdf5_xdmf" 471 PARTITIONERTYPE = "ptscotch" 472""" 473 474class TestPlexHDF5XDMFParmetisHomogeneous(BaseTestPlexHDF5Homogeneous, 475 unittest.TestCase): 476 OUTFORMAT = "hdf5_xdmf" 477 PARTITIONERTYPE = "parmetis" 478 479class TestPlexHDF5PETSCSimpleHeterogeneous(BaseTestPlexHDF5Heterogeneous, 480 unittest.TestCase): 481 OUTFORMAT = "hdf5_petsc" 482 PARTITIONERTYPE = "simple" 483 484""" 485Skipping. PTScotch produces different distributions when run 486in a sequence in a single session. 487 488class TestPlexHDF5PETSCPTScotchHeterogeneous(BaseTestPlexHDF5Heterogeneous, 489 unittest.TestCase): 490 OUTFORMAT = "hdf5_petsc" 491 PARTITIONERTYPE = "ptscotch" 492""" 493 494class TestPlexHDF5PETSCParmetisHeterogeneous(BaseTestPlexHDF5Heterogeneous, 495 unittest.TestCase): 496 OUTFORMAT = "hdf5_petsc" 497 PARTITIONERTYPE = "parmetis" 498 499class TestPlexHDF5XDMFSimpleHeterogeneous(BaseTestPlexHDF5Heterogeneous, 500 unittest.TestCase): 501 OUTFORMAT = "hdf5_xdmf" 502 PARTITIONERTYPE = "simple" 503 504class TestPlexHDF5XDMFPTScotchHeterogeneous(BaseTestPlexHDF5Heterogeneous, 505 unittest.TestCase): 506 OUTFORMAT = "hdf5_xdmf" 507 PARTITIONERTYPE = "ptscotch" 508 509class TestPlexHDF5XDMFParmetisHeterogeneous(BaseTestPlexHDF5Heterogeneous, 510 unittest.TestCase): 511 OUTFORMAT = "hdf5_xdmf" 512 PARTITIONERTYPE = "parmetis" 513 514# -------------------------------------------------------------------- 515 516if __name__ == '__main__': 517 unittest.main() 518