1import petsc4py 2from petsc4py import PETSc 3import unittest 4import os 5import filecmp 6import numpy as np 7 8# -------------------------------------------------------------------- 9 10ERR_ARG_OUTOFRANGE = 63 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 self.plex.orient() 138 139 h_min = 1.0e-30 140 h_max = 1.0e+30 141 a_max = 1.0e+10 142 target = 10.0 143 p = 1.0 144 beta = 1.3 145 hausd = 0.01 146 self.plex.metricSetIsotropic(False) 147 self.plex.metricSetRestrictAnisotropyFirst(False) 148 self.plex.metricSetNoInsertion(False) 149 self.plex.metricSetNoSwapping(False) 150 self.plex.metricSetNoMovement(False) 151 self.plex.metricSetNoSurf(False) 152 self.plex.metricSetVerbosity(-1) 153 self.plex.metricSetNumIterations(3) 154 self.plex.metricSetMinimumMagnitude(h_min) 155 self.plex.metricSetMaximumMagnitude(h_max) 156 self.plex.metricSetMaximumAnisotropy(a_max) 157 self.plex.metricSetTargetComplexity(target) 158 self.plex.metricSetNormalizationOrder(p) 159 self.plex.metricSetGradationFactor(beta) 160 self.plex.metricSetHausdorffNumber(hausd) 161 162 self.assertFalse(self.plex.metricIsIsotropic()) 163 self.assertFalse(self.plex.metricRestrictAnisotropyFirst()) 164 self.assertFalse(self.plex.metricNoInsertion()) 165 self.assertFalse(self.plex.metricNoSwapping()) 166 self.assertFalse(self.plex.metricNoMovement()) 167 self.assertFalse(self.plex.metricNoSurf()) 168 assert self.plex.metricGetVerbosity() == -1 169 assert self.plex.metricGetNumIterations() == 3 170 assert np.isclose(self.plex.metricGetMinimumMagnitude(), h_min) 171 assert np.isclose(self.plex.metricGetMaximumMagnitude(), h_max) 172 assert np.isclose(self.plex.metricGetMaximumAnisotropy(), a_max) 173 assert np.isclose(self.plex.metricGetTargetComplexity(), target) 174 assert np.isclose(self.plex.metricGetNormalizationOrder(), p) 175 assert np.isclose(self.plex.metricGetGradationFactor(), beta) 176 assert np.isclose(self.plex.metricGetHausdorffNumber(), hausd) 177 178 metric1 = self.plex.metricCreateUniform(1.0) 179 metric2 = self.plex.metricCreateUniform(2.0) 180 metric = self.plex.metricAverage2(metric1, metric2) 181 metric2.array[:] *= 0.75 182 assert np.allclose(metric.array, metric2.array) 183 metric = self.plex.metricIntersection2(metric1, metric2) 184 assert np.allclose(metric.array, metric1.array) 185 metric = self.plex.metricEnforceSPD(metric) 186 assert np.allclose(metric.array, metric1.array) 187 nMetric = self.plex.metricNormalize(metric, restrictSizes=False, restrictAnisotropy=False) 188 metric.scale(pow(target, 2.0/self.DIM)) 189 assert np.allclose(metric.array, nMetric.array) 190 191 def testAdapt(self): 192 if self.DIM == 1: return 193 self.plex.orient() 194 plex = self.plex.refine() 195 plex.distribute() 196 if self.CELLS is None and not plex.isSimplex(): return 197 if sum(self.DOFS) > 1: return 198 metric = plex.metricCreateUniform(9.0) 199 try: 200 newplex = plex.adaptMetric(metric,"") 201 except PETSc.Error as exc: 202 if exc.ierr != ERR_ARG_OUTOFRANGE: raise 203 204 205# -------------------------------------------------------------------- 206 207class BaseTestPlex_2D(BaseTestPlex): 208 DIM = 2 209 CELLS = [[0, 1, 3], [1, 3, 4], [1, 2, 4], [2, 4, 5], 210 [3, 4, 6], [4, 6, 7], [4, 5, 7], [5, 7, 8]] 211 COORDS = [[0.0, 0.0], [0.5, 0.0], [1.0, 0.0], 212 [0.0, 0.5], [0.5, 0.5], [1.0, 0.5], 213 [0.0, 1.0], [0.5, 1.0], [1.0, 1.0]] 214 DOFS = [1, 0, 0] 215 216class BaseTestPlex_3D(BaseTestPlex): 217 DIM = 3 218 CELLS = [[0, 2, 3, 7], [0, 2, 6, 7], [0, 4, 6, 7], 219 [0, 1, 3, 7], [0, 1, 5, 7], [0, 4, 5, 7]] 220 COORDS = [[0., 0., 0.], [1., 0., 0.], [0., 1., 0.], [1., 1., 0.], 221 [0., 0., 1.], [1., 0., 1.], [0., 1., 1.], [1., 1., 1.]] 222 DOFS = [1, 0, 0, 0] 223 224# -------------------------------------------------------------------- 225 226class TestPlex_1D(BaseTestPlex, unittest.TestCase): 227 pass 228 229class TestPlex_2D(BaseTestPlex_2D, unittest.TestCase): 230 pass 231 232class TestPlex_3D(BaseTestPlex_3D, unittest.TestCase): 233 pass 234 235class TestPlex_2D_P3(BaseTestPlex_2D, unittest.TestCase): 236 DOFS = [1, 2, 1] 237 238class TestPlex_3D_P3(BaseTestPlex_3D, unittest.TestCase): 239 DOFS = [1, 2, 1, 0] 240 241class TestPlex_3D_P4(BaseTestPlex_3D, unittest.TestCase): 242 DOFS = [1, 3, 3, 1] 243 244class TestPlex_2D_BoxTensor(BaseTestPlex_2D, unittest.TestCase): 245 CELLS = None 246 COORDS = None 247 def setUp(self): 248 self.plex = PETSc.DMPlex().createBoxMesh([3,3], simplex=False) 249 250class TestPlex_3D_BoxTensor(BaseTestPlex_3D, unittest.TestCase): 251 CELLS = None 252 COORDS = None 253 def setUp(self): 254 self.plex = PETSc.DMPlex().createBoxMesh([3,3,3], simplex=False) 255 256try: 257 raise PETSc.Error 258 PETSc.DMPlex().createBoxMesh([2,2], simplex=True, comm=PETSc.COMM_SELF).destroy() 259except PETSc.Error: 260 pass 261else: 262 class TestPlex_2D_Box(BaseTestPlex_2D, unittest.TestCase): 263 CELLS = None 264 COORDS = None 265 def setUp(self): 266 self.plex = PETSc.DMPlex().createBoxMesh([1,1], simplex=True) 267 268 class TestPlex_2D_Boundary(BaseTestPlex_2D, unittest.TestCase): 269 CELLS = None 270 COORDS = None 271 def setUp(self): 272 boundary = PETSc.DMPlex().create(self.COMM) 273 boundary.createSquareBoundary([0., 0.], [1., 1.], [2, 2]) 274 boundary.setDimension(self.DIM-1) 275 self.plex = PETSc.DMPlex().generate(boundary) 276 277 class TestPlex_3D_Box(BaseTestPlex_3D, unittest.TestCase): 278 CELLS = None 279 COORDS = None 280 def setUp(self): 281 self.plex = PETSc.DMPlex().createBoxMesh([1,1,1], simplex=True) 282 283 class TestPlex_3D_Boundary(BaseTestPlex_3D, unittest.TestCase): 284 CELLS = None 285 COORDS = None 286 def setUp(self): 287 boundary = PETSc.DMPlex().create(self.COMM) 288 boundary.createCubeBoundary([0., 0., 0.], [1., 1., 1.], [1, 1, 1]) 289 boundary.setDimension(self.DIM-1) 290 self.plex = PETSc.DMPlex().generate(boundary) 291 292# -------------------------------------------------------------------- 293 294PETSC_DIR = petsc4py.get_config()['PETSC_DIR'] 295 296def check_dtype(method): 297 def wrapper(self, *args, **kwargs): 298 if PETSc.ScalarType is PETSc.ComplexType: 299 return 300 else: 301 return method(self, *args, **kwargs) 302 return wrapper 303 304def check_package(method): 305 def wrapper(self, *args, **kwargs): 306 if not PETSc.Sys.hasExternalPackage("hdf5"): 307 return 308 elif self.PARTITIONERTYPE != "simple" and \ 309 not PETSc.Sys.hasExternalPackage(self.PARTITIONERTYPE): 310 return 311 else: 312 return method(self, *args, **kwargs) 313 return wrapper 314 315def check_nsize(method): 316 def wrapper(self, *args, **kwargs): 317 if PETSc.COMM_WORLD.size != self.NSIZE: 318 return 319 else: 320 return method(self, *args, **kwargs) 321 return wrapper 322 323class BaseTestPlexHDF5(object): 324 NSIZE = 4 325 NTIMES = 3 326 327 def setUp(self): 328 self.txtvwr = PETSc.Viewer() 329 330 def tearDown(self): 331 if not PETSc.COMM_WORLD.rank: 332 if os.path.exists(self.outfile()): 333 os.remove(self.outfile()) 334 if os.path.exists(self.tmp_output_file()): 335 os.remove(self.tmp_output_file()) 336 self.txtvwr = None 337 338 def _name(self): 339 return "%s_outformat-%s_%s" % (self.SUFFIX, 340 self.OUTFORMAT, 341 self.PARTITIONERTYPE) 342 343 def infile(self): 344 return os.path.join(PETSC_DIR, "share/petsc/datafiles/", 345 "meshes/blockcylinder-50.h5") 346 347 def outfile(self): 348 return os.path.join("./temp_test_dmplex_%s.h5" % self._name()) 349 350 def informat(self): 351 return PETSc.Viewer.Format.HDF5_XDMF 352 353 def outformat(self): 354 d = {"hdf5_petsc": PETSc.Viewer.Format.HDF5_PETSC, 355 "hdf5_xdmf": PETSc.Viewer.Format.HDF5_XDMF} 356 return d[self.OUTFORMAT] 357 358 def partitionerType(self): 359 d = {"simple": PETSc.Partitioner.Type.SIMPLE, 360 "ptscotch": PETSc.Partitioner.Type.PTSCOTCH, 361 "parmetis": PETSc.Partitioner.Type.PARMETIS} 362 return d[self.PARTITIONERTYPE] 363 364 def ref_output_file(self): 365 return os.path.join(PETSC_DIR, "src/dm/impls/plex/tutorials/", 366 "output/ex5_%s.out" % self._name()) 367 368 def tmp_output_file(self): 369 return os.path.join("./temp_test_dmplex_%s.out" % self._name()) 370 371 def outputText(self, msg, comm): 372 if not comm.rank: 373 with open(self.tmp_output_file(), 'a') as f: 374 f.write(msg) 375 376 def outputPlex(self, plex): 377 self.txtvwr.createASCII(self.tmp_output_file(), 378 mode='a', comm=plex.comm) 379 plex.view(viewer=self.txtvwr) 380 self.txtvwr.destroy() 381 382 @check_dtype 383 @check_package 384 @check_nsize 385 def testViewLoadCycle(self): 386 grank = PETSc.COMM_WORLD.rank 387 for i in range(self.NTIMES): 388 if i == 0: 389 infname = self.infile() 390 informt = self.informat() 391 else: 392 infname = self.outfile() 393 informt = self.outformat() 394 if self.HETEROGENEOUS: 395 mycolor = (grank > self.NTIMES - i) 396 else: 397 mycolor = 0 398 try: 399 import mpi4py 400 except ImportError: 401 self.skipTest('mpi4py') # throws special exception to signal test skip 402 mpicomm = PETSc.COMM_WORLD.tompi4py() 403 comm = PETSc.Comm(comm=mpicomm.Split(color=mycolor, key=grank)) 404 if mycolor == 0: 405 self.outputText("Begin cycle %d\n" % i, comm) 406 plex = PETSc.DMPlex() 407 vwr = PETSc.ViewerHDF5() 408 # Create plex 409 plex.create(comm=comm) 410 plex.setName("DMPlex Object") 411 # Load data from XDMF into dm in parallel 412 vwr.create(infname, mode='r', comm=comm) 413 vwr.pushFormat(format=informt) 414 plex.load(viewer=vwr) 415 plex.setOptionsPrefix("loaded_") 416 plex.distributeSetDefault(False) 417 plex.setFromOptions() 418 vwr.popFormat() 419 vwr.destroy() 420 self.outputPlex(plex) 421 # Test DM is indeed distributed 422 flg = plex.isDistributed() 423 self.outputText("Loaded mesh distributed? %s\n" % 424 str(flg).upper(), comm) 425 # Interpolate 426 plex.interpolate() 427 plex.setOptionsPrefix("interpolated_") 428 plex.setFromOptions() 429 self.outputPlex(plex) 430 # Redistribute 431 part = plex.getPartitioner() 432 part.setType(self.partitionerType()) 433 _ = plex.distribute(overlap=0) 434 plex.setName("DMPlex Object") 435 plex.setOptionsPrefix("redistributed_") 436 plex.setFromOptions() 437 self.outputPlex(plex) 438 # Save redistributed dm to XDMF in parallel 439 vwr.create(self.outfile(), mode='w', comm=comm) 440 vwr.pushFormat(format=self.outformat()) 441 plex.setName("DMPlex Object") 442 plex.view(viewer=vwr) 443 vwr.popFormat() 444 vwr.destroy() 445 # Destroy plex 446 plex.destroy() 447 self.outputText("End cycle %d\n--------\n" % i, comm) 448 PETSc.COMM_WORLD.Barrier() 449 # Check that the output is identical to that of plex/tutorial/ex5.c. 450 self.assertTrue(filecmp.cmp(self.tmp_output_file(), 451 self.ref_output_file(), shallow=False), 452 'Contents of the files not the same.') 453 PETSc.COMM_WORLD.Barrier() 454 455class BaseTestPlexHDF5Homogeneous(BaseTestPlexHDF5): 456 """Test save on N / load on N.""" 457 SUFFIX = 0 458 HETEROGENEOUS = False 459 460class BaseTestPlexHDF5Heterogeneous(BaseTestPlexHDF5): 461 """Test save on N / load on M.""" 462 SUFFIX = 1 463 HETEROGENEOUS = True 464 465class TestPlexHDF5PETSCSimpleHomogeneous(BaseTestPlexHDF5Homogeneous, 466 unittest.TestCase): 467 OUTFORMAT = "hdf5_petsc" 468 PARTITIONERTYPE = "simple" 469 470""" 471Skipping. PTScotch produces different distributions when run 472in a sequence in a single session. 473 474class TestPlexHDF5PETSCPTScotchHomogeneous(BaseTestPlexHDF5Homogeneous, 475 unittest.TestCase): 476 OUTFORMAT = "hdf5_petsc" 477 PARTITIONERTYPE = "ptscotch" 478""" 479 480class TestPlexHDF5PETSCParmetisHomogeneous(BaseTestPlexHDF5Homogeneous, 481 unittest.TestCase): 482 OUTFORMAT = "hdf5_petsc" 483 PARTITIONERTYPE = "parmetis" 484 485class TestPlexHDF5XDMFSimpleHomogeneous(BaseTestPlexHDF5Homogeneous, 486 unittest.TestCase): 487 OUTFORMAT = "hdf5_xdmf" 488 PARTITIONERTYPE = "simple" 489 490""" 491Skipping. PTScotch produces different distributions when run 492in a sequence in a single session. 493 494class TestPlexHDF5XDMFPTScotchHomogeneous(BaseTestPlexHDF5Homogeneous, 495 unittest.TestCase): 496 OUTFORMAT = "hdf5_xdmf" 497 PARTITIONERTYPE = "ptscotch" 498""" 499 500class TestPlexHDF5XDMFParmetisHomogeneous(BaseTestPlexHDF5Homogeneous, 501 unittest.TestCase): 502 OUTFORMAT = "hdf5_xdmf" 503 PARTITIONERTYPE = "parmetis" 504 505class TestPlexHDF5PETSCSimpleHeterogeneous(BaseTestPlexHDF5Heterogeneous, 506 unittest.TestCase): 507 OUTFORMAT = "hdf5_petsc" 508 PARTITIONERTYPE = "simple" 509 510""" 511Skipping. PTScotch produces different distributions when run 512in a sequence in a single session. 513 514class TestPlexHDF5PETSCPTScotchHeterogeneous(BaseTestPlexHDF5Heterogeneous, 515 unittest.TestCase): 516 OUTFORMAT = "hdf5_petsc" 517 PARTITIONERTYPE = "ptscotch" 518""" 519 520class TestPlexHDF5PETSCParmetisHeterogeneous(BaseTestPlexHDF5Heterogeneous, 521 unittest.TestCase): 522 OUTFORMAT = "hdf5_petsc" 523 PARTITIONERTYPE = "parmetis" 524 525class TestPlexHDF5XDMFSimpleHeterogeneous(BaseTestPlexHDF5Heterogeneous, 526 unittest.TestCase): 527 OUTFORMAT = "hdf5_xdmf" 528 PARTITIONERTYPE = "simple" 529 530class TestPlexHDF5XDMFPTScotchHeterogeneous(BaseTestPlexHDF5Heterogeneous, 531 unittest.TestCase): 532 OUTFORMAT = "hdf5_xdmf" 533 PARTITIONERTYPE = "ptscotch" 534 535class TestPlexHDF5XDMFParmetisHeterogeneous(BaseTestPlexHDF5Heterogeneous, 536 unittest.TestCase): 537 OUTFORMAT = "hdf5_xdmf" 538 PARTITIONERTYPE = "parmetis" 539 540# -------------------------------------------------------------------- 541 542if __name__ == '__main__': 543 unittest.main() 544