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