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