PETSc Tutorial - The ACTS Toolkit

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Profiling PETScEfficient Matrix CreationCreate matrix with MatCreate()Set type with MatSetType()Determine the number of nonzeros in each rowloop over the grid for finite differencesloop over the elements for finite elementsneed only local+ghost informationPreallocate matrixMatSeqAIJSetPreallocation()MatMPIAIJSetPreallocation()M. Knepley (ANL) Tutorial ACTS ’06 45 / 166
Profiling PETScIndicating Expected NonzerosSequential Sparse MatricesMatSeqAIJPreallocation(Mat A, int nz, int nnz[])nz: expected number of nonzeros in any rownz(i): expected number of nonzeros in row iM. Knepley (ANL) Tutorial ACTS ’06 46 / 166
Page 1 and 2: PETSc TutorialPETSc TeamPresented b
Page 3 and 4: Part IGetting Started with PETScM.
Page 5 and 6: What is PETSc?What I Need From YouT
Page 7 and 8: What is PETSc?How Can We Help?Provi
Page 9 and 10: What is PETSc?How Can We Help?Provi
Page 11 and 12: What is PETSc?What is PETSc?A freel
Page 13 and 14: What is PETSc?TimelineActive Develo
Page 15 and 16: What is PETSc?What Can We Handle?PE
Page 17 and 18: Who uses and develops PETSc?Who Use
Page 19 and 20: How can I get PETSc?Downloading PET
Page 21 and 22: How can I get PETSc?Unpacking PETSc
Page 23 and 24: How do I Configure PETSc?Configurin
Page 25 and 26: How do I Configure PETSc?Automatic
Page 27 and 28: Building PETScHow do I Build PETSc?
Page 29 and 30: Exercise 4How do I Build PETSc?Reco
Page 31 and 32: Using MPIHow do I run an example?Th
Page 33 and 34: How do I run an example?Alternative
Page 35 and 36: How do I run an example?Common Moni
Page 37 and 38: Exercise 6How do I run an example?C
Page 39 and 40: Part IICommon PETSc UsageM. Knepley
Page 41 and 42: Debugging PETScInteracting with the
Page 43 and 44: Exercise 1Debugging PETScUse the de
Page 45 and 46: Profiling PETScUsing Stages and Eve
Page 47 and 48: Profiling PETScAdding A Logging Eve
Page 49: Profiling PETScMatrix Memory Preall
Page 53 and 54: Profiling PETScIndicating Expected
Page 55 and 56: Exercise 2Profiling PETScReturn to
Page 57 and 58: PETSc principles and designPETSc St
Page 59 and 60: PETSc principles and designLevels o
Page 61 and 62: PETSc principles and designSymmetry
Page 63 and 64: PETSc principles and designExperime
Page 65 and 66: CollectivityPETSc principles and de
Page 67 and 68: PETSc principles and designBasic Pe
Page 69 and 70: Initial OperationsApplication Integ
Page 71 and 72: Integration StagesInitial Operation
Page 73 and 74: ProfilingInitial OperationsUse -log
Page 75 and 76: Vector AlgebraVector AlgebraWhat ar
Page 77 and 78: Creating a VectorVector AlgebraVec
Page 79 and 80: Vector AssemblyVector AlgebraA thre
Page 81 and 82: Vector AlgebraA Better Way to Set t
Page 83 and 84: Vector AlgebraWorking With Local Ve
Page 85 and 86: VecGetArray in F77Vector Algebra#in
Page 87 and 88: Matrix AlgebraMatrix AlgebraWhat ar
Page 89 and 90: Matrix AlgebraMatrix PolymorphismTh
Page 91 and 92: Matrix AlgebraOne Way to Set the El
Page 93 and 94: Matrix AlgebraA Better Way to Set t
Page 95 and 96: SolversAlgebraic SolvesExplicit:Fie
Page 97 and 98: Nonlinear SolversNewton MethodsAlge
Page 99 and 100: Algebraic Solves3rd Party Solvers i
Page 101 and 102:
More AbstractionsHigher Level Abstr
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Part VAdvanced PETScM. Knepley (ANL
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SNES FunctionNonlinear EquationsThe
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SNES VariantsNonlinear EquationsLin
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Nonlinear EquationsSNES Example: Dr
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Nonlinear EquationsDriven Cavity Re
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What is a DA?Structured GridsDA is
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Creating a DAStructured GridsDACrea
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Structured GridsDA Global Numbering
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DA VectorsStructured GridsThe DA ob
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DA Local FunctionStructured GridsTh
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DA StencilsStructured GridsBoth the
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Structured GridsMapping Between Glo
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Structured GridsDA Example: BratuPe
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Part VIPETSc ExtensibilityM. Kneple
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Linking to PETScExtending the Build
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Extending ClassesAdding an Implemen
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Extending ClassesAdding a New Subty
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Extending ClassesAdding a New TypeS
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Extending ClassesAdding a New TypeT
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Marc Garbey’s ProblemProblem Doma
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Revision 1.1Marc Garbey’s Problem
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Revision 1.6Marc Garbey’s Problem
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Marc Garbey’s ProblemMesh Indepen
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Marc Garbey’s ProblemForcing Func
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Marc Garbey’s ProblemNeumann Solu
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Part VIIIFuture PlansM. Knepley (AN
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PETSc PartsTo make the new function
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Mesh CapabilitiesMesh2D Delaunay ge
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How does Sieve Work?MeshApplication
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How does Field Work?MeshApplication
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Page 173 and 174:
AdvantagesMeshSieve/Field operation
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Page 181 and 182:
MeshWhat is Sieve Good For?Parallel
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Page 193 and 194:
IntegrationMeshTwo main integration
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Sieve and PETScMeshSieve is the uns
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Sieve and PETScMeshSieve is the uns
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Jacobian EvaluationMeshPetscScalar
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Weak Form LanguagesA Language for W
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ExamplesWeak Form LanguagesPoisson
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