PETSc Tutorial - The ACTS Toolkit

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Debugging PETScCorrectness DebuggingAutomatic generation of tracebacksDetecting memory corruption and leaksOptional user-defined error handlersM. Knepley (ANL) Tutorial ACTS ’06 35 / 166
Debugging PETScInteracting with the DebuggerLaunch the debugger-start in debugger [gdb,dbx,noxterm]-on error attach debugger [gdb,dbx,noxterm]Attach the debugger only to some parallel processes-debugger nodes 0,1Set the display (often necessary on a cluster)-display khan.mcs.anl.gov:0.0M. Knepley (ANL) Tutorial ACTS ’06 36 / 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: Part IICommon PETSc UsageM. Knepley
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 and 50: Profiling PETScMatrix Memory Preall
Page 51 and 52: Profiling PETScIndicating Expected
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
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Matrix AlgebraOne Way to Set the El
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Matrix AlgebraA Better Way to Set t
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SolversAlgebraic SolvesExplicit:Fie
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Nonlinear SolversNewton MethodsAlge
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Algebraic Solves3rd Party Solvers i
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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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AdvantagesMeshSieve/Field operation
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Page 181 and 182:
MeshWhat is Sieve Good For?Parallel
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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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