Questions tagged [petsc]

PETSc is an open source suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

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Is it possible to predict the null space of a structure from contributing elements null spaces?

I am trying to solve an almost incompressible problem with heterogeneous properties by domain decomposition. Solution with CG converges slowly or divergerces completely. My problem becomes ill-...
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62 views

Solving saddle point problem having non-invertible top-left block with a PETSc nested matrix

My system is a symmetric FE problem with lagrange multipliers: $Z=\begin{pmatrix}A & C^T \\ C & 0\end{pmatrix}$ The matrix $A$ is positive semi-definite, non-invertible. The whole matrix is ...
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0answers
80 views

PETSc SNES for user defined state

How to use PETSc SNES (scalable nonlinear equation solver), when the solution is not a vector but a user defined state? I am implementing a non-linear mechanics problem (geometrically exact shell 5-...
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243 views

Method with low memory requirement for large-scale eigenvalue problem

I am working on the flow stability problem. In this work the main complication is solving generalized eigenvalue problem for a large scale Non-Hermitian matrix. I need only one eigenvalue (most left ...
3
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0answers
157 views

Is there an easy way to read a PetscBag into a python dict?

I'm using a PetscBag to store the input parameters of my program. At some point, I'm going to need to use python to plot these parameters against some output parameters, and ...
2
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1answer
177 views

Solving nonlinear PDE with finite difference based on Newton-Krylov

I am now working on solving MHD equations with finite difference method, which include nonlinear equations: $$ \frac{\partial\rho}{\partial t}+\nabla\cdot\left[\left(\rho_0+\rho\right){v}\right]-\...
2
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0answers
167 views

Is it worth switching to timesteppers provided by PETSc if I can't write down a Jacobian for my problem? Case study with “the amoeba” toy problem

I am considering using petsc4py instead of scipy.integrate.odeint (which is a wrapper for Fortran solvers) for a problem ...
2
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0answers
161 views

preconditioned Uzawa method with Petsc

I am trying to improve the resolution of a Stokes problem (P2/P1 on unstructured mesh) defined by the matrix $M$: $M= \begin{pmatrix} A_u & 0 & B_u \\ 0 & A_v & B_v\\ B_u^T & B_v^...
2
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564 views

Jacobian-Free Newton-Krylov vs explicitly forming jacobian in DG

For a given discontinuous galerkin (DG) implementation for Navier-Stokes, targeting 10,000 to 1,000,000 4th order cells in 3D, I'm using PETSc's suite of linear/non-linear solvers on the back-end. It ...
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587 views

Cusp Library performance worse than PETSC (GMRES 200 iterations) Why?

I wanted to compare the speeds of the GMRES implementations in the CUSP and the PETSc libraries. The matrix (A) used for testing was a 3d Laplacian matrix obtained by using the 7 point stencil on a ...
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0answers
32 views

Orientation of cones and transitive closures of a dmplex in Petsc

From the Petsc manual pages, I fail to understand what the orientations of cones and transitive closures mean. In particular, how can I relate these numbers to the orientation of the length/area/...
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183 views

Getting started with FEM: Ill-conditioned matrix when evaluating flux terms in conservation law?

I have a system of conservation laws of the form $$ \frac{\partial \mathbf{q}}{\partial t} + \nabla \cdot \mathbf{F}\!\left(\mathbf{q}\right) = 0 $$ I want to use finite elements to solve this ...
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60 views

Parallel dense solve with submatrices from mesh refinement with Petsc

For a Bounday Element Method problem I require the solution of a system of linear equations with multiple right-hand sides. Though this is a dense system, I still want to do it via Petsc in parallel. ...
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101 views

PETSc - difference between PetscNew and PetscMalloc

I wonder what is the difference between both functions. In C++, the difference between new and malloc is easier: new allocates memory by calling the constructor. What about PETSc ? In the example, ...
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48 views

Petsc matrix with DM objects takes too much memory

I have been learning petsc recently and made a simple solver for stokes equation on 3D staggered grid. My code is running on server with 200GB ram, but if I run a solver on 256^3 grid, memory used by ...
0
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1answer
71 views

Access PETSc data in totalview?

Is it possible to view the data stored in the various PETSc data types from within totalview? Ordinarily, PETSc types are integers which act as pointers to the actual data (obviously my understanding ...