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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How to reuse the symbolic factorization when using MUMPS in petsc?

I have a problem when using petsc. I want to solve a series of linear equations. A1x1=b1, A2x2=b2, A3*x3=b3 ... The A1,A2,A3 have the same sparstiy pattern. I want to use MUMPS to solve the system. In ...
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6 votes
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PETSc-like library for Julia

I want to build an application for Material Point Method (and probably other meshfree methods too) in Julia and I am looking for library for direct and iterative solvers that can help me with it. One ...
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Output solution vector in Petsc

I am using petsc to solve a linear elasticity problem discretized by finite elements.The initial mesh is read by a mesh file and the distribution in each processor is done using METIS.I am using only ...
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2 votes
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276 views

How to solve a linear problem A x = b in PETSC when matrix A has zero diagonal enteries?

I am solving a structural mechanics problem that involves setting constraints, and I use Lagrange multipliers to set it. Consequently, some diagonal entries of the tangent stiffness matrix vanish, and ...
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2 votes
2 answers
111 views

Petsc Mat object in class

[Relatively new to Petsc] I am writing an object oriented project and my idea is to have parallel objects when the user constructs the object with MPI arguments. So have member data Mat and fill/...
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Parallelisation strategies for mixed FE formulations

Mixed FE formulations with LBB-stable elements require two different meshes for the primary and the constraint variables, for example, displacement and pressure. With continuous approximation for the ...
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Issue solving nonlinear equation containing a quotient

I have a coupled set of PDEs that need to be solved as part of a larger problem. I am currently approaching this by computing spatial derivatives with finite differences and using PETSc's nonlinear ...
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How to delete $n^{th}$ row and $n^{th}$ column of a matrix K in Petsc and restructure it?

I have a matrix K in Petsc. I want to delete the $n^{th}$ row and $n^{th}$ column of this matrix and restructure it. I am a beginner in Petsc. Can you suggest how to do it? Example: I have matrix K ...
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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 ...
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3 votes
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137 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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What method to solve a sparse complex symmetric (non-Hermitian) system?

I have a sparse system (about 78% of zero entries) that is complex and symmetric (but not Hermitian). The following figure shows the structure of the problem. The off-diagonal blocks are incidence ...
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Why PETSc/MPI uses only 1 processor a number of times, rather than using several as prescribed by mpiexec [closed]

I am a beginner to PETSc and MPI, so after installing PETSc I was compiling some basic tutorial. But whenever I give the number of processors i.e mpiexec -n 4 ./ex1 ...
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1 vote
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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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1 answer
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Send Petsc sequential matrix to another MPI rank

I am doing specific tests on matrices, so forgive me if this question doesn't seem related to Petsc typical use. I have a SEQAIJ matrix on one process and I need ...
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3 votes
1 answer
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PETSc - Manipulate BAIJ matrix locally

My program loads a parallel PETSc matrix $A$ on several MPI processes, each holding a block submatrix $A_i$. I would like to retrieve the local submatrix $A_i$, the one corresponding to the current ...
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2 votes
1 answer
354 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]-\...
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PCJACOBI works but the default PCBJACOBI failed in PETSc

I am using PETSc and libmesh to solve a simple linear elastic problem with quite complicated geometry, using linear tetrahedral elements. I am always using the KSP CG as the solver. I noticed that ...
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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 ...
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2 votes
1 answer
127 views

is it more efficient to use ghosted vector in PETSC for PDE solving on unstructured mesh?

In a traditional PDE solver on unstructured meshes, we know exactly the sparse pattern of the Jacobian matrix, and we know that the amount of data to communicate is far smaller than the amount of ...
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How to access solution to linear system in PETSc?

I have just started with PETSc hence it might seem like a very stupid question but I couldn't find any answer in manual. After Calling KSPSolve, where can I access the soluition for my linear system? ...
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3 votes
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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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1 vote
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243 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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Efficiency of parallel direct linear solver

I am currently working on solving a positive definite symmetric systems in parallel. The parallel direct solver I used is MUMPS. However, the performance and efficiency of the parallel direct solver ...
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2 votes
2 answers
2k views

Which python library for GPU sparse linear system solver library

I have a fluid dynamic solver written in python which I want to accelerate by moving the most expensive computations to the GPU. Ideally all arrays and sparse matrices used in my code should remain on ...
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Which iterative method and preconditioner from petsc should be used when solving linear algebra in parallel?

I am currently trying to parallelize the incompressible flow solver code. However, when I run the code I realise that the parallel code takes much longer time than sequential code to finish one ...
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Why does PETSc take unexpectedly long to set up its KSP solver with a custom preconditioner? [closed]

I am attempting to solve a large system, $\bf{Ax} = \bf{b}$ with the help of PETSc. Due to the size of the problem, I'm using a matrix-free approach, where $\bf{A}$ is just a shell. I'm also providing ...
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1 vote
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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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1 vote
3 answers
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Practical reference on sparse linear solvers for PDEs (Navier-Stokes, Poisson) and on learning PETSc

My background is mainly engineering and applied research and I have been a developer or some CFD software, but mostly at high level without worrying about linear solvers and the like. This has been ...
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1 vote
2 answers
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Linear solvers: How to deal with a singular system? (Poisson equation with Neumann boundary conditions)

The question is in the context of iterative numerical solution of large PDE systems with Finite Differences or Finite Elements: Stating the Poisson equation with Neumann boundary conditions will lead ...
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1 vote
1 answer
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How to deal with multi-region problems (in PETSc)

Consider a problem where space is filled with a liquid and a solid phase, with a large, complicated geometry. On each of the phases, there's an electrical potential/poisson equation. The equations are ...
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1 vote
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Algebraic multigrid in PETSc

Consider a potential/poisson equation on a very large, complicated geometry. Currently, an self-written FEM and linear solvers from NumPy are used. Performance is, of course, not good enough for ...
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1 vote
1 answer
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Why does PETSc matrix memory allocation improve performance so much?

Context In the Portable, Extensible Toolkit for Scientific Computing (PETSc), the user often creates matrices and vectors. These objects are then used as input for other routines like iterative ...
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2 votes
1 answer
652 views

Distributed (MPI) matrix matrix multiplication

I perform matrix matrix multiplications (between rank-3 and rank-2 arrays) in fortran using following subroutine, ...
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0 votes
1 answer
326 views

setting COMM_WORLD size from petsc4py without mpiexec command line

I would like to create a parallel solver using petsc4py as one component of a larger application. I can easily get PETSc.COMM_WORLD.getSize() to be 4 by calling mpiexec -n 4 python my_prog.py ...
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3 votes
1 answer
309 views

SLEPc eigensolvers take long time to converge for large sparse symmetric matrices

I am leveraging the SLEPc library for solving the first $k$ (where $k = 3$ or $4$) eigenvalues and their corresponding vectors for a matrix of size 200,000. The matrix is sparse and symmetric. I ...
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1 vote
1 answer
366 views

What is the default smoother for the "PCMG" preconditioner in PETSc?

For a large parallel sparse matrix (mpiaij type matrix) in my code, I was experimenting with various preconditioners to see which one would do best with GMRES/BiCGSTAB. I tried the PCMG ...
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9 votes
3 answers
2k views

Are there any "light-weight" FEM packages around?

Basically, FEM seems to be a problem that is pretty much "solved". There are numerous powerful frameworks existing, like Trilinos, PETSc, FEniCS, Libmesh or MOOSE. One thing they have in common: They ...
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5 votes
2 answers
585 views

PetSc vs Sundials for serial numerical computations?

I am currently working on a physics problem that turns into a non-linear boundary value problem. I need an efficient numerical solver that I could run on my laptop with i5 dual core CPU. I am ...
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1 vote
1 answer
251 views

The alternative to using PETSc's SNES solvers in parallel without using the DMDA methods

I am using the PETSc libraries, in particular using the SNES solver package to solve a nonlinear matrix equation. Is there a way of parallelising the solution to this problem problem without using ...
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1 vote
0 answers
130 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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1 vote
1 answer
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PETCs - How should one initialize PetscRandom?

The documentation of PETSc shows an example of usage: ...
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1 answer
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PETSc - how computing a random number between 0 and 1?

In PETSc, I need to generate a random number between 1 and 0. With the include cstdlib, the classical trick is: ...
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2 votes
0 answers
179 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 ...
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3 votes
1 answer
156 views

Get a matrix with absolute values in PETSc [closed]

Is there any function to create or change a matrix, to have $A_{ij} = \text{abs}(A_{ij})$ in PETSc? If possible it should work with MPIAIJ matrices, not only local.
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5 votes
1 answer
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Can Variational Inequalities handle non-symmetric matrices?

I am trying to enforce the discrete maximum principle (i.e., ensuring non-negative concentrations) for diffusion-type problems that have an anisotropic diffusivity tensor (e.g., tensor dispersion from ...
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2 votes
0 answers
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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^...
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2 votes
1 answer
625 views

How to convert MPIAIJ to SEQAIJ matrix in petsc/petsc4py?

I am curious, if there is a function to convert MPIAIJ (distributed matrices in AIJ format) to a SEQAIJ matrix that lie on a single processor. It is possible to do such an operation for PETSc vectors ...
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3 votes
1 answer
380 views

Sparse matrix vector product using PETSC

I am trying to do a simple parallel sparse matrix vector multiplications using PETSC. My sparse matrix is a simple tridiagonal laplacian matrix, which is distributed over multiple processors using ...
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3 votes
1 answer
832 views

Why is MPI/PETSc only showing 1 processor even though it works for helloworld?

I am a beginner with Unix and MPI. For the serial program, I run the program by typing make in /directory/buildagain and then <...
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7 votes
2 answers
331 views

Comparing various implementations/software packages for large-scale finite element simulations

I currently use FEniCS and Deal.II to solve various FEM problems. I am also writing my own implementation of these problems by directly implementing the data structures, routines, and solvers within ...
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