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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About PETSc installation

I have downloaded and unzipped PETSc from PETSc Website in my home directory (OS is CentOS 6.3 64bit ) and followed given commands on Installation page "./configure --with-cc=gcc --with-fc=gfortran -...
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MPI-based Implementations of FFT

In a numerical computation, I am required to take a multi-dimensional FFT on a distributed-memory cluster. The data is currently distributed using a distributed array in PETSc (DMDA). I initial ...
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PETSc's makefile system can't find MKL

I'm learning PETSc and trying to make the examples written in C. However, when I use the provided makefile, I get the following error: ...
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Solving a simple Ax=b system in parallel with PETSc

I am new to the PETSc package. I have a ~4000x4000 matrix A in matrix-market format and I want to get PETSc to solve this using multiple processors. I know how to solve the system on a single ...
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CPU benchmarks for numerical kernels

CPU benchmarks available online mostly focus on desktop apps/games and rarely on serial/parallel numerical kernels, specially sparse ones (e.g., MatMult). Some benchmarks like NAS/SciMark exists but ...
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Using algebraic multigrid for preconditioning convection-diffusion operators

I implemented a Navier Stokes based on FEM discretization and PETSc for solving the linear system of equations. To create an efficient solution procedure, I follow the paper "Efficient ...
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How to get sparse complex matrices from my code to PETSc efficiently

What is the most efficient way to get a complex sparse matrix from my Fortran code to PETSc? I understand that this is problem dependent, so I tried to give as many relevant details as possible below. ...
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How can I estimate the condition number of a large sparse matrix using PETSc?

I have a PETSc Mat and would like to estimate its condition number.
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Using same memory space for global and local Petsc DA Vectors

I have constructed a local and global distributed array in Petsc 3.2 using: DMCreateGlobalVector(da, &v); DMCreateLocalVector(da, &lv); In order to ...
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Is there a way to inspect the graph of a sparse matrix with PETSc?

I am currently trying to code the CA-CG method within the PETSc framework. A mandatory step in this process is the implementation of the "matrix powers kernel" algorithm for a generic sparse matrix. ...
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Factor a non-symmetric matrix into the product of a sparse symmetric matrix and a diagonal matrix plus a low rank correction

I have a non-symmetric matrix, where the non-symmetry only appears at a subset of points. This arises due to the particular manner on which boundary conditions are applied in a Cartesian grid method. ...
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Debugging Shell matrix

I am trying to solve complex valued Poisson equation $$(C + \nabla. D \nabla )u = f \text{ ;where C, D, u and f are complex numbers.} $$ I am breaking this eqn into real valued problem, which is of ...
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What are d_nz and o_nz in PETSc's MatMPIAIJSetPreallocation function?

I'm working from ex2.c of PETSc's example codes. On line 65, the code specifies: MatMPIAIJSetPreallocation(A,5,PETSC_NULL,5,PETSC_NULL); I looked up the ...
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Memory footprint for DMDA objects in PETSc

Why does DMDA objects require so much memory on PETSc 3.2-p7. When running the code: ...
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How to work with function pointers in Fortran in scientific programs

Here is a typical usage of function pointers in C. I would like to do something similar in Fortran. I have some ideas, but I would like to know if there is some canonical way to do so. The function ...
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351 views

Is the sparsity pattern of a linear system important for iterative (KSP) solvers?

Pretty much the question. Given a general sparse, non-symmetric (both numerically and structurally) matrix, how important is the sparsity pattern (i.e. row/column permutation of matrix/vector) for ...
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891 views

32bit/64bit issue when working with Numpy and petsc4py

When indexing PETSc.Mat A with an array c ( numpy.ndarray with ...
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Does PETSc ever make use of LAPACK libraries for sparse matrix math?

Does compiling PETSc with an external BLAS/LAPACK library significantly affect performance on sparse matrices, or does it only use those libraries for dense matrix math?
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Petsc's xxxSetxxx methods: Own Pointer or Copy Values?

In PETSC, there are many xxxSetyyy methods, e.g. MatSetLocalToGlobalMapping(A,rmap,cmap). I wonder whether contents of rmap and cmap (or generally yyy, that set to xxx) pointing to are copied to ...
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How do I print a PetscBag to a specific file?

I have a PetscBag in my program that I want to write to a filename I have stored as a string. If I want to write to stdout, there is a pre-made PetscViewer macro ...
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456 views

When is MatGetArray/VecGetArray useful?

In petsc, there are already SetValues(Local) methods. But when does one need GetArray methods? A related question: to copy a portion of a Mat/Vec to part of another Mat/Vec, it is usually suggested ...
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How should I build a 2D 5-point stencil Laplacian matrix in parallel?

I'm making a simple eigenvalue solver with SLEPc, using a 5-point stencil and the finite difference method. I want to be able to assemble the matrix in parallel. My first thought was just to use <...
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Do I need KSPSetOperators after PCSetOperators?

What I did is Create some PC named pc, and PCSetOperators(pc,A,A,..); Create KSP named ksp; KSPSetPC(ksp,pc); After the above process, am I still obliged to KSPSetOperators(ksp,A,A,..), or I can ...
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What is the difference between MATSEQMAIJ and MATSEQAIJ in PETSc?

What is the difference between MATSEQMAIJ and MATSEQAIJ in PETSc? Also, where can I find more information on each of the MatTypes? I went to the MatType documentation, but it didn't have anything but ...
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Efficiency of using petsc4py vs. c/c++/fortran

How much slower is petsc4py vs c/c++/fortran? I realize it will depend significantly on the code being executed, but what about something simple like a matrix-vector product?
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How do you change the desired accuracy of a TS object in PETSc?

I'm currently getting very long propagation times when attempting to use the Time Stepping propagators in Petsc 3.2, and in the interest of speeding things up, I'm curious how I can reduce the ...
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What does MatGetOwnershipRange() do for sequential matrices?

I'm writing a petsc code using a sequential matrix type. Since I want it to be easy to parallelize, I put some stuff in the code that is useless now, but will make it easier to parallelize later. One ...
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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 ...
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MatMatMult and KSPSolve for MATMPIDENSE matrices

I'm trying to use MATMPIDENSE matrices to solve a system of type Ax=b, but I have some problems. The KSP documentation says that KSPSolve for dense matrices requires to set a 'gmres' solver and a 'lu' ...
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218 views

Error message when trying to get PETSc to draw to an X terminal by passing -mat_view_draw

I've made a matrix, and now I want to draw it on the screen to make a basic check of correctness. The documentation for MatAssemblyEnd() states that I can pass an ...
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1answer
569 views

Implicitly casting PetscReal to the real part of PetscComplex

The version of Petsc installed on my machine has PetscScalar set to be complex. I am making a matrix which has all real entries. Something like the following code compiles: ...
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Why can't I compile a function using the CHKERRQ macro in PETSc?

I wrote a function to read in the runtime parameters my program takes. This function is in a different file than my main program; the two object files are linked after compilation. When I compile the ...
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What should a PetscBag be used for?

I've been trying to use a PetscBag to read in a number of options I want to pass to a program I'm writing. Before I came across the documentation for PetscBag, I was planning on using a struct and a ...
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Can PetscBags be used with 64 bit versions of petsc?

I was looking at the documentation for PetscBagCreate(), and it says that The size of the A struct must be small enough to fit in a PetscInt; by default ...
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What does PetscBagSetFromOptions() do?

I'm writing a program that uses PETSc and SLEPc, and I was looking for a convienient way to read in options from the command line. The description of ...
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Overlapping communication and computation in PETSc and/or Trilinos?

I am just learning about these packages, so forgive me if this is a trivial/silly question. Our group is working re-developing our code from the ground up using modern software practices. Currently ...
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612 views

Petsc not compiling c++ files

I'm having a problem where petsc is complaining about the type of PetscScalar (I get a whole bunch of errors from the c++ standard library that revolve around PetscScalar not defined). I believe it ...
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How do I read a binary file into PETSc as a matrix?

I created a binary matrix using the following loop in c ...
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How useful is PETSc for Dense Matrices?

Wherever I have seen, PETSc tutorial/documents etc. say that it is useful for linear algebra and usually specifies that sparse systems will benefit. What about dense matrices? I am concerned about ...
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How do I compute the parallel overhead of a parallel code run on a single processor when no sequential code is available?

I'm profiling the performance of PETSc's linear solvers. As I understand it, $$\text{speedup}=\frac{\text{Sequential Time}}{\text{Parallel Time}}.$$ I know that running the parallel code on one ...
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What are the main differences between PETSc and Trilinos?

As far as I can tell, the two big generic US Department of Energy computational science software frameworks are PETSc and Trilinos. They seem similar at first glance, beyond differences in language (...
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How to measure the overall performance of a PETSc program using the -log_summary flag?

When I run a PETSc example in parallel with the flag "-log_summary", the first two tables of information look something like this: ...
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Problems running a PETSc example in parallel

After configuring and building PETSc, I have successfully been able to run several examples. In particular, I am working with this example. I have been able to run the program using the following ...
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How to run a PETSc example?

I just installed the PETSc library. This is what I did from the home directory ~ ...
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Why is my iterative linear solver not converging?

What can go wrong when using preconditoned Krylov methods from KSP (PETSc's linear solver package) to solve a sparse linear system such as those obtained by discretizing and linearizing partial ...
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Is it possible to dynamically resize a sparse matrix in the Petsc library?

This may be a Petsc newbie question, but... I'm using Petsc to solve a large sparse linear system. The initial creation of the matrix is fairly slow, which I'm given to understand is largely due to ...
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Which libraries have good high-level support for multigrid?

I'm planning to use multigrid to calulate some eigenvalues and vectors, and I noticed PETSc has high-level support for multigrid. The PETSc documentation says that this part of PETSc should not be ...
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Why is my parallel solver slower than my sequential solver?

I was playing around with PETSc and noticed that when I run my program with more than one process via MPI it seems to run even slower! How can I check to see what is going on?

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