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18
votes
1answer
2k views

How to Run MPI-3.0 in shared memory mode like OpenMP

I am parallelizing code to numerically solve a 5 Dimensional population balance model. Currently I have a very good MPICH2 parallelized code in FORTRAN but as we increase parameter values the arrays ...
15
votes
1answer
3k views

Comparing Jacobi and Gauss-Seidel methods for nonlinear iterations

It is well known that for certain linear systems Jacobi and Gauss-Seidel iterative methods have the same convergence behavior, e.g. Stein-Rosenberg Theorem. I am wondering if similar results exist for ...
13
votes
0answers
410 views

Sequential approach to solving coupled PDEs

I'm dealing with a coupled system of three transient, non-linear convection-diffusion equations. Let's just say to simplify the problem that they take the following form: $$ -\nabla\cdot(D_{1}(u_{2},...
13
votes
0answers
343 views

Operator Splitting methods for DAEs

After doing some research, I've found that most of the literature on operator splitting methods (e.g. Strang Splitting, Fractional Step, etc.) are specifically designed for a standard problem type of ...
12
votes
0answers
3k views

Optimized open source BLAS / LAPACK package

I was wondering what is a more optimized open source BLAS/LAPACK package with respect to modern multi-core processors (Haswell and beyond). Is there any distribution that can attain performance close ...
12
votes
0answers
525 views

Fast Eigenvalue and SVD Solver for Structured Matrices

I am looking for a fast Eigenvalue and SVD solver for small dense structured matrices (Hankel and Toeplitz). I have searched for efficient implementations in libraries like MKL but I am not able to ...
11
votes
1answer
171 views

Benchmark problems for eigenvalue reordering algorithms sought

Every real matrix $A$ can be reduce to real Schur form $T = U^T A U$ using an orthogonal similiary transform $U$. Here the matrix $T$ is quasi-triangular form with 1 by 1 or 2 by 2 blocks on the main ...
11
votes
1answer
437 views

DG local equation, how to interpret mean-averaged test function

In the paper http://www.sciencedirect.com/science/article/pii/S0045782509003521, an HDG element-local equation is described on page 584 equation (4), with one of the equations taking the following ...
10
votes
0answers
595 views

Implementing std::nextafter: Should denormals-are-zero mode affect it? If so, how?

This might be the wrong stackexchange site for this question. math.SE, cs.SE, programmers.SE, and of course stackoverflow are all possibilities. I'm hoping to reach an audience that might actually ...
10
votes
0answers
116 views

Are there any standardized file formats for point group character tables?

Character tables are an important tool for symmetry analysis in many computational chemistry software packages. Are there any standardized file formats for point group character tables? This may seem ...
10
votes
0answers
409 views

Updating matrix diagonal with Woodbury matrix identity and maintaining numerical accuracy

I have a dense matrix A and its corresponding inverse $A^{-1}$. The Woodbury matrix identity states: $$ (A + UCV)^{-1} = A^{-1} - A^{-1}U(C^{-1} + VA^{-1}U)^{-1}VA^{-1} $$ I wish to perform small ...
9
votes
1answer
192 views

How to compute Singular value decomposition of a large matrix with Python

Language: Python3 Problem: I have a matrix Q of shape [51200 rows x 51200 cols] stored in a binary file, each of the element in this matrix has a data type of complex64. To load the data into memory I ...
9
votes
0answers
186 views

Imbalance of variables in Mixing Newton's method and Linear solver for a Non-linear system

Problem Solving a non-linear system of equations. The number of variables is the same as the number of equations. When I fix a set of variables (say $\vec{y}$) and keep another set free (say $\vec{...
9
votes
0answers
113 views

Review of modern homotopy methods and practical techniques

I'm hoping someone can recommend recent literature concerning homotopy methods for solving systems of nonlinear equations. Already by the time of Layne Watson's 1986 paper there were a lot of methods,...
9
votes
0answers
576 views

Numerical implementation of the Dirichlet-to-Neumann map

I am solving the Dirichlet problem $$ \begin{cases} \Delta u = 0, \\ u|_{\partial D} = f, \end{cases} $$ in a $2d$ domain $D$ using the finite element method. What I want to get is the ...
9
votes
0answers
267 views

Numerical integration using interval arithmetic, nowadays

Is there now a package for rigorous numerical integration that uses interval arithmetic and has access to a well-developed library of special functions? By "well-developed", I mean something that, at ...
9
votes
1answer
381 views

Increasing V-cycles for constant Coarsest Grid Size and increasing Fine Grid size

Problem statement I implemented geometric multigrid for $-\nabla^{2}=f$ where $f=\frac{3\pi^{2}}{4}sin \frac{\pi x}{2} sin \frac{\pi y}{2} sin \frac{\pi z}{2}$ on $\Omega \in [0,1]$ on a unit cube. ...
9
votes
0answers
196 views

Time advance in Adaptive Mesh Refinement method

I am working on solving complex system of 2D PDEs governing the behaviour of plasma in a gas lamp during discharge. Recent tests have shown that because of steep gradients in temperature field and ...
9
votes
0answers
248 views

Wanted: sequences of linear systems for recycling Krylov solver analysis

In the solution of sequences of linear systems $$A_ix_i=b_i\quad\text{for}\quad i=1,2,\dots$$ with Krylov subspace methods, data can be recycled from already solved linear systems in order to speed up ...
9
votes
0answers
414 views

Simple turbulence model appropriate for buoyancy-driven cavity like problem

Which turbulence model is suitable for resolving incompressible buoyancy-driven flow of a fluid within an cylindrical ampoule? I prefer turbulence model which is sufficiently simple so that fully ...
9
votes
0answers
338 views

Energy conservation in the solution of the Helmholtz equation

This might be a silly question, but I know very little about the theoretical properties finite elements, so here goes. Suppose you were to solve the Helmholtz equation (let's say in 2D) with a ...
9
votes
0answers
443 views

What's a good numerical/optimization software package for solving the 2-D optimal stopping problem?

I am looking for a numerical software package to help me solve the 2-dimensional "free boundary" PDEs that arise in optimal stopping problems. In one dimension a standard optimal stopping problem in ...
9
votes
0answers
144 views

Potential Reduction and Primal Path following methods

In both the potential reduction and primal path following interior point methods for linear programming, a barrier function is constructed which contains the terms $-\sum \log x_j$ where $x_j$ are the ...
9
votes
0answers
156 views

Fast algorithms to solve Markov Decision Processes

In my master thesis I used an Algorithm called Approximative Dynamic Programming [1] to solve equations of the form $$ \max_{\pi}\mathbb{E}^{\pi}\left\{\sum_{t=0}^{T}\gamma^tC_t^{\pi}(S_t,A_t^{\pi}(...
9
votes
1answer
224 views

Suggestions for numerical integral over Pólya Distribution

This problem arises from a Bayesian statistical modeling project. In order to compute with my model, I need to perform an integration in which part of the integrand is the "Pólya" or "Dirichlet-...
8
votes
0answers
132 views

What are some good debugging habits for numerical simulation?

I'm currently writing a lid drive cavity CFD code on python. Currently, my code has some issues (values jumping bear b.c). I was wondering what are some good habits in debugging numerical codes. ...
8
votes
0answers
85 views

How to construct an effective preconditioner for this particular problem

A quick introduction to my problem I am currently developing a method for simulation of water waves in three dimensions based on potential flow theory. The computational bottleneck of the method is ...
8
votes
0answers
569 views

Fast Automatic Differentiation for numpy?

I would like to use automatic differentiation to calculate gradients to function written in numpy. I've come across a number of packages, including autograd tangent chainer But none of them seem ...
8
votes
0answers
106 views

Finding the smallest root of a function on $[0, \infty)$

I would like to find the smallest real root of a 1-D real-valued function $f(x)$ on the domain $x\in [0,\infty)$. In this problem, I can make the following guarantees on $f$: $f$ does have a root at ...
8
votes
0answers
338 views

Speed and accuracy of Strassen vs Winograd matrix multiplication algorithms

I am doing work which requires as fast matrix multiplication as possible and just want to double-check with this community that the Winograd variant of Strassen's MM algorithm is the fastest practical ...
8
votes
0answers
332 views

Eigenvalue with largest imaginary part

Iterative eigensolvers such as ARPACK, give the option to find a subset of the eigenvalues which have the largest imaginary part. My question is how do these algorithms work. As I understand it, ...
8
votes
0answers
242 views

What can be done with Finite Element Method and not with the Finite Volume Method, and vice versa?

What are some applications where you would absolutely go for either FEM, but not FVM, or vice versa? What are some applications where both methods are equally suited? I worked with the FEM so far and ...
8
votes
0answers
162 views

Tucker factorisation to compare multiple PCA decompositions?

This is an entry-level question for multiway matrix decompositions. I have a set/population $k$ of entities (here biological cells) for each of which I also have a number ($l$) of flavours of length $...
8
votes
0answers
507 views

DIIS method to accelerate SCF convergence for stretched geometries

I am implementing from scratch an Hartree-Fock calculation in the STO-3G basis set to perform Born-Oppenheimer molecular dynamics. I have a Restricted Hartree-Fock procedure that can reproduce very ...
8
votes
0answers
160 views

Accelerated convergence for Sparse NMF

In the Non-Negative Matrix factorization (NMF), you basically compute an approximation of a given matrix $V \in \mathbb{R}_{+}^{n \times m}$ into matrices $W$ and $H$ such that $W \in \mathbb{R}_{+}^{...
8
votes
0answers
524 views

What is the source of the error in the Sherman-Morrison formula application?

The Sherman-Morrison formula $$ (A+uv^T)^{-1} = A^{-1} - \frac{A^{-1}uv^TA^{-1}}{1+v^TA^{-1}u} $$ results in small errors in relation to the standard matrix inverse operation after each application, ...
8
votes
1answer
100 views

Choosing how many iterations to use in VEGAS

I'm using VEGAS integration, specifically the GSL implementation, for some QCD calculations, and I've been investigating the behavior of the algorithm for various numbers of iterations in an attempt ...
7
votes
0answers
257 views

Finding points inside cells of power (generalized Voronoi) diagram

Suppose we have a set of points $p_1,\ldots,p_n\in\mathbb R^d$ as well as a set of weights $w_1,\ldots,w_n\in\mathbb R$. Recall that the power cell associated to the pair $(p_k,w_k)$ is given by: $$\...
7
votes
0answers
134 views

Is a complete bacteria simulation with an exascale supercomputer possible?

Will it be possible to simulate a complete (at least simple) bacteria atom by atom on an exascale supercomputer? or is it possible already today with the largest systems? Here, I've read that ...
7
votes
0answers
166 views

fastest way to compute many small dot products

I have two n-by-3 blocks contiguous in memory ("n vectors of length 3") and I'd like to compute the dot product between each of the rows as fast as possible. In numpy, using ...
7
votes
0answers
182 views

How to check if my stiffness matrix is correct

I built the stiffness matrix for the Poisson equation on a 2-dimensional domain with the shape of "almost" an octagon, using pyramid basis functions. I used almost to intend the fact that I have an "...
7
votes
0answers
120 views

“Geometry of ill-conditioning” for least-squares problems

It is an idea that dates back to Demmel, 1987 that the condition number of a problem is often related to the distance to the closest ill-posed problems. In Section 3 of the above paper, the author ...
7
votes
0answers
114 views

Implementation of Lanczos method that returns tridiagonal matrix

The Lanczos method can be used to obtain extremal eigenpairs of sparse symmetric or hermitian matrices. I know there are several implementations of the Lanczos method (as well as Arnoldi, Davidson, ...
7
votes
0answers
72 views

Why not use the preconditioned residual as termination criterion for preconditioned CG?

I have a Poisson equation with wildly varying material parameters (1 .. 1000), wildly varying element sizes (5 nm .. 100 um) and some quite anisotropic (tetrahedral) elements (100 nm x 100 um). I use (...
7
votes
0answers
73 views

Quadrature methods for peaky integrands

Consider $$ I = \int_{-L}^L f(x)dx, $$ where $f(x)$ is real-valued and analytic on $[-L,L]$, but it has a pole in the complex plane whose real part lies in $[-L,L]$. Call it $z_0$, and assume it is a ...
7
votes
0answers
151 views

Solving a coupled eigen value problem

I have the following problem: $$\begin{bmatrix}A &B \\C& D\end{bmatrix}\begin{bmatrix}x\\y\end{bmatrix} = \begin{bmatrix}\lambda I_m & 0 \\ 0& \mu I_n\end{bmatrix}\begin{bmatrix}x \\y\...
7
votes
0answers
550 views

Understanding Boundary Condition in FEM

I am trying to understand Dirichlet and Neumann boundary conditions in FEM and I wanted to know if my inference is correct. To articulate my understanding, lets consider a simple case of TE and TM ...
6
votes
0answers
75 views

Can automatic differentiation be used on the parameters of an optimization problem?

If I wanted to perform an optimization using a Newton-based solver where the Hessian and gradient of a function are known analytically, and then use a package such as Adept to compute a Jacobian ...
6
votes
0answers
97 views

A Question About a Claim from 1991 Computational EM paper about the Cancellation of certain Boundary Terms

Please let me know if this is not the appropriate site for this question. I found questions regarding EFIE/MFIE/CFIE on this site, so I thought my question might fit. I am studying the paper by Putnam ...
6
votes
0answers
262 views

Symmetric sparse direct solvers in scipy

scipy.linalg.solve, in its newer versions, has a parameter assume_a that can be used to specify that the matrix $A$ is symmetric ...

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