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In floating point arithmetic, why does numerical imprecision result from adding a small term to a difference of large terms?

I have been reading the book Computer Simulation of Liquids by Allen and Tildesley. Starting on page 71, the authors discuss the various algorithms that are used to integrate Newton's equations of ...
2k views

Is C slower than Fortran on the spectral norm shootout (using gcc, intel and other compilers)?

The conclusion here: How much better are Fortran compilers really? is that gfortran and gcc are as fast for simple code. So I wanted try something more complicated. I took the spectral norm shootout ...
2k views

Mathematically, why does mass matrix / load vector lumping work?

I know that people often replace consistent mass matrices with lumped diagonal matrices. In the past, I've also implemented a code where the load vector is assembled in a lumped fashion rather than ...
415 views

Testing suites for numerical applications in C++?

Recently, I've been pushing my group to include more testing when writing their code. There were several major bugs that took a lot longer to catch than probably speaking was necessary, because we ...
9k views

Understanding the “rate of convergence” for iterative methods

According to Wikipedia the rate of convergence is expressed as a specific ratio of vector norms. I'm trying to understand the difference between "linear" and "quadratic" rates, at different points of ...
5k views

What is the purpose of the test function in Finite Element Analysis?

In the wave equation: $$c^2 \nabla \cdot \nabla u(x,t) - \frac{\partial^2 u(x,t)}{\partial t^2} = f(x,t)$$ Why do we first multiply by a test function $v(x,t)$ before integrating?
3k views

Is the Thomas algorithm the fastest way to solve a symmetric diagonally dominant sparse tridiagonal linear system

I am wondering if the Thomas algorithm is the fastest way (provably?) to solve a symmetric diagonally dominate sparse tridiagonal system in terms of algorithmic complexity (not looking for ...
2k views

C++ or Python for a development of CFD library

What would you say would be the advantages/disadvantages of two approaches to coding a general (finite volume, fem, dg) library for Computational Continuum Mechanics? This is how I see things right ...
4k views

Strong vs. weak solutions of PDEs

The strong form of a PDE requires that the unknown solution belongs in $H^2$. But the weak form requires only that the unknown solution belongs in $H^1$. How do you reconcile this?
1k views

Is there any benefit to compiling LAPACK from source versus installing the prebuilt package from Ubuntu?

I know that ATLAS is able to optimize itself for the machine it is compiled on and thus maximum benefits are found by compiling from source. Is there any benefit to compiling LAPACK from source? It ...
2k views

Does the “cofactor technique” for inverting a matrix have any practical significance?

The title is the question. This technique involves using the "matrix of cofactors", or "adjugate matrix", and gives explicit formulae for the components of the inverse of a square matrix. It is not ...
1k views

SVD for finding the largest eigenvalue of a 50x50 matrix — am I wasting significant amounts of time?

I've got a program that computes the largest eigenvalue of many real symmetric 50x50 matrices by performing singular-value decompositions on all of them. The SVD is a bottleneck in the program. Are ...
346 views

How to create a random 3D domain representing a plant's root structure?

I would like to model laminar flow of water from roots to the stem of a plant. At the very end of the roots, the tubes vary from millimeter to centimeter scale in diameter and length. As we get closer ...
6k views

FLOP counting for library functions

When evaluating the number of FLOPs in a simple function, one can often just go down the expression tallying basic arithmetic operators. However, in the case of mathematical statements involving even ...
926 views

What are the guidelines for conducting computational experiments?

Physics, biology, chemistry etc. have different sets of rules for making experiments: what events are considered relevant, how to avoid contamination of samples, how to create and fix a reproducing ...
986 views

Estimating hardware error probability

Say I run a supercomputer computation on 100k cores for 4 hours on http://www.nersc.gov/users/computational-systems/edison/configuration, exchanging about 4 PB of data over the network and performing ...
4k views

Pressure as a Lagrange Multiplier

In the incompressible Navier-Stokes equations, \begin{align*} \rho\left(\mathbf{u}_t + (\mathbf{u} \cdot \nabla)\mathbf{u}\right) &= - \nabla p + \mu\Delta\mathbf{u} + \mathbf{f}\\ \nabla\cdot\...
12k views

I have this confusion about Armijo rule used in line search. I was reading back tracking line search but didn't get what this Armijo rule is all about. Can anyone elaborate what Armijo rule is? The ...
5k views

What is a common file/data format for a mesh (for FEM)?

I'm developing an FEM simulation. For early testing, I will use simple self-written mesher and visualisation of the mesh graph. But I want to prepare my program to use data generated by an existing ...
1k views

On Finding Open Source Projects To Contribute To

This question has been asked a billion times on Stackoverflow however, the focus has always been on Non-Numerical Coding. I am looking for a project to contribute to within the confines of Numerical ...
336 views

Rapidly determining whether or not a dense matrix is of low rank

In a software project that I'm working on, certain computations are vastly easier for dense low-rank matrices. Some problem instances involve dense low-rank matrices, but they're given to me in full, ...
5k views

Why does Matlab's integral outperform integrate.quad in Scipy?

I am experiencing some frustration over the way matlab handles numerical integration vs. Scipy. I observe the following differences in my test code below: Matlab's version runs on average 24 times ...
2k views

Are HDF5 files suitable for git revision control?

I am not familiar with the file format used in HDF5, but I am wondering if HDF5 files are suitable for revision control with git (or for example Mercurial or Subversion)? I guess what I mean is: are ...
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What are possible methods to solve compressible Euler equations

I would like to write my own solver for compressible Euler equations, and most importantly I want it to work robustly in all situations. I would like it to be FE based (DG is ok). What are the ...
2k views

Compute all eigenvalues of a very big and very sparse adjacency matrix

I have two graphs with nearly n~100000 nodes each. In both graphs, each node is connected to exactly 3 other nodes so the adjacency matrix is symmetric and very sparse. The hard part is I need all ...
927 views

How is Krylov-accelerated Multigrid (using MG as a preconditioner) motivated?

Multigrid (MG) may be used to solve a linear system $Ax=b$ by constructing an initial guess $x_0$ and repeating the following for $i=0,1..$ until convergence: Compute the residual $r_i = b-Ax_i$ ...
302 views

Computing slightly oscillatory series to high precision?

Suppose I have the following interesting function: $$f(x) = \sum_{k\geq1} \frac{\cos k x}{k^2(2-\cos kx)}.$$ It has some unpleasant properties, like its derivative not being continous at rational ...
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Which time-integration methods should we use for hyperbolic PDEs?

If we employ the Method of Lines for discretization (separate time and space discretization) of hyperbolic PDEs we obtain after spatial discretization by our favorite numerical method (fx. Finite ...
1k views

Best practice for storing hierarchical simulation data

TL,DR What is the accepted best practice in scientific computing circles for storing large quantities of hierarchically structured data? For example, SQL does not play nicely with large sparse ...