# All Questions

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### How can I reduce the communication bottleneck of a parallel explicit finite difference scheme?

Suppose i was trying to solve a parabolic PDE (heat equation) on a rectangular domain using an explicit finite difference scheme. I am storing my solution vector in a matrix form (because it closely ...
2k views

### How can one parallelize a multigrid method for solving a linear system of equations?

As I understand it, the multigrid method solves a linear system by solving a coarser version of the same problem (there by eliminating low frequency error) then projecting back to the fine grid to ...
1k views

### Is there a standard rating system for scientific journal publications?

I have heard that some journals are rated more highly than others. Is this true? And if so, what are the criteria for judging the value of one peer reviewed journal over another? How do I find out ...
704 views

### Surface Mesh Library

I'm thinking a bit about the Front Tracking method used for simulation of Two phase flow with sharp interfaces. The literature tells me that the main issue is the surface mesh representation (...
1k views

### Computational Complexity of Image Segmentation algorithms

I have a question. I need to calculate the computational complexity of image segmentation algorithms. Can anyone please help me? For example, I have a screen-size picture with white background ...
2k views

### How do I compile a program that contains both MPI and OPENMP

I have a fortran 90 code that distributes blocks of computations (from a matrix) to multiple nodes in a cluster using MPI, but in each node, the for loops are executed in parallel using openmp. I ...
2k views

### finite volume method: unstructured mesh vs octree adaptation + cell cutting

I'm working with the OpenFOAM C++ Computational Continuum Mechanics library (it can deal with fluid-solid interaction, MHD flows...) which uses arbitrary unstructured meshes. This was driven by the ...
1k views

### Looking for a library or algorithms to perfom clipping 3D unstructured meshes by a set of surfaces

We have a 3D (volume) unstructured, possibly hybrid, degenerative irregular mesh data structure that we are capable of generating (mostly composed of hexahedra and general polyhedra, using a mix of ...
832 views

### Complex numerical analysis

What numerical analysis situations become more/less stable, have faster/slower convergence, or are otherwise quite different when dealing with functions of complex variable instead of functions of a ...
2k views

### Reference implementation of Nédélec-Elements

Does anybody know of an implementation of Nédélec elements that does not come along with a huge bulk of additional software? Is there a small library written in a language like Python, Matlab, or ...
1k views

### Scalability of Fast Fourier Transform (FFT)

To use the Fast Fourier Transform (FFT) on uniformly sampled data, e.g. in connection with PDE solvers, it is well known that the FFT is an $\mathcal{O}(n\log(n)$) algorithm. How well do the FFT scale ...
533 views

### Which is computed faster, $a^b$, $\log_a c$ or $\sqrt[b]{c}$?

Which is computed faster, $a^b$ or $\log_a c$ or $\sqrt[b]{c}$? $a$, $b$ and $c$ are positive reals with $b>1$. What kinds of algorithms will you use in the comparison? What are their complexities?...
116 views

### Up-/downdating methods for a series of normal equations

In an application I have to solve a series of positive definite linear systems of the form $A^TA x = A^Tb$ (i.e. normal equations). The next system is obtained from the previous one by adding and/or ...
6k views

### How to derive the Weak Formulation of a Partial Differential Equation for Finite Element Method?

I have taken a basic introduction to Finite Element Method, which did not emphasize a sophisticated understanding of a 'weak formulation'. I understand that with the galerkin method, we multiply both ...
747 views

### Is it preferable to concentrate on studying math or computation?

Concurrent to my research on Krylov Subspace Methods, I have the option of exploring mathematics behind HPC a step ahead or the theory of computation (hardware, OS, compilers etc.). Currently, I know ...
547 views

### Fitting a grid to an STM image

Suppose I have a scan from an STM image (very much like the things you see here). Suppose I have a simple square lattice with lattice parameter a. What I'd like to do is to numerically find the ...
4k views

### Efficient solution of mixed integer linear programs

Many important problems can be expressed as a mixed integer linear program. Unfortunately computing the optimal solution to this class of problems is NP-Complete. Luckily there are approximation ...
861 views

### When is automatic differentiation cheap?

Automatic differentiation allows us to numerically evaluate the derivative of a program on a particular input. There is a theorem that this computation can done at a cost less than five times the cost ...
2k views

### Scientific Programming on Mac using Objective-C/Cocoa for MATLAB Users

I want to get started on scientific programming on the Mac using Objective-C. I am very familiar with MATLAB which makes it easy to store complex-valued waveform data in vectors and generating plots. ...
6k views

### State of the Mac OS in Scientific Computing and HPC

Back towards the dawn of OS X, there seemed to be a great deal of hubbub, at least in the Mac world (I was nowhere near scientific computing at the time) about the Mac OS as a platform for scientific ...
3k views

### What is the advantage of multigrid over domain decomposition preconditioners, and vice versa?

This is mostly aimed for elliptic PDEs over convex domains, so that I can get a good overview of the two methods.
135 views

### Probabilistic algorithms for matrix approximation

Considering regular matrix approximation inequality || $A - QQ^TA$|| < e where we try to approximate matrix $A$ by a lower rank orthonormal matrix $Q$. I've read an article on probabilistic ...
3k views

### What is a good stop criterion when using an iterative method to find eigenvalues?

I read this answer, and realized I have been using the difference between sucessive iterates to define a stop criterion for an iterative method of finding eigenvalues/vectors. What are good stop ...
2k views

### Solution oscillations with a small timestep in backward Euler

I am using backward Euler in a FEM scheme for a convection-diffusion problem. On a given mesh, I can take arbitrarily large time steps, as expected. But if I decrease time step, at some point it will ...
316 views

### What are the possible numerical schemes for a diffusion equation with a nonlinear reaction term?

For some simple convex domain $\Omega$ in 2D, we have some $u(x)$ satisfying the following equation: $$-\mathrm{div}(A\nabla u)+cu^n = f$$ with certain Dirichlet and/or Neumann boundary conditions....
147 views

### Looking for an understandable discussion of creating Maximum Entropy classifiers

Texts, articles, and papers on Maximum Entropy Classifiers tend to come in two varieties: the more popular "upper level", and the more technical. The popular variety are good at explaining the ...
13k views

### 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 ...
239 views

### Quadrature rules, methodologies, and references

There is at least one quite comprehensive encyclopaedia of quadrature rules that doesn't seem to have been updated in quite a while and has restricted access. This source refers to several classical ...
857 views

### How can I choose a good Riemann solver when numerically solving a system of hyperbolic PDEs?

Many numerical methods for hyperbolic PDEs are based on the use of Riemann solvers. Such solvers are essential for accurately capturing shock waves. There are a range of such solvers available for ...
1k views

### Are 8 Gauss points required for second order hexahedral finite elements?

Is it possible to get second order accuracy for hexahedral finite elements with fewer than 8 Gauss points without introducing unphysical modes? A single central Gauss point introduces an unphysical ...
477 views

### Is there a Moore's law for floating-point precision, and what would it imply?

Moore's law states that the number of transistors on an integrated circuit grow exponentially, roughly doubling at a period of 20 months. This affects the amount of memory available and the speed of ...
430 views

### Testing a simple polygon for monotonicity in linear time question

I'm looking for the algorithm of Preparata and Supowit for testing a simple polygon for monotonicity in linear time. I've found it referenced in many textbooks but I can't find the algorithm itself. ...
1k views

### Implementing Euler's method for initial value ODEs

In my physics class, I had to calculate the trajectory of a projectile that was fired (very fast) with $v_0$ in an angle off a planet (radius $R$, mass $M$) from the surface. The projectile would ...
2k views

### numerical integration with possible division by 'zero'

I am trying to integrate $$\int^1_0 t^{2n+2}\exp\left({\frac{\alpha r_0}{t}}\right)dt$$ which is a simple transformation of $$\int^{\infty}_1 x^{2n}\exp(-\alpha r_0 x)dx$$ using $t = \frac1{x}$ ...
752 views

### 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 ...
358 views

### Approximate a distribution function from a finite sample

Say I have a simulation that produces a single floating point number as a result, and a different number is produced each time the simulation runs. These numbers are randomly distributed according to ...
215 views

### Discretization of Classical Density Functional Theory (CDFT) problems

I formulate questions about ion densities in biological and materials problems using Classical Density Functional Theory, as in this paper which is also on the arXiv. The discretization in that paper ...
58 views

### Assembled human ESTs for annotation

I am annotating protein-coding genes in a region of the human genome and am looking for a set of assembled ESTs I can use as evidence for constructing gene models. A quick search of NCBI's SRA shows 4,...
1k views

### 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 ...
367 views

### best way to optimize a function with linear/non-linear parameters

I am trying to fit some raw data using a function of the form $f(r) = \sum_{i=1}^{K} d_kS_k(n_k,\alpha_k,r)$ where $S_k(n_k,\alpha_k,r) = \frac{\alpha_k ^{n_k+3}}{(n_k+2)!}r^{n_k}\exp(-\alpha_kr)$ ...
244 views

### Evaluating $\binom{100}{i}a^i(1-a)^{(100-i)}$ in GMP-GNU

I want to calculate $\binom{100}{i}a^i(1-a)^{(100-i)}$ for different $i$ with $a=0.001$ using GMP-GNU. How can this be done?
368 views

### What is a good way to understand the overall structure of a code base?

Sometimes it is useful in my work to modify someone else open-source code or find out how to develop specific things for your own application. However, not all software have good documentation. What ...
96 views

### Applicability of combinatorial and support preconditioner

There are several correspondences between matrices and graphs, e.g., each matrix is the adjacancy matrix of a weighted graph. The terms support preconditioner or combinatorial preconditioner refer to ...
2k views

### Is there an open source set of ODE solvers for C that use the native C99 complex type?

I've been using GSL as the foundation of many of my simulations, but it's a little bit overkill for my purposes and it defines its own complex type for legacy reasons. Rather than code my own Runge-...
2k views

### Parallel I/O options, in particular parallel HDF5

I have an application that can be trivially parallelized but its performance is to a large extent I/O bound. The application reads a single input array stored in a file that is typically 2-5 GB in ...
7k views

### What does the priority of a PBS job really mean?

The qsub command which submits PBS jobs has a -p option that allows you to set the priority. From the man page: Defines the ...
669 views

### What numerical quadrature to choose to integrate a function with singularities?

For example, I would like to numerically compute the $L^2$-norm of $\displaystyle u = \frac{1}{(x^2+y^2+z^2)^{1/3}}$ in some domain that includes zero, I tried Gauss quadrature and it fails, it is ...
233 views

### Enumerating hexahedral cell vertices and faces in arbitrary dimension

I have a Cartesian mesh in $d$ dimensions, and I would like to enumerate all the subcells of a given hexahedral cell. If I am just enumerating the vertices of a cell (or cells that contain a vertex) I ...