# All Questions

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### I/O Strategies for computational problems with large data sets?

My research group focuses on molecular dynamics, which obviously can generate gigabytes of data as part of a single trajectory which must then be analyzed. Several of the problems we're concerned ...
604 views

### Perron-Frobenius theorem on general real symmetric matrices

From the Perron-Frobenius theorem, it might be concluded that the spectral radius is the largest eigenvalue for positive matrices, ie, matrices with strictly positive entries. In other words, the ...
2k views

### Why can't Householder reflections diagonalize a matrix?

When computing the QR factorization in practice, one uses Householder reflections to zero out the lower portion of a matrix. I know that for computing eigenvalues of symmetric matrices, the best you ...
69 views

### Understanding how Numpy does SVD [duplicate]

Possible Duplicate: Understanding how Numpy does SVD I have been using different methods to calculate both the rank of a matrix and the solution of a matrix system of equations. I came across the ...
7k views

### Understanding how Numpy does SVD

I have been using different methods to calculate both the rank of a matrix and the solution of a matrix system of equations. I came across the function linalg.svd. Comparing this to my own effort of ...
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### Gradient descent to stationary, or accumulation point

I recently came across the notion of an accumulation point as a result of a certain gradient descent variation. The following definition was found: An accumulation point $P$ is such that there are an ...
321 views

### Convert ODE into discrete probabilistic model

how can I turn an ODE equation into a discrete probabilistic model? I take for example the Verhulst equation for the growth of a population. $$\frac{dP}{dt} = rP(1-P/K)$$ I was thinking to simulate ...
952 views

### Mesh domain decompositions / mesh partitioning

I have some experience with mpmetis from METIS. It is pretty good software which offers unstructured mesh grid partitioning. But obtained results always minimize edgecuts or total communication volume....
6k views

### solving coupled ODEs with initial-value and final-value constraints

The essence of my question is the following: I have a system of two ODEs. One has an initial-value constraint and the other has a final-value constraint. This can be thought of as a single system with ...
5k views

### How does the computational cost of an mpi_allgather operation compare with a gather/scatter operation?

I'm working on a problem that can be parallelized by using a single mpi_allgather operation or one mpi_scatter and one mpi_gather operation. These operations are called within a while loop, so they ...
3k views

### What is the corresponding LAPACK function behind Matlab [Q,R,E]=qr(A)?

I currently trying to cheaply compute a good rank estimate for a matrix $A$. Therefore I compute a columnt pivoting QR decompostion using [Q,R,E]=qr(A) in ...
159 views

### reverse-lookup Digital Object Identifier given table of citations? [closed]

I asked this question on stackoverflow a few weeks ago, but have not gotten a useable answer, even after a colleague added a 150pt bounty. Is it possible to query the doi for each record in a table ...
945 views

### How do I write dimensionally agnostic code?

I often find myself writing very similar code for one, two, and three dimensional versions of a given operation/algorithm. Maintaining all of these versions can become tedious. Simple code ...
327 views

### Linear regression with quadratic constraints

What methods are suggested to solve problems of the form $\min || {A} x - y ||_k$, subject to $x^T P x \leq c$, and/or $x^T Q x = d$?
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### Nonlinear least squares with box constraints

What are recommended ways of doing nonlinear least squares, min $\sum err_i(p)^2$, with box constraints $lo_j <= p_j <= hi_j$ ? It seems to me (fools rush in) that one could make the box ...
3k views

### To what extent is generic and meta-programming using C++ templates useful in computational science?

The C++ language provides generic programming and metaprogramming through templates. These techniques have found their way into many large-scale scientific computing packages (e.g., MPQC, LAMMPS, CGAL,...
901 views

### Multidimensional Minimization: GNU GSL C++ error code 27 for - iteration is not making progress towards solution

I am trying to find the minimum of the function using GNU scientific library, package Multidimensional Minimization. The method I am using is Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm which is ...
915 views

### A Comparison between GMRES, QMR and LU for Dense Matrices

As I see it, there are 3 ways to solve unstructured dense system of equations: GMRES, QMR and LU. Has anyone done a comparison for these three? As far as I know, LU is the preferred choice and it is ...