2
votes
4answers
55 views

Minimisation problem in thousands of dimensions

I need to find the minimum of a function (a log-likelihood from a Potts model) in tens of thousands of dimensions. The function evaluation is quite fast, takes about $10^{-3} s$, and there is a ...
-1
votes
0answers
11 views

Speeding up the evaluation of a symbolic expression while retaining the precision

I have an expression DesignMatrixMult which is 2*2 matrix (in general it will be a n*n matrix). The expression is in terms of four symbolic variables q1/q2/x1/x2. ...
2
votes
5answers
77 views

Recommendations for input file format for science applications

Assuming that a program is written in either C, C++, Fortran or python, what do you think is the best format for the input file given that users could be relatively diverse, i.e. not familiar with the ...
0
votes
2answers
31 views

What is 'SOLVER' in R and Statistics/Analytics ?

**strong text**a) I tried to research on what exactly is a SOLVER only to find a not clear-cut simple answer. My doubts still remain after going through several sites full of discussions about it. I ...
0
votes
0answers
19 views

Matlab: Get the Hessian matrix using Multistart

I am using Multistart in Matlab with the fmincon command to estimate some parameters to my maximum likelihood function. The issue that I have with Multistart is ...
0
votes
1answer
42 views

Translate a 3D point along a heading

I need to translate a point (P1) in 3D a certain amount, call it stepSize, along a vector described by a heading composed of ...
2
votes
2answers
76 views

Solving Lx = b for big sparse Laplacian matrices

What algorithm is more practically suited in terms of performance for solving the $\mathbf{Lx=b}$ equation, where $\mathbf{L}$ is a generic Laplacian matrix (associated to a strongly connected graph, ...
1
vote
0answers
25 views

What is a general method for identifying how connected parts of a binary volume are?

I have a binary volume consisting of a number of disconnected objects. (coming from a noisy, anatomic dataset) However, some of the objects are 'somewhat' connected. Picture a big cylinder and a ...
1
vote
1answer
26 views

CUDA Fortran: Multi GPU Programming and memory allocation

I am writing a program that is supposed to use multiple GPUs on a single node using CUDA Fortran. Although I've looked through the Portland Group CUDA Fortran Reference, I am still unclear about how ...
-1
votes
0answers
21 views

Navier Stokes Equations - Cnoidal Waves and Stokes V Waves

I am working on my undergraduate research and am trying to solve Navier-Stokes Equations for shallow water conditions. However whilst reading different implementation guides I came across the terms ...
0
votes
0answers
16 views

Modelling: How much Cd2+ will a cell be able to chelate with phytochelatins? [on hold]

I am involved in a synthetic biology project where I have to do modelling with ODEs. The biological process I want to model is the chelation of Cd2+ with phytochelatins, to know how much can be ...
0
votes
0answers
42 views

LU Factorization update when adding columns

I am looking for a way to update the LU factorization of a general $m \times n$ matrix after adding a column to the matrix. I have to iterate this procedure so I will begin with a matrix that is $m ...
0
votes
0answers
21 views

Updating the LU Factorization [duplicate]

I am looking for a way to update the LU factorization of a general m×n matrix after adding a column to the matrix. I have to iterate this procedure so I will begin with a matrix that is m×1 and go all ...
3
votes
1answer
45 views

Books and references on implementing finite difference codes for PDEs

Are there any good books or references on implementing finite difference methods for PDEs? Specifically, I'm looking for something comparable to Gockenbach's book Understanding and Implementing the ...
0
votes
0answers
30 views

'Python' and 'R' with Bioinformatics [on hold]

What is the relevance of 'python' and 'R' with bioinformatics/computational biology ? Would it solve most of the problems/tasks associated with statistical analysis, data analytics (are these both ...
0
votes
0answers
11 views

What are the specific generic properties do Ansys consider while running a Non Linear Analysis?

When Working on Ansys Non Linear Static Structural Analysis, I couldn't comprehend while defining and assigning material properties to corresponding bodies. When I give different random values for ...
0
votes
0answers
12 views

NASTRAN RBE3 element specify UM option

In NASTRAN model while creating RBE3 element, how do I specify UM option? I need to constrain certain degrees of freedom in using UM (m-set).
1
vote
2answers
90 views

Exascale computer today

There is a lot of talk about exascale computing these days, and whether we will be able to reach that goal by 2018, 2019 or whatever. I have what is probably a naive question. What are the issues ...
0
votes
1answer
66 views

Future of a degree in computational science and engineering [on hold]

I have done my bachelor in Computer Engineering and I am about to start a MSc in "Computational science and engineering" (Specializations: Computer Science,Bioinformatics,Biomedical Engineering). I ...
1
vote
1answer
20 views

Speedier alternative to “skimage.morphology._pnpoly import points_inside_poly”?

I am using scikit-image's points_inside_poly function, and in my code I am calling it enough times that it takes up about 50% of ...
0
votes
1answer
57 views

Beginning Computer Programming [on hold]

I was 7 years old when I learnt BASIC. Then I learnt C and Visual Basic till the age of 13. I stopped programming for 4 years continuously, and don't remember much about it now. I have lost the skill, ...
2
votes
2answers
64 views

Simulating interaction of Smart Fluids with Solids

Is it possible to simulate interaction of Smart Fluids with Solids? Is there a software capable of doing so? What I Know: The two software that I know of are Autodesk Simulation Mechanical and ...
0
votes
1answer
51 views

Python: Computation time Issue with mpi4py

I am using in Python mpi4py to process in parallel 20 minimization functions. Each of the 20 worker processes the same algorithm but with different random initial ...
0
votes
1answer
26 views

Writing a 3D array from Petsc

I am trying to do something fairly simple somehow I have made it hard. Is there an example of how to send a 3D array to a binary file?
3
votes
0answers
40 views

Dimensionality reduction of the domain of f(x)

I'm wondering if there is something analogous to a PCA for data sets where there is a dependent variable. (Though I am interested in any method of dimensionality reduction, PCA is just an example.) ...
4
votes
3answers
91 views

Machine precision and local error

I'm working with an RKF45 integrator that I have programmed using CUDA C++ on my GPU and am pondering a few questions as I'm trying to track down some issues with my code. I'm using double ...
0
votes
1answer
49 views

a circular plot from a vector which represents the temperature along the radius surface, which is the same for every radius

I have calculated the temperature of the section of a cylinder, which is subjected to a heat flow on its upper surface. Getting the temperature distribution in the 2D section. As shown in the ...
1
vote
0answers
49 views

How to get proper parameters of SPH simulation?

I'm implementing basic fluid flow simulator using SPH method basing on e.g. https://www10.informatik.uni-erlangen.de/Publications/Theses/2010/Staubach_BA10.pdf. So far I've implemented: uniform ...
0
votes
3answers
36 views

Algorithm: Extracting motion frequency from video

I was wondering if anyone knows of any algorithms or projects that can detect the frequency of a motion from a video clip. Like if I had a video of a bouncing ball with constant frequency, could an ...
5
votes
1answer
99 views

Lagrange Multipliers in Multi-body Finite Element Code

I'm working on a Multibody dynamics code using the finite element method to simulate the behaviour of flexible beams (using this paper if anyone is interested/ it is relevant). I'd like to model ...
2
votes
0answers
43 views

Accurate computation of $\frac{\mathrm{B}_{x,y}(\alpha + 1,\beta)}{\mathrm{B}_{x,y}(\alpha,\beta)}$ for large paramers?

I need to calculate these ratios: $$\frac{\mathrm{B}_{x,y}(\alpha + 1,\beta)}{\mathrm{B}_{x,y}(\alpha,\beta)} \tag{1}$$ where $\alpha,\beta > 0$ and $0\le x\le y \le 1$. Here ...
1
vote
1answer
50 views

Integer simplification of irrational inequality

I'm doing work in computational geometry where the robustness of the algorithm is important. On two separate occasions now have I come across a scenario where I compare the numerical size of two ...
2
votes
1answer
60 views

Unwrap cylinder to plane in Paraview

I want to extract the data from the boundary surface of a cylinder (in a .vtu file) and plot it onto a plane, where the coordinates are theta (rotation angle) and ...
0
votes
0answers
30 views

How much time does DSYEV take to diagonalise a $N \times N $

I have been using a DSYEV, for some time. My instructor told me to calculate how much time does DSYEV take to diagonalise a $N \times N $. I know, in our case matrix M is symmetric. Standard ...
3
votes
1answer
57 views

Constructing explicit Runge Kutta methods of order 9 and higher

Some older books I've seen say that the minimum number of stages of an explicit Runge-Kutta method of a specified order is unknown for orders $\geq 9$. Is this still true? What libraries are there ...
1
vote
0answers
30 views

Histogram separation energy equation based on Bhattacharyya

I am working in level set method, specially Lankton method paper. I try to implement Histogram Separation (HS) Energy problem (Part III.C). It based on Bhattacharyya to control the evolution of ...
4
votes
1answer
64 views

Applying Dirichlet b.c. to the Eigenvalue-Problem

If you use a FEM (on the variational formulation), you can discretize some continuous eigenvalue problem, $$L u = \lambda u \ \ \text{on} \ \Omega,$$ into some discrete, generalized eigenvalue ...
0
votes
0answers
16 views

Compute hypergeometric function ratio: $\frac{_{2}F_{1}(a+1,b;c;x)}{_{2}F_{1}(a,b;c;x)}$, for large positive $a,b,c$? [duplicate]

I need a numerically stable way to compute the following ratio: $$\frac{_{2}F_{1}(a+1,b;c;x)}{_{2}F_{1}(a,b;c;x)}$$ All the parameters are real positive numbers, with $0 < a,b,c$ and $0 < x ...
5
votes
6answers
2k views

Computational Science Jokes [closed]

I've noticed some other SE sites have a canonical "what's you're favorite joke" question in them: Math Overflow's "Do good math jokes exist?" Cross Validated's "What is your favorite data analysis ...
1
vote
1answer
26 views

BLAS/LAPACK Non absolute sum

I need to know if there is some function in BLAS/LAPACK or some other Scientific Library that returns a non absolute sum of a vector/matrix. I've found the 'asum', but it returns only the absolute ...
3
votes
2answers
107 views

Looking for Runge-Kutta 8th order in C/C++

I would like to use Runge-Kutta 8th order method (89) in a celestial mechanics / astrodynamics application, written in C++, using a Windows machine. Therefore I wonder if anyone knows a good library / ...
0
votes
2answers
130 views

Most efficient library to diagonalize exactly large hermitian or unitary matrices

I am working on a physics problem which requires obtaining the exact eigenvalues and eigenvectors of Hermitian and Unitary matrices numerically. Naturally I would like to ask the experts what are the ...
1
vote
1answer
41 views

Maximum function evaluation with NLOPT in Python

I am having an issue with the implementation of NLOPT in Python. My objective is to minimize a somewhat complicated Maximum Likelihood function. My function is called mle and there are 6 parameters ...
8
votes
2answers
209 views

How to plan & incorporate project management tools into research code

I'm entering my 3rd year of my PhD program, and up until now my research code (numerical inverse problems/medical imaging/image processing/etc) consists mostly of disorganized MATLAB scripts and ...
0
votes
2answers
68 views

Numerical minimization of scalar-valued function in 3d

I am finding minimum of the potential function $f=f_1+f_2$, where $f_i: \mathbb{R}^3\to\mathbb{R}$. I was about to use Levenberg-Marquardt as the quick starting point, since it is already implemented ...
1
vote
0answers
19 views

Printing a plot in Octave-3.8.1 breaks LaTeX labels [closed]

Since upgrading to Octave 3.8 I have been unable to export plots with LaTeX labels. When the figure is displayed the labels render fine but when I try to export the figure using the ...
0
votes
1answer
96 views

Finding optimal velocity profile using Dynamic Programming

While continuously reading about Dynamic Programming I have a problem, implementing it in a practical application. Let's assume we want to optimize our way to school which we go daily by bicycle. ...
4
votes
4answers
74 views

Measurement error library

Is there a python library that would keep track of uncertainty in measured data? i.e. if I put in a figure of a±b is there an easy way to track the propagation of error through calculations.
3
votes
2answers
105 views

Finding shortest path in a time/distance map

I get a distance map output after using a Fast Marching Method. The PDE involved is the Eikonal equation which take the form : $$\begin{cases} c(x).|\nabla u| =1\\ u(x) =\phi(x) ...
0
votes
1answer
37 views

Gradient descent on the PDF of the multivariate normal distribution

I want to perform gradient descent optimization of the probability of a sample under a multivariate normal probability density function. For your convenience I state the PDF here: ...

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