# All Questions

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### Can MPI messages be prioritized?

As far as I understand, the order in which non-blocking point-to-point MPI messages (Isend and Irecv) are received is consistent with the order in which they are sent. Are there any techniques for ...
212 views

### Exit_status=15 , what does it mean? [closed]

I have a job which stops unexpectedly with Exit_status=15. What is the most probable error ?
782 views

### Solving sparse matrix systems which can be reordered to block diagonal form

I have a class of matrices $A$ which are created by a domain decomposition method. Each matrix represents several subproblems of equal size, and I know that for some permutation matrix $P$, $PAP^T$ ...
3k views

### How to parallelize the computation of eigenvalues of a sparse symmetric matrix in MATLAB?

I have a similarity matrix which is symmetric and sparse. How can I parallelize the computation of the eigenvalues of this matrix in MATLAB?
157 views

### How to detect the multiplicity for the eigenvalues?

Suppose A is a general sparse matrix, and I want to compute the eigenvalues. I do not know how to detect the multiplicity for the eigenvalues. As far as I know, for a special case, finding the ...
564 views

### Recommended Route for Mastering Inverse PDE Problems

I would like to master Inverse PDE Problems particularly with the use of Finite Elements. My problem is I don't know where to start. Should I begin by reading a book on Inverse Problems or on PDE-...
1k views

### Book reference for Numerical Analysis

I've had a glimpse of Numerical Analysis (majorly, Numerical Methods like root finding, quadratic equations and other preliminary stuff) in my Calculus class but now, I find myself wanting more ...
3k views

### How to get all intersections between two simple polygons in O(n+k)

Basically the formulation of the problem I'd like to solve is very simple. Given 2 simple polygons (without self-intersections) report all intersecting edge pairs in O(n+k) time, where n - is a total ...
385 views

### SciComp Modeling Jobs

The meta seemed to suggest that career advice is ok . . . so here goes. I have a couple of close friends in the ML and mathematical modeling fields just finishing PhD's and starting out on the job ...
219 views

### What does MatGetOwnershipRange() do for sequential matrices?

I'm writing a petsc code using a sequential matrix type. Since I want it to be easy to parallelize, I put some stuff in the code that is useless now, but will make it easier to parallelize later. One ...
112 views

### Are there any QM macromolecule simulation methods that can use an electron density map as input?

I am not an xray crystallographer, but from what I've heard there's often a good deal of guess work and intuition involved in the process of fitting a ball-and-stick molecular model to a crystal-...
4k views

### Portable multicore/NUMA memory allocation/initialization best practices

When memory bandwidth limited computations are performed in shared memory environments (e.g. threaded via OpenMP, Pthreads, or TBB), there is a dilemma of how to ensure that the memory is correctly ...
359 views

### Rank structure in the Schur complement

I am doing research on the structure in the Schur complements and find an interesting phenomenon: Suppose that A is from 5--pt laplacian. If I use nested dissection ordering and multifrontal method ...
16k views

### Fastest Delaunay triangulation libraries for sets of 3D points

Which is the fastest library for performing delaunay triangulation of sets with millions if 3D points? Are there also GPU versions available? From the other side, having the voronoi tessellation of ...
102 views

### Efficient principal pivots

It was suggested I should try posting this question here from Mathematics Background I'm working on a numerical linear algebra package in C#. I'm trying to implement a variety of "principal ...
2k views

### Gauss-Seidel iterations node spacing

I am working on an assignment where I am determining the temperature distribution of a chip on a substrate. When I decrease the nodal spacing the results change drastically. The smaller the nodal ...
2k views

### Higher-order numerical integration on a triangle/tetrahedron/simplex

Let $T$ be a triangle and let $f$ be a smooth function on $T$. We can use mid-point quadrature $\int f dx \approx |T|\cdot f(x_M)$, where $x_M$ is the middle-point of $T$. Can you provide me with (a ...
813 views

### Construction of $C^1$/$H^2$-conforming finite element basis for triangular or tetrahedral mesh

In the paper Hierarchical Conforming Finite Element Methods for the Biharmonic Equation, P. Oswald claimed Clough-Tocher type elements has $C^1$-continuity while being a cubic polynomial on each ...
2k views

### Where do the laws of quantum mechanics break down in simulations?

As someone who holds a BA in physics I was somewhat scandalized when I began working with molecular simulations. It was a bit of a shock to discover that even the most detailed and computationally ...
14k views

### scipy.optimize.fmin_bfgs: “Desired error not necessarily achieved due to precision loss”

I am getting the warning in the post subject when attempting to optimize a function in Python with the scipy.optimize.fmin_bfgs function. The complete output: Warning: Desired error not necessarily ...
186 views

### How to establish that an iterative method can be applied to large matrices whose size may reach 10^3?

I have an iterative method for computing the Moore-Penrose generalized inverse of matrices, that is $$X_{k+1} = ((I-\beta X_{k}A)^t) + X_{k}$$ with initial approximation: $$X_{0} = \beta AA^t$$ ...
1k views

### Why would a computational scientist need to implement their own version of std::complex?

Many of the better-known C++ libraries in computational science such as Eigen, Trilinos, and deal.II use the standard C++ template header library object, ...
1k views

### Why does std::complex<> initialize its value to 0 upon default construction?

Doing so strikes me as a waste of time. Consider std::complex<double> *a = new std::complex<double>[1<<28]; This could be near-instantaneous ...
251 views

### Forced viscous damping in elastodynamics

I have an 2D elastodynamics problem, that is a problem which is driven by the Cauchy equation: $$\rho\ddot u-\mathrm{div}\sigma=\rho f$$ where $u$ is the displacement, $\sigma$ the Cauchy stress ...
2k views

### Compute smallest eigenvectors of a matrix

It appears that matlab's eigs is giving me bad approximations of the smallest eigenvectors of a matrix. I assume I can use some slower methods which would also be ...
43 views

### The region of allowed values ​​for solving the equation in Mathematica

In[2]:= Solve[sqrt(2x-9) == sqrt(4x+3), x] Out[2]= {{x -> -6}} But mathematically there is no solution, since sqrt (-21) is not defined. There is a flag that ...
4k views

### Problems that can be reduced to the Traveling Salesman Problem

Which search/optimization problems can be reduced to the famous "Traveling Salesman Problem"? For instance, I have a collection of N particles, in 3D, and there is a function (Van der Waals energy) ...
197 views

### MatMatMult and KSPSolve for MATMPIDENSE matrices

I'm trying to use MATMPIDENSE matrices to solve a system of type Ax=b, but I have some problems. The KSP documentation says that KSPSolve for dense matrices requires to set a 'gmres' solver and a 'lu' ...
69 views

### Are there any open standards for data exchange between components of a spatial model?

I'm just getting into climate research, and am amazed at how much poorly documented legacy code is used. This kind of thing means that models more or less have to be maintained by the people who wrote ...
4k views

### How to find QR decomposition of a rectangular matrix in overdetermined linear system solution?

While trying to find cell-centered gradients in finite volume method computation of incompressible fluid flow I get over-determined linear system. This is a well known "cell based least-square" ...
1k views

### Reporting curve-fit results in a scientific paper

(I hope this question fits this site; if not, accept my apologies). I ran a certain simulation, and got a time series y(t), t = 0, 1, ... 20. After trying some functions, I found that: ...
1k views

### Comparing algorithms for tridiagonal linear systems solution

Below there are two algorithms for solving tridiagonal linear systems of the form  \left[ \begin{array}{ccccc|c} b_1 & c_1 & & & &d_1\\ a_2 & b_2 & c_2 & & &...
322 views

### Generating a tuple in Maple

I am trying to generate a 2 tuple using maple. Can anyone give me the command to generate this? Thank you very much.