# All Questions

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### Do I need KSPSetOperators after PCSetOperators?

What I did is Create some PC named pc, and PCSetOperators(pc,A,A,..); Create KSP named ksp; KSPSetPC(ksp,pc); After the above process, am I still obliged to KSPSetOperators(ksp,A,A,..), or I can ...
514 views

### How to estimate the maximum argument of eigenvalues?

How to estimate $$\max_i |\mathrm{Arg}(-\lambda_i)|,$$ where $\{\lambda_i\}$ are eigenvalues of a large sparse matrix $A$ all lying in the left complex half-plane?
217 views

### What is the difference between MATSEQMAIJ and MATSEQAIJ in PETSc?

What is the difference between MATSEQMAIJ and MATSEQAIJ in PETSc? Also, where can I find more information on each of the MatTypes? I went to the MatType documentation, but it didn't have anything but ...
5k views

### When is building a cluster in the cloud cheaper than building one in my lab for MD simulations?

An Amazon EC2 compute cluster costs about \$800-\$1000 (depending on duty cycle) per physical CPU core over the course of 3 years. In our last round of hardware acquisition, my lab picked up 48 cores ...
239 views

### 3D to 2D projections, a generalization

Given some data points in 3D, $X\in\mathbb{R}^{n\times 3}$, could one say that $$Y=XP,$$ for some $P\in\mathbb{R}^{3\times 2}$ actually corresponds to a particular viewpoint on a 3D data? Basically, ...
113 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-...
1k views

### Meaning of search methods and optimization methods

I was wondering what differences and relations are between "search methods" and "optimization methods"? Especially when solving an optimization problem? I emphasize the context of solving ...
208 views

### Solving PSD matrix in Newton's method

I have functions defined as follows: $f1(A) = \sum\|x_i-x_j\|_A = \sum\sqrt{(x_i-x_j)^TA(x_i-x_j)}$ and $f2(A) = \sum\|x_k-x_l\|^2_A$ where A is PSD matrix, x are number vectors. Task is to minimize ...
2k views

### Efficiency of using petsc4py vs. c/c++/fortran

How much slower is petsc4py vs c/c++/fortran? I realize it will depend significantly on the code being executed, but what about something simple like a matrix-vector product?
1k views

### How do I vectorize this 4-D matrix operation in Matlab?

I need to do a large number of matrix operations in Matlab, but one of the matrices is 4-D and my normal instincts for correct vectorization are failing me. Right now I'm using a loop. Maybe somebody ...
3k views

### Hill climbing and coordinate descent/ascent

From Wikipedia: In computer science, hill climbing is a mathematical optimization technique which belongs to the family of local search. It is an iterative algorithm that starts with an ...
4k views

### Meaning of (meta)heuristic methods

For optimization, from Wikipedia: In computer science, metaheuristic designates a computational method that optimizes a problem by iteratively trying to improve a candidate solution with regard ...
167 views

### Permissive Math Library for Parameter Statistics in C++

I am looking for recommendations for a C++ math library, with a permissive licence, well suited to calculating a wide variety of statistics on segmentations of timebased parameter data. I would be ...
163 views

### System Speed - Refactoring [closed]

Could the runtime of methods within a system potentially be reduced via refactoring during development (pre-public release)? i.e. Let's assume that methodX() takes ...
218 views

### Is it possible to run a Solver Foundation solver against a model containing linear and non-linear elements?

This is a follow up question to one I made previously about non-linear equations and ranged real numbers in Solver Foundation. I acknowledge that where possible, rewriting a problem that is non-...
108 views

### How do you change the desired accuracy of a TS object in PETSc?

I'm currently getting very long propagation times when attempting to use the Time Stepping propagators in Petsc 3.2, and in the interest of speeding things up, I'm curious how I can reduce the ...
905 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

### Calculating Lagrange coefficients for SVM in Python

I'm trying to write a full SVM implementation in Python and I have a few issues computing the Lagrange coefficients. First let me rephrase what I understand from the algorithm to make sure I'm on the ...
928 views

### Practical efficacy of parallel back substitution

The fact that the back substitution is not done in parallel is not important, because it uses a negligible amount of computer time when N is large, compared to the forward elimination. This is a ...
413 views

### Generalized least squares gradient of a vector field

For computing the gradient of a scalar field, one can use the weighted least squares method as described in the paper Revisiting the Least-squares Procedure for Gradient Reconstruction on Unstructured ...
134 views

### Matching Similar Items from a Set

I'm trying to match items. Given a set of $n$ items I can rank on a scale from 0 to 100 of how similar they are to one another. For instance, if item $n_1$ is milk and item $n_2$ is also milk, then ...
487 views

### How to do FEM in sector elements?

Suppose we have an element in the polar coordinate as $0\leq r\leq 1$, $0\leq\theta\leq \alpha$. What are the correct basis functions in this element? For this kind of mesh, there are a lot of ...
842 views

### Projecting out the null-space of $A$ from $b$ in $Ax=b$

Given the system $$Ax=b,$$ where $A\in\mathbb{R}^{n\times n}$, I read that, in case Jacobi iteration is used as a solver, the method will not converge if $b$ has a non-zero component in the null-space ...
168 views

71 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 ...