# All Questions

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### C++ Best practices for dealing with many constants, variables in scientific codes

I am developing a code to simulate fluid flow with biological substances present in the flow. This involves the standard Navier-Stokes equations coupled to some additional biological models. There are ...
678 views

### 20% performance penalty for a nice software design

I'm writing a small library for sparse matrix computations as a way to teach myself to make the best use of object-oriented programming. I've worked really hard on having a nice object model, where ...
2k views

### Parsing protein structure data in C

My background is in genomics, but I have recently been working with problems related to protein structure. I wrote a few relevant programs in C, building my own PDB file parser from scratch in the ...
2k views

### Finding a global minimum of a smooth, bounded, non-convex 2D function that is costly to evaluate

I have a bounded non-convex 2-D function which I'd like to find the minimum of. The function is quite smooth. Evaluating it is costly. An acceptable error is about 3% of the function's domain in each ...
4k views

### The definition of stiff ODE system

Consider an IVP for ODE system $y'=f(x,y)$, $y(x_0)=y_0$. Most commonly this problem is considered stiff when Jacobi matrix $\frac{\partial f}{\partial y}(x_0,y_0)$ has both eigenvalues with very ...
921 views

### Scripted Mesh Generation Software

I'm looking for a mesh generation software that is free and open source, provides a sane scripting interface for domain specification, works for complex geometries, can generate 2D and 3D meshes, ...
3k views

### Disadvantages of common discretization schemes for CFD simulations

The other day, my computational fluid dynamics instructor was absent and he sent in his PhD candidate to substitute for him. In the lecture he gave, he seemed to indicate several disadvantages ...
309 views

### Desktop software with HPC resources for back end number crunching

Our workgroup produces a desktop application that simulates building energy performance. It is a .NET application and when the user is running a lot of simulations, they can be quite time consuming. ...
349 views

### Databases of results for numerical codes

In the numerical methods literature, many research papers consist of a description of a new algorithmic variation, followed by a few test problems comparing the new method with one or two existing ...
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 ...
2k views

### For which statistical methods are GPUs faster than CPUs?

I have just installed a Nvidia GT660 graphic card on my desktop and, after some struggle, I manage to interface it with R. I have been playing with several R packages that use GPUs, especially ...
3k views

### Discontinuous Galerkin: Nodal vs Modal advantages and disadvantages

There are two general approaches to representing solutions in the discontinuous galerkin method: nodal and modal. Modal: Solutions are represented by sums of modal coefficients multiplied by a set of ...
3k views

### Problems where Conjugate gradient works much better than GMRES

I am interested in cases where Conjugate gradient works much better than GMRES method. In general, CG is preferable choice in many cases of SPD (symmetric-positive-definite) because it requires less ...
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 ...
2k views

### Is there a good, easy-to-use, high quality open source CFD solver out there?

My thesis is on developing numerical methods for model reduction in combustion. I run my methods purely on the chemistry part of combustion simulations, and I have plenty of case studies for 0-D ...
3k views

### Drawbacks of Newton-Raphson approximation with approximate numerical derivative

Suppose I have some function $f$ and I want to find $x$ such that $f(x)\approx 0$. I might use the Newton-Raphson method. But this requires that I know the derivative function $f'(x)$. An analytic ...
3k views

### Should I rent computing resources, or buy my own computers

Since this question is related to computation, I decided to post here. Hopefully it will be seen as appropriate. I've just started running atmospheric and oceanic models, and I realize that I need ...
2k views

### Example of a continuous function that is difficult to approximate with polynomials

For teaching purposes I'd need a continuous function of a single variable that is "difficult" to approximate with polynomials, i.e. one would need very high powers in a power series to "fit" this ...
2k views

### BDF vs implicit Runge Kutta time stepping

Are there any reasons for why one should choose high order implicit Runge Kutta (IMRK) over BDF time stepping? BDF seems much easier to me as $q$ stage IMRK needs $q$ linear solves per time step. ...
25k views

### Euclidean distance in Octave

I would like to know if there is a quick way to compute the Euclidean distance of two vectors in Octave. It seems that there is no special function for that, so should I just use the formula with <...
5k views

### uniform vs. non-uniform grid

It is probably a student level question but I can't exactly make it cleat to myself. Why is it more accurate to use non-uniform grids in the numerical methods? I am thinking in the context of some ...
5k views

### Row major versus Column major layout of matrices

In programming dense matrix computations, is there any reason to choose a row-major layout of the over the column-major layout? I know that depending on the layout of the matrix chosen, we need to ...
1k views

### Does Computational Science involve programming?

I read about computational science on Wikipedia, but my understanding is not very clear. Does computational science involve programming? How different is computational science from computational ...
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 ...
4k views

### Finding which triangles points are in

Suppose I have a 2D mesh consisting of nonoverlapping triangles $\{T_k\}_{k=1}^N$, and a set of points $\{p_i\}_{i=1}^M \subset \cup_{k=1}^N T_K$. What is the best way to determine which triangle each ...
872 views

### Practical example of why it is not good to invert a matrix

I am aware about that inverting a matrix to solve a linear system is not a good idea, since it is not as accurate and as efficient as directly solving the system or using LU, Cholesky or QR ...
5k views

### What are differences between 'a priori' and 'posteriori' error estimate in numerical analysis?

I have learnt about Finite Element Method (also a little on other numerical methods) but I don't know what are exactly definition of these two errors and differences between them?
6k views

### What is the general idea of Nitsche's method in numerical analysis?

I know that the Nitsche's method is a very attractive methods since it allows to take into account Dirichlet type boundary conditions or contact with friction boundary conditions in a weak way without ...
7k views

### Profiling CFD code with Callgrind

I'm using Valgrind + Callgrind to profile a solver I have written. As the Valgrind user manual states, I've compiled my code with the debugging options for the compiler: "Without debugging info, ...
483 views

### Are there operator splitting approaches for multiphysics PDEs that achieve high order convergence?

Given an evolution PDE $$u_t = Au + Bu$$ where $A,B$ are (possibly nonlinear) differential operators that don't commute, a common numerical approach is to alternate between solving $$u_t = Au$$ ...
7k views

### Null-space of a rectangular dense matrix

Given a dense matrix $$A \in R^{m \times n}, m >> n; max(m) \approx 100000$$ what is the best way to find its null-space basis within some tolerance $\epsilon$? Based on that basis can I then ...
1k views

### Boost::mpi or C MPI for high performance scientific applications?

The thing I dislike most about MPI is dealing with datatypes (i.e. data maps/masks) because they don't fit that nicely with object oriented C++. boost::mpi only ...
561 views

### How should I study creating and programming HPC systems?

I'm in a field that doesn't necessarily do a great deal of HPC work, and when it does encounter it, it's often the result of researchers from other fields exploring new applications to their methods ...
4k views

### When is Newton-Krylov not an appropriate solver?

Recently I have been comparing different non-linear solvers from scipy and was particularly impressed with the Newton-Krylov example in the Scipy Cookbook in which they solve a second order ...
762 views

### Strategies for unit testing and test-driven development

I'm a huge advocate of test-driven development in scientific computing. It's utility in practice is just staggering, and really alleviates the classic troubles that code developers know. However, ...
1k views

### When should implicit methods be used in the integration of hyperbolic PDEs?

Numerical methods for solving PDEs (or ODEs) fall into two broad categories: explicit and implicit methods. Implicit methods allow larger stable timesteps but require more work per step. For ...
4k views

### Apply PCA on very large sparse matrix

I am doing a text classification task with R, and I obtain a document-term matrix with size 22490 by 120,000 (only 4 million non-zero entries, less than 1% entries). Now I want to reduce the ...
266 views

### What are the best practices for algorithms and implementation of multi-physics simulations?

Multi-physics simulation involves coupling multiple "physics", often with different space and/or time scales. Additionally, the single-physics codes are often written by different teams. The most ...
860 views

### How do you debug numerical code, what could be source of this oscillatory error?

Quiet a lot of insight can be gained form experience, I was just wondering if anybody has seen something similar to this before. The plot shows the initial condition (green) for the advection-...
256 views

### Uses of power series maps

I'm from the field of accelerator physics, specifically related to circular storage rings for synchrotron light sources. High energy electrons circulate around the ring, guided by magnetic fields. ...
775 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 ...
3k views

### Python OSS alternatives for Matlab Neural Network Toolbox. Any intercomparisons?

I'd like to be independent of commercial software for my scientific work. I find a dependence an commercial packages such as Matlab and its toolboxes unsatisfactory, because I do not know if I will ...
1k views

### Can the solution of a linear system of equations be approximated for only the first few variables?

I have a linear system of equations of size mxm, where m is large. However, the variables that I'm interested in are just the first n variables (n is small compared to m). Is there a way I can ...
1k views

### Why does the numerical solution of an ODE move away from an unstable equilibrium?

I wish to simulate the behaviour of a double-pendulum-like system. The system is a 2-degrees-of-freedom robot manipulator that is not actuated and will, therefore, behave mostly like a double-pendulum ...
837 views

### Robust computation of the mean of two numbers in floating-point?

Let x, y be two floating-point numbers. What's the right way to compute their mean? The naive way ...
2k views

### multigrid method to solve PDE

I need simple explanation of the Multigrid Method or some literature about this. I am familiar with iterational methods including BiCGStab,CG,GS,Jacobi and preconditioning, but I am a beginner with ...
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.
6k views

### Implicit finite difference schemes for advection equation

There are numerous FD schemes for the advection equation $\frac{\partial T}{\partial t}+u\frac{\partial T}{\partial x}=0$ discuss in the web. For instance here: http://farside.ph.utexas.edu/teaching/...
1k views

### (how to) write simulations that run faster?

I have started using python as the programming language for doing all my assignments in CFD. I have a very little experience in programming. I am from mechanical engineering background and am pursuing ...
5k views

### Linear programming feasibility problem with strict positivity constraints

There is a system of linear constraints ${\bf Ax} \leq {\bf b}$ . I wish to find a strictly positive vector ${\bf x} > 0$ that satisfies these constraints. That means, $x_i > 0$ is required for ...

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