Questions tagged [software]

Questions about libraries and standalone software designed or well-suited for scientific or numerical calculations.

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4
votes
3answers
356 views

Overlapping communication and computation in PETSc and/or Trilinos?

I am just learning about these packages, so forgive me if this is a trivial/silly question. Our group is working re-developing our code from the ground up using modern software practices. Currently ...
5
votes
5answers
347 views

Will MPI continue to be a popular basis writing scalable massively parallel solvers on future many-core CPUs? [duplicate]

Possible Duplicate: What programming paradigms should I be investing in if I want my code to run on petascale machines in the future? Having entered the multi-core era (som already refers to as ...
11
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4answers
4k views

Algebraic Multigrid Code

I would like to understand more details about the implementation of Algebraic Multigrid Methods (AMG). I have been reading "A Multigrid Tutorial", which is quite good and explain all the details of ...
13
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5answers
572 views

How much should scientific software be optimized?

For applications requiring significant computational resources, high performance can be a critical factor when it comes to delivering scientific results or achieving "break-throughs" in reasonable ...
13
votes
5answers
1k views

On Finding Open Source Projects To Contribute To

This question has been asked a billion times on Stackoverflow however, the focus has always been on Non-Numerical Coding. I am looking for a project to contribute to within the confines of Numerical ...
2
votes
1answer
201 views

Power series approximation for any function such as $-e^{x^{2}}$ in some easily-accessed open-source software?

My comrades repeatedly encourages monotonous problems where the issue is the same: chain-rule and some basic arithmetic. Is there some computational way to derive power series approximations? Suppose ...
5
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6answers
19k views

How can I plot piece-wise defined function in some easily-accessed open-source tool?

I want to plot $$f_{n}(x) = \begin{cases} x-n & \text{for } n \leq x \leq n+1 \\ 2-x+n & \text{for } n+1\leq x \leq n+2 \\ 0 &...
24
votes
12answers
20k views

Is it possible to use Octave to learn MATLAB programming?

I want to learn MATLAB programming so that I can conduct some researh/analysis on my own and also, so that I can study/modify some MATLAB scripts that I have found online etc. However, the problem is ...
2
votes
0answers
169 views

How to print out a network in peersim? [closed]

Peersim is a peer-to-peer network simulator. I'm simply trying to get the program to print out the network (an edge list is fine). Presumably this is possible, since there is an in-built ...
2
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2answers
1k views

Lanczos solver implementations in MATLAB/C++ give different results

I have transferred my MATLAB Lanczos solver for symmetric eigenvalue solvers to C++ with the help of Intel MKL and MTL4 libraries. I have some wrapper templates for MKL routines. However during the ...
19
votes
6answers
1k views

What is the best way to do reproducible research if you need proprietary libraries?

Reproducible research in computation aims to make the code needed to generate the results in a computational paper available to other researchers so that they can run this code to reproduce the ...
39
votes
11answers
2k views

Venues for publishing papers that emphasize software

Software is a fundamental part of computational science, and is increasingly recognized as an essential part of the scientific record. Given the value of using existing and well-tested code, it seems ...
6
votes
3answers
708 views

Surface Mesh Library

I'm thinking a bit about the Front Tracking method used for simulation of Two phase flow with sharp interfaces. The literature tells me that the main issue is the surface mesh representation (...
18
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5answers
6k views

State of the Mac OS in Scientific Computing and HPC

Back towards the dawn of OS X, there seemed to be a great deal of hubbub, at least in the Mac world (I was nowhere near scientific computing at the time) about the Mac OS as a platform for scientific ...
5
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3answers
1k views

Implementing Euler's method for initial value ODEs

In my physics class, I had to calculate the trajectory of a projectile that was fired (very fast) with $v_0$ in an angle off a planet (radius $R$, mass $M$) from the surface. The projectile would ...
25
votes
5answers
712 views

Is there software that can autogenerate numerically-accurate floating point C routines from symbolic formulae?

Given a real function of real variables, is there software available that can automatically generate numerically-accurate code to calculate the function over all inputs on a machine equipped with IEEE ...
8
votes
2answers
370 views

What is a good way to understand the overall structure of a code base?

Sometimes it is useful in my work to modify someone else open-source code or find out how to develop specific things for your own application. However, not all software have good documentation. What ...
8
votes
3answers
2k views

Scientific Programming on Mac using Objective-C/Cocoa for MATLAB Users

I want to get started on scientific programming on the Mac using Objective-C. I am very familiar with MATLAB which makes it easy to store complex-valued waveform data in vectors and generating plots. ...
25
votes
5answers
7k views

What are the main differences between PETSc and Trilinos?

As far as I can tell, the two big generic US Department of Energy computational science software frameworks are PETSc and Trilinos. They seem similar at first glance, beyond differences in language (...
17
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5answers
3k 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 ...
26
votes
8answers
4k views

What software is good to use for parallel debugging?

I'm not running any parallel code right now, but I anticipate running parallel code in the future using a hybrid of OpenMP and MPI. Debuggers have been invaluable tools for me when running serial ...
27
votes
10answers
759 views

Recommendations and experiences on which license to choose for software?

Developers of software have the choice to choose an appropriate license in accordance with the goal(s) of the work. Can anyone give some recommendations/experiences on which license to pick for ...
165
votes
8answers
132k views

Recommendations for a usable, fast C++ matrix library?

Does anyone have recommendations on a usable, fast C++ matrix library? What I mean by usable is the following: Matrix objects have an intuitive interface (ex.: I can use rows and columns while ...
47
votes
8answers
2k views

What are good ways to document scientific software?

Many times, when I've inherited or encountered scientific code written by other people (or occasionally, even my own work), I've noticed that documentation is either sparse or nonexistent. If I'm ...
3
votes
3answers
244 views

Evaluating $\binom{100}{i}a^i(1-a)^{(100-i)}$ in GMP-GNU

I want to calculate $\binom{100}{i}a^i(1-a)^{(100-i)}$ for different $i$ with $a=0.001$ using GMP-GNU. How can this be done?
16
votes
2answers
305 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 ...

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