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Questions tagged [scientific-computing]

Use this tag for questions about using computers in science. Many of these questions also fit on scicomp.stackexchange.com.

Scientific computing encompasses numerical methods, physical simulations, data processing and visualization, and the many other ways in which computers are used to do scientific research.

There is an entire Stack Exchange site devoted to questions about scientific applications of computers. These sorts of questions may get more specialized attention at that site.

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How to generate a massive amount of high quality Random Numbers?

I'm working on a random walk simulation of particles moving in a lattice. For that reason I must create a massive amount of random numbers, about 10^12 and above. Currently I'm using the possibilities C++11 provides with . When profiling my…
dani
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Java Multi-Threading Beginner Questions

I am working on a scientific application that has readily separable parts that can proceed in parallel. So, I've written those parts to each run as independent threads, though not for what appears to be the standard reason for separating things…
Carl
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HDF5 Storage Overhead

I'm writing a large number of small datasets to an HDF5 file, and the resulting filesize is about 10x what I would expect from a naive tabulation of the data I'm putting in. My data is organized hierarchically as follows: group 0 -> subgroup 0 …
apdnu
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How do I incorporate TDD into my workflow as a scientific programmer / student / researcher?

I'm busy! Most of my time is spent using analytical techniques, or on course work, and when I switch over to programming mode I need to generate code quickly. Since, the Primary Investigator for the lab I'm in doesn't care if I'm using TDD or an…
bias
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Solving floating-point rounding issues C++

I develop a scientific application (simulation of chromosomes moving in a cell nucleus). The chromosomes are divided in small fragments that rotate around a random axis using 4x4 rotation matrices. The problem is that the simulation performs…
user703016
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Discrete Laplacian (del2 equivalent) in Python

I need the Python / Numpy equivalent of Matlab (Octave) discrete Laplacian operator (function) del2(). I tried couple Python solutions, none of which seem to match the output of del2. On Octave I have image = [3 4 6 7; 8 9 10 11; 12 13 14 15;16 17…
BBSysDyn
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What is the performance penalty of using std::vector in C++?

Typically, I'm interested in knowing if the the standard template library incurs performance/speed overheads in codes for numerical/scientific computing. For eg. Is declaring an array as double 2dmatrix [10][10] going to give me more performance…
atmaere
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Plot Mandelbrot with matplotlib / pyplot / numpy / python

I am new to python and learning by following Python "Scientific lecture notes Release 2013.1" tutorial. Please help me solve this Mandelbrot problem in the srcreenshot below (Pg 71). Please provide step-wise commands with explanation if possible…
nilesh
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Data persistency of scientific simulation data, Mongodb + HDF5?

I'm developing a Monte Carlo simulation software package that involves multiple physics and simulators. I need to do online analysis, track of the dependency of derived data on raw data, and perform queries like "give me the waveforms for…
Shen Chen
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Scientific Plotting in Python

I have a large data set of tuples containing (time of event, latitude, longitude) that I need to visualize. I was hoping to generate a 'movie'-like xy-plot, but was wondering if anyone has a better idea or if there is an easy way to do this in…
user100046
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"Logbook" for scientific simulations

I'm using C++ to perform scientific simulation on some things. At this moment, due to the increasing number of parameters, I found necessary to have a "logbook": a file where all the information about a given simulation is stored (not the output;…
Jorge Leitao
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Is there any 3D visualization library or toolkit for C? (No C++ please!)

Basically I'm interested in knowing if there exists any openGL 3D visualization toolkit for C for scientific uses?
chutsu
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A good web resource for learning Direct Compute?

I am interested in getting my hands dirty with numeric computation using Microsoft's Direct Compute framework. The whole concept seems to be a rather poorly documented business. Are there any useful resources, such as web-tutorials or ebooks where…
Martin
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Averaging Data in Bins

I have two lists: 1 is a depth list and the other is a chlorophyll list, which correspond to each other. I want to average chlorophyll data every 0.5 m depth. chl = [0.4,0.1,0.04,0.05,0.4,0.2,0.6,0.09,0.23,0.43,0.65,0.22,0.12,0.2,0.33] depth =…
Adam
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Scientific Programming with Ruby

I was doing the mathematical calculations with python or octave because of availability of really nice functions and libraries at hand. But recently I gained interest in ruby and I wonder if there is an equivalent in Ruby to the numpy, scipy in…
systemsfault
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