The efficiency tag has no wiki summary.
2
votes
1answer
27 views
Trying to implement a simple/efficient combinations function in MATLAB
So, recently, I have found myself in the position of having to implement a combinations function in MATLAB. What I mean by this is the following: I simply need to list all possible combinations for an ...
4
votes
2answers
105 views
Efficiency of Repeated Sparse Matrix-Vector Products
I recently read Wolfgang's answer to the question found here and found myself wondering about a related followup question.
Assume you have two sparse matrices $A$ and $B$. You need to do the ...
5
votes
3answers
206 views
Fast and accurate double precision implementation of incomplete gamma function
What is the state of the art way of implementing double precision special functions? I need the following integral:
$$
F_m(t) = \int_0^1 u^{2m} e^{-tu^2} d u
= {\gamma(m+{1\over 2}, ...
4
votes
3answers
161 views
How to efficiently structure simulation data in memory for cells with varying degrees of freedom?
For a discontinuous Galerkin-based simulation I need to store cell-based simulation data in memory. Since the order of the polynomial approximation $N_p$ may vary between cells, I wonder what the most ...
9
votes
1answer
141 views
Costs of lookups versus calculations
I am interested in setting up calculations to check if a distance criterion is satisfied: that is, the distance between a vector ${\bf x}_i$ and anther vector ${\bf x}_j$ should be less than some ...
6
votes
1answer
1k views
What are the advantages and disadvantages of the particle decomposition and domain decomposition parallelization algorithms?
I am running molecular dynamics (MD) simulations using several software packages, like Gromacs and DL_POLY.
Gromacs now supports both the particle decomposition and domain decomposition algorithms. ...
15
votes
2answers
410 views
What is the computational cost of $\sqrt{x}$ in standard libraries?
One of the major issues that we have to deal with in molecular simulations is the calculation of distance-dependent forces. If we can restrict the force and distance functions to have even powers of ...
12
votes
3answers
692 views
I/O Strategies for computational problems with large data sets?
My research group focuses on molecular dynamics, which obviously can generate gigabytes of data as part of a single trajectory which must then be analyzed.
Several of the problems we're concerned ...
2
votes
3answers
90 views
Inverse compression for space-time trade off
A bit of a strange question - but I am developing an application where speed is critical, not memory - I have the ability to blow up to 3 TB on the data storage that this application will use and I am ...
2
votes
2answers
204 views
Modern Computer Efficiency vs Modern Nervous Systems
I am currently working on an evolutionary system and most of what I have heard is that a computer like mine at the moment would be able to simulate a bee sized brain (not taking into account the time ...
-1
votes
1answer
91 views
Space Time tradeoff [closed]
I am wondering if you can answer a math question that I require answered for an evolutionary program that I am writing.
With regards to the phenomenon known as the "space-time tradeoff" (wiki it) - ...
6
votes
2answers
141 views
When is automatic differentiation cheap?
Automatic differentiation allows us to numerically evaluate the derivative of a program on a particular input. There is a theorem that this computation can done at a cost less than five times the cost ...
