Skip to main content

performance tuning - Speeding up construction of simple tridiagonal matrix


I have the following code to construct a tridiagonal matrix:


ClearAll[th];
th[nwells_ /; EvenQ@nwells] := Module[
{size = nwells, bdiag},

bdiag = RandomReal[{0, 99}, size - 1];
SparseArray[
{
Band[{1, 1}] -> bdiag,
Band[{1, 2}] -> -0.5,
Band[{2, 1}] -> -0.5},
{size - 1, size - 1}
]
]


This will be executed millions of times (bdiag is actually something that will change each time, so this is unavoidable). I'd like to speed it up as much as possible. Any ideas? I am interested in values of nwells of the order of 100 to 1000.


EDIT: Let us compare the time taken by the Band version, by MrW's version and Rojo's version for varying sizes:


{
Table[{i, Do[th[i], {100}] // AbsoluteTiming // First}, {i, 100,
5000, 200}],
Table[{i, Do[banded[i], {100}] // AbsoluteTiming // First}, {i, 100,
5000, 200}],
Table[{i, Do[banded2[i], {100}] // AbsoluteTiming // First}, {i, 100,
5000, 200}]
} // ListLogPlot[#, AxesLabel -> {"size", "t"}] &


Mathematica graphics


(the slowest one is mine). Note the logarithmic axis. Evidently, the Band method falls behind more and more with larger system sizes.


Also, using Band unpacks:


On["Packing"]
th[3000]; // AbsoluteTiming
banded[3000]; // AbsoluteTiming

Mathematica graphics


This occurs when Band is used to insert the (packed) bdiag list into the diagonal.




Answer



This question came up in Chat the other day. Here is the solution I proposed.


banded[n_Integer?EvenQ] :=
With[
{main = RandomReal[99, n - 1],
side = SparseArray[{}, n - 2, -0.5]},
SparseArray[{i_, i_} :> main[[i]], n - 1] +
Sum[side ~DiagonalMatrix~ i, {i, {-1, 1}}]
]


This uses several tricks and observations. Credit for the first goes to Norbert Pozar, who showed me that this is a very fast way to construct a diagonal SparseArray from a list x:


SparseArray[{i_, i_} :> x[[i]], Length @ x]

The second is my own observation that a DiagonalMatrix made from a SparseArray list is also created quickly. This in enhanced by creating the list with SparseArray[{}, n - 2, -0.5], where the "background" of the array is the element to be repeated, rather than ConstantArray or Table. One can see below that only minimal evaluation takes place:


SparseArray[{}, 10^6, -0.5] // InputForm


SparseArray[Automatic, {1000000}, -0.5, {1, {{0, 0}, {}}, {}}]

DiagonalMatrix is particularly fast with this input form.



These "tricks" are combined with the knowledge that adding sparse SparseArrays is fast, and that Band can be rather slow (again thanks to Norbert Pozar) to create a solution that is about fifty times faster than the original.


Comments

Popular posts from this blog

plotting - How to draw lines between specified dots on ListPlot?

I would like to create a plot where I have unconnected dots and some connected. So far, I have figured out how to draw the dots. My code is the following: ListPlot[{{1, 1}, {2, 2}, {3, 3}, {4, 4}, {1, 4}, {2, 5}, {3, 6}, {4, 7}, {1, 7}, {2, 8}, {3, 9}, {4, 10}, {1, 10}, {2, 11}, {3, 12}, {4,13}, {2.5, 7}}, Ticks -> {{1, 2, 3, 4}, None}, AxesStyle -> Thin, TicksStyle -> Directive[Black, Bold, 12], Mesh -> Full] I have thought using ListLinePlot command, but I don't know how to specify to the command to draw only selected lines between the dots. Do have any suggestions/hints on how to do that? Thank you. Answer One possibility would be to use Epilog with Line : ListPlot[ {{1, 1}, {2, 2}, {3, 3}, {4, 4}, {1, 4}, {2, 5}, {3, 6}, {4, 7}, {1, 7}, {2, 8}, {3, 9}, {4, 10}, {1, 10}, {2, 11}, {3, 12}, {4, 13}, {2.5, 7}}, Ticks -> {{1, 2, 3, 4}, None}, AxesStyle -> Thin, TicksStyle -> Directive[Black, Bold, 12], Mesh -> Full, Epilog -> { Line[ ...

equation solving - Invert and fit implicitly defined curve

I need to fit an implicitly defined curve. I thought I could get some data out of Solve , and then using FindFit . Therefore, I would like to find the relation the parametric curve defined by $F(x,y)=0$: Solve[-(1/2) + 1/2 (0.41202 BesselK[0, 0.1 Sqrt[x^2 + y^2]] + (0.101483 x BesselK[1, 0.1 Sqrt[x^2 + y^2]])/Sqrt[x^2 + y^2]) == 0, y] But I can't get an output: Solve was unable to solve the system with inexact coefficients or the system obtained by direct rationalization of inexact numbers present in the system. Since many of the methods used by Solve require exact input, providing Solve with an exact version of the system may help. >> Edit: In particular, I would like to fit the data coming from the curve with the expression of another curve, and not with a function $f(x)$. In particular, since this clearly looks like a cardioid , I would like it to fit to something like it. What other strategies could I try?

dynamic - How can I make a clickable ArrayPlot that returns input?

I would like to create a dynamic ArrayPlot so that the rectangles, when clicked, provide the input. Can I use ArrayPlot for this? Or is there something else I should have to use? Answer ArrayPlot is much more than just a simple array like Grid : it represents a ranged 2D dataset, and its visualization can be finetuned by options like DataReversed and DataRange . These features make it quite complicated to reproduce the same layout and order with Grid . Here I offer AnnotatedArrayPlot which comes in handy when your dataset is more than just a flat 2D array. The dynamic interface allows highlighting individual cells and possibly interacting with them. AnnotatedArrayPlot works the same way as ArrayPlot and accepts the same options plus Enabled , HighlightCoordinates , HighlightStyle and HighlightElementFunction . data = {{Missing["HasSomeMoreData"], GrayLevel[ 1], {RGBColor[0, 1, 1], RGBColor[0, 0, 1], GrayLevel[1]}, RGBColor[0, 1, 0]}, {GrayLevel[0], GrayLevel...