Questions on optimizing Mathematica code for higher performance. This may mean faster execution, lower memory usage or both. Not to be confused with mathematical optimization.

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0
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1answer
88 views

Accessing the elements in a table is slower than calculating each time?

This is a follow-up of How to accelerate combinations and sum calculations here? I have tried all tricks but when N reaches 35 the time is still intimidating in a 16-core server, which is far better ...
2
votes
3answers
93 views
1
vote
0answers
78 views

Using Map instead of For?

Since i am new to mathematica i tried to do some code with several for-loops. However i saw that mathematica is not efficient with for loops and discovered some functions like map etc. So my question ...
4
votes
1answer
203 views

Mathematica 10.X benchmark report for high-end surface pro 4/surface book?

Recently, I am seriously considering purchasing the high-end surface device (with intel i7 and maximal RAM). Mathematica will be one of the main applications. Since it is not a full or traditional ...
2
votes
1answer
59 views

How to accelerate combinations and sum calculations here?

I have a 4d matrix H defined as below (embedded with combinations and sums) ...
1
vote
1answer
56 views

Fast Eigensystem calculation

I have a code which finds the eigensystem for a matrix H = H0 + x HInt, where x is a variable which turns on the interaction. H0 is diagonal, and HInt is a sparse matrix (with about 400 states, I hope ...
0
votes
0answers
42 views

Parallelization and efficiency improvement

Hey i am new to mathematica and at the moment i am writing some test code. It works but it is unrefined. I try to make it more efficient by using parallelization or other techniques. I wanted to ask ...
6
votes
2answers
99 views

Speed up AbsoluteTime with string input

I have millions of strings representing dates in the form: "05-Mar-2004 10:15:00". I would like to convert these to absolute times. For example: ...
24
votes
0answers
2k views

Mathematica performance on Mac

I recently got a trial version of both Mathematica 9 and MATLAB 13a for Windows. I was stunned by the performance difference in the Windows and the Mac version. It was a simple test in matrix ...
2
votes
1answer
81 views
1
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0answers
33 views

Fast Creation of Label Matrix for Use With ComponentMeasurements?

I am taking a lot of measurements from regions of interest in microscopy images and am finding that generating binary masks to use with ComponentMeasurements is rather slow (at least it's slow the way ...
15
votes
1answer
135 views

Is it better to completely forget about the existence of PowersRepresentations?

I noticed that in several cases the performance of PowersRepresentations is hugely worse than that of IntegerPartitions. (Mma 10....
5
votes
0answers
51 views

Is there a way to tell how much time FindRoot is spending calculating Jacobians?

I am solving a large number of trascendental equations by scanning FindRoot over a bunch of seeds and a bunch of different parameter values, and I would like to ...
0
votes
1answer
78 views

Problems with NMaximize [duplicate]

The Objective function I would like to Maximize takes less than a second to evaluate. There are several packages needed to evaluate it, so I'm not showing it here. ...
1
vote
1answer
128 views

Speed Up Sampling of Perimeter of Polygon

I have a polygon whose vertices (points) are defined by some image coordinates that I have manually selected. The polygon is used to create a mask for a region of interest in a microscopy image. ...
11
votes
1answer
155 views

Why FoldList 5 times faster than Apply for matrix multiplication? [duplicate]

Consider this list of $2\times 2$ matrices: list=RandomReal[{-2,2},{500,2,2}]; Now compare timings of Apply and ...
4
votes
1answer
287 views

Writing Faster Mathematica Code - Sow and Reap?

I am applying Select function to a large list called xyCoordinateCentreCircle. The dimensions of the list are: ...
3
votes
0answers
116 views

Mathematica Newmark Optimization

Here is my Mathematica code which implements the Newmark method to solve a equation of motion. The variable "ag" contains the accelerations from an earthquake record. Is it possible to optimize this ...
1
vote
0answers
63 views

How to speed up NDSolve?

I have a program where I need to iterate NDSolve thousands of times for different configurations of a diffusion problem. The thing is, I only need about 3 digits of accuracy. I looked thru previous ...
0
votes
1answer
70 views

Faster code for calculat in Integral include derivative

I saw this question How I can get faster I tried help that. But I can not understand. I want to write a faster code for: ...
13
votes
3answers
544 views

Particles bouncing in a 3D box

I made this Manipulate code which shows a pack of particles randomly moving inside a box. It has a huge performance issue. What should be the best way in doing "...
10
votes
1answer
140 views

RandomInteger: speed with long lists

I noticed an interesting effect with RandomInteger when looking at the time to create 10^8 random integers. The following code lines all take about 0.5 seconds on a ...
18
votes
1answer
502 views

Numerical inverse Laplace-Hankel transform

When trying to reproduce the result of this paper about numerical solution of Lamb's problem, I encountered the following double integral (to be more precise, the 0-order inverse Hankel-Laplace ...
8
votes
0answers
132 views

Exporting a high-resolution GraphPlot of a very large graph (65,536 nodes)

Problem I have a very large graph of 65,536 vertices. GraphPlot yields: But the vertices are too dense to see in any detail, and attempting to use any of the on-...
0
votes
1answer
77 views

Why are CoefficientRules and MonomialList so slow?

Why is CoefficientRules so slow in this example (v10.2 on OS X 10.11.4)? ...
6
votes
1answer
137 views

Calculate the ESP Grid based on Density Grid

I want to build a fast way to convert a density grid file into a grid file of the respective electrostatic potential (ESP; also known as MEP, the molecular electrostatic potential). This ...
2
votes
3answers
114 views

Strong glitch with Evaluate in Manipulate

I'm experiencing a strong evaluation problem for a Manipulate box and I can't find the best solution yet. Here's a MWE to show the glitch : ...
8
votes
0answers
89 views

More efficient way to generate lattice graph with edges between visible vertices?

Given a nXn lattice, I need to generate the graph such that there is an edge between two vertices iff they are directly "visible" to each other, i.e., there is no vertex between them. I'm using <...
1
vote
1answer
168 views

Why timing of FindRoot is almost the same even if the function is speedup significantly

This question is almost the same issue as this one. However, it seems that it didn't draw enough attention. Now I encountered the same problem. I previously make this post, I will copy the code here. ...
1
vote
0answers
58 views

How to speedup Plot3D with precompiled argument

I have a huge problem with my code: I estimate it to take hours to run. The scheme of the code is the following (I left the steps the same, but took much simpler functions): ...
5
votes
1answer
155 views

Efficiently importing data into Mathematica

I have a graph data file infile.txt. 3 2 0 1 1 2 3 2 0 1 2 1 3 2 1 0 1 2 3 3 0 1 1 0 1 2 3 3 0 1 1 0 2 1 3 4 0 1 1 0 1 2 2 1 ...
3
votes
0answers
74 views

What is the good source to study advanced custom coding in Mathematica [duplicate]

My question is, probably, too general ... I deal a lot with complicated symbolic evaluations, integrations, plotting. I have troubles with optimizing my codes. They come out way too slow. Google and ...
9
votes
1answer
199 views

Fast implementation of Metropolis-Hastings update with multiple sets

This is an optimisation question rather than something I am unable to do. I have a naive, primitive working version of the code (I submit it below) but I am trying to make it work faster. I am asking ...
2
votes
1answer
68 views

Can this simple loop with several counters be improved or parallelized

I am running the following calculations. The timing for H = 2000 is about 8 days on my machine. Can this be parallelized or improved upon in some other way. Also I am trying to avoid storing the ...
6
votes
2answers
356 views

Performance of calculation of means squared displacement

How can I improve the performance of the following code which calculates the mean squared displacement for coordinates stored in data? Here for each time difference ...
64
votes
2answers
3k views

Profiling from Mathematica

I've always wished I could do some profiling like you get in Wolfram Workbench, but directly from Mathematica, without using or having Workbench. If it is possible, how can I do it?
9
votes
0answers
121 views

Is there a linter to help write good Mathematica code?

I don't do much real programming, but I've recently been turned on to Atom, which has linter plugins for over 50 languages to make coding easier (most drawing on pre-existing lint-like programs). In ...
8
votes
1answer
94 views

DatePlus and DayPlus perform much worse than my user-defined-function

I was debugging a function speed, and discovered that the time bottleneck was in DatePlus. I tried to change to DayPlus and get ...
3
votes
1answer
99 views

Speed up computation of sum from large matrix

I have a 3x3 matrix (252^3) of data (densities) and I want to compute a correlation xi from nearest neighbours as well as a sum involving a check whether the density is in a certain bin. The ...
9
votes
3answers
348 views

Give a element rank list of a list

SeedRandom[417] list1 = RandomChoice[Range[22, 28], 4] {22, 24, 26, 23} We can get the rank list ...
5
votes
0answers
79 views

Is it possible to speedup these simple linear algebra operations

I'm trying to numerically solve some equations using splitting operator method. The solver I construct iteratively constructs a matrix and feeds it to LinearSolve. ...
2
votes
0answers
89 views

Optimization of custom probability distibutions?

Consider the two tests: Timing[Do[RandomVariate[NormalDistribution[0.5, 0.3]], {200}]] {0.001188, Null} ...
2
votes
1answer
65 views

Twin Prime Max Gaps (Performance Tuning)

Ok, let's build a foundation here: A common way of testing primality, is dividing by all primes smaller than the number's square root. For instance, $97$ is prime because dividing by none of the ...
0
votes
0answers
48 views

How to calculate a continuous function once and access values later?

I have a function that involves a numerical calculation: h[v_]:=NIntegrate[f[x]*Log[p[x, v]], {x, -Infinity, Infinity}] I need to visualize how well a bunch of ...
4
votes
0answers
67 views

Sudden changes in performance

Last week Mathematica was working fine. At the beginning of this week I went on a trip and it slowed down. I ran Needs["Benchmarking`"] BenchmarkReport[] The ...
2
votes
0answers
74 views

FourierCoefficient performance

I encountered weird performance issue while using FourierCoefficient[]. I narrowed it down to calculating $n$-th coefficient for $\cos(nx)$. ...
3
votes
2answers
145 views

Fast way to evaluate the PDF of a multivariable distribution

I'm trying to evaluate the PDF of a truncated multi-normal distribution. My distribution has 8 dimensions and each value must be ≥ 0. ...