Questions on parallel computing in Mathematica.

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7
votes
0answers
238 views

Using Compile to speed up Function with PermutationProduct

I have the following fairly simple routine dot involving PermutationProduct that I wish to speed up using ...
2
votes
2answers
430 views

Difference between sub MathKernel and MathKernel

When I try to run Mathematica processes in parallel on a Linux based server, I see that my server allows 7 MathKernels and 28 sub MathKernels. I was wondering what the difference is and how I can take ...
5
votes
1answer
219 views

Build recursion in parallel?

Problem Let's define a simple recursion. f[1] = 1; f[n_] := f[n] = f[n - 1]*n; If I evaluate f in parallel ...
1
vote
1answer
201 views

Version differences in Parallelize

I am having a problem which I guess is due to version difference. I have to generate a list of unitary matrices, which I can do easily. However I came to know about ...
4
votes
0answers
83 views

Mathlink and Parallelization [duplicate]

Possible Duplicate: How to run mathlink external commands in parallel? Abstract I have a binary file compiled to work with MathLink. I can install the file and run the component functions ...
2
votes
1answer
160 views

Server running WolframLightWeightGrid manager loses licensing information

"Once more into the breach..," I have 2 identical Xserves running OS X Server 10.6.8 each with 2 quad core Intel Xenon processors a total of 16 kernels. I have configured both servers identically ...
5
votes
2answers
194 views

Computers running Wolfram lightweight grid manager won't fall asleep

I have a computing environment comprised of: 27" iMac with dual cores running Mac OS X 10.6.8 and 2 XServes each with 2 quad cores running Max OS X Server 10.6.8 All networking by ethernet to a Time ...
13
votes
1answer
481 views

Parallel compiled functions running on parallel sub-kernels

Question Why is it, that compiled, Listable, parallel functions which work perfectly fine on the main kernel, do not run in parallel on sub-kernels? Details ...
6
votes
2answers
170 views

ParallelTable running on outermost index only

I need to run a simple ParallelTable: ...
0
votes
1answer
440 views

On the parallelization of matrix multiplications in Mathematica 8

I have installed Mathematica 8, but I think the commands for parallelizations do not work! Even when I try to test the example in the Help of Mathematica, I face with ParallelDo::nopar: No ...
2
votes
1answer
203 views

how to nest parallelized computations on a cluster?

I am lucky to have access to a computational cluster and I could submit my job to many-many cores. As I need to evaluate a numerical integral within a numerical integral, I would like to know if I can ...
0
votes
2answers
739 views

nested numerical integration: not valid limits?

I encountered an error when I was hoping for some Mathematica (8.0.4) magic sparing me to code up numerical integration, function approximation and root-finding myself. The broader context and the ...
19
votes
3answers
1k views

Does parallel programming use up large quantities of memory in Mathematica?

When I start Mathematica with a fresh kernel and load a program I am developing to analyze biology data, the amount of used system memory is 1.9 GB (free memory is 14.5 GB). These memory values are ...
13
votes
2answers
770 views

Speeding up random walk for many particles

I am trying to speed up this code for many particles to take a random walk. I'm not sure why it is so slow for such a simple task. I got a few hints from colleagues to reduce the precision of the ...
3
votes
3answers
311 views

How can I suppress Print in parallel evaluation?

When using a function that includes Print statements, one can suppress the output by ...
4
votes
1answer
225 views

DistributeDefinitions doesn't work as expected when used for table iterator bounds?

I am new to parallelization in Mathematica, so this question may reflect some elementary confusion. I am attempting to parallelize a rather complicated module which, as part of its internal ...
7
votes
1answer
266 views

Setting $RecursionLimit across all parallel kernels

I'm trying to optimize an elliptic curve factoring method by running it in parallel. There is a recursive step which required me to set the recursion limit higher than 256, however when I try and run ...
29
votes
3answers
1k views

Are built-in Mathematica functions already parallelized?

I've been noticing something strange since updating to Mathematica 8, and that is that occaisionally I'll see that the MathKernel is using up to 800% CPU in my Activity Monitor on OS X (I have 8 ...
5
votes
1answer
430 views

Export to file from ParallelDo loop

I currently have a Mathematica code similar to: ...
12
votes
2answers
274 views

Parallelization of distinct array write access from subkernels

I'm working on an implementation of a multivariate FFT, which is (or at least should be) highly parallelizable due to the row-column-algorithm. However, i can't figure out how to implement that. The ...
30
votes
1answer
836 views

Transferring a large amount of data in parallel calculations

This question is inspired by one of @whuber's answers Consider the following code: ...
6
votes
2answers
520 views

Filling global arrays in parallel calculations

I want to parallelize heavy computations which has to be done many times, the result should be arrays of data. Each calculation does not depend on others (but uses the same variables though). The ...
10
votes
1answer
588 views

Nesting Parallel processes

I just attempted to run code that had nested ParallelMap[] functions. It generates the error message: ParallelMap::subpar: Parallel computations cannot be nested; proceeding with sequential ...
10
votes
2answers
1k views

CUDA and GPU hardware and compatibility questions?

We have iMac desktops and have just begun to parallelize computations across them see: Wolfram Light Weight Grid and parallel computing. This still does not look like it will give us the performance ...
9
votes
1answer
1k views

Wolfram Light Weight Grid and parallel computing

I have attempted to set up and use the Wolfram Lightweight Grid Manager so I can do parallel computing from Mathematica using 2 remote processors on another machine on my local network. My ...
0
votes
1answer
261 views

How to distribute definitions when loading external *.m packages

i'm struggling with the following. I use ParallelTable and it works transparently as it automatically distributes the needed definitions. However, I run into ...
13
votes
2answers
1k views

List of Parallelize[]-able functions

The question is clear and is inspired by this question and the first comment on this question. Although there are many tricks for parallelizing things that are not ...
6
votes
1answer
555 views

Efficiency of ParallelDo when a global variable./matrix is being updated

(Disclaimer: I realize that the addition of matrices a and b below can be done very fast just by typing a+b. The code below is just meant to illustrate behavior similar to what I observe in much more ...
7
votes
2answers
902 views

ParallelTable and Table do not give same result

I have a question regarding the use of Parallelize. In the help one can read that “Parallelize[Table[expr,iter, …]] (which is ...
12
votes
6answers
787 views

Efficient conditional Mean[] on a large data set

Consider a list, AK6, that has 382 sublists of length varying from 2500 to 3000. Each "subsublist" is as such : ...
14
votes
1answer
2k views

Parallelizing Numerical Integration in Mathematica

I have an ugly, six dimensional function that I need to integrate numerically. It works, but it currently take twelve hours to complete the calculation. Is there any good way to parallelize the ...
6
votes
1answer
308 views

PrintTemporary in ParallelTable

I thought of a possible answer to Monitor doesn't work with ParallelTable but it doesn't work as I hoped it would. This accumulates print cells instead of deleting them as intended. Can it be ...
15
votes
3answers
1k views

Monitor doesn't work with ParallelTable

I can't monitor ParallelTable: Monitor[ParallelTable[Pause[3]; i, {i, 1, 10}], i] just displays i until it is finished. Do ...
18
votes
2answers
458 views

Parallelize evaluation of function with memoization

I have a complicated function that I need multiple times, so I want to memoize it and have the first evaluation done in parallel. Unlike in my example below it's not a continuous function, so ...
0
votes
3answers
345 views

Silence debug output from Parallelize?

I have this script, which does a bunch of image aligning in parallel: https://gist.github.com/8848a25a15da013ed1ad However, on EVERY print, Mathematica also prints from what Kernel the message came ...
26
votes
1answer
526 views

Is it safe to launch/close kernels in the middle of a parallel calculation?

It appears that it is possible to launch additional kernels (or close existing ones) during a parallel calculation. The newly launched kernels will be utilized for the rest of the calculation. ...
27
votes
4answers
2k views

Is it possible to speed up ContourPlot on multi-core machines?

It is not very difficult to face a function for which ContourPlot works too slow. And it seems natural that this function can be parallelized well. Anyway, naive ...
10
votes
5answers
767 views

Connecting to and disconnecting from a continuously running kernel, on demand

I realized that there are lots of advantages to driving C/C++/FORTRAN code directly from Mathematica as LibraryLink functions (instead of running them from the command line or a shell script, as I ...
14
votes
4answers
386 views

How can we implement “Sleep Sort”?

Inspired by Implement Sleep Sort: Sleep Sort is an integer sorting algorithm I found on the Internet. It opens an output stream, and for each input numbers in parallel, delay for the number ...
18
votes
4answers
851 views

How to collect result continuously (interruptible calculation) when running parallel calculations?

This is the most common pattern to compute a table of results: Table[function[p], {p, parameters}] (regardless of how it's implemented, it could be a ...
12
votes
2answers
236 views

Tuning ParallelMap when IO and computationally bound

I'm currently doing work on processing a number of images taken frame-by-frame from a video. As a result, I have a directory of around 16K PNG images that at most ~300K. That said, I have a routine, ...
41
votes
4answers
2k views

Speeding up this fractal-generating code

I used the code below (which is a sample from this gist containing more similar code) in my answer to my own question about Mandelbrot-like sets for functions other than the simple quadratic on ...
11
votes
1answer
688 views

How to run mathlink external commands in parallel?

I have an external function called increment (for the sake of illustration) that I call from Mathematica using MathLink. I.e., ...