Questions on parallel computing in Mathematica.

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31
votes
1answer
865 views

Transferring a large amount of data in parallel calculations

This question is inspired by one of @whuber's answers Consider the following code: ...
8
votes
2answers
933 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 ...
19
votes
1answer
1k views

Why won't Parallelize speed up my code?

What reasons are there that can cause parallelized Mathematica code not to run with full performance?
18
votes
4answers
863 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 ...
6
votes
2answers
540 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 ...
29
votes
3answers
2k 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 ...
16
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 ...
13
votes
6answers
801 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 : ...
9
votes
3answers
317 views

Why is this parallel evaluation with Dispatch[] so slow?

Can you efficiently parallelize this? The parallel versions are much slower than the sequential version, and I'm not sure why. Does SetSharedVariable allow ...
5
votes
1answer
225 views

How to avoid unpacking from Language`ExtendedFullDefinition

Consider this code: LaunchKernels[]; On["Packing"] a = RandomReal[{0., 1.}, {64, 30000}]; ParallelMap[Fourier, a]; // AbsoluteTiming Developer...
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
705 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., ...
10
votes
5answers
778 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 ...
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 ...
10
votes
1answer
607 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 ...
7
votes
3answers
352 views

Efficient way to utilise Parallel features to make use of many cores

Let's say I have 100 cores/kernels as my disposal and want to compute a function of two variables f[x,y] over {x,1,10}, ...
2
votes
2answers
134 views

Definitions inside ParallelTable?

How can I make definitions inside ParallelTable to use them outside? For example, if I execute: ...
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 ...
12
votes
3answers
624 views

Mathematica Parellelization on HPC

I'm currently using Mathematica on a High Performance Cluster (HPC) which consists of many compute nodes each with around 16 cores. I currently run my Mathematica script on 20 of the nodes that ...
13
votes
2answers
777 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 ...
6
votes
1answer
197 views

Parallel optimization of Markov Chain Monte Carlo

I'm trying to reduce the computation time of a MCMC simulation. Essentially I have a set of particles performing a random walk in a periodic random potential. The particles are independent and every ...
9
votes
2answers
270 views

Why is ParallelMap way slower than Map

I recently tried to use ParallelMap instead of Map and to my surprise encountered that ...
2
votes
2answers
108 views

Executing several input cell simultaneously with parallelization

How can I execute more than one input cell simultaneously using different processor. For example consider this two cells ...
1
vote
0answers
512 views

Threads vs Cores: How many kernels need to launch in parallel Mathematica?

I have a dual-core intel machine. I would like to test how many parallel local kernels should be launch to get the optimized performance. Knowing that the HyperThreading technology of Intel could run ...
18
votes
2answers
464 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 ...
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 ...
15
votes
2answers
1k views

Parallelization problem in LinearSolve and Minimize

My CPU has got 8 cores (it is Intel Core i7-2600 3.40 GHz). When I try to solve a linear matrix equation using LinearSolve for large matrices, Mathematica just uses 4 cores to solve the problem (CPU ...
14
votes
4answers
388 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 ...
14
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
245 views

Launching remote slave kernels on HPC causes slow down

I had a post earlier regarding how I can run Mathematica at a HPC cluster (running PBSpro) by having a single MathKernel launch ...
7
votes
2answers
496 views

Writing data to a common file during parallel processing

I am executing a loop, and in each loop I have to store a parameter in a file. It is like ...
5
votes
2answers
194 views

Parallelizing or optimizing a script for calculating the size of all pairwise intersections between collections of sets

I need to speed up or parallelize an operation that looks essentially like this: ...
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 ...
12
votes
2answers
279 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 ...
11
votes
2answers
276 views

Package found with `Needs`, but not with `ParallelNeeds`

I want to use a self-written package in a parallel computation. However while Needs["mypackage`"] works without problems, ...
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 ...
5
votes
2answers
197 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 ...
3
votes
1answer
553 views

Are there any openCL test suites?

I have a new ATI gpu that I have been trying on 3 different distributed computing projects. I get errors on each work unit. The errors indicate No Protocol which could be caused by a bad environment ...
3
votes
3answers
319 views

How can I suppress Print in parallel evaluation?

When using a function that includes Print statements, one can suppress the output by ...
2
votes
1answer
165 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 ...
8
votes
1answer
119 views

Experimental`NumericalFunction in NMinimize solution

I try to make a number of optimizations using this code: ...
6
votes
2answers
224 views

Does Eigenvalues evaluate in a parallelized way?

I use mathematica on a computer with linux operating system. The computer has 2 cpus and each cpu has 4 cores, so there are totally 8 cores available. Now I got confused with whether the evaluation ...
6
votes
1answer
338 views

Export graphics in parallel

I run a heavy simulation, using NDSolve and the method of lines. This means that the result of NDSolve is a list of, say, ...
6
votes
1answer
571 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 ...
6
votes
1answer
313 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 ...
5
votes
1answer
222 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 ...
4
votes
1answer
255 views

Why is parallel slower?

I always assumed that distributing a computation is faster, but it isn't necessarily true. When I do Sum[i,{i,10^4}] I retrieve an answer much faster then if I do ...
4
votes
0answers
140 views

Raster with ColorFunction is blank when Dynamic Updating is disabled

UPDATE Today I was having these WaveletScalogram problems again. I think this is ultimately some kind of interaction issue with Dynamic. I have narrowed it down to ...
3
votes
1answer
133 views

Issue in ParallelTable after evaluating another function using NDSolve and FindRoot. What is wrong with this inverse?

I am trying to find the inverse of a function which is defined through NDSolve and NIntegrate. The question is pretty similar ...
3
votes
2answers
430 views