Questions on parallel computing in Mathematica.

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2
votes
1answer
176 views

Understanding a slowdown associated with wrapping a set of nested Do loops with a ParallelDo expression

I have a set of set of nested Do loops that require data from three different arrays (though the position from each array is fixed per cycle of the outer Do loop). Let's call these arrays: ListA, ...
2
votes
1answer
115 views

Parallel computing NInverseFourierTransForm

I am running the code below, and it works perfectly. I have some function in Fourier space, and I take the numerical InverseFourierTransform. However, I will have ...
6
votes
1answer
97 views

Is it safe to use older version subkernels with a newer version main kernel?

At the moment we only have access to version 8 of the Lightweight Grid (i.e. version 8 of the Mathematica kernel). Is it safe to run version 8 subkernels together with a version 9 main kernel? It ...
3
votes
1answer
74 views

local logfiles for remote kernels

I'd like remote slave kernels to produce log files on my local machine, subject to the following constraints: 1) I don't want to install a distributed filesystem or do other administrative work on ...
2
votes
1answer
97 views

How can I set the kernel for CreatePalette?

I have written some code that requests some calculations from an SQL server every N seconds and uses a palette: CreatePalette[Dynamic[DateListPlot[...]]] I ...
11
votes
3answers
321 views

Suspecting bug in Parallel Framework

I've reduced my actual problem to: ParallelEvaluate[ Module[{slot=1}, Slot[slot] ] ] gives error messages that I think shouldn't be there. It seems I can ...
2
votes
1answer
599 views

3 hour calculation? ParallelMap & ParallelTable

I'm having some problems with slow Mathematica code... I'm basically doing a computation that's is expected to take 3 hours (!) in my Core i7 with 4 processors... I'm basically computing an index (of ...
7
votes
1answer
404 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, ...
7
votes
1answer
243 views

how can I avoid CPU waste (by master kernel) using WaitNext?

I'm using WaitNext in Mathematica for parallel processing on Mac OS X. I have 4 processors on my MacBook and LaunchKernels[] ...
1
vote
1answer
109 views

Draw from HistogramDistribution with ParallelTable

I wanted to check something, but ran into troubles using HistogramDistribution in combination with ParallelTable. The code does the following: Compute a HistogramDistribution of some sample and use ...
7
votes
1answer
231 views

How to make this code threadsafe?

I have the following code, schematically: ...
2
votes
1answer
366 views

Light Weight Grid and core limitation

I am trying to figure out what would be best for running some simulations using multiple computers where each has it's own mma 8 licence. The main part of the computation involves a parallelized table ...
5
votes
1answer
416 views

Progress indicator with shared variables

I'm trying to create a custom progress indicator for a parallelized computation, using Dynamic and SetSharedVariables to display ...
12
votes
2answers
444 views

Tell ParallelMap[] to use just specific kernels

Is there a way to tell ParallelMap to use just some specific kernels (as is possible for ParallelEvaluate)? Background: I have ...
1
vote
0answers
191 views

Parallel linear algebra with arbitrary precision

Is it possible to do parallel linear algebra with arbitrary precision within Mathematica (in a simple manner, as is done for the machine precision)?
3
votes
1answer
316 views

Why can't Mathematica parallelize this?

The following code makes mathematica print "ParallelTable::nopar1: [...] cannot be parallelized; proceeding with sequential evaluation." ...
1
vote
0answers
265 views

Return Functions from parallel execution of module

I wrote a module which numerically solves an ODE using NDSolve. The result from this is e.g. either ...
7
votes
2answers
317 views

Use of Cellular Automaton or Discrete Convolution to calculate Potts Energy of a 2D Matrix

In a project of Monte Carlo Modelling of Grain Growth (Link) one of the most costly subroutines is the calculation of the Potts-Energy of an Monte Carlo Grid cell by comparing the center cell value ...
4
votes
1answer
379 views

using interpolation functions in ParallelMap

Edit I am editing the question to give a simple workable example. It is at the bottom under the heading Example. The original question is now headed withe Background. Background I am trying to ...
4
votes
1answer
292 views

ParallelTable and Precision

I'm using ParallelTable[] to calculate a function over a range of my parameters , ($\omega,\ell$). This seems to be working well (in terms of speed increase) except ...
9
votes
1answer
272 views

Is there a way to convert mathematica code to OpenMP or OpenACC?

I see that Mathematica has limited support for things like OpenCL and CUDA, but what about other standards like OpenMP or OpenACC?
2
votes
1answer
260 views

Clearing distributed definitions from remote kernels

The documentation shows the following example to "Remove a distributed definition..." Oh, course this doesn't work without redefining the function prior to re distributing the definition. The ...
7
votes
1answer
521 views

Communication between parallel kernels

Greetings. This is my first post here, also, I am not a seasoned programmer, so any advice pertaining to coding that is not directly related to the problem (stated below) is welcome. I am having ...
6
votes
1answer
297 views

MapThread and parallel computing

This time I have a very short question. Is there a deeper reason why ParallelMapThread does not exist? Regards, Frink
11
votes
2answers
335 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, ...
17
votes
2answers
2k 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 ...
3
votes
1answer
179 views

How do I fix Needs[“OpenCLLink`”] failure?

In Mathematica 8.0.4 under Mac OS X 10.8.2, when I evaluate Needs["OpenCLLink`"] I get error ...
10
votes
1answer
738 views

Is there a simple example using OpenCLLink that shows performance advantages?

OpenCLLink allows Mathematica to use the OpenCL parallel computing language. I have done some tests on simple examples, but so far, the CPU regularly outperforms ...
3
votes
1answer
624 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 ...
8
votes
0answers
254 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
576 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
269 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
231 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
86 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
185 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
229 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 ...
16
votes
1answer
628 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
205 views

ParallelTable running on outermost index only

I need to run a simple ParallelTable: ...
0
votes
1answer
589 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
242 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
869 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 ...
22
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 ...
14
votes
2answers
851 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
413 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
305 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
304 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 ...
31
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 ...
5
votes
1answer
577 views

Export to file from ParallelDo loop

I currently have a Mathematica code similar to: ...
12
votes
2answers
290 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 ...
35
votes
1answer
1k views

Transferring a large amount of data in parallel calculations

This question is inspired by one of @whuber's answers Consider the following code: ...