Questions on parallel computing in Mathematica.

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2
votes
1answer
240 views

How can I prevent these warnings while using ParallelTable

I have this code to find all the permutations of a set of letters that form legal words. ...
7
votes
1answer
285 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
3answers
425 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
1answer
221 views

Parallelization of REvaluate[]?

Is there a way to run several RLink computations via REvaluate[] in parallel, e.g. with ParallelTable[]?
13
votes
3answers
794 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 ...
2
votes
1answer
141 views

Mathematica 9.0 problem: ParallelTable with SQLExecute

I have run into the following problem: when I try to run the following code in Mathematica 9 I get SQL connection error on all kernels. The code is: ...
0
votes
1answer
263 views

Why does my attempt at parallelization not work?

I want to run some function with different parameters, parallel on 4 cores (i5). When I run it without using Parallelize, processor has ~25% utilization. It's a ...
10
votes
1answer
434 views

Parallelization and Hadoop

The short question: Has anyone used Mathematica in conjunction with Hadoop and does Mathematica's built in parallelization play well with Hadoop? The long version: So I have a Mathematica program ...
4
votes
2answers
761 views

why I can't define a commutator operator in this way?

I am trying to define some operators I used frequently.For example, I defined a KroneckerProduct operator as $ \otimes $ as follows: a_$ \otimes $b_:=a.b-b.a and this works fine. Then I want to ...
3
votes
1answer
267 views

Determining the partitioning of Do loop iterations between kernels?

Say I have some Do loop that I'd like to evaluate in parallel: Do[Something, {i, 1, M}]. I'd like to split this list up into ...
1
vote
1answer
150 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
105 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
93 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
70 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
87 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
306 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
556 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 ...
6
votes
1answer
374 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
235 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
107 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
225 views

How to make this code threadsafe?

I have the following code, schematically: ...
2
votes
1answer
329 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
368 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
426 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
183 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
276 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
233 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 ...
6
votes
2answers
304 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 ...
3
votes
1answer
330 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
269 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 ...
7
votes
1answer
237 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
221 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
457 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 ...
5
votes
1answer
247 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
304 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, ...
15
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
168 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
679 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
588 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 ...
7
votes
0answers
245 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
505 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
256 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
218 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
85 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
170 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
212 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 ...
15
votes
1answer
537 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
185 views

ParallelTable running on outermost index only

I need to run a simple ParallelTable: ...
0
votes
1answer
513 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
223 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 ...