Questions on parallel computing in Mathematica.

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2
votes
0answers
316 views

ParallelSum in Mathematica 9 vs 10

Here's part of a package I'm working on: ...
0
votes
0answers
94 views

strange timing behavior

The following code is from a book about Mathematica. ...
0
votes
0answers
61 views

Shared variable impacting speed? [duplicate]

I am using a shared variable as a progress indicator ( via SetSharedVariable[counter] and then Dynamic[counter]), to keep track ...
3
votes
0answers
295 views

Death of parallel sub-kernels

EDIT : Finally, the new Mathematica 10.0 seems to fix it. I have a little parallelization problem. I wrote a code to generate a quasicrystal by dynamical generation. Here the code: ...
28
votes
1answer
1k views

Mma 10: Half the parallel power (Macs)?

Here is a comparison of the parallel kernels launched under Mathematica under v9 and v10, on the same identical current 2014 R2-D2 Mac Pro ... [ Update: Valerio has commented that the same issue ...
3
votes
1answer
283 views

Parallel kernel and front end

I have a piece of code which looks like this: ParallelTable[ Monitor[ Table[ <code here> ,{i,i1,i2]; ,i]; ] so basically a ...
2
votes
0answers
53 views

Timing of ParallelDo versus Do: simple example [duplicate]

I'm trying to understand why a simple do-loop takes substantially longer when done in parallel than sequentially: ...
2
votes
1answer
127 views

ParallelEvaluate: Evaluation Rules and Increment

I'm trying to understand how ParallelEvaluate works, considering the two following snippets: ...
4
votes
0answers
258 views

How to force the compilation language to be C++ (not C) in CreateExecutable or CreateLibrary

I'm trying to speed up a section of a Mathematica 9.0.1 notebook by performing some calculations in C++ with the Cilk Plus and Threading Building Blocks tools available for the Intel C++ 14.0 compiler ...
0
votes
0answers
16 views

How can I set global computation options ($MaxPiecewiseCases) for parallel kernels? [duplicate]

I'm trying to do a calculation in parallel that requires setting $MaxPiecewiseCases. How can I do this? This small test case doesn't work for me: ...
0
votes
0answers
33 views

Notebook stops using extra kernels after some time

Have a mathematica .nb job where I've programmed to run on parallel. Everything goes fine for about an hour but after this most kernels just stop being used by the program. I can see this happing in ...
1
vote
1answer
38 views

$IterationLimit and parallel computing

Short question: How can you set $IterationLimit for parallel computation? I thought just setting $IterationLimit = Infinity ...
0
votes
0answers
347 views

Cluster integration: Problem connecting to Sun Grid Engine

I'm trying to launch some kernels in a cluster engine running Sun Grid Engine using Cluster integration. But I'm getting the error "Cannot find components required for SGE". ...
1
vote
0answers
195 views

Diagonalization in parallel

I would like to diagonalize one unitary non-sparse matrix of size 12870 with complex number entries (not symbols, this is really a numerical problem). Is is possible to make eigensystem run in ...
0
votes
1answer
77 views

A problem with parallelize

I am experimenting with Parallelize and ParallelTable This is the code I am using: ...
25
votes
1answer
2k 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?
0
votes
1answer
112 views

ParallelTable not firing

...
1
vote
1answer
94 views

Using parallel computing to build a matrix recursively

I am trying to compute the product of a sequence of matrices using the command ParallelDo. Of course, if I use the simpler command ...
2
votes
0answers
112 views

ParallelTable and expensive functions

I would like to build up a 2D-Table using ParallelTable as follows ...
0
votes
1answer
73 views

ParallelTable and plotting result of own define funtion

I define function which return a list of numbers ...
3
votes
1answer
91 views

ParallelTable Works in Regular Notebook but Gives Error When Packaged

Consider the following: ...
0
votes
1answer
553 views

Parallel computation of NDSolve and a problem

I used this code to solve a system of differential equations: ...
3
votes
1answer
577 views

Parallel computation of a system of differential equation

I need to solve a system of differential equations which contains, at minimum, ten thousands of differential equations. Actually, I am trying to solve density matrix equation $$\frac{d}{d t}\rho(t) = ...
6
votes
1answer
150 views

Garbage collection for memoized functions on subkernels

I have a top-level function which operates on some data: findBestIntegers[data_]:=ParallelMap[optimize,data] which makes parallelized calls to an optimization ...
0
votes
1answer
109 views

Can ParallelDo speed up a counting problem?

How to make parallelize the following code keeping the same "idea". The example I have in mind is more complicated, but I would like to know if a program of this structure can be parallelized? ...
0
votes
0answers
110 views

How to parallelize this code

Here I obtained one code which should tests some zeros of the poly for various g, but sometimes I have to many cycles because of step and I need to parallelize the running on all cores. Classical ...
3
votes
1answer
99 views

Creating a parallelizable DiscretePlot

To my knowledge, DiscretePlot cannot be parallelized, although one can simulate the default behavior of DiscretePlot and get the ...
1
vote
2answers
245 views

Do multiple instances of Mathematica run completely independently?

Let me simplify the problem I am trying to solve so that the issue I face is highlighted. Say, I want to generate $n$ samples of a Gaussian random variable. I have a script (say ...
14
votes
1answer
388 views

Making Monte Carlo simulation with ParallelTable

I would like to to MonteCarlo simulations of various regressions - basically, doing OLS under various conditions to test approaches. On my macpro 2x 2.8 GHz quad core Xeon, 32 Gb RAM DDR2 @ 667 Mhz, ...
3
votes
0answers
106 views

LibraryLink parallel performance

I'm trying to use a LibraryLink function in parallel. It is an embarrassingly parallel problem, so that no dependency between those parallel tasks. However I can only get the parallel efficiency about ...
0
votes
2answers
142 views

Distributing value of variable to specific kernel

I want to distribute the value of a variable to a specific kernel in a parallel computing setup. Using DistributeDefinitions of course does the job, but it ...
11
votes
5answers
2k views

What is the fastest way to extract a substring from a huge string?

I develop an algorithm to find the most common substrings of a given length n up to a certain distance l in front of a pattern p in a huge sequence S. E.g. I want to find the most common hexamers ...
1
vote
3answers
135 views

Where Statement

Is there a "parallel" way to perform these operations? Indices = {} For[i = 1, i <= Length[w], i++, If[w[[i]] < 0, AppendTo[Indices, i]]] Which gives a ...
2
votes
1answer
151 views

Launching external program in background process with ParallelSubmit

I work on the implementation of an image processing pipeline in Mathematica in which I also would like to use external programs to do certain processing steps. As an example I have macros for the ...
2
votes
1answer
175 views

SSH known hosts in Windows (Error code = 124)

I had to re-install Raspbian OS and now it has new SSH key. SSH clients usually let ignore this fact and save the new key, but not now. Mathematica gives no way to go if the Host Key was changed. I ...
6
votes
1answer
471 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 ...
8
votes
1answer
188 views

Experimental`NumericalFunction in NMinimize solution

I try to make a number of optimizations using this code: ...
0
votes
0answers
44 views

Updating List with Do works but not with ParallelDo [duplicate]

I am trying to find 5 minimas for some function. I can obtain the results if I implement a simple Do function. I tried to speed it up by using ParallelDo and then my code returns spurious results. ...
5
votes
1answer
203 views

Parallel evaluation of Image and Rasterize problem

The following command: ParallelTable[Image[Graphics[{{Red, Disk[{5, 5}, 4]}}]], {i, 10}] shows a very strange behaviour. It starts a new Mathematica process on ...
3
votes
0answers
468 views

Remote kernel shuts down after several seconds

I have Mathematica 9 installed on two Windows Server 2008 R2 machines. Now i want to try using one of them as a frontend with local kernels and the other one for remote kernels. OpenSSH 6.5 for ...
3
votes
0answers
206 views

Launching Remote Kernels takes a lot of time

I recently played around with establishing a remote kernel setup without using mathematica grid. To do this I use the LaunchKernels[] command and ...
4
votes
1answer
135 views

TimeConstrained for parallel computations

The Mathematica manual states TimeConstrained takes account only of CPU time spent inside the main Mathematica kernel process; it does not include additional ...
3
votes
1answer
609 views

Parallel evaluation and memory use

I have never used Mathematica's parallel evaluation before and have some trouble getting it to work properly. For the record, I am running Mathematica 9 on Linux with an Intel Core i7 processor (4 ...
4
votes
1answer
135 views

Parallelize[Mapindexed[]], level={-1}? Sal Mangano's 《Cookbook》

It is easy to Parallelize[] Map[] & MapIndexed[], as having been shown in MMA9 Help for ParallelMap[] and Parallelize[]. For MapIndexed[], the default levelspec is {1}. However there are many ...
4
votes
2answers
232 views

Using Multiple Kernels When Making Plots

I am running a notebook that makes multiple plots. I define a function and then I want to plot that function for different choices of parameters, using RegionPlot. ...
0
votes
0answers
46 views

How to construct a list in a For Loop nested in a Parallel Loop [duplicate]

I've the following problem I cannot solve. I allocate an empty matrix, v, of size n x m. Then I want to do a Parallel loop (ex. ParallelDo), and do some operations (described by a function ...
4
votes
0answers
220 views

Discriminant of Characteristic Polynomial

I'm doing a calculation which finds the characteristic polynomial of a matrix with rather complex entries and then determines the discriminant of that polynomial. For smaller matrices up to around 7x7 ...
6
votes
1answer
124 views

Finer granularity with ParallelDo

ParallelDo only parallelizes by the innermost variable. Is it possible to distribute the calculation over all the points (all the variable) separately? let me ...
3
votes
2answers
192 views

Definitions inside ParallelTable?

How can I make definitions inside ParallelTable to use them outside? For example, if I execute: ...
1
vote
1answer
272 views

ParallelTable and DistributeDefinitions

I have a function in the following form: function[...] := With[ {...}, Table[ anotherfunction[i, j, ...], {i, ...}, {j, ...}, ... ] ] If ...