Questions on parallel computing in Mathematica.

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6
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0answers
90 views

Partial Differential Equation in Parallel

is there any native way to implement multi-core parallel solving of PDE in Wolfram Mathematica? WM 10 now supports Finite Elements Method, but it is actually useless without parallelization. Usually ...
2
votes
0answers
90 views

ParallelSum in Mathematica 9 vs 10

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

strange timing behavior

The following code is from a book about Mathematica. ...
0
votes
0answers
34 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 ...
0
votes
0answers
56 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: ...
15
votes
1answer
423 views

Mma 10: Half the parallel power (Mac Pro)?

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 ... Under v9.01 ...
2
votes
0answers
40 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
77 views

ParallelEvaluate: Evaluation Rules and Increment

I'm trying to understand how ParallelEvaluate works, considering the two following snippets: ...
4
votes
0answers
90 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
15 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
28 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
24 views

$IterationLimit and parallel computing

Short question: How can you set $IterationLimit for parallel computation? I thought just setting $IterationLimit = Infinity ...
0
votes
0answers
43 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
68 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
41 views

A problem with parallelize

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

ParallelTable not firing

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1
vote
1answer
50 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 ...
0
votes
0answers
44 views

Need to parallelize function f in a iteration

I don't have experience using Mathematica for parallel calculation. I need to do something simple to parallelize the calculation of f which is calculate each time n iterates: ...
0
votes
0answers
41 views

How to parallelize a the calculation of a vector function which is inside a recursive formula

I need some help with parallelizing the calculation of a vector function F which is inside a recursive formula. An example of the code is below for few iterations. ...
2
votes
0answers
64 views

ParallelTable and expensive functions

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

ParallelTable and plotting result of own define funtion

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

ParallelTable Works in Regular Notebook but Gives Error When Packaged

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

Parallel computation of NDSolve and a problem

I used this code to solve a system of differential equations: ...
0
votes
1answer
127 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. It's like something ...
6
votes
1answer
94 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 ...
2
votes
1answer
115 views

Copy a variable to a specific kernel in Mathematica [closed]

I would like to copy some parameter from the main Kernel of Mathematica to the parallel kernels available. So I'm running now a command like: ...
0
votes
1answer
79 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? ...
1
vote
0answers
71 views

ParallelTable, ParallelDo and ParallelMap all fail on simple evaluations, a BUG? [closed]

Sorry I am relatively new to the parallel functionality mathematica.. Here is to code: ...
0
votes
0answers
61 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 ...
0
votes
0answers
28 views

KernelObject::rdead on local kernels

I'm trying to parallelize some tasks which involve fetching data from a URL and processing it. This is the code: ...
3
votes
1answer
56 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
116 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
302 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, ...
0
votes
0answers
443 views

Fastest way to create a NxNxNxN dimensional matrix

I have a function that outputs a complex number Func[x_,y_]:= blah blah; I have constructed a table of all possible values of this function. ...
2
votes
0answers
57 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
66 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
1k 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
115 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 ...
0
votes
1answer
56 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
81 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 ...
0
votes
0answers
43 views

Aborting Multiple Trial Divisions if a Factor is found

I am using Mathematica to perform trial divisions on large Mersenne numbers using specific prime numbers (e.g., primes of the form 8n+1 or 8n-1) and would like the program to abort once a factor is ...
0
votes
0answers
63 views

coding simple structures, potential problems (multithreading) and how to solve them

This post contains two parts. In the first part I will explain what I am trying to do. In the second part I will explain what I fear. My questions are about these fears. Are they justified and if yes ...
6
votes
1answer
182 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
115 views

Experimental`NumericalFunction in NMinimize solution

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

save data in parallel table [duplicate]

Suppose we have a table such as: Table[a[i,j]= 3 i^2+5 j,{i,1,100},{j,1,1000}]; after running this command we will have access to a[i,j], for example: ...
1
vote
0answers
80 views

Parallel numerically integrated function can't be plotted

I've been working on a problem where I need to integrate a function numerically. The function is quite complex and it takes almost an hour for Mathematica to make a plot. To speed the process up I ...
0
votes
0answers
30 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. ...
4
votes
1answer
90 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 ...
2
votes
0answers
168 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 ...