Questions on parallel computing in Mathematica.

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40
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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: ...
26
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?
25
votes
4answers
1k 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 ...
11
votes
2answers
2k 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 ...
36
votes
3answers
3k 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 cores)...
50
votes
4answers
3k 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 Math....
10
votes
3answers
442 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 ...
33
votes
3answers
897 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 ...
25
votes
3answers
2k 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
999 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 : ...
4
votes
2answers
229 views

Elegant way to partition list to be faster than `ParallelTable` (using `ParallelSubmit`), or some alternative?

Suppose you have a function fun[x_] := (Pause[.05*x]; x^2); of which you know that its evaluation time increases with its argument - in this case obviously ...
12
votes
1answer
1k 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., ...
7
votes
0answers
2k 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 ...
7
votes
2answers
1k 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 ...
6
votes
1answer
109 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 ...
4
votes
2answers
228 views

Mysterious behaviour of ParallelTable

This question is related to Export bug in combination with ParallelTable?. The following code shows an even stranger bug than in the upper question. The y-axis should always be logarithmic, but in ...
2
votes
1answer
94 views

Changing a Part of a variable within ParallelDo

I want to evaluate nested do as a parallel computations. My formula looks like: ...
16
votes
5answers
1k 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 ...
24
votes
2answers
2k 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 ...
11
votes
1answer
2k 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 ...
8
votes
4answers
596 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}, ...
9
votes
1answer
611 views

Does Mathematica take advantage of hyper-threading (if it is available)?

I do not know much about computer architecture, but some Intel processors have hyper-threading technology, which can apparently improve parallelization for applications that take advantage of it. In ...
9
votes
2answers
1k 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 ...
10
votes
1answer
1k 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 ...
8
votes
1answer
203 views

Export bug in combination with ParallelTable?

I am programming with Mathematica 10.3.1.0 on Windows 10 Professional 64 Bit and have an i7-4940-MX 3,1 GHz processor (4 cores). When I use in the example code below ...
5
votes
2answers
319 views

NDSolve in Mathematica won't use all the cores avaiable

When I solve a system of differential equations in Matlab, the task manager shows that all the CPU cores are in use. This is not true when I solve the same system in Mathematica. I have six cores. ...
6
votes
1answer
360 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...
35
votes
5answers
3k 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 <...
15
votes
3answers
1k 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 ...
30
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 ...
15
votes
4answers
452 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
947 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 ...
10
votes
1answer
319 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 ...
4
votes
1answer
51 views

Cell evaluation and parallel kernels

Is it possible to simply force Mathematica to evaluate one cell with let's say kernel A and another cell with kernel B etc. so that they can be evaluated in parallel? There is a similar answer here ...
13
votes
2answers
335 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 ...
13
votes
3answers
428 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
1answer
747 views

ParallelEvaluate for function minimization

Is there a parallelized version of a minimization routine available in Mathematica? The objective function is non-linear and the gradients have to be numerically computed. Every function evaluation ...
8
votes
1answer
484 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 ...
6
votes
1answer
551 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 ...
5
votes
1answer
496 views

Is there a method to send different Cell evaluation to different core?

I am running Mathematica on a computer with multi CPU and every CPU has multicore. I am wondering if there exist a method to send different cell evaluation to different core? So if I already have a ...
3
votes
2answers
205 views

Definitions inside ParallelTable?

How can I make definitions inside ParallelTable to use them outside? For example, if I execute: ...
2
votes
2answers
257 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 ...
6
votes
2answers
445 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 ...
5
votes
1answer
809 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 <...
1
vote
1answer
893 views

ParallelTable 70 times slower on 16 cores than Table on single core

Consider these code(sorry it's messy), why the ParallelTable version is 70 times slower than the Table version? ...
22
votes
3answers
2k 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 ...
8
votes
2answers
283 views

Distribute and analyze large datasets

I need to analyze very large datasets, and they obviously don't fit in a computer memory. I need to produce some statistics on these datasets, and this brings me here: How can I make some statistical ...
19
votes
1answer
250 views

Two, maybe related, issues with ParallelTable

I will use a very simple example for demonstrating two issues I face with ParallelTable, one with respect to the speed and one with respect to the use of memory. These issues might be related. Let us ...
12
votes
1answer
165 views

DistributeDefinitions and synchronization in Mathematica 10

The command DistributeDefinitions[z] installs all current definitions for z on the local kernels. A simple example: we assign ...
7
votes
1answer
392 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 ...