Questions on parallel computing in Mathematica.

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3
votes
0answers
48 views

Problem with Parallelization when using Packages

I tried to find a solution to my problem in several answers posted in MSE but due to lack of my knowledge on parallelization territory, I couldn't figure out solution to my problem. I have a big code ...
11
votes
1answer
138 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 ...
0
votes
0answers
44 views

Can parallelization speed up FindClusters?

I have a clustering task that would take FindClusters 2-3 months1 to complete. Can this calculation be sped up with parallelization? (FWIW, the data to be ...
9
votes
3answers
1k views

Parallelization works, but does not use all CPU power

I've written code which involves Parallelize@Cases. When I evaluate, I find that all 16 cores are being used, but not fully; in other words all cores are active, but the total CPU usage is only 50%. ...
2
votes
0answers
22 views

ParallelDo issue with SQLExecute (SQLite) [on hold]

This code run as expected if I use Do[...], but if I use instead ParallelDo[...], as in the code bellow, the SQL INSERT statements seems to be completely ignored. In both cases, the filename is ...
12
votes
3answers
420 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, ...
6
votes
1answer
37 views

How to ensure that a package is always loaded on startup, even in parallel kernels?

Is there a robust way to ensure that a package is always loaded on startup, even in parallel kernels? Parallel kernels do not read Kernel/init.m.
3
votes
1answer
40 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 ...
4
votes
1answer
476 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 ...
2
votes
0answers
26 views

Where do DistributeDefinitions and ParallelNeeds put their definitions for newly-launched kernels to find

I'm sorry to keep banging on the definition distribution bell, but here is another (hopefully well-focused enough) question on that vein. If one is trying to distribute the definitions in a package ...
0
votes
0answers
16 views

ParallelDo does not work, when using variables from other parts of the script

I have a script doing a large amount of calculations with very big matrices that takes so long; so, I want to parallelize pieces of the script to be executed on multiple kernels. For instance, the ...
6
votes
1answer
52 views

Run several input cells in parallel

I have a notebook with several input cells that produce data which is then plotted into separate graphs. Since I do not want to save the results, because it makes the file huge, I keep the ...
0
votes
0answers
21 views

Make an existing solution for monitoring parallel jobs robust against dying kernels

Is there any chance to make the solution by @David here http://mathematica.stackexchange.com/a/1562/21606 more robust in the following sense: In my case, some parallel kernels die regularly during ...
5
votes
1answer
46 views

How to understand the different output of two UnsetShared?

Update From technical support, Thank you for contacting Wolfram Technical Support. I understand that you are reporting an issue with UnsetShared deleting the shared variable after a second ...
6
votes
1answer
131 views

Calculate the ESP Grid based on Density Grid

I want to build a fast way to convert a density grid file into a grid file of the respective electrostatic potential (ESP; also known as MEP, the molecular electrostatic potential). This ...
2
votes
0answers
50 views

KernelObject appears dead problem [closed]

my cluster got 24 cores And I use this setting to do parallel computing ...
4
votes
1answer
101 views

Can a package append its context to $DistributedContexts?

I am writing a package (for reference, this one) which I use extensively in parallel computations, and to lighten the coding load on the 'run-time' notebook, I want my package to sit on the ...
3
votes
0answers
35 views

How to make use of multithread feature of Eigenvalues in ParallelDo or ParallelTable [duplicate]

In mathematica, Eigenvalues is implemented internally using intel MKL. When running Eigenvalues[RandomReal[1.,{2000,2000}] ...
2
votes
1answer
66 views

Can this simple loop with several counters be improved or parallelized

I am running the following calculations. The timing for H = 2000 is about 8 days on my machine. Can this be parallelized or improved upon in some other way. Also I am trying to avoid storing the ...
4
votes
1answer
49 views

How to Export from ParallelDo? [duplicate]

I'm running a simulation with parallel, and I want the results from each parameter set exported to a file whenever it's done (because the parameter space is huge and my computer doesn't have enough ...
6
votes
1answer
103 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 ...
3
votes
1answer
45 views

Execute a function in parallel on different cores?

Suppose I have a function f which takes a list and does something with it: ...
10
votes
2answers
198 views

ParallelTable behaves differently when it is run inside a package

I've been butting my head against some very weird behaviour by ParallelTable, and its interaction with packages, over the past few weeks, and making relatively ...
1
vote
0answers
37 views

mathematica example for parallel run

I want to run a parallel mathematica example via a PBS script. I am not expert in this application, instead as a system administrator, I have to be sure that users are able to submit parallel jobs to ...
4
votes
1answer
44 views

$DistributedContexts and ParallelEvaluate

This is a small question regarding the relationship between the $DistributedContexts variable and the ParallelEvaluate command. ...
34
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 ...
4
votes
0answers
39 views

Is there a clean way to parallelize multi-index tables?

The documentation of ParallelTable indicates that if you want to parallelize the evaluation of a table of more than one dimension, such as ...
4
votes
2answers
218 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 ...
3
votes
1answer
30 views

Skipping commented in a stream from OpenRead

Is there a solution to skip comments in text files that are imported with OpenRead? I know there are solutions for Importand ...
4
votes
1answer
47 views

How can I access memoized values from parallel evaluation? [duplicate]

I want to evaluate a table of functions with ParallelTable. Here is the serial code: ...
3
votes
1answer
71 views

How to simultaneously monitoring parallel computations in different Kernels?

I have a question about monitoring parallel processes. Let's suppose that I am running the following code with 5 active Kernels. ...
8
votes
1answer
192 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 ...
4
votes
2answers
224 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 ...
1
vote
1answer
38 views

Customized `ParallelTable` - Automate `ParallelSubmit` - Possibly an issue with `HoldAllComplete` attribute

Related to this question and in particular its answer I am trying to wrap everything into a new parallelTab function that takes into account some cost per job, ...
0
votes
1answer
48 views

Improving performance Importing Table

I am currently working on mathematica script on a Raspberry Pi, which will periodically (10 secs) be launched by a bash script. However the runtime of my script really isn't the best. It's actually ...
2
votes
1answer
90 views

How to create parallel loops

My knowledge in parallel computing is very limited. I tried to figure out how to proceed using the mathematica help but did not really find what I needed. The programme looks as shown below. There are ...
1
vote
1answer
65 views

First come, first save in ParallelTable parallelization

Short version of the question: In C++'s OpenMP, I know how to get what I want, but I'm wondering whether Mathematica has the same option. It's called "dynamic scheduling" when parallelizing. Long ...
0
votes
0answers
62 views

How to determine side-effects in parallel computation? Possibly associated to Kernel not closing reliably

I have written a bunch of code to simulate some measurements. To speed things up, I intended to obtain the measurement values via a ParallelTable. However, it turns ...
3
votes
1answer
57 views

Side effects with ParallelDo

Hi guys I've the following problem with ParallelDo: if I run the code: ...
1
vote
0answers
48 views

ParallelTable gets slower when rerun in a module

Question: Why does the performance of ParallelTable within a Module drop so horribly when the module is RERUN several times? ...
6
votes
2answers
427 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 ...
7
votes
1answer
411 views

Causes “libGL error: failed to load driver: swrast” an Huge Overhead in Parallel under Version 10.3?

Under Linux (SUSE Linux Enterprise 11) for Mathematica Version 10.2/10.3 I observe the following error in parallel ...
1
vote
1answer
84 views
5
votes
2answers
52 views

Why ParallelEvaluate[x = 0; {$KernelID, Dynamic[x]}] returns {{1,x},{2,x}}?

I'd expect that ParallelEvaluate[x = 0; {$KernelID, Dynamic[x]}] returns {{1, 0}, {2, 0}}, and that if in a parallel ...
2
votes
2answers
256 views

Follow each pixel brightness in set of images (Memory constrained)

I have a set of 2700 consecutive png images (8bit, 2048*2048 pixels). I would like to visualize the intensity variation of each pixel vs. image number. Here is an example of 10 images: ...
5
votes
1answer
179 views

How does Mathematica detect the number of cores in a system?

I'm running Mathematica 10.3.1.0 on a machine with 16 cores, but Mathematica (in the Parallel settings) says "Number of processor cores is 8." It's a 16-core Opteron 6300 chip on an Ubuntu system. All ...
39
votes
9answers
2k views

What would you ask Mathematica to do on a big system?

Our hardware supplier has given us the opportunity to test Mathematica on a big Windows system. The specs will be 1 to 4 TB of working memory and 12 sockets with 18 cores each. I got 1 full week of ...
3
votes
1answer
54 views

Shared variable can not be distributed again after UnsetShared

I see a weired behavior in my MM 10.3 version. Can someone reproduce it or explain what is going on? The code is easy: ...
10
votes
1answer
316 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 ...
0
votes
1answer
55 views

Strange behavior of ParallelTable

I was trying to carry out the following calculations: ...