Questions on parallel computing in Mathematica.
8
votes
2answers
114 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 ...
8
votes
1answer
172 views
How to run an external program in parallel with a Mathematica package?
Under Mathematica 8 (Linux x84_64) I was able to run an external program in parallel from a Mathematica package. However this procedure breaks down under Mathematica 9.
Within my Mathematica package ...
4
votes
2answers
107 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 ...
1
vote
0answers
86 views
3
votes
0answers
78 views
Mathlink and multithreading
In order to make my computations faster I have developed a C/C++ application calling Mathematica kernel and performing many operations using Mathematica functions for equation solving.
Now I want to ...
5
votes
0answers
107 views
Parallelizing is much slower than single kernel evaluation?
Starting with a vector of matrices, tVec, I would like to parallelize the multiplication of each element with the same matrix ...
2
votes
0answers
69 views
Raster with ColorFunction is blank when Dynamic Updating is disabled
UPDATE
Today I was having these WaveletScalogram problems again. I think this is ultimately some kind of interaction issue with Dynamic. I have narrowed it down to ...
0
votes
0answers
77 views
Parallelization issues
I'm programming an algorithm where I have to evaluate, at each iteration, a characteristic of a subgroup of data. An evaluation of a subgroup takes 2-3 secondes and I have 200 sugroups to test per ...
2
votes
1answer
96 views
Mathematica 7: Problems when evaluating Fourier inside a ParallelTable
after I got such a great response for my first question on this site, I'm very encouraged to asked my second one!
So here it is, very generally: To speed up a "row-wise" (i.e. 1D) operation on a ...
2
votes
1answer
87 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.
...
4
votes
1answer
97 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 ...
3
votes
3answers
114 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
2answers
117 views
Parallelization of REvaluate[]?
Is there a way to run several RLink computations via REvaluate[] in parallel, e.g. with ParallelTable[]?
7
votes
2answers
165 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
72 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
164 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 ...
9
votes
1answer
211 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 ...
3
votes
2answers
182 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
67 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
97 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
70 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
62 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
53 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
66 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
254 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 ...
1
vote
1answer
216 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
222 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
187 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[] ...
0
votes
0answers
139 views
Best Parallel Kernel Configuration
I wrote a code snippet which counts prime numbers in any given interval because the built-in PrimePihas a limited bounds.
...
0
votes
1answer
70 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
190 views
2
votes
1answer
183 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 ...
2
votes
1answer
131 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
285 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
133 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)?
2
votes
1answer
148 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
99 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
209 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 ...
2
votes
1answer
198 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 ...
1
vote
1answer
140 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 ...
6
votes
0answers
101 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
98 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
270 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 ...
4
votes
1answer
105 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
9
votes
2answers
126 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
611 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
125 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
360 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
403 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 ...
8
votes
0answers
178 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 ...
