Questions tagged [parallelization]

Questions on parallel computing in Mathematica.

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6
votes
2answers
59 views

Choose the number of kernels used by ParallelTable

By default, on my system, ParallelTable uses 4 kernels. Is it possible to change the number of kernels used, for example using only 3 instead of 4?
4
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0answers
50 views

Is there something wrong with DistributeDefinitions?

I have the following code, which fails to distribute the DownValues for the symbol f. Could anybody please explain what is wrong. ...
4
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0answers
31 views

Difference in computation speed of Eigensystem not to expectation for ParallelTable and Table

I was trying to compute the time it takes for Eigensystem to evaluate while being inside a ParallelTable, as it is well-known LAPACK subroutine has an inbuilt Parallelization to it. And the difference ...
0
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1answer
28 views

Evaluating values from a indexed ParametricNDSolve solution in parallel

I have a ParametricNDsolve solution for a differential equation for a huge system given by s1. I have no problem in evaluating ...
2
votes
1answer
36 views

DecompositionNDSolveValue analogue for NDEigenvalues

In FEMAddOns there is a function DecompositionNDSolveValue to solve stationary PDEs on a cluster. Is there a similar way to solve the eigenvalue problem for a system of ODEs in parallel kernels, ...
1
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0answers
107 views

Simplify Vs FullSimplify

I performed an integral and received an extremely long answer. I tried running FullSimplify on the answer, and after 72 hours gave up. Does ...
1
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2answers
62 views

How to Parallel submit nested do loop

This is the first time I'm trying to parallel compute something on Mathematica. So this question might be silly. I have a nested Do loop of the form: ...
3
votes
1answer
54 views

Tracking progress of ParallelTable Computations

I have a notebook where I work with large datasets, where the data is stored as an A x B array of signals, where each signal is often 1000 samples long. In the past I would track the progress of ...
8
votes
1answer
437 views

Parallel computing: cores vs threads

I'm running Mathematica on a machine wtih 48 cores and 96 threads. I want to limit the number of threads the computation can have access to. If I give LaunchKernels[1] it correctly launches a single ...
2
votes
1answer
34 views

Filtering solutions using the Select function [closed]

I have a certain code that output in the following format: {{a1,b1},{a2,b2},{a3,b3},...,{an,bn}} Where $a_1$ and $b_1$ etc are numbers. Now I want to filter ...
1
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0answers
25 views

Parallelization option gives Import error for Package files

I have an issue when trying to use parallelization when loading a stand-alone Package. To simplify the question I have a few scenarios: The first scenario, with single-kernel evaluation, works fine: ...
3
votes
0answers
50 views

Parallelize import of many files

I'm trying to speed up the import of a large number of files, using ParallelTable to store them in a indexed variable, eqDump. The files are in the folder "Frames" and are named "Conf_Run.1000", "...
2
votes
0answers
66 views

Aborting any computation that takes too long

One of the biggest annoyances in Mathematica is that it will often hang up without any way to abort (i.e. Alt + . or other methods can't stop the computation). Is ...
1
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0answers
27 views

How to close a specific Kernel after completion of evaluation in ParallelDo

I have a particular code that I have to run over several different parameters. I am using ParallelDo to parallelize the process. Due to the nature of the evaluations some Kernels finish the ...
0
votes
1answer
19 views

Defining specific evaluation task to specific parallel kernel

Is it possible to specify particular task to a particular kernel to be evaluated in parallel?
0
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0answers
35 views

Why ParallelTable warns where Table runs quietly?

I have a code involving ParametricNDSolveValue and FindRoot to find a trajectory [actually, trajectory of a line that everywhere ...
1
vote
1answer
28 views

A problem with nested tables and parallelization

My code contains the structure Table[....,Table[....,{m1,1,N}],{m2,1,M}] and I would like to use ParallelTable to improve timing. Empirically, I know that ...
7
votes
2answers
139 views

Parallelize GroupBy

I have a huge list longList that I want to split into two parts depending on whether an element of the list satisfies the condition: ...
1
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0answers
18 views

Command line instances sharing variables [closed]

I have a Mathematica notebook that I have been running on my desktop and am working on moving it over to a high-performance cluster. One part of the code is a random walk algorithm that uses a ...
1
vote
0answers
28 views

ParalleTable can't use 100% CPU

I have two notebook. A.nb and B.nb. When I run the ParalleTable in A.nb, it will use 100% CPU. But I change some items in A.nb to get B.nb. When I run B.nb, it only used 50% CPU. I can't find the ...
2
votes
0answers
43 views

How can I parallelize this calculation?

I need to compute a sum function: $$E=\frac{(2 \gamma )}{\delta ^2} \sum _{m,n,p,q=0}^{\text{mMax}-1} a_m a_n a_p a_q \text{A}(m) \text{A}(n) \text{A}(p) \text{A}(q) \text{D}\left(\frac{1}{2} (m+n+p+q)...
2
votes
1answer
45 views

ParallelTable does not evaluate DLL functions

I have a function programed in C which I load in MMA with ...
0
votes
0answers
47 views

7X7 matrix of distinct cubed integers with identical row and column sums

Problem: find a 7X7 matrix of distinct cubed integers with identical row and column sums. Well, I have the following code (that came from @kglr from my previous question): ...
0
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0answers
25 views

Closing sleeping kernels in parallel computation

I want to close the kernels which have completed their jobs in parallel computation. I have a test code as following: ...
0
votes
2answers
78 views

Solving a system of equations using the data generated by PowersRepresentations and ParallelTable

First of all, it is possible to check the code that I am asking for because I know that $x=3051$ must yield at least a solution to the problem. Well, I have the following system of equations: Now, I ...
0
votes
0answers
39 views

Parallel Computation: Kill kernels which have completed the jobs while others keep running

I launch 20 parallel kernels in the background using nohup math -run "<<file.m" &> file.out The nature of computation is integration over various ...
0
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0answers
40 views

Efficiency of Parallelization

I'm trying to evaluate an expression by a repeated application of a list of rules. Like tmp1=exp//.rules; Here exp is a list. ...
0
votes
1answer
101 views

Update initial conditions recursively/sequentially within ParallelTable using NDSolve

I am modelling 3D motion of particles inside a force-field using second-order coupled PDEs, which I solve from time t=t0 to t=t1 with initial conditions x0,y0,z0. I have a total number of "particles" ...
2
votes
0answers
692 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 it possible to make eigensystem run in ...
3
votes
0answers
105 views

Wolfram math on windows using PBSPro cluster

A user wishes to use math application running on our PBSPpro cluster. Our cluster is accessible to linux users, running qsub to submit their jobs. We have math10.4 for our cluster users, with ...
2
votes
0answers
211 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 ...
5
votes
1answer
572 views

Why is $ProcessorCount different than the selected number of cores in PBS?

By using ParallelTable and submitting my Mathematica code to a cluster, I noticed that it was enhancing the speed even when I selected a single core in a single ...
1
vote
0answers
61 views

Launching specific remote kernels in parallel

For some reason I found that my numerical integration runs much faster on Mathematica 9 than on Mathematica 10. Since I sent my calculation to a cluster with 24 cores with the following command <...
5
votes
1answer
386 views

gridMathematica on cluster with PBS Pro

I'm running my script (say "cluster.m") on the University cluster with PBS Pro installed. The script uses simple Parallelize like this: ...
12
votes
1answer
302 views

Can Predict/Classify be parallelized?

Being able to parallelize Predict /Classify would be useful on multiple fronts: Performance/Scale Streaming Pedagogical ...
5
votes
1answer
826 views

How to change front end setting “Parallel Kernel Configuration” in the code?

I'm trying to run Mathematica parallel on multiple nodes on a HPC, and I use the remote kernel tab in the "Parallel Kernel Configuration" settings to set the communication between different nodes(...
8
votes
1answer
575 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 ...
2
votes
0answers
72 views

How to sync parallel kernels across multiple nodes on an HPC

I'm hoping to parallelise my Mathematica script across multiple nodes on an HPC, but I can't get it to work. My code has the following schematic form: ...
14
votes
1answer
521 views

How to constrain memory usage on HPC?

I found the performance of built-in function MemoryConstrained is very poor. It stops the evaluation after the memory limit has already been exceeded greatly than ...
0
votes
0answers
120 views

Parallel computation on an HPC

This is my first time using an HPC and I am completely lost as to how to successfully launch a master kernel and a set of slave kernels. So far I have a .sh called <...
14
votes
0answers
531 views

Mathematica HPC on AWS vs. Azure

I am looking for advice on deploying Mathematica for HPC in an on-demand cloud environment. I occasionally have Mathematica projects that require parallel computing and large amounts of RAM. These ...
1
vote
0answers
46 views

Trouble parallellising on HPC

I'm trying to carry out a parallel computation using Mathematica's inbuilt parallel functions, ParallelTable, etc. The problem is that the HPC doesn't seem to like ...
5
votes
1answer
180 views

Eigensystem on HPC

I am submitting Mathematica jobs to an HPC. I have a large matrix that is a function of (x,y) and I am diagonalizing it for around 500 points in the plane. My initial idea was to request a node with ...
18
votes
3answers
3k 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 ...
0
votes
0answers
604 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". ...
0
votes
0answers
76 views

Parameter sweeps on a HPC cluster

I have a mathematica *.wl file set up, such that there are a couple of parameters defined in the beginning, and, when run, it produces a few outputs. I can run this script on a Slurm-run HPC cluster ...
5
votes
1answer
159 views

Right syntax to launch multiple kernels on SLURM cluster

I have access to a SLURM based cluster where I allocate 2 nodes, each with 12 processors. I am looking for a way to launch all 24 kernels to utilize the resources to the maximum for parallel ...
1
vote
0answers
181 views

How to use Mathematica with Slurm?

We have a cluster that uses Slurm. On each node we have put a license that allows for 128 computation kernels (we have a Mathematica for Sites License). How can we run Mathematica on more than one ...
0
votes
0answers
34 views

Converting Do expression to ParallelDo

I'm trying to use ParallelDo to speed up my code, but a problem confused me. In the following code I use Do and get the expected ...
2
votes
1answer
56 views

Vectorized RootFind for interpolated function

I've spent the last few days trying to vectorize my code to speed up root-finding on a grid. Apologies in advance if my code is poorly formatted. I have a fair amount of setup for the problem. It ...

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