Questions tagged [high-performance-clusters]

Questions about using Mathematica on high-performance computing clusters.

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How does one monitor a RemoteBatchSubmit[] calculation? How do I get ExternalStorageUpload[] to work remotely?

I am using RemoteBatchSubmit to run a long numerical Mathematica calculation on Amazon Web Services (AWS). By default, ...
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2 votes
0 answers
38 views

HPC doesn't read .mx file

I am trying to work in an HPC cluster. Mathematica works fine and I can export tables that I need. However, I had one interpolated data saved in as a mx file. I ...
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how to generate .m file in mathematica without (**); Run the mathematica script on HPC

For example, I write a simple script in Mathematica like this: x = 4; y = 5; x*y. I want to get the output of x*y. I saved it as ...
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  • 55
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Indexing of NDEigensystem Result on a Cluster

I am trying to run on a cluster (where the version 11 of Mathematica is available) a code involving the following calculation: ...
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  • 71
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1 answer
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Does the Solve function as applied to simultaneous equations benefit from multi-node / GPU parallel computing?

I use the Solve function to find solutions for systems of simultaneous equations with dozens or hundreds of equations and variables. This is successful though very slow (weeks) on a conventional ...
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22 votes
1 answer
414 views

Intuitive explanation of RemoteBatchSubmit[] in AWS for total novices?

When I read Wolfram's post about the new features in MMA 12.2 I was intrigued by RemoteBatchSubmit[]. He wrote: I have only ever used MMA from my laptop, and never used any other cloud computing or ...
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3 votes
2 answers
177 views

What is the cheapest method to get cloud computing, remote kernels, HPC access, connection to clusters or GPUs?

I want to be able to run parallelisable tasks quicker and on better hardware. Are there any services that can easily do this with my personal copy of Mathematica?
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  • 309
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Is it possible to generate and export plots in a high-performance cluster environment?

I have access to a cluster that uses SLURM. I am not very knowledgeable about using clusters, so figuring out how to submit Mathematica jobs was a challenge but eventually something was worked out. ...
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  • 379
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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 ...
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6 votes
1 answer
450 views

Right syntax to launch multiple kernels on SLURM cluster

Important: sometimes you may need to modify the kernel location. In my case I had to find the kernel location explicitly by executing which wolfram command in the ...
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  • 8,528
3 votes
0 answers
457 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 ...
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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 ...
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2 votes
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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: ...
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  • 291
1 vote
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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 ...
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  • 291
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Reading a .m file from the terminal in an HPC

I've written a Mathematica notebook and subsequently saved it as a .m file, so that I can run it on an HPC. When I opened it, the ...
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  • 291
1 vote
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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 <...
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  • 291
5 votes
1 answer
462 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: ...
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3 votes
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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 ...
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16 votes
0 answers
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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 ...
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1 vote
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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 <...
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2 votes
0 answers
245 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 ...
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  • 301
12 votes
1 answer
363 views

Can Predict/Classify be parallelized?

Being able to parallelize Predict /Classify would be useful on multiple fronts: Performance/Scale Streaming Pedagogical ...
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6 votes
1 answer
196 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 ...
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  • 141
1 vote
1 answer
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Mathematica on a cluster

I try to run mathematica on a grid. Since this is my first time working on a cluster, I have no plan what to do. I have to run a job (pbs-file). ...
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  • 11
2 votes
0 answers
823 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 ...
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  • 785
14 votes
1 answer
567 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 ...
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5 votes
1 answer
620 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 ...
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  • 728
6 votes
1 answer
958 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(...
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8 votes
0 answers
588 views

Is it possible to run Mathematica on an HPC cluster with Torque?

I'm installing Wolfram gridMathematica for use in a high-performance computing (HPC) cluster which uses TORQUE Resource Manager for scheduling. Mathematica seems to support PBS pro; has anyone had ...
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  • 313
8 votes
1 answer
645 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 ...
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  • 2,055
19 votes
3 answers
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 ...
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  • 2,055