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software:matlab:farber [2019-08-29 14:33] – [Desktop] anita | software:matlab:farber [2020-10-29 11:16] – [Interactive parallel toolbox example] anita | ||
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For use on Farber, MATLAB projects should be developed using a Desktop installation of MATLAB and then copied to Farber | For use on Farber, MATLAB projects should be developed using a Desktop installation of MATLAB and then copied to Farber | ||
- | to be run in batch. | + | to be run in batch. |
Details on how to run these two scripts in batch are given with the resulting output files. | Details on how to run these two scripts in batch are given with the resulting output files. | ||
- | section with UNIX commands you can use to watch your jobs and gather [[#timing and core count]] numbers. | + | section with UNIX commands you can use to watch your jobs and gather [[#timings-and-core-count | timing and core count]] numbers. |
It is important to know how much memory with be needed and how many cores will be used to set your resource requirements. If you do not ask for enough memory your job will fail. If you do not ask for enough cores, the job will take longer. | It is important to know how much memory with be needed and how many cores will be used to set your resource requirements. If you do not ask for enough memory your job will fail. If you do not ask for enough cores, the job will take longer. | ||
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second example shows an interactive session, which starts multiple MATLAB pool of workers to execute the function as a parallel toolbox loop, **'' | second example shows an interactive session, which starts multiple MATLAB pool of workers to execute the function as a parallel toolbox loop, **'' | ||
- | You can run [[: | + | You can run [[#desktop |MATLAB as a desktop (GUI)]] application on Farber, but is not recommended as the graphics is slow to display especially with a slower network connection. |
Many MATLAB research projects fall in the the "high throughput computing" | Many MATLAB research projects fall in the the "high throughput computing" | ||
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end | end | ||
</ | </ | ||
- | See [[maxNumCompThreads|Setting maximum number of computational threads]]</ | + | See [[maxNumCompThreadsGridEngine|Setting maximum number of computational threads]]</ |
<note tip> | <note tip> | ||
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====== Interactive job ====== | ====== Interactive job ====== | ||
- | Here are specific details for running MATLAB as an interactive job on a compute node. You should have a copy of your [[#MATLAB project directory]] on the cluster. | + | Here are specific details for running MATLAB as an interactive job on a compute node. You should have a copy of your [[#MATLAB project directory]] on the cluster |
===== Command-line ===== | ===== Command-line ===== | ||
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</ | </ | ||
- | ==== Grid Engine script | + | ====== Batch job serial example ====== |
Second, write a shell script file to set the Matlab environment and start Matlab running your script file. The following script file will set the Matlab environment and run the command in the [[# | Second, write a shell script file to set the Matlab environment and start Matlab running your script file. The following script file will set the Matlab environment and run the command in the [[# | ||
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If everyone in your group carefully set these values, multiply jobs can run concurrently on the node. | If everyone in your group carefully set these values, multiply jobs can run concurrently on the node. | ||
- | See [[maxNumCompThreads|Setting maximum number of computational threads]] | + | See [[maxNumCompThreadsGridEngine|Setting maximum number of computational threads]] |
</ | </ | ||
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</ | </ | ||
- | <note warning> | + | <note warning> |
In this example you will only need a license for the base Matlab, and the parallel toolbox needs one license. | In this example you will only need a license for the base Matlab, and the parallel toolbox needs one license. | ||
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- | ===== Batch parallel example ===== | + | ====== Batch parallel example |
The Matlab parallel toolbox uses JVM to manage the workers and communicate while you are running. | The Matlab parallel toolbox uses JVM to manage the workers and communicate while you are running. | ||
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- | ===== Interactive example ===== | + | ====== Interactive example |
The basic steps to running a [[: | The basic steps to running a [[: | ||
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- | ===== MCR array job example ===== | + | ====== MCR array job example |
Most Matlab functions can be compiled using the Matlab Compiler (MCC) and then deployed to run on the compute nodes in the MATLAB Compiler Runtime (MCR). | Most Matlab functions can be compiled using the Matlab Compiler (MCC) and then deployed to run on the compute nodes in the MATLAB Compiler Runtime (MCR). |