# Difference between revisions of "SW:Matlab matlabsubmit"

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= Example 2: Utilizing Matlab workers (single node) = | = Example 2: Utilizing Matlab workers (single node) = | ||

− | To utilize additional workers used by Matlab's parallel features such as ''parfor'',''spmd'', and ''distributed'' matlabsubmit provides | + | To utilize additional workers used by Matlab's parallel features such as ''parfor'',''spmd'', and ''distributed'', '''matlabsubmit''' provides an option to specify the number of workers. This is done using the ''-w <N>'' flag (where <N> represents the number of workers). The following example shows a simple case of using 8 workers. |

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<pre> | <pre> | ||

+ | -bash-4.1$ matlabsubmit -w 8 test.m | ||

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Running Matlab script with following parameters | Running Matlab script with following parameters | ||

----------------------------------------------- | ----------------------------------------------- | ||

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Workers : 8 | Workers : 8 | ||

Nodes : 1 | Nodes : 1 | ||

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#threads : 1 | #threads : 1 | ||

=============================================== | =============================================== | ||

− | + | sbatch -o MatlabSubmitLOG2/slurm.out --job-name=matlabsubmitID-2_test --ntasks=9 --ntasks-per-node=9 --cpus-per-task=1 --mem=16000 --time=02:00:00 MatlabSubmitLOG2/submission_script | |

− | + | Submitted batch job 3759571 | |

− | + | (from job_submit) your job is charged as below | |

− | + | Project Account: 122839393845 | |

− | + | Account Balance: 17504.211670 | |

− | + | Requested SUs: 18 | |

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----------------------------------------------- | ----------------------------------------------- | ||

− | matlabsubmit ID : | + | matlabsubmit ID : 2 |

− | matlab output file : | + | matlab output file : MatlabSubmitLOG2/matlab.log |

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</pre> | </pre> | ||

− | In this example, matlabsubmit will first execute | + | In this example, '''matlabsubmit''' will first execute Matlab code to create a ''parpool'' with 8 workers (using the local profile). As can be seen in the output, in this case, '''matlabsubmit''' requests 9 cores: 1 core for the client and 8 cores for the workers. The only exception is when the user requests all the workers on a node ( 28 on terra). In that case, matlabsubmit will request all cores (instead of one extra for the client). |

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= Example 3: Utilizing Matlab workers (multi node) = | = Example 3: Utilizing Matlab workers (multi node) = |

## Revision as of 15:59, 24 February 2020

# Example 1: basic use

The following example shows the simplest use of matlabsubmit. It will execute matlab script *test.m* using default values for batch resources and Matlab resources. matlabsubmit will also print some useful information to the screen. As can be seen in the example, it will show the Matlab resources requested (e.g. #threads, #workers), the submit command that will be used to submit the job, the batch scheduler JobID, and the location of output generated by Matlab and the batch scheduler.

-bash-4.1$ matlabsubmit test.m =============================================== Running Matlab script with following parameters ----------------------------------------------- Script : test.m Workers : 0 Nodes : 1 #threads : 8 =============================================== sbatch -o MatlabSubmitLOG1/slurm.out --job-name=matlabsubmitID-1_test --ntasks=1 --ntasks-per-node=1 --cpus-per-task=8 --mem=16000 --time=02:00:00 MatlabSubmitLOG1/submission_script Submitted batch job 3759554 (from job_submit) your job is charged as below Project Account: 122839393845 Account Balance: 17504.211670 Requested SUs: 16 ----------------------------------------------- matlabsubmit ID : 1 Matlab output file : MatlabSubmitLOG1/matlab.log -bash-4.1$

The matlab script *test.m* has to be in the current directory. Control will be returned immediately after executing the matlabsubmit command. To check the run status or kill a job, use the respective batch scheduler commands (e.g. **squeue** and **scancel**). matlabsubmit will create a sub directory named **MatlabSubmitLOG<N>** (where **N** is the matlabsubmit ID). In this directory matlabsubmit will store all its relevant files; the generated batch script, matlab driver, and redirected output and error. A listing of this directory will show the following files:

**slurm.err**redirected error**slurm.out**redirected output (both LSF and Matlab)**matlab.log**redirected Matlab screen output**matlabsubmit_wrapper.m**Matlab code that sets #threads and calls user function**submission_script**the generated LSF batch script**batch_job_id-<SLURM_JOBID>**dummy file to show the actual Slurm job id this matlabsubmit job is associated to.

# Example 2: Utilizing Matlab workers (single node)

To utilize additional workers used by Matlab's parallel features such as *parfor*,*spmd*, and *distributed*, **matlabsubmit** provides an option to specify the number of workers. This is done using the *-w <N>* flag (where <N> represents the number of workers). The following example shows a simple case of using 8 workers.

-bash-4.1$ matlabsubmit -w 8 test.m Running Matlab script with following parameters ----------------------------------------------- Script : test.m Workers : 8 Nodes : 1 #threads : 1 =============================================== sbatch -o MatlabSubmitLOG2/slurm.out --job-name=matlabsubmitID-2_test --ntasks=9 --ntasks-per-node=9 --cpus-per-task=1 --mem=16000 --time=02:00:00 MatlabSubmitLOG2/submission_script Submitted batch job 3759571 (from job_submit) your job is charged as below Project Account: 122839393845 Account Balance: 17504.211670 Requested SUs: 18 ----------------------------------------------- matlabsubmit ID : 2 matlab output file : MatlabSubmitLOG2/matlab.log

In this example, **matlabsubmit** will first execute Matlab code to create a *parpool* with 8 workers (using the local profile). As can be seen in the output, in this case, **matlabsubmit** requests 9 cores: 1 core for the client and 8 cores for the workers. The only exception is when the user requests all the workers on a node ( 28 on terra). In that case, matlabsubmit will request all cores (instead of one extra for the client).

# Example 3: Utilizing Matlab workers (multi node)

matlabsubmit provides excellent options for Matlab runs that need more than 20 workers (maximum for single node) and/or when the Matlab workers need to be distributed among multiple nodes. Reasons for distributing workers among different nodes include: need to use certain resources such as gpu on multiple nodes, enable multi threading on every worker, and use the available memory on multiple nodes. The following example shows how to run a matlab simulation that utilizes 24 workers, where every node will run 4 workers (i.e. the workers will be distributed among 24/4 = 6 nodes).

-bash-4.1$ matlabsubmit -w 24 -p 4 test.m =============================================== Running Matlab script with following parameters ----------------------------------------------- Script : test.m Workers : 24 Nodes : 6 Mem/proc : 2500 #threads : 1 =============================================== ... starting matlab batch. This might take some time. See MatlabSubmitLOG8/matlab-batch-commands.log ...Starting Matlab from host: login4 MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2016 The MathWorks, Inc. R2016a (9.0.0.341360) 64-bit (glnxa64) February 11, 2016 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. ... Interactive Matlab session, multi threading reduced to 4 Academic License commandToRun = bsub -L /bin/bash -J Job1 -o '/general/home/pennings/Job1/Job1.log' -n 25 -M 2500 -R rusage[mem=2500] -R "span[ptile=4]" -W 02:00 "source /general/home/pennings/Job1/mdce_envvars ; /general/software/x86_64/tamusc/Matlab/toolbox/tamu/profiles/lsfgeneric/communicatingJobWrapper.sh" job = Job Properties: ID: 1 Type: pool Username: pennings State: running SubmitTime: Mon Aug 01 12:15:15 CDT 2016 StartTime: Running Duration: 0 days 0h 0m 0s NumWorkersRange: [25 25] AutoAttachFiles: true Auto Attached Files: /general/home/pennings/MatlabSubmitLOG8/matlabsubmit_wrapper.m /general/home/pennings/test.m AttachedFiles: {} AdditionalPaths: {} Associated Tasks: Number Pending: 25 Number Running: 0 Number Finished: 0 Task ID of Errors: [] Task ID of Warnings: [] ----------------------------------------------- matlabsubmit JOBID : 8 batch output file (client) : Job1/Task1.diary.txt batch output files (workers) : Job1/Task[2-25].diary.txt Done -bash-4.1$

As can be seen the output is very different from the previous examples. When a job uses multiple nodes the approach matlabsubmit uses is a bit different. matlabsubmit will start a regular *interactive* matlab session and from within it will run the Matlab *batch* command using the **TAMUG** cluster profile. It will then exit Matlab while the Matlab script is executed on the compute nodes.

The contents of the MatlabSubmitLOG directory are also slightly different. A listing will show the following files:

**matlab-batch-commands.log**screen output from Matlab**matlabsubmit_driver.m**Matlab code that sets up the cluster profile and calls Matlab*batch***matlabsubmit_wrapper.m**Matlab code that sets #threads and calls user function**submission_script**The actual command to start Matlab

In addition to the MatlabSubmitLOG directory created by matlabsubmit, Matlab will also create a directory named **Job<N>** used by the cluster profile to store meta data, log files, and screen output. The ***.diary.txt** text files will show screen output for the client and all the workers.