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HPRC developed a tool named matlabsubmit to run Matlab simulations on the HPRC compute nodes without the need to create your own batch script and without the need to start a Matlab session. matlabsubmit will automatically generate a batch script with the correct requirements. In addition, matlabsubmit will also generate boilerplate Matlab code to set up the environment (e.g. the number of computational threads) and, if needed, will start a parpool using the correct Cluster Profile (local if all workers fit on a single node and a cluster profile when workers are distribued over multiple nodes)

To submit your Matlab script, use the following command:

[ NetID@cluster ~]$ matlabsubmit myscript.m

In the above example, matlabsubmit will use all default values for runtime, memory requirements, the number of workers, etc. To specify resources, you can use the command-line options of matlabsubmmit. For example:

[ NetID@cluster ~]$ matlabsubmit -t 07:00 -s 4 myscript.m

will set the wall-time to 7 hours and makes sure Matlab will use 4 computational threads for its run ( matlabsubmit will also request 4 cores).

To see all options for matlabsubmit use the -h flag

[ NetID@cluster ~]$ matlabsubmit -h
Usage: /sw/hprc/sw/Matlab/bin/matlabsubmit [options] SCRIPTNAME

This tool automates the process of running Matlab codes on the compute nodes.

  -h Shows this message
  -m set the amount of requested memory in MEGA bytes(e.g. -m 20000)
  -t sets the walltime; form hh:mm (e.g. -t 03:27)
  -w sets the number of ADDITIONAL workers
  -g indicates script needs GPU  (no value needed)
  -b sets the billing account to use 
  -s set number of threads for multithreading (default: 8 ( 1  when -w > 0)
  -p set number of workers per node
  -f run function call instead of script
  -x add explicit batch scheduler option

  memory   : 2000 per core 
  time     : 02:00
  workers  : 0
  gpu      : no gpu 
  threading: on, 8 threads

NOTE when using the -f flag to execute a function instead of a script, the function call must be enclosed with double quotes when it contains parentheses. For example: matlabsubmit -f "myfunc(21)"

When executing, matlabsubmit will do the following:

  • generate boilerplate Matlab code to setup the Matlab environment (e.g. #threads, #workers)
  • generate a batch script with all resources set correctly and the command to run Matlab
  • submit the generated batch script to the batch scheduler and return control back to the user


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

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 (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- 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 flag (where 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 workers than fit a single node and/or when the Matlab workers need to be distributed among multiple nodes. Some examples for distributing workers among multiple nodes include

  • hybrid runs: where every worker uses multiple computational threads
  • memory requirements: where the job needs more memory than fits on a single node.
  • GPU needs: where every worker needs to utilize the GPU on a node

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 8 -p 4 test.m
Running Matlab script with following parameters
Script     : test.m
Workers    : 8
Nodes      : 2
#threads   : 1

... starting matlab batch. This might take some time. See MatlabSubmitLOG5/matlab-batch-commands.log
...Starting Matlab from host: tlogin-0502.cluster
MATLAB is selecting SOFTWARE OPENGL rendering.

                                                                                < M A T L A B (R) >
                                                                      Copyright 1984-2019 The MathWorks, Inc.
                                                                  R2019b Update 3 ( 64-bit (glnxa64)
                                                                                 November 27, 2019

To get started, type doc.
For product information, visit

... Interactive Matlab session, multi threading reduced to 8

submitstring =

    '--cpus-per-task=1 --ntasks=9 --ntasks-per-node=4 --mem=5334 --time=2:00:00  '


As can be seen the output is very different from the previous examples ( some of the ouput has been removed for readability). 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 a specialized 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 used by the cluster profile to store metadata, log files, and screen output. The *.diary.txt text files will show screen output for the client and all the workers. All the Job directories can be found in your $SCRATCH/MatlabJobs/ directory where is the name of the used cluster profile. For R2019b it will be $SCRATCH/MatlabJobs/TAMU2019b. Note: for older versions, the profile is always TAMU

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