Submit LSF command from matlab script

I want to subbmit LSF command from matlab:

command = 'bsub -q normal -G example sleep 100';

% Execute the command using system

[status, result] = system(command);

in the result i get command not found

[Damian Pietrus]

Integrating MATLAB with LSF requires a support package which can be accessed here:

https://github.com/mathworks/matlab-parallel-lsf-plugin

Is your MATLAB client (where you're submitting the command from) on the cluster or off-cluster?

[lior]

I dont want to use cluster and parallel computing on matlab.

There is way to send job to LSF without using cluster and parllel computing on matlab?

Answer 1

[Swastik Sarkar]

Hi @lior,

The "command not found" error likely results from a PATH issue. To diagnose this, verify the directory containing bsub by executing the following in a terminal where bsub is accessible:

which bsub

'bsub' not found.

Next, check if this directory is included in the PATH variable of the MATLAB Client using:

getenv("PATH")

ans = '/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'

This is likely the cause of the error being encountered. Below is a demonstration of a similar error using the ls command:

system("ls -al")

total 8
drwxr-xr-x 2 matlab matlabgroup 4096 Aug 30 12:35 .
drwx------ 3 matlab matlabgroup 4096 Aug 30 12:35 ..

ans = 0

    
system("which ls")

/usr/bin/ls

ans = 0

    
getenv("PATH") % You will notice that the above directory is present here.

ans = '/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'

    
setenv("PATH", "") % Setting to PATH to empty string to simulate a “No command found”

system("ls -al") % Command not found

/bin/bash: line 1: ls: No such file or directory

ans = 127

This issue can be resolved by specifying the absolute path of bsub, thereby eliminating the dependency on the PATH variable. Below is an example using ls:

getenv("PATH") % Verifying PATH is empty

ans =

  0x0 empty char array

system("/usr/bin/ls -al")

total 8
drwxr-xr-x 2 matlab matlabgroup 4096 Aug 30 12:35 .
drwx------ 3 matlab matlabgroup 4096 Aug 30 12:35 ..

ans = 0

A more official method to communicate with LSF is to use the Parallel Computing Toolbox plugin for LSF, as mentioned by @Damian Pietrus. This approach allows MATLAB to construct the necessary bsub command. The plugin can be found here:

https://www.mathworks.com/matlabcentral/fileexchange/127374-parallel-computing-toolbox-plugin-for-lsf

Hope this helps.