Submit LSF command from matlab script

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lior
lior 2024-2-29
编辑： Swastik Sarkar 2024-8-30
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
  2 个评论
Damian Pietrus
Damian Pietrus 2024-3-19
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
lior 2024-4-24
编辑：lior 2024-4-24
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?

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回答（1 个）

Swastik Sarkar
Swastik Sarkar 2024-8-30
编辑：Swastik Sarkar 2024-8-30
Ran in:
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.

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