Hi Neda,
I understand that you are facing issues with running a .sbatch file inside a matlab script using "system" command.
The issue you're encountering might be related to how the `system` command in MATLAB interacts with the environment and resource allocation on the HPC system. Here are some steps you can take to troubleshoot and resolve the issue:
1. Check Environment Variables
Ensure that the environment variables and modules loaded in your terminal session are also available when MATLAB runs the `system` command. Sometimes, the environment within MATLAB might differ from the one in your terminal.
2. Use Full Paths
Ensure that you use full paths for the `sbatch` command and the `.sbatch` file within MATLAB. This helps avoid any issues related to the current working directory.
3. Debugging Output
Capture and print the output of the `system` command to see more detailed error messages. This can help you diagnose what might be going wrong.
Example MATLAB Script
Here's an example MATLAB script that incorporates these suggestions:
% Full path to the sbatch command and the .sbatch file
sbatchCmd = '/usr/bin/sbatch'; % Adjust this path as necessary
sbatchFile = '/path/to/my.sbatch'; % Adjust this path as necessary
% Construct the command string
cmd = sprintf('%s %s', sbatchCmd, sbatchFile);
% Execute the system command and capture the output
[status, result] = system(cmd);
% Display the status and result
disp(['Status: ', num2str(status)]);
disp(['Result: ', result]);
% Check for errors
if status ~= 0
error('Failed to submit job: %s', result);
end
4. Use a Wrapper Script
If the above suggestions do not resolve the issue, consider creating a wrapper shell script that sets up the environment and then calls `sbatch`. This script can be invoked from MATLAB.
Wrapper Script Example (`submit_job.sh`):
#!/bin/bash
# Load necessary modules
module load parallel
# Submit the sbatch job
sbatch /path/to/my.sbatch
MATLAB Script to Call Wrapper:
% Full path to the wrapper script
wrapperScript = '/path/to/submit_job.sh'; % Adjust this path as necessary
% Execute the system command and capture the output
[status, result] = system(wrapperScript);
% Display the status and result
disp(['Status: ', num2str(status)]);
disp(['Result: ', result]);
% Check for errors
if status ~= 0
error('Failed to submit job: %s', result);
end
5. Check CPU Binding and Resource Allocation
The error message suggests an issue with CPU binding. Ensure that the resources requested in the `.sbatch` file are appropriate and available on the HPC system.
6. Verify Permissions
Ensure that MATLAB has the necessary permissions to execute the `sbatch` command and that the `.sbatch` file is accessible from the MATLAB environment.
By following these steps, you should be able to diagnose and resolve the issue with running `.sbatch` files from within a MATLAB script.
I hope above information helps you.
Thank you.
