MATLAB and SIMPA Configuration Issue: Encountering KeyError and Java Environment Setup Error on NeSI GPU

[LumiXIE]

Hello everyone,

I am currently working on photoacoustic imaging simulations using SIMPA on the NeSI GPU environment. However, I have encountered an issue that I need some assistance with. The issue seems to be related to the MATLAB configuration and the Java Runtime Environment (JRE).

Issue Summary:
When executing the SIMPA code, I encounter the following error: KeyError: 'time_series_data'

Additionally, I receive the following warning: Warning: Cannot locate Java Runtime Environment (JRE)

This occurs when I try to run the following command: /opt/nesi/share/MATLAB/R2021b/bin/matlab -nodisplay -nosplash -automation -r "addpath('/path/to/simpa/code'); simulate_2D('/path/to/data'); exit;"

Debugging Steps:
MATLAB on NeSI: As I am using NeSI GPU, MATLAB is pre-installed, and I cannot directly install k-Wave or add it to the toolbox path. However, I manually installed k-Wave (version 1.4) and added it with the following setup:

module load MATLAB/2021b

matlab -nodisplay

addpath('/nesi/project/uoa04354/k-wave-source');

MATLAB Startup Check: I tried running matlab -n to check if MATLAB starts correctly, but encountered an error indicating that -n is not a valid argument, and the matlab.m script could not be executed.

Java Runtime Issue: The warning suggests that MATLAB cannot locate the Java Runtime Environment (JRE). I checked if Java is installed on the system and tried using the version -java command in MATLAB to confirm its Java version. However, it seems MATLAB cannot find the correct Java Runtime.

MATLAB_JAVA Environment Variable: I attempted to set the MATLAB_JAVA environment variable to the correct Java path, but the issue persists.

Request for Help:
Has anyone experienced similar configuration issues? I believe it may be related to MATLAB not properly loading Java or a compatibility issue.

If anyone knows how to configure the Java environment correctly or troubleshoot the MATLAB startup process, I would appreciate any guidance.

For those who have successfully run SIMPA and k-Wave on NeSI GPU, could you kindly share your setup process or environment configuration details?

Thank you in advance for your help. I look forward to your suggestions.

Best regards,
Lumi