Sorry, I didn't encountered a similar issue before. But I think this problem may not come from MODIS data. Generally, MODIS data can be used directly in pyVPRM. By comparing with my running log, this code should occur after all MODIS tile data in a chunk has been read and processed, and tile merging is in progress. So I thought maybe we could try these methods to solve this problem:
1. Check super computer's memory.
2. Clean files in /wrf_preprocessor/out after a failed run.
3. Check rasterio and rioxarray installed with conda, and I think the most likely cause is a version conflict in the environment package.
4. Install pyVPRM in python 3.12 is recommended.
These are based on my previous experience in building pyPVRM. I hope it can help you.