Hello Jin,
unfortunately, using ELMO-defined species in ISAM is not possible in either CMAQv5.4 or CMAQv5.5. It is a feature that is planned for the next CMAQ release in 2026. While full SOA apportionment was already supported in CMAQv5.4, there were a few subsequent bug fixes (released in CMAQv5.4.0.1 and CMAQv5.4.0.2) that are incorporated in CMAQv5.5 so we recommend using that latest version for your work.
Given that using ELMO-defined species in ISAM is not possible, you will have to address the error you reported above. When you compiled CMAQ ISAM, did you use the “large” I/O API library (as described here) recommended for DDM3D and ISAM applications with many output variables?