Your build script does looks correct.
As far as your control file, it will not work the way you have it. You have to define the tags one at a time and there can only be 1 name in the TAG NAME field. For example:
TAG NAME |GR1
TAG CLASSES |SULFATE, OZONE, NITRATE, PM25_IONS
REGION(S) |EVERYWHERE
EMIS STREAM(S) |AGRICULTURE
Fliu was on the right track, except this user created identical “EMIS STREAM(S)” calls for each tag, which would oversubscribe the emissions and crash. You can assign multiple emissions to one TAG NAME, and that will calculate the cumulative impact. You can’t assign the same mass in multiple places.
Note that we are in the processes of releasing a major update for ISAM that will drastically change OZONE predictions in the next few weeks. The update is finished, its just going through review. So, while it will be helpful to use the old code to resolve issues like you are having, I would wait for the new release before interpreting the results. The problem we are solving with the update is documented in the “Known Issues” in the repository. The update also includes some error checking for the control file, which should give you some more clues in situations like yours.