A run with ORCHIDEE will create additional files that you won't see in your output file structure created by libIGCM. For example, all write statements in the code which say WRITE(numout,*) will be printed to the file out_orchidee. By default, this file is not saved after every run. Sometimes, however, it contains very useful information for debugging. There is an easy way to save it.

In your submission file, there is a COMP directory. Inside that directory, there is a stomate.card.

[OutputText]
List=   (out_orchidee, run.def, used_run.def, stomate_forcing.nc)

You can see here that I've added two files to the two that are there by default: out_orchidee and run.def. After the run is over, you can find the out_orchidee and run.def for every period in the output directory: JOBNAME/SBG/Debug.