Q: Our jobs are crashing on our cluster because the stdout file is too big (more than 20meg). Is there a way to tell eman to generate a “less verbose” output?

A: Sorry. Not really. Clusters shouldn't really limit the size of stdout like that... The only real option I can think of would be to redirect stdout of the 'refine' command directly to a file, however, since it calls other subshells, I'm not 100% positive if the subprograms would also go to the file...