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PSS/E prints it's output to different "devices" depending on the activity: progress, prompt, and report. The progress output is the one producing the messages you're referring to. To change how the program interacts with these devices there are some API commands.
ierr = progress_output(islct, filarg, options)
ierr = prompt_output(islct, filarg, options)
ierr = report_output(islct, filarg, options)
You can disable these output devices by setting ISLCT=6. However, it's good practice is to save these log files in case something goes awry or for future analysis (i.e. ISLCT=2 & filarg=output file name).
Having the output go to the PSS/E GUI can slow things down when there's a lot of text being printed. Check out the API documentation for more details.
