Hi Hongyang
In recent CP2K versions, you can control the appearance of such warnings with the keyword EPS_CHECK_DIAG in the &GLOBAL section.
The output is not overwritten by such warnings. These warning are just added to the normal output, but can be overwhelming if there are many.
HTH
Matthias
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Hi Hongyang
I did not observed an overwriting of the output file with such warnings so far. Therefore, I guess it is rather a problem of your local system or environment.
Best
Matthias
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