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You'll need to edit E3SM/components/cmake/build_model.cmake (or the appropriate Depends file) as follows:

if (COMP_NAME STREQUAL "name-of-component")
  e3sm_add_flags("${SOURCE_FILE}" "-flag1 -flag2 ...")
endif()

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You'll need to edit E3SM/components/cmake/build_model.cmake (or the appropriate Depends file)  as follows:

if (COMP_NAME STREQUAL "name-of-component")
  e3sm_remove_flags("${SOURCE_FILE}" "-flag1 -flag2 ...")
endif()

Permanently change compile flags for a generated file (.F90.in)

You'll need to edit E3SM/components/cmake/build_model.cmake (or the appropriate Depends file) as follows:

if (COMP_NAME STREQUAL "name-of-component")
  e3sm_add_flags("${CMAKE_CURRENT_BINARY_DIR}/${BASEFILENAME}.F90" "-flag1 -flag2 ...")
endif()

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