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Haveri District administration has ordered the schools to close on May 20 and 21 due to the yellow alert.
The schools in Udupi, Dharwad, and Shivamogga will remain shut on Friday.
The heavy downpour continued to wreak havoc in various parts of Karnataka including Bengaluru for the third day.
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Many dams including the Krishnaraja Sagar, Kabini, Harangi, Hemavathi, Almatti, Narayanapura, Bhadra, Tungabhadra, Ghataprabha, and Malaprabha were inching towards filling to the brim due to the heavy rains.
Meanwhile, the Weather Department has forecast thunderstorms and lightning with light to moderate spells of rain and gusty winds in Bengaluru, Dakshina Kannada, Uttara Kannada, Bagalkote, Chikkamagaluru, Mysuru, Haveri, Gadag, Raichur, Mandya, Chitradurga, Davangere, Koppal, Ballari and Shivamogga.
(With PTI inputs)