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Error: database disk image is malformed for every large database after a few SELECT instruction
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>  The timestamp on the file does not change. I understand that SELECT should not write to the database but somehow the file get corrupted after several searches without timestamp changed. 

Which suggests to me that your storage device is likely to blame. Only recently i had to dispose of a flaky SSD which would occasionally randomly corrupt files which were never written to by the OS.

> This problem appears on 4 different desktops with the same system but different databases

It's not clear from that statement whether you're running the same external drive on multiple computers or whether they're accessing the db via a network, but my suspicion is the former. If that's the case, and multiple computers are failing in the same way with that same device, there's even more reason to suspect the storage device.