MLClose() intMLClose(MLINKlink) closes a MathLink connection. Calling MLClose() does not necessarily terminate a program at the other end of the link. Any data buffered in the link is sent when MLClose() is called. Programs should close all links they have opened before terminating. See the Mathematica book: Section 2.12.12, Section 2.12.14. See also: MLDeinitializeMLDeinitializeMainBookLinkOldButtonDataMLDeinitialize.
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