Could the global variable shared between two kernels in the same aocx file?

I think the linker script is only needed when several files are involved. Even a named section is created? how to guarantee the host does not use the section when calling device malloc function?

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You might want to put the data into a named section and get the linker script(s) to assign it to a fixed address.

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According to the Altera SDK for OpenCL Programming Guide", the atomic operation is supported, is it true?

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Also there are no atomic RMW cycles on the Avalon bus, so you need to use something else to ensure correct sequencing of accesses.

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If the kernel will write to/read from the DDR directly and sequentially, the coherence will preserve?

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You'll need to worry about cache coherenceny.

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