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can I run daemon on xeon phi? And can I communicate with this daemon?
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Are you thinking of any daemon in particular? There are a number of daemons that run on the coprocessor already - including the coi_daemon, sshd and nfsiod.
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I wanted to run my daemon in native model, but I thought that it will not work, beacuse daemon use external libraries, which I don't compile for MIC architecture. Do I understand correctly?
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Yes if the external libraries are compatible with Xeon Phi(TM) coprocessor. But normally you need to recompile those libraries, and transfer them to the coprocessor.
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Thanks

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