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I've got wlan0 and wlan1. Each interface should connect to a different SSID.

I would like to use wpa_supplicant for both.

I can put the two networks in /etc/wpa_supplicant.conf, but how do I tell which one each interface should use?

(RHEL 6.3)

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You create two separate wpa_supplicant.conf files, one for each interface. Then you specify which conf file goes with which interface when you invoke wpa_supplicant. You use the -N option to show that you want to start describing a new interface.

This example comes right out of the wpa_supplicant(8) man page:

wpa_supplicant \
    -c wpa1.conf -i wlan0 -D hostap -N \
    -c wpa2.conf -i ath0 -D madwifi
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