OK, I think I have found the reason for this bug. It is not due to stage
2 in power nap, but rather stage 1 - during powersave mode the ethernet
configuration for the card is changed, which deactivates wake-on-lan.

Since power nap first enters in stage1 then stage2, when the computer is
turned off (or suspended) in stage 2, the wake-on-lan is deactivated...
Of course I do *not* see this when manually shutting down, because my
typing on the console or through ssh gets the computer out of powersave
mode.

Here is the log file which demonstrates this. It is produced by a while
loop which logs the end of /var/log/powernap.log and the result of
"ethtool eth0" every 5 seconds. As you can see below the first two
logged entries (at t=0s and t=5s) have "Wake-on: g" but at t=+10s there
is "Wake-on: d" which I assume means deactivated...

=> I am not sure where power nap changes this, isn't it supposed to just
change speed ?

####### Time series of /var/log/powernap.log and "ethtool eth0"  at 5s
intervals #########

samedi 28 avril 2012, 11:24:08 (UTC+0200)
2012-04-28_11:23:45 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [3] seconds
2012-04-28_11:23:46 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [2] seconds
2012-04-28_11:23:46 WARNING  Taking action [/usr/sbin/powernap]
2012-04-28_11:23:50 WARNING  Taking recover action [/usr/sbin/pm-powersave 
false]
2012-04-28_11:23:59 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:00 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:02 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:05 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:06 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:08 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
Settings for eth0:
        Supported ports: [ TP MII ]
        Supported link modes:   10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Supported pause frame use: No
        Supports auto-negotiation: Yes
        Advertised link modes:  10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Advertised pause frame use: Symmetric Receive-only
        Advertised auto-negotiation: Yes
        Link partner advertised link modes:  10baseT/Half 10baseT/Full 
                                             100baseT/Half 100baseT/Full 
                                             1000baseT/Half 1000baseT/Full 
        Link partner advertised pause frame use: Symmetric Receive-only
        Link partner advertised auto-negotiation: Yes
        Speed: 1000Mb/s
        Duplex: Full
        Port: MII
        PHYAD: 0
        Transceiver: internal
        Auto-negotiation: on
        Supports Wake-on: pumbg
        Wake-on: g
        Current message level: 0x00000033 (51)
                               drv probe ifdown ifup
        Link detected: yes


samedi 28 avril 2012, 11:24:13 (UTC+0200)
2012-04-28_11:23:50 WARNING  Taking recover action [/usr/sbin/pm-powersave 
false]
2012-04-28_11:23:59 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:00 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:02 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:05 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:06 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:08 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:10 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:11 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:12 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
Settings for eth0:
        Supported ports: [ TP MII ]
        Supported link modes:   10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Supported pause frame use: No
        Supports auto-negotiation: Yes
        Advertised link modes:  10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Advertised pause frame use: Symmetric Receive-only
        Advertised auto-negotiation: Yes
        Link partner advertised link modes:  10baseT/Half 10baseT/Full 
                                             100baseT/Half 100baseT/Full 
                                             1000baseT/Half 1000baseT/Full 
        Link partner advertised pause frame use: Symmetric Receive-only
        Link partner advertised auto-negotiation: Yes
        Speed: 1000Mb/s
        Duplex: Full
        Port: MII
        PHYAD: 0
        Transceiver: internal
        Auto-negotiation: on
        Supports Wake-on: pumbg
        Wake-on: g
        Current message level: 0x00000033 (51)
                               drv probe ifdown ifup
        Link detected: yes


samedi 28 avril 2012, 11:24:18 (UTC+0200)
2012-04-28_11:24:02 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:05 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:06 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:08 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:10 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:11 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:12 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:13 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [3] seconds
2012-04-28_11:24:15 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [2] seconds
2012-04-28_11:24:15 WARNING  Taking action [/usr/sbin/powernap]
Settings for eth0:
        Supported ports: [ TP MII ]
        Supported link modes:   10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Supported pause frame use: No
        Supports auto-negotiation: Yes
        Advertised link modes:  10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Advertised pause frame use: Symmetric Receive-only
        Advertised auto-negotiation: Yes
        Link partner advertised link modes:  10baseT/Half 10baseT/Full 
                                             100baseT/Half 100baseT/Full 
                                             1000baseT/Half 1000baseT/Full 
        Link partner advertised pause frame use: Symmetric Receive-only
        Link partner advertised auto-negotiation: Yes
        Speed: 1000Mb/s
        Duplex: Full
        Port: MII
        PHYAD: 0
        Transceiver: internal
        Auto-negotiation: on
        Supports Wake-on: pumbg
        Wake-on: d
        Current message level: 0x00000033 (51)
                               drv probe ifdown ifup
        Link detected: yes


samedi 28 avril 2012, 11:24:23 (UTC+0200)
2012-04-28_11:24:02 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:05 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:06 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:08 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:10 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [6] seconds
2012-04-28_11:24:11 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [5] seconds
2012-04-28_11:24:12 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [4] seconds
2012-04-28_11:24:13 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [3] seconds
2012-04-28_11:24:15 WARNING  Entered into GRACE PERIOD. Action 
[/usr/sbin/powernap] will be taken in [2] seconds
2012-04-28_11:24:15 WARNING  Taking action [/usr/sbin/powernap]
Settings for eth0:
        Supported ports: [ TP MII ]
        Supported link modes:   10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Supported pause frame use: No
        Supports auto-negotiation: Yes
        Advertised link modes:  10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Advertised pause frame use: Symmetric Receive-only
        Advertised auto-negotiation: Yes
        Link partner advertised link modes:  10baseT/Half 10baseT/Full 
                                             100baseT/Half 100baseT/Full 
                                             1000baseT/Half 1000baseT/Full 
        Link partner advertised pause frame use: Symmetric Receive-only
        Link partner advertised auto-negotiation: Yes
        Speed: 1000Mb/s
        Duplex: Full
        Port: MII
        PHYAD: 0
        Transceiver: internal
        Auto-negotiation: on
        Supports Wake-on: pumbg
        Wake-on: d
        Current message level: 0x00000033 (51)
                               drv probe ifdown ifup
        Link detected: yes

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https://bugs.launchpad.net/bugs/989175

Title:
  Powernap prevents waking from WakeOnLAN

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