Patchwork [2.6.32.3] ahci: AHCI and RAID mode SATA patch for Intel Cougar Point DeviceIDs

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Submitter Krzysztof Halasa
Date Jan. 13, 2010, 3:15 p.m.
Message ID <m3my0i6nou.fsf@intrepid.localdomain>
Download mbox | patch
Permalink /patch/42827/
State Not Applicable
Delegated to: David Miller
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Comments

Krzysztof Halasa - Jan. 13, 2010, 3:15 p.m.
Jeff Garzik <jgarzik@pobox.com> writes:

> Well, two lines of thinking here:
>
> * some of lines of Intel chips do not separate AHCI into a separate
> PCI ID rather legacy IDE interface.  When an AHCI interface exists and
> AHCI/IDE share the same PCI ID, we default to using AHCI.  Thus, some
> of those PCI ID matches in ahci.c's PCI table may not get caught by
> the generic PCI class match at the end of the table.
>
> * the cost carrying redundant PCI IDs seems low, harmless, and
> potentially helpful.

Also people may use things like this:
Jeff Garzik - Jan. 13, 2010, 5:08 p.m.
On 01/13/2010 10:15 AM, Krzysztof Halasa wrote:
> Jeff Garzik<jgarzik@pobox.com>  writes:
>
>> Well, two lines of thinking here:
>>
>> * some of lines of Intel chips do not separate AHCI into a separate
>> PCI ID rather legacy IDE interface.  When an AHCI interface exists and
>> AHCI/IDE share the same PCI ID, we default to using AHCI.  Thus, some
>> of those PCI ID matches in ahci.c's PCI table may not get caught by
>> the generic PCI class match at the end of the table.
>>
>> * the cost carrying redundant PCI IDs seems low, harmless, and
>> potentially helpful.
>
> Also people may use things like this:
>
> diff --git a/drivers/ata/ahci.c b/drivers/ata/ahci.c
> index a3241a1..0616bbb 100644
> --- a/drivers/ata/ahci.c
> +++ b/drivers/ata/ahci.c
> @@ -561,9 +561,11 @@ static const struct pci_device_id ahci_pci_tbl[] = {
>   	{ PCI_VDEVICE(INTEL, 0x3b2c), board_ahci }, /* PCH RAID */
>   	{ PCI_VDEVICE(INTEL, 0x3b2f), board_ahci }, /* PCH AHCI */
>
> +#ifdef DOESNT_WORK_FOR_ME
>   	/* JMicron 360/1/3/5/6, match class to avoid IDE function */
>   	{ PCI_VENDOR_ID_JMICRON, PCI_ANY_ID, PCI_ANY_ID, PCI_ANY_ID,
>   	  PCI_CLASS_STORAGE_SATA_AHCI, 0xffffff, board_ahci_ign_iferr },
> +#endif
>
>   	/* ATI */
>   	{ PCI_VDEVICE(ATI, 0x4380), board_ahci_sb600 }, /* ATI SB600 */
> @@ -667,9 +669,11 @@ static const struct pci_device_id ahci_pci_tbl[] = {
>   	/* Promise */
>   	{ PCI_VDEVICE(PROMISE, 0x3f20), board_ahci },	/* PDC42819 */
>
> +#ifdef DOESNT_WORK_FOR_ME
>   	/* Generic, PCI class code for AHCI */
>   	{ PCI_ANY_ID, PCI_ANY_ID, PCI_ANY_ID, PCI_ANY_ID,
>   	  PCI_CLASS_STORAGE_SATA_AHCI, 0xffffff, board_ahci },
> +#endif
>

I'm not sure I understand your point.  Are there ahci problems with the 
generic entries, that remain unresolved?

	Jeff




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Krzysztof Halasa - Jan. 13, 2010, 6:18 p.m.
Jeff Garzik <jgarzik@pobox.com> writes:

> I'm not sure I understand your point.  Are there ahci problems with
> the generic entries, that remain unresolved?

It seems JMB363 on MSI Neo2 motherboard (P45 + ICH10R) still doesn't
work correctly, flooding the kernel logs. No SATA devices connected,
a CD-ROM connected to PATA (and it works fine). I've sent a report to
the IDE  list some time ago, please let me know if you need more details
or testing etc.

JMB363 set in BIOS setup to non-RAID mode (it seems this means disabling
the JMB BIOS). Last tested with 2.6.32.1 x86-64 SMP. IRQ 16 is shared.

Currently the IRQ in PCI registers is 10 (JMB363 SATA is not handled),
I can enable and check again if needed.

02:00.0 SATA controller: JMicron Technologies, Inc. 20360/20363 Serial ATA Controller (rev 03) (prog-if 01 [AHCI 1.0])
        Subsystem: Micro-Star International Co., Ltd. Device 7512
        Control: I/O+ Mem+ BusMaster+ the_rest-
        Status: Cap+ the_rest-
        Latency: 0, Cache Line Size: 32 bytes
        Interrupt: pin A routed to IRQ 10
        Region 5: Memory at fe9fe000 (32-bit, non-prefetchable) [size=8K]
        Capabilities: <access denied>

ahci 0000:02:00.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16
ahci 0000:02:00.0: AHCI 0001.0000 32 slots 2 ports 3 Gbps 0x3 impl SATA mode
ahci 0000:02:00.0: flags: 64bit ncq pm led clo pmp pio slum part
ahci 0000:02:00.0: setting latency timer to 64
scsi6 : ahci
scsi7 : ahci
ata7: SATA max UDMA/133 abar m8192@0xfe9fe000 port 0xfe9fe100 irq 16
ata8: SATA max UDMA/133 abar m8192@0xfe9fe000 port 0xfe9fe180 irq 16
ata8: SATA link down (SStatus 0 SControl 300)
ata7: SATA link down (SStatus 0 SControl 300)

then every few seconds (ata8 only, nothing on ata7):

ata8: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { CommWake DevExch }
ata8: hard resetting link
ata8: SATA link down (SStatus 0 SControl 300)
ata8: EH complete
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { CommWake DevExch }
ata8: hard resetting link
ata8: SATA link down (SStatus 0 SControl 300)
ata8: EH complete
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4060000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { PHYInt CommWake DevExch }
ata8: limiting SATA link speed to 1.5 Gbps
ata8: hard resetting link
ata8: SATA link down (SStatus 0 SControl 310)
ata8: EH complete
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { CommWake DevExch }
ata8: limiting SATA link speed to 1.5 Gbps
ata8: hard resetting link
ata8: SATA link down (SStatus 0 SControl 310)
ata8: EH complete
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { CommWake DevExch }
ata8: limiting SATA link speed to 1.5 Gbps
ata8: hard resetting link
ata8: SATA link down (SStatus 0 SControl 310)
ata8: EH complete
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { CommWake DevExch }
ata8: limiting SATA link speed to 1.5 Gbps
ata8: hard resetting link
ata8: SATA link down (SStatus 0 SControl 310)
ata8: EH complete
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { CommWake DevExch }
ata8: limiting SATA link speed to 1.5 Gbps
ata8: hard resetting link
ata8: SATA link down (SStatus 0 SControl 310)
ata8: EH complete
ata8: exception Emask 0x10 SAct 0x0 SErr 0x4060000 action 0xe frozen
ata8: irq_stat 0x00000040, connection status changed
ata8: SError: { PHYInt CommWake DevExch }
ata8: limiting SATA link speed to 1.5 Gbps

It seems it worked without the above few times (according to the logs),
though I can't repeat it even with the same kernel version.
Maybe setting the mode to RAID (= enabling the JMB BIOS) would fix it?
I can check if there is non-zero possibility.

I can't rule out a hw problem, though I think other people had similar
problems with this chip.
Robert Hancock - Jan. 13, 2010, 11:57 p.m.
On Wed, Jan 13, 2010 at 12:18 PM, Krzysztof Halasa <khc@pm.waw.pl> wrote:
> Jeff Garzik <jgarzik@pobox.com> writes:
>
>> I'm not sure I understand your point.  Are there ahci problems with
>> the generic entries, that remain unresolved?
>
> It seems JMB363 on MSI Neo2 motherboard (P45 + ICH10R) still doesn't
> work correctly, flooding the kernel logs. No SATA devices connected,
> a CD-ROM connected to PATA (and it works fine). I've sent a report to
> the IDE  list some time ago, please let me know if you need more details
> or testing etc.
>
> JMB363 set in BIOS setup to non-RAID mode (it seems this means disabling
> the JMB BIOS). Last tested with 2.6.32.1 x86-64 SMP. IRQ 16 is shared.
>
> Currently the IRQ in PCI registers is 10 (JMB363 SATA is not handled),
> I can enable and check again if needed.
>
> 02:00.0 SATA controller: JMicron Technologies, Inc. 20360/20363 Serial ATA Controller (rev 03) (prog-if 01 [AHCI 1.0])
>        Subsystem: Micro-Star International Co., Ltd. Device 7512
>        Control: I/O+ Mem+ BusMaster+ the_rest-
>        Status: Cap+ the_rest-
>        Latency: 0, Cache Line Size: 32 bytes
>        Interrupt: pin A routed to IRQ 10
>        Region 5: Memory at fe9fe000 (32-bit, non-prefetchable) [size=8K]
>        Capabilities: <access denied>
>
> ahci 0000:02:00.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16
> ahci 0000:02:00.0: AHCI 0001.0000 32 slots 2 ports 3 Gbps 0x3 impl SATA mode
> ahci 0000:02:00.0: flags: 64bit ncq pm led clo pmp pio slum part
> ahci 0000:02:00.0: setting latency timer to 64
> scsi6 : ahci
> scsi7 : ahci
> ata7: SATA max UDMA/133 abar m8192@0xfe9fe000 port 0xfe9fe100 irq 16
> ata8: SATA max UDMA/133 abar m8192@0xfe9fe000 port 0xfe9fe180 irq 16
> ata8: SATA link down (SStatus 0 SControl 300)
> ata7: SATA link down (SStatus 0 SControl 300)
>
> then every few seconds (ata8 only, nothing on ata7):
>
> ata8: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
> ata8: irq_stat 0x00000040, connection status changed
> ata8: SError: { CommWake DevExch }
> ata8: hard resetting link
> ata8: SATA link down (SStatus 0 SControl 300)
> ata8: EH complete

That would seem like a board-specific problem, as I have an Asus
P7P55D PRO board with the same JMicron controller and I don't see any
such errors. The JMicron BIOS isn't enabled.

The behavior here is strange, the controller reports a connection
status change interrupt with CommWake which should indicate that some
device completed the handshake with the controller, but then the SATA
link shows down. I assume there's nothing plugged into the two JMicron
SATA ports?
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Krzysztof Halasa - Jan. 14, 2010, 2:40 p.m.
Robert Hancock <hancockrwd@gmail.com> writes:

> The behavior here is strange, the controller reports a connection
> status change interrupt with CommWake which should indicate that some
> device completed the handshake with the controller, but then the SATA
> link shows down. I assume there's nothing plugged into the two JMicron
> SATA ports?

Precisely nothing. Only the PATA is connected.
Robert Hancock - Jan. 15, 2010, 12:15 a.m.
On Thu, Jan 14, 2010 at 8:40 AM, Krzysztof Halasa <khc@pm.waw.pl> wrote:
> Robert Hancock <hancockrwd@gmail.com> writes:
>
>> The behavior here is strange, the controller reports a connection
>> status change interrupt with CommWake which should indicate that some
>> device completed the handshake with the controller, but then the SATA
>> link shows down. I assume there's nothing plugged into the two JMicron
>> SATA ports?
>
> Precisely nothing. Only the PATA is connected.

It would be interesting to see what happens if you actually plug
something into that port that's having the issues, and see what
happens. I'm kind of inclined to suspect it's a hardware fault, though
it would likely require a report from someone else with the same or
similar board model to confirm that..
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Krzysztof Halasa - Jan. 15, 2010, 9:43 p.m.
Robert Hancock <hancockrwd@gmail.com> writes:

> It would be interesting to see what happens if you actually plug
> something into that port that's having the issues, and see what
> happens. I'm kind of inclined to suspect it's a hardware fault, though
> it would likely require a report from someone else with the same or
> similar board model to confirm that..

2.6.32.3 with the patch disabling JMB363 and "catch all AHCI" applied.
Nothing connected to SATA, only PATA in use.

I understand the following doesn't set the AHCI_HFLAG_IGN_IRQ_IF_ERR
and thus doesn't ignore PORT_IRQ_IF_ERR, but the latter doesn't seem to
be set.

# echo -n 197b 2363 > new_id

ahci 0000:02:00.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16
ahci 0000:02:00.0: AHCI 0001.0000 32 slots 2 ports 3 Gbps 0x3 impl SATA mode
ahci 0000:02:00.0: flags: 64bit ncq pm led clo pmp pio slum part 
ahci 0000:02:00.0: setting latency timer to 64
scsi9 : ahci
scsi10 : ahci
ata9: SATA max UDMA/133 abar m8192@0xfe9fe000 port 0xfe9fe100 irq 16
ata10: SATA max UDMA/133 abar m8192@0xfe9fe000 port 0xfe9fe180 irq 16
ata10: SATA link down (SStatus 0 SControl 300)
ata9: SATA link down (SStatus 0 SControl 300)

ata10: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
ata10: irq_stat 0x00000040, connection status changed
ata10: SError: { CommWake DevExch }
ata10: hard resetting link
ata10: SATA link down (SStatus 0 SControl 300)
ata10: EH complete
ata10: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
ata10: irq_stat 0x00000040, connection status changed
ata10: SError: { CommWake DevExch }
ata10: limiting SATA link speed to 1.5 Gbps
ata10: hard resetting link
ata10: SATA link down (SStatus 0 SControl 310)
ata10: EH complete
...

sometimes the two lines become:

ata10: exception Emask 0x10 SAct 0x0 SErr 0x4060000 action 0xe frozen
ata10: SError: { PHYInt CommWake DevExch }

Now plugging something into the mb connector (1.5 Gbps device, the same
which my VT6421A-based miniPCI card doesn't like):

ata10: exception Emask 0x10 SAct 0x0 SErr 0x4050000 action 0xe frozen
ata10: irq_stat 0x00400040, connection status changed
ata10: SError: { PHYRdyChg CommWake DevExch }
ata10: hard resetting link
ata10: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
ata10.00: ATA-7: Kingston SSDNow V Series 64GB, B090428a, max UDMA/100
ata10.00: 125045424 sectors, multi 1: LBA
ata10.00: configured for UDMA/100
ata10: EH complete
scsi 10:0:0:0: Direct-Access     ATA      Kingston SSDNow  B090 PQ: 0 ANSI: 5
sd 10:0:0:0: Attached scsi generic sg8 type 0
sd 10:0:0:0: [sdh] 125045424 512-byte logical blocks: (64.0 GB/59.6 GiB)
sd 10:0:0:0: [sdh] Write Protect is off
sd 10:0:0:0: [sdh] Mode Sense: 00 3a 00 00
sd 10:0:0:0: [sdh] Write cache: disabled, read cache: enabled, doesn't support DPO or FUA
sd 10:0:0:0: [sdh] Attached SCSI disk

Absolutely no problems with fs access, expected linear transfer speed
etc.

Well, let's unplug it. Power down first:

ata10: exception Emask 0x10 SAct 0x0 SErr 0x990000 action 0xe frozen
ata10: irq_stat 0x00400000, PHY RDY changed
ata10: SError: { PHYRdyChg 10B8B Dispar LinkSeq }
ata10: hard resetting link
ata10: SATA link down (SStatus 0 SControl 300)
ata10: hard resetting link
ata10: SATA link down (SStatus 0 SControl 300)
ata10: limiting SATA link speed to 1.5 Gbps
ata10: hard resetting link
ata10: SATA link down (SStatus 0 SControl 310)
ata10.00: disabled
ata10: EH complete
ata10.00: detaching (SCSI 10:0:0:0)
sd 10:0:0:0: [sdh] Stopping disk
sd 10:0:0:0: [sdh] START_STOP FAILED
sd 10:0:0:0: [sdh] Result: hostbyte=DID_BAD_TARGET driverbyte=DRIVER_OK

Seems stable at this point, no additional messages.

Then removing the plug from (unpowered) SSD - IRQs start appearing again
every few seconds. Mostly:

ata10: exception Emask 0x10 SAct 0x0 SErr 0x4000000 action 0xe frozen
ata10: irq_stat 0x00000040, connection status changed
ata10: SError: { DevExch }
ata10: limiting SATA link speed to 1.5 Gbps
ata10: hard resetting link
ata10: SATA link down (SStatus 0 SControl 310)
ata10: EH complete

sometimes SErr 0x4060000 and 0x4040000

Fine, so let's connect it again (device still not powered):
Messages stopped.

Disconnected again, messages started, reconnected, stopped.

Am I to use the SSD as a passive SATA terminator?

Any further ideas welcome :-)
Robert Hancock - Jan. 16, 2010, 1:32 a.m.
On Fri, Jan 15, 2010 at 3:43 PM, Krzysztof Halasa <khc@pm.waw.pl> wrote:
> Robert Hancock <hancockrwd@gmail.com> writes:
>
>> It would be interesting to see what happens if you actually plug
>> something into that port that's having the issues, and see what
>> happens. I'm kind of inclined to suspect it's a hardware fault, though
>> it would likely require a report from someone else with the same or
>> similar board model to confirm that..
>
> 2.6.32.3 with the patch disabling JMB363 and "catch all AHCI" applied.
> Nothing connected to SATA, only PATA in use.
>
> I understand the following doesn't set the AHCI_HFLAG_IGN_IRQ_IF_ERR
> and thus doesn't ignore PORT_IRQ_IF_ERR, but the latter doesn't seem to
> be set.
>
> # echo -n 197b 2363 > new_id
>
> ahci 0000:02:00.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16
> ahci 0000:02:00.0: AHCI 0001.0000 32 slots 2 ports 3 Gbps 0x3 impl SATA mode
> ahci 0000:02:00.0: flags: 64bit ncq pm led clo pmp pio slum part
> ahci 0000:02:00.0: setting latency timer to 64
> scsi9 : ahci
> scsi10 : ahci
> ata9: SATA max UDMA/133 abar m8192@0xfe9fe000 port 0xfe9fe100 irq 16
> ata10: SATA max UDMA/133 abar m8192@0xfe9fe000 port 0xfe9fe180 irq 16
> ata10: SATA link down (SStatus 0 SControl 300)
> ata9: SATA link down (SStatus 0 SControl 300)
>
> ata10: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
> ata10: irq_stat 0x00000040, connection status changed
> ata10: SError: { CommWake DevExch }
> ata10: hard resetting link
> ata10: SATA link down (SStatus 0 SControl 300)
> ata10: EH complete
> ata10: exception Emask 0x10 SAct 0x0 SErr 0x4040000 action 0xe frozen
> ata10: irq_stat 0x00000040, connection status changed
> ata10: SError: { CommWake DevExch }
> ata10: limiting SATA link speed to 1.5 Gbps
> ata10: hard resetting link
> ata10: SATA link down (SStatus 0 SControl 310)
> ata10: EH complete
> ...
>
> sometimes the two lines become:
>
> ata10: exception Emask 0x10 SAct 0x0 SErr 0x4060000 action 0xe frozen
> ata10: SError: { PHYInt CommWake DevExch }
>
> Now plugging something into the mb connector (1.5 Gbps device, the same
> which my VT6421A-based miniPCI card doesn't like):
>
> ata10: exception Emask 0x10 SAct 0x0 SErr 0x4050000 action 0xe frozen
> ata10: irq_stat 0x00400040, connection status changed
> ata10: SError: { PHYRdyChg CommWake DevExch }
> ata10: hard resetting link
> ata10: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
> ata10.00: ATA-7: Kingston SSDNow V Series 64GB, B090428a, max UDMA/100
> ata10.00: 125045424 sectors, multi 1: LBA
> ata10.00: configured for UDMA/100
> ata10: EH complete
> scsi 10:0:0:0: Direct-Access     ATA      Kingston SSDNow  B090 PQ: 0 ANSI: 5
> sd 10:0:0:0: Attached scsi generic sg8 type 0
> sd 10:0:0:0: [sdh] 125045424 512-byte logical blocks: (64.0 GB/59.6 GiB)
> sd 10:0:0:0: [sdh] Write Protect is off
> sd 10:0:0:0: [sdh] Mode Sense: 00 3a 00 00
> sd 10:0:0:0: [sdh] Write cache: disabled, read cache: enabled, doesn't support DPO or FUA
> sd 10:0:0:0: [sdh] Attached SCSI disk
>
> Absolutely no problems with fs access, expected linear transfer speed
> etc.
>
> Well, let's unplug it. Power down first:
>
> ata10: exception Emask 0x10 SAct 0x0 SErr 0x990000 action 0xe frozen
> ata10: irq_stat 0x00400000, PHY RDY changed
> ata10: SError: { PHYRdyChg 10B8B Dispar LinkSeq }
> ata10: hard resetting link
> ata10: SATA link down (SStatus 0 SControl 300)
> ata10: hard resetting link
> ata10: SATA link down (SStatus 0 SControl 300)
> ata10: limiting SATA link speed to 1.5 Gbps
> ata10: hard resetting link
> ata10: SATA link down (SStatus 0 SControl 310)
> ata10.00: disabled
> ata10: EH complete
> ata10.00: detaching (SCSI 10:0:0:0)
> sd 10:0:0:0: [sdh] Stopping disk
> sd 10:0:0:0: [sdh] START_STOP FAILED
> sd 10:0:0:0: [sdh] Result: hostbyte=DID_BAD_TARGET driverbyte=DRIVER_OK
>
> Seems stable at this point, no additional messages.
>
> Then removing the plug from (unpowered) SSD - IRQs start appearing again
> every few seconds. Mostly:
>
> ata10: exception Emask 0x10 SAct 0x0 SErr 0x4000000 action 0xe frozen
> ata10: irq_stat 0x00000040, connection status changed
> ata10: SError: { DevExch }
> ata10: limiting SATA link speed to 1.5 Gbps
> ata10: hard resetting link
> ata10: SATA link down (SStatus 0 SControl 310)
> ata10: EH complete
>
> sometimes SErr 0x4060000 and 0x4040000
>
> Fine, so let's connect it again (device still not powered):
> Messages stopped.
>
> Disconnected again, messages started, reconnected, stopped.
>
> Am I to use the SSD as a passive SATA terminator?
>
> Any further ideas welcome :-)

Hmm.. From those test results I really suspect some kind of hardware
fault. Could be a defective motherboard - I don't know if that chip
needs any terminating resistors on the motherboard for the SATA signal
lines or something, if so, could be they weren't installed properly..
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Krzysztof Halasa - Jan. 16, 2010, 6:02 p.m.
Robert Hancock <hancockrwd@gmail.com> writes:

> Hmm.. From those test results I really suspect some kind of hardware
> fault. Could be a defective motherboard - I don't know if that chip
> needs any terminating resistors on the motherboard for the SATA signal
> lines or something, if so, could be they weren't installed properly..

Unfortunately I can't find a JMB363 datasheet on the net, but there is
a certain mb (p965t-a) schematic available.
It seems JMB363 doesn't need terminators on SATA RX/TX lines, there is
capacitative coupling only (10 nF in each line).

The port in question (SATA#2) on my mb (P45 Neo2) uses pins 56 (RXP)
57 (RXN) and 60 (TXN) 61 (TXP). No visible irregularity, the traces look
like they should, go straigt to the capacitors, and then to 0R R-packs
and to the connector. It looks exactly the same for both ports. There is
no short circuit past the capacitors (from the connector side). I'd say
quite low probability that there is something wrong with these signals.

It seems the chip uses extra 12k resistors for SATA (p965t-a calls the
pins SJ_REXT[12]), pin 44 for port#1 and 55 for port#2. Both look sane.
I will check the suspected connections with the machine powered off
later.

The RX and TX trace pairs go next to each other for up to 10 mm, could
that be a problem at these frequencies? If so it would show up on
all/many such boards certainly? Can't find any report.

OTOH other people have similar problems with other boards: e.g.
ASUS P5KC: http://ubuntuforums.org/showthread.php?t=766217
           https://bugs.launchpad.net/ubuntu/+source/linux/+bug/377633

(unknown boards)
https://archlinux-fr.org/doku.php?id=securisation:logcheck
http://forum.ubuntu-fr.org/viewtopic.php?pid=2739616
http://ubuntu-ky.ubuntuforums.org/showthread.php?p=7243061
The last one claims:
this started after an upgrade to ubuntu 9.04 and is stll here after re-installing
ubuntu 8.10.
this was fixed by re-installing ubuntu 8.10 only using the kernal,
2.6.27-7-generic.
I don't know if JMB36x is involved in this case, and how reliable the
info is.

Investigating as time permits.

Patch

diff --git a/drivers/ata/ahci.c b/drivers/ata/ahci.c
index a3241a1..0616bbb 100644
--- a/drivers/ata/ahci.c
+++ b/drivers/ata/ahci.c
@@ -561,9 +561,11 @@  static const struct pci_device_id ahci_pci_tbl[] = {
 	{ PCI_VDEVICE(INTEL, 0x3b2c), board_ahci }, /* PCH RAID */
 	{ PCI_VDEVICE(INTEL, 0x3b2f), board_ahci }, /* PCH AHCI */
 
+#ifdef DOESNT_WORK_FOR_ME
 	/* JMicron 360/1/3/5/6, match class to avoid IDE function */
 	{ PCI_VENDOR_ID_JMICRON, PCI_ANY_ID, PCI_ANY_ID, PCI_ANY_ID,
 	  PCI_CLASS_STORAGE_SATA_AHCI, 0xffffff, board_ahci_ign_iferr },
+#endif
 
 	/* ATI */
 	{ PCI_VDEVICE(ATI, 0x4380), board_ahci_sb600 }, /* ATI SB600 */
@@ -667,9 +669,11 @@  static const struct pci_device_id ahci_pci_tbl[] = {
 	/* Promise */
 	{ PCI_VDEVICE(PROMISE, 0x3f20), board_ahci },	/* PDC42819 */
 
+#ifdef DOESNT_WORK_FOR_ME
 	/* Generic, PCI class code for AHCI */
 	{ PCI_ANY_ID, PCI_ANY_ID, PCI_ANY_ID, PCI_ANY_ID,
 	  PCI_CLASS_STORAGE_SATA_AHCI, 0xffffff, board_ahci },
+#endif
 
 	{ }	/* terminate list */
 };