diff --git a/arch/ia64/pci/pci.c b/arch/ia64/pci/pci.c
index 729298f4b234..7de76dd352fe 100644
--- a/arch/ia64/pci/pci.c
+++ b/arch/ia64/pci/pci.c
@@ -537,7 +537,7 @@ pcibios_align_resource (void *data, struct resource *res,
 /*
  * PCI BIOS setup, always defaults to SAL interface
  */
-char * __devinit
+char * __init
 pcibios_setup (char *str)
 {
 	return str;
diff --git a/arch/mn10300/include/asm/pci.h b/arch/mn10300/include/asm/pci.h
index e58b9a46e1b1..35d2ed6396f6 100644
--- a/arch/mn10300/include/asm/pci.h
+++ b/arch/mn10300/include/asm/pci.h
@@ -70,10 +70,6 @@ struct pci_dev;
  */
 #define PCI_DMA_BUS_IS_PHYS	(1)
 
-
-/* This is always fine. */
-#define pci_dac_dma_supported(pci_dev, mask)	(0)
-
 /* Return the index of the PCI controller for device. */
 static inline int pci_controller_num(struct pci_dev *dev)
 {
diff --git a/arch/x86/pci/acpi.c b/arch/x86/pci/acpi.c
index b26626dc517c..1014eb4bfc37 100644
--- a/arch/x86/pci/acpi.c
+++ b/arch/x86/pci/acpi.c
@@ -68,6 +68,10 @@ setup_resource(struct acpi_resource *acpi_res, void *data)
 	unsigned long flags;
 	struct resource *root;
 	int max_root_bus_resources = PCI_BUS_NUM_RESOURCES;
+	u64 start, end;
+
+	if (bus_has_transparent_bridge(info->bus))
+		max_root_bus_resources -= 3;
 
 	status = resource_to_addr(acpi_res, &addr);
 	if (!ACPI_SUCCESS(status))
@@ -84,25 +88,24 @@ setup_resource(struct acpi_resource *acpi_res, void *data)
 	} else
 		return AE_OK;
 
-	res = &info->res[info->res_num];
-	res->name = info->name;
-	res->flags = flags;
-	res->start = addr.minimum + addr.translation_offset;
-	res->end = res->start + addr.address_length - 1;
-	res->child = NULL;
-
-	if (bus_has_transparent_bridge(info->bus))
-		max_root_bus_resources -= 3;
+	start = addr.minimum + addr.translation_offset;
+	end = start + addr.address_length - 1;
 	if (info->res_num >= max_root_bus_resources) {
 		printk(KERN_WARNING "PCI: Failed to allocate 0x%lx-0x%lx "
 			"from %s for %s due to _CRS returning more than "
-			"%d resource descriptors\n", (unsigned long) res->start,
-			(unsigned long) res->end, root->name, info->name,
+			"%d resource descriptors\n", (unsigned long) start,
+			(unsigned long) end, root->name, info->name,
 			max_root_bus_resources);
-		info->res_num++;
 		return AE_OK;
 	}
 
+	res = &info->res[info->res_num];
+	res->name = info->name;
+	res->flags = flags;
+	res->start = start;
+	res->end = end;
+	res->child = NULL;
+
 	if (insert_resource(root, res)) {
 		printk(KERN_ERR "PCI: Failed to allocate 0x%lx-0x%lx "
 			"from %s for %s\n", (unsigned long) res->start,
@@ -114,23 +117,6 @@ setup_resource(struct acpi_resource *acpi_res, void *data)
 	return AE_OK;
 }
 
-static void
-adjust_transparent_bridge_resources(struct pci_bus *bus)
-{
-	struct pci_dev *dev;
-
-	list_for_each_entry(dev, &bus->devices, bus_list) {
-		int i;
-		u16 class = dev->class >> 8;
-
-		if (class == PCI_CLASS_BRIDGE_PCI && dev->transparent) {
-			for(i = 3; i < PCI_BUS_NUM_RESOURCES; i++)
-				dev->subordinate->resource[i] =
-						dev->bus->resource[i - 3];
-		}
-	}
-}
-
 static void
 get_current_resources(struct acpi_device *device, int busnum,
 			int domain, struct pci_bus *bus)
@@ -158,8 +144,6 @@ get_current_resources(struct acpi_device *device, int busnum,
 	info.res_num = 0;
 	acpi_walk_resources(device->handle, METHOD_NAME__CRS, setup_resource,
 				&info);
-	if (info.res_num)
-		adjust_transparent_bridge_resources(bus);
 
 	return;
 
@@ -222,8 +206,15 @@ struct pci_bus * __devinit pci_acpi_scan_root(struct acpi_device *device, int do
 		 */
 		memcpy(bus->sysdata, sd, sizeof(*sd));
 		kfree(sd);
-	} else
-		bus = pci_scan_bus_parented(NULL, busnum, &pci_root_ops, sd);
+	} else {
+		bus = pci_create_bus(NULL, busnum, &pci_root_ops, sd);
+		if (bus) {
+			if (pci_probe & PCI_USE__CRS)
+				get_current_resources(device, busnum, domain,
+							bus);
+			bus->subordinate = pci_scan_child_bus(bus);
+		}
+	}
 
 	if (!bus)
 		kfree(sd);
@@ -238,8 +229,6 @@ struct pci_bus * __devinit pci_acpi_scan_root(struct acpi_device *device, int do
 #endif
 	}
 
-	if (bus && (pci_probe & PCI_USE__CRS))
-		get_current_resources(device, busnum, domain, bus);
 	return bus;
 }
 
diff --git a/arch/x86/pci/amd_bus.c b/arch/x86/pci/amd_bus.c
index f893d6a6e803..3ffa10df20b9 100644
--- a/arch/x86/pci/amd_bus.c
+++ b/arch/x86/pci/amd_bus.c
@@ -100,8 +100,9 @@ void x86_pci_root_bus_res_quirks(struct pci_bus *b)
 	int j;
 	struct pci_root_info *info;
 
-	/* don't go for it if _CRS is used */
-	if (pci_probe & PCI_USE__CRS)
+	/* don't go for it if _CRS is used already */
+	if (b->resource[0] != &ioport_resource ||
+	    b->resource[1] != &iomem_resource)
 		return;
 
 	/* if only one root bus, don't need to anything */
@@ -116,6 +117,9 @@ void x86_pci_root_bus_res_quirks(struct pci_bus *b)
 	if (i == pci_root_num)
 		return;
 
+	printk(KERN_DEBUG "PCI: peer root bus %02x res updated from pci conf\n",
+			b->number);
+
 	info = &pci_root_info[i];
 	for (j = 0; j < info->res_num; j++) {
 		struct resource *res;
diff --git a/drivers/pci/hotplug/pci_hotplug_core.c b/drivers/pci/hotplug/pci_hotplug_core.c
index 844580489d4d..5c5043f239cf 100644
--- a/drivers/pci/hotplug/pci_hotplug_core.c
+++ b/drivers/pci/hotplug/pci_hotplug_core.c
@@ -555,6 +555,8 @@ static struct hotplug_slot *get_slot_from_name (const char *name)
  * @slot: pointer to the &struct hotplug_slot to register
  * @devnr: device number
  * @name: name registered with kobject core
+ * @owner: caller module owner
+ * @mod_name: caller module name
  *
  * Registers a hotplug slot with the pci hotplug subsystem, which will allow
  * userspace interaction to the slot.
diff --git a/drivers/pci/msi.c b/drivers/pci/msi.c
index d9f06fbfa0bf..d986afb7032b 100644
--- a/drivers/pci/msi.c
+++ b/drivers/pci/msi.c
@@ -127,17 +127,23 @@ static inline __attribute_const__ u32 msi_enabled_mask(u16 control)
  * reliably as devices without an INTx disable bit will then generate a
  * level IRQ which will never be cleared.
  */
-static void msi_mask_irq(struct msi_desc *desc, u32 mask, u32 flag)
+static u32 __msi_mask_irq(struct msi_desc *desc, u32 mask, u32 flag)
 {
 	u32 mask_bits = desc->masked;
 
 	if (!desc->msi_attrib.maskbit)
-		return;
+		return 0;
 
 	mask_bits &= ~mask;
 	mask_bits |= flag;
 	pci_write_config_dword(desc->dev, desc->mask_pos, mask_bits);
-	desc->masked = mask_bits;
+
+	return mask_bits;
+}
+
+static void msi_mask_irq(struct msi_desc *desc, u32 mask, u32 flag)
+{
+	desc->masked = __msi_mask_irq(desc, mask, flag);
 }
 
 /*
@@ -147,15 +153,21 @@ static void msi_mask_irq(struct msi_desc *desc, u32 mask, u32 flag)
  * file.  This saves a few milliseconds when initialising devices with lots
  * of MSI-X interrupts.
  */
-static void msix_mask_irq(struct msi_desc *desc, u32 flag)
+static u32 __msix_mask_irq(struct msi_desc *desc, u32 flag)
 {
 	u32 mask_bits = desc->masked;
 	unsigned offset = desc->msi_attrib.entry_nr * PCI_MSIX_ENTRY_SIZE +
-					PCI_MSIX_ENTRY_VECTOR_CTRL_OFFSET;
+						PCI_MSIX_ENTRY_VECTOR_CTRL;
 	mask_bits &= ~1;
 	mask_bits |= flag;
 	writel(mask_bits, desc->mask_base + offset);
-	desc->masked = mask_bits;
+
+	return mask_bits;
+}
+
+static void msix_mask_irq(struct msi_desc *desc, u32 flag)
+{
+	desc->masked = __msix_mask_irq(desc, flag);
 }
 
 static void msi_set_mask_bit(unsigned irq, u32 flag)
@@ -188,9 +200,9 @@ void read_msi_msg_desc(struct irq_desc *desc, struct msi_msg *msg)
 		void __iomem *base = entry->mask_base +
 			entry->msi_attrib.entry_nr * PCI_MSIX_ENTRY_SIZE;
 
-		msg->address_lo = readl(base + PCI_MSIX_ENTRY_LOWER_ADDR_OFFSET);
-		msg->address_hi = readl(base + PCI_MSIX_ENTRY_UPPER_ADDR_OFFSET);
-		msg->data = readl(base + PCI_MSIX_ENTRY_DATA_OFFSET);
+		msg->address_lo = readl(base + PCI_MSIX_ENTRY_LOWER_ADDR);
+		msg->address_hi = readl(base + PCI_MSIX_ENTRY_UPPER_ADDR);
+		msg->data = readl(base + PCI_MSIX_ENTRY_DATA);
 	} else {
 		struct pci_dev *dev = entry->dev;
 		int pos = entry->msi_attrib.pos;
@@ -225,11 +237,9 @@ void write_msi_msg_desc(struct irq_desc *desc, struct msi_msg *msg)
 		base = entry->mask_base +
 			entry->msi_attrib.entry_nr * PCI_MSIX_ENTRY_SIZE;
 
-		writel(msg->address_lo,
-			base + PCI_MSIX_ENTRY_LOWER_ADDR_OFFSET);
-		writel(msg->address_hi,
-			base + PCI_MSIX_ENTRY_UPPER_ADDR_OFFSET);
-		writel(msg->data, base + PCI_MSIX_ENTRY_DATA_OFFSET);
+		writel(msg->address_lo, base + PCI_MSIX_ENTRY_LOWER_ADDR);
+		writel(msg->address_hi, base + PCI_MSIX_ENTRY_UPPER_ADDR);
+		writel(msg->data, base + PCI_MSIX_ENTRY_DATA);
 	} else {
 		struct pci_dev *dev = entry->dev;
 		int pos = entry->msi_attrib.pos;
@@ -385,6 +395,7 @@ static int msi_capability_init(struct pci_dev *dev, int nvec)
 	/* Configure MSI capability structure */
 	ret = arch_setup_msi_irqs(dev, nvec, PCI_CAP_ID_MSI);
 	if (ret) {
+		msi_mask_irq(entry, mask, ~mask);
 		msi_free_irqs(dev);
 		return ret;
 	}
@@ -439,8 +450,14 @@ static int msix_capability_init(struct pci_dev *dev,
 
 	for (i = 0; i < nvec; i++) {
 		entry = alloc_msi_entry(dev);
-		if (!entry)
-			break;
+		if (!entry) {
+			if (!i)
+				iounmap(base);
+			else
+				msi_free_irqs(dev);
+			/* No enough memory. Don't try again */
+			return -ENOMEM;
+		}
 
  		j = entries[i].entry;
 		entry->msi_attrib.is_msix = 1;
@@ -487,7 +504,7 @@ static int msix_capability_init(struct pci_dev *dev,
 		set_irq_msi(entry->irq, entry);
 		j = entries[i].entry;
 		entry->masked = readl(base + j * PCI_MSIX_ENTRY_SIZE +
-					PCI_MSIX_ENTRY_VECTOR_CTRL_OFFSET);
+						PCI_MSIX_ENTRY_VECTOR_CTRL);
 		msix_mask_irq(entry, 1);
 		i++;
 	}
@@ -611,9 +628,11 @@ void pci_msi_shutdown(struct pci_dev *dev)
 	pci_intx_for_msi(dev, 1);
 	dev->msi_enabled = 0;
 
+	/* Return the device with MSI unmasked as initial states */
 	pci_read_config_word(dev, pos + PCI_MSI_FLAGS, &ctrl);
 	mask = msi_capable_mask(ctrl);
-	msi_mask_irq(desc, mask, ~mask);
+	/* Keep cached state to be restored */
+	__msi_mask_irq(desc, mask, ~mask);
 
 	/* Restore dev->irq to its default pin-assertion irq */
 	dev->irq = desc->msi_attrib.default_irq;
@@ -653,7 +672,6 @@ static int msi_free_irqs(struct pci_dev* dev)
 
 	list_for_each_entry_safe(entry, tmp, &dev->msi_list, list) {
 		if (entry->msi_attrib.is_msix) {
-			msix_mask_irq(entry, 1);
 			if (list_is_last(&entry->list, &dev->msi_list))
 				iounmap(entry->mask_base);
 		}
@@ -741,9 +759,17 @@ static void msix_free_all_irqs(struct pci_dev *dev)
 
 void pci_msix_shutdown(struct pci_dev* dev)
 {
+	struct msi_desc *entry;
+
 	if (!pci_msi_enable || !dev || !dev->msix_enabled)
 		return;
 
+	/* Return the device with MSI-X masked as initial states */
+	list_for_each_entry(entry, &dev->msi_list, list) {
+		/* Keep cached states to be restored */
+		__msix_mask_irq(entry, 1);
+	}
+
 	msix_set_enable(dev, 0);
 	pci_intx_for_msi(dev, 1);
 	dev->msix_enabled = 0;
diff --git a/drivers/pci/msi.h b/drivers/pci/msi.h
index a0662842550b..de27c1cb5a2b 100644
--- a/drivers/pci/msi.h
+++ b/drivers/pci/msi.h
@@ -6,11 +6,11 @@
 #ifndef MSI_H
 #define MSI_H
 
-#define PCI_MSIX_ENTRY_SIZE			16
-#define  PCI_MSIX_ENTRY_LOWER_ADDR_OFFSET	0
-#define  PCI_MSIX_ENTRY_UPPER_ADDR_OFFSET	4
-#define  PCI_MSIX_ENTRY_DATA_OFFSET		8
-#define  PCI_MSIX_ENTRY_VECTOR_CTRL_OFFSET	12
+#define PCI_MSIX_ENTRY_SIZE		16
+#define  PCI_MSIX_ENTRY_LOWER_ADDR	0
+#define  PCI_MSIX_ENTRY_UPPER_ADDR	4
+#define  PCI_MSIX_ENTRY_DATA		8
+#define  PCI_MSIX_ENTRY_VECTOR_CTRL	12
 
 #define msi_control_reg(base)		(base + PCI_MSI_FLAGS)
 #define msi_lower_address_reg(base)	(base + PCI_MSI_ADDRESS_LO)
diff --git a/drivers/pci/pci.c b/drivers/pci/pci.c
index 6c93af5ced18..dbd0f947f497 100644
--- a/drivers/pci/pci.c
+++ b/drivers/pci/pci.c
@@ -1517,11 +1517,20 @@ void pci_enable_ari(struct pci_dev *dev)
  *
  * Perform INTx swizzling for a device behind one level of bridge.  This is
  * required by section 9.1 of the PCI-to-PCI bridge specification for devices
- * behind bridges on add-in cards.
+ * behind bridges on add-in cards.  For devices with ARI enabled, the slot
+ * number is always 0 (see the Implementation Note in section 2.2.8.1 of
+ * the PCI Express Base Specification, Revision 2.1)
  */
 u8 pci_swizzle_interrupt_pin(struct pci_dev *dev, u8 pin)
 {
-	return (((pin - 1) + PCI_SLOT(dev->devfn)) % 4) + 1;
+	int slot;
+
+	if (pci_ari_enabled(dev->bus))
+		slot = 0;
+	else
+		slot = PCI_SLOT(dev->devfn);
+
+	return (((pin - 1) + slot) % 4) + 1;
 }
 
 int
@@ -2171,7 +2180,7 @@ static int pci_parent_bus_reset(struct pci_dev *dev, int probe)
 	u16 ctrl;
 	struct pci_dev *pdev;
 
-	if (dev->subordinate)
+	if (pci_is_root_bus(dev->bus) || dev->subordinate || !dev->bus->self)
 		return -ENOTTY;
 
 	list_for_each_entry(pdev, &dev->bus->devices, bus_list)
diff --git a/drivers/pci/pcie/aer/ecrc.c b/drivers/pci/pcie/aer/ecrc.c
index ece97df4df6d..a928d8ab6bda 100644
--- a/drivers/pci/pcie/aer/ecrc.c
+++ b/drivers/pci/pcie/aer/ecrc.c
@@ -106,7 +106,7 @@ void pcie_set_ecrc_checking(struct pci_dev *dev)
 		disable_ecrc_checking(dev);
 		break;
 	case ECRC_POLICY_ON:
-		enable_ecrc_checking(dev);;
+		enable_ecrc_checking(dev);
 		break;
 	default:
 		return;
diff --git a/drivers/pci/quirks.c b/drivers/pci/quirks.c
index 56552d74abea..06b965623962 100644
--- a/drivers/pci/quirks.c
+++ b/drivers/pci/quirks.c
@@ -1058,6 +1058,11 @@ static void __devinit quirk_no_ata_d3(struct pci_dev *pdev)
 }
 DECLARE_PCI_FIXUP_EARLY(PCI_VENDOR_ID_SERVERWORKS, PCI_ANY_ID, quirk_no_ata_d3);
 DECLARE_PCI_FIXUP_EARLY(PCI_VENDOR_ID_ATI, PCI_ANY_ID, quirk_no_ata_d3);
+/* ALi loses some register settings that we cannot then restore */
+DECLARE_PCI_FIXUP_EARLY(PCI_VENDOR_ID_AL, PCI_ANY_ID, quirk_no_ata_d3);
+/* VIA comes back fine but we need to keep it alive or ACPI GTM failures
+   occur when mode detecting */
+DECLARE_PCI_FIXUP_EARLY(PCI_VENDOR_ID_VIA, PCI_ANY_ID, quirk_no_ata_d3);
 
 /* This was originally an Alpha specific thing, but it really fits here.
  * The i82375 PCI/EISA bridge appears as non-classified. Fix that.
diff --git a/drivers/pci/slot.c b/drivers/pci/slot.c
index eddb0748b0ea..8c02b6c53bdb 100644
--- a/drivers/pci/slot.c
+++ b/drivers/pci/slot.c
@@ -311,7 +311,7 @@ EXPORT_SYMBOL_GPL(pci_destroy_slot);
 #include <linux/pci_hotplug.h>
 /**
  * pci_hp_create_link - create symbolic link to the hotplug driver module.
- * @slot: struct pci_slot
+ * @pci_slot: struct pci_slot
  *
  * Helper function for pci_hotplug_core.c to create symbolic link to
  * the hotplug driver module.
@@ -334,7 +334,7 @@ EXPORT_SYMBOL_GPL(pci_hp_create_module_link);
 
 /**
  * pci_hp_remove_link - remove symbolic link to the hotplug driver module.
- * @slot: struct pci_slot
+ * @pci_slot: struct pci_slot
  *
  * Helper function for pci_hotplug_core.c to remove symbolic link to
  * the hotplug driver module.
diff --git a/include/linux/pci.h b/include/linux/pci.h
index d304ddf412d0..115fb7ba5089 100644
--- a/include/linux/pci.h
+++ b/include/linux/pci.h
@@ -1145,7 +1145,7 @@ static inline void pci_set_drvdata(struct pci_dev *pdev, void *data)
 /* If you want to know what to call your pci_dev, ask this function.
  * Again, it's a wrapper around the generic device.
  */
-static inline const char *pci_name(struct pci_dev *pdev)
+static inline const char *pci_name(const struct pci_dev *pdev)
 {
 	return dev_name(&pdev->dev);
 }