PCI - how does it work at the hardware level?   

http://www.fpga4fun.com/PCI.html

How does PCI worked in Linux?

From the documentation Documentation/PCI/pci.txt - here are the setup/teardown details:
(how to write a PCI drivers?)

Once the driver knows about a PCI device and takes ownership, the
driver generally needs to perform the following initialization:

        Enable the device
        Request MMIO/IOP resources
        Set the DMA mask size (for both coherent and streaming DMA)
        Allocate and initialize shared control data (pci_allocate_coherent())
        Access device configuration space (if needed)
        Register IRQ handler (request_irq())
        Initialize non-PCI (i.e. LAN/SCSI/etc parts of the chip)
        Enable DMA/processing engines

When done using the device, and perhaps the module needs to be unloaded,
the driver needs to take the follow steps:

        Disable the device from generating IRQs
        Release the IRQ (free_irq())
        Stop all DMA activity
        Release DMA buffers (both streaming and coherent)
        Unregister from other subsystems (e.g. scsi or netdev)
        Release MMIO/IOP resources
        Disable the device

On the other hand, how to write a userspace PCI drivers:

http://lwn.net/Articles/197523/

What are the commands to control the PCI?

Inside the linux/pci_regs.h:

/*
 * Under PCI, each device has 256 bytes of configuration address space,
 * of which the first 64 bytes are standardized as follows:
 */
#define PCI_VENDOR_ID           0x00    /* 16 bits */
#define PCI_DEVICE_ID           0x02    /* 16 bits */
#define PCI_COMMAND             0x04    /* 16 bits */
#define  PCI_COMMAND_IO         0x1     /* Enable response in I/O space */
#define  PCI_COMMAND_MEMORY     0x2     /* Enable response in Memory space */
#define  PCI_COMMAND_MASTER     0x4     /* Enable bus mastering */
#define  PCI_COMMAND_SPECIAL    0x8     /* Enable response to special cycles */
#define  PCI_COMMAND_INVALIDATE 0x10    /* Use memory write and invalidate */
   
#define  PCI_COMMAND_VGA_PALETTE 0x20   /* Enable palette snooping */
                 
#define  PCI_COMMAND_PARITY     0x40    /* Enable parity checking */
#define  PCI_COMMAND_WAIT       0x80    /* Enable address/data stepping */
#define  PCI_COMMAND_SERR       0x100   /* Enable SERR */
#define  PCI_COMMAND_FAST_BACK  0x200   /* Enable back-to-back writes */
#define  PCI_COMMAND_INTX_DISABLE 0x400 /* INTx Emulation Disable */

#define PCI_STATUS              0x06    /* 16 bits */
#define  PCI_STATUS_CAP_LIST    0x10    /* Support Capability List */
#define  PCI_STATUS_66MHZ       0x20    /* Support 66 Mhz PCI 2.1 bus */
#define  PCI_STATUS_UDF         0x40    /* Support User Definable Features [obsolete] */
#define  PCI_STATUS_FAST_BACK   0x80    /* Accept fast-back to back */
#define  PCI_STATUS_PARITY      0x100   /* Detected parity error */
#define  PCI_STATUS_DEVSEL_MASK 0x600   /* DEVSEL timing */
#define  PCI_STATUS_DEVSEL_FAST         0x000
#define  PCI_STATUS_DEVSEL_MEDIUM       0x200
#define  PCI_STATUS_DEVSEL_SLOW         0x400
#define  PCI_STATUS_SIG_TARGET_ABORT    0x800 /* Set on target abort */
#define  PCI_STATUS_REC_TARGET_ABORT    0x1000 /* Master ack of " */
#define  PCI_STATUS_REC_MASTER_ABORT    0x2000 /* Set on master abort */
#define  PCI_STATUS_SIG_SYSTEM_ERROR    0x4000 /* Set when we drive SERR */
#define  PCI_STATUS_DETECTED_PARITY     0x8000 /* Set on parity error */

#define PCI_CLASS_REVISION      0x08    /* High 24 bits are class, low 8 revision */
#define PCI_REVISION_ID         0x08    /* Revision ID */
#define PCI_CLASS_PROG          0x09    /* Reg. Level Programming Interface */
#define PCI_CLASS_DEVICE        0x0a    /* Device class */

#define PCI_CACHE_LINE_SIZE     0x0c    /* 8 bits */
#define PCI_LATENCY_TIMER       0x0d    /* 8 bits */
#define PCI_HEADER_TYPE         0x0e    /* 8 bits */
#define  PCI_HEADER_TYPE_NORMAL         0
#define  PCI_HEADER_TYPE_BRIDGE         1
#define  PCI_HEADER_TYPE_CARDBUS        2

#define PCI_BIST                0x0f    /* 8 bits */
#define  PCI_BIST_CODE_MASK     0x0f    /* Return result */
#define  PCI_BIST_START         0x40    /* 1 to start BIST, 2 secs or less */
#define  PCI_BIST_CAPABLE       0x80    /* 1 if BIST capable */

/*
 * Base addresses specify locations in memory or I/O space.
 * Decoded size can be determined by writing a value of
 * 0xffffffff to the register, and reading it back.  Only
 * 1 bits are decoded.
 */
#define PCI_BASE_ADDRESS_0      0x10    /* 32 bits */
#define PCI_BASE_ADDRESS_1      0x14    /* 32 bits [htype 0,1 only] */
#define PCI_BASE_ADDRESS_2      0x18    /* 32 bits [htype 0 only] */
#define PCI_BASE_ADDRESS_3      0x1c    /* 32 bits */
#define PCI_BASE_ADDRESS_4      0x20    /* 32 bits */
#define PCI_BASE_ADDRESS_5      0x24    /* 32 bits */
#define  PCI_BASE_ADDRESS_SPACE         0x01    /* 0 = memory, 1 = I/O */
#define  PCI_BASE_ADDRESS_SPACE_IO      0x01
#define  PCI_BASE_ADDRESS_SPACE_MEMORY  0x00
#define  PCI_BASE_ADDRESS_MEM_TYPE_MASK 0x06
#define  PCI_BASE_ADDRESS_MEM_TYPE_32   0x00    /* 32 bit address */
#define  PCI_BASE_ADDRESS_MEM_TYPE_1M   0x02    /* Below 1M [obsolete] */
#define  PCI_BASE_ADDRESS_MEM_TYPE_64   0x04    /* 64 bit address */
#define  PCI_BASE_ADDRESS_MEM_PREFETCH  0x08    /* prefetchable? */
#define  PCI_BASE_ADDRESS_MEM_MASK      (~0x0fUL)
#define  PCI_BASE_ADDRESS_IO_MASK       (~0x03UL)
/* bit 1 is reserved if address_space = 1 */




/* Capability lists */

#define PCI_CAP_LIST_ID         0       /* Capability ID */
#define  PCI_CAP_ID_PM          0x01    /* Power Management */
#define  PCI_CAP_ID_AGP         0x02    /* Accelerated Graphics Port */
#define  PCI_CAP_ID_VPD         0x03    /* Vital Product Data */
#define  PCI_CAP_ID_SLOTID      0x04    /* Slot Identification */
#define  PCI_CAP_ID_MSI         0x05    /* Message Signalled Interrupts */
#define  PCI_CAP_ID_CHSWP       0x06    /* CompactPCI HotSwap */
#define  PCI_CAP_ID_PCIX        0x07    /* PCI-X */
#define  PCI_CAP_ID_HT          0x08    /* HyperTransport */
#define  PCI_CAP_ID_VNDR        0x09    /* Vendor specific */
#define  PCI_CAP_ID_DBG         0x0A    /* Debug port */
#define  PCI_CAP_ID_CCRC        0x0B    /* CompactPCI Central Resource Control */
#define  PCI_CAP_ID_SHPC        0x0C    /* PCI Standard Hot-Plug Controller */
#define  PCI_CAP_ID_SSVID       0x0D    /* Bridge subsystem vendor/device ID */
#define  PCI_CAP_ID_AGP3        0x0E    /* AGP Target PCI-PCI bridge */
#define  PCI_CAP_ID_EXP         0x10    /* PCI Express */
#define  PCI_CAP_ID_MSIX        0x11    /* MSI-X */
#define PCI_CAP_LIST_NEXT       1       /* Next capability in the list */
#define PCI_CAP_FLAGS           2       /* Capability defined flags (16 bits) */
#define PCI_CAP_SIZEOF          4

/* Power Management Registers */


/* Power Management Registers */

#define PCI_PM_PMC              2       /* PM Capabilities Register */
#define  PCI_PM_CAP_VER_MASK    0x0007  /* Version */
#define  PCI_PM_CAP_PME_CLOCK   0x0008  /* PME clock required */
#define  PCI_PM_CAP_RESERVED    0x0010  /* Reserved field */
#define  PCI_PM_CAP_DSI         0x0020  /* Device specific initialization */
#define  PCI_PM_CAP_AUX_POWER   0x01C0  /* Auxilliary power support mask */
#define  PCI_PM_CAP_D1          0x0200  /* D1 power state support */
#define  PCI_PM_CAP_D2          0x0400  /* D2 power state support */
#define  PCI_PM_CAP_PME         0x0800  /* PME pin supported */
#define  PCI_PM_CAP_PME_MASK    0xF800  /* PME Mask of all supported states */
#define  PCI_PM_CAP_PME_D0      0x0800  /* PME# from D0 */
#define  PCI_PM_CAP_PME_D1      0x1000  /* PME# from D1 */
#define  PCI_PM_CAP_PME_D2      0x2000  /* PME# from D2 */
#define  PCI_PM_CAP_PME_D3      0x4000  /* PME# from D3 (hot) */
#define  PCI_PM_CAP_PME_D3cold  0x8000  /* PME# from D3 (cold) */
#define  PCI_PM_CAP_PME_SHIFT   11      /* Start of the PME Mask in PMC */
#define PCI_PM_CTRL             4       /* PM control and status register */
#define  PCI_PM_CTRL_STATE_MASK 0x0003  /* Current power state (D0 to D3) */
#define  PCI_PM_CTRL_NO_SOFT_RESET      0x0008  /* No reset for D3hot->D0 */
#define  PCI_PM_CTRL_PME_ENABLE 0x0100  /* PME pin enable */
#define  PCI_PM_CTRL_DATA_SEL_MASK      0x1e00  /* Data select (??) */
#define  PCI_PM_CTRL_DATA_SCALE_MASK    0x6000  /* Data scale (??) */
#define  PCI_PM_CTRL_PME_STATUS 0x8000  /* PME pin status */
#define PCI_PM_PPB_EXTENSIONS   6       /* PPB support extensions (??) */
#define  PCI_PM_PPB_B2_B3       0x40    /* Stop clock when in D3hot (??) */
#define  PCI_PM_BPCC_ENABLE     0x80    /* Bus power/clock control enable (??) */
#define PCI_PM_DATA_REGISTER    7       /* (??) */
#define PCI_PM_SIZEOF           8





/* AGP registers */

#define PCI_AGP_VERSION         2       /* BCD version number */
#define PCI_AGP_RFU             3       /* Rest of capability flags */
#define PCI_AGP_STATUS          4       /* Status register */
#define  PCI_AGP_STATUS_RQ_MASK 0xff000000      /* Maximum number of requests - 1 */
#define  PCI_AGP_STATUS_SBA     0x0200  /* Sideband addressing supported */
#define  PCI_AGP_STATUS_64BIT   0x0020  /* 64-bit addressing supported */
#define  PCI_AGP_STATUS_FW      0x0010  /* FW transfers supported */
#define  PCI_AGP_STATUS_RATE4   0x0004  /* 4x transfer rate supported */
#define  PCI_AGP_STATUS_RATE2   0x0002  /* 2x transfer rate supported */
#define  PCI_AGP_STATUS_RATE1   0x0001  /* 1x transfer rate supported */
#define PCI_AGP_COMMAND         8       /* Control register */
#define  PCI_AGP_COMMAND_RQ_MASK 0xff000000  /* Master: Maximum number of requests */
#define  PCI_AGP_COMMAND_SBA    0x0200  /* Sideband addressing enabled */
#define  PCI_AGP_COMMAND_AGP    0x0100  /* Allow processing of AGP transactions */
#define  PCI_AGP_COMMAND_64BIT  0x0020  /* Allow processing of 64-bit addresses */
#define  PCI_AGP_COMMAND_FW     0x0010  /* Force FW transfers */
#define  PCI_AGP_COMMAND_RATE4  0x0004  /* Use 4x rate */
#define  PCI_AGP_COMMAND_RATE2  0x0002  /* Use 2x rate */
#define  PCI_AGP_COMMAND_RATE1  0x0001  /* Use 1x rate */
#define PCI_AGP_SIZEOF          12






#define  PCI_IO_RANGE_MASK      (~0x0fUL)
#define PCI_SEC_STATUS          0x1e    /* Secondary status register, only bit 14 used */
#define PCI_MEMORY_BASE         0x20    /* Memory range behind */
#define PCI_MEMORY_LIMIT        0x22
#define  PCI_MEMORY_RANGE_TYPE_MASK 0x0fUL
#define  PCI_MEMORY_RANGE_MASK  (~0x0fUL)
#define PCI_PREF_MEMORY_BASE    0x24    /* Prefetchable memory range behind */
#define PCI_PREF_MEMORY_LIMIT   0x26
#define  PCI_PREF_RANGE_TYPE_MASK 0x0fUL
#define  PCI_PREF_RANGE_TYPE_32 0x00
#define  PCI_PREF_RANGE_TYPE_64 0x01
#define  PCI_PREF_RANGE_MASK    (~0x0fUL)
#define PCI_PREF_BASE_UPPER32   0x28    /* Upper half of prefetchable memory range */
#define PCI_PREF_LIMIT_UPPER32  0x2c
#define PCI_IO_BASE_UPPER16     0x30    /* Upper half of I/O addresses */
#define PCI_IO_LIMIT_UPPER16    0x32
/* 0x34 same as for htype 0 */
/* 0x35-0x3b is reserved */
#define PCI_ROM_ADDRESS1        0x38    /* Same as PCI_ROM_ADDRESS, but for htype 1 */
/* 0x3c-0x3d are same as for htype 0 */
#define PCI_BRIDGE_CONTROL      0x3e
#define  PCI_BRIDGE_CTL_PARITY  0x01    /* Enable parity detection on secondary interface */
#define  PCI_BRIDGE_CTL_SERR    0x02    /* The same for SERR forwarding */
#define  PCI_BRIDGE_CTL_ISA     0x04    /* Enable ISA mode */


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