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Top Forums Shell Programming and Scripting mapped reads using samtools flagstat options Post 302711219 by DGPickett on Friday 5th of October 2012 02:06:55 PM
Old 10-05-2012
Mapped files are read by VM page faults, so at least one per page. I suppose an aggressive OS might map ahead or in larger blocks to assist fastest sequential access at the cost of some extra VM churn. For instance, to optimize large SAN blocks and RAIS striped access, it might read 65K starting with the page of the next byte, or based at the modulo 65K address of that byte, into newly mapped pages. This exploits buffers and caching on the SAN and disk drives, as wells as being RAID tolerant by writing whole striped blocks across N drives.
 

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MD(4)							     Kernel Interfaces Manual							     MD(4)

NAME
md - Multiple Device driver aka Linux Software Raid SYNOPSIS
/dev/mdn /dev/md/n DESCRIPTION
The md driver provides virtual devices that are created from one or more independent underlying devices. This array of devices often con- tains redundancy, and hence the acronym RAID which stands for a Redundant Array of Independent Devices. md supports RAID levels 1 (mirroring) 4 (striped array with parity device) and 5 (striped array with distributed parity information). If a single underlying device fails while using one of these levels, the array will continue to function. md also supports a number of pseudo RAID (non-redundant) configurations including RAID0 (striped array), LINEAR (catenated array) and MUL- TIPATH (a set of different interfaces to the same device). MD SUPER BLOCK With the exception of Legacy Arrays described below, each device that is incorporated into an MD array has a super block written towards the end of the device. This superblock records information about the structure and state of the array so that the array can be reliably re-assembled after a shutdown. The superblock is 4K long and is written into a 64K aligned block that starts at least 64K and less than 128K from the end of the device (i.e. to get the address of the superblock round the size of the device down to a multiple of 64K and then subtract 64K). The available size of each device is the amount of space before the super block, so between 64K and 128K is lost when a device in incorporated into an MD array. The superblock contains, among other things: LEVEL The manner in which the devices are arranged into the array (linear, raid0, raid1, raid4, raid5, multipath). UUID a 128 bit Universally Unique Identifier that identifies the array that this device is part of. LEGACY ARRAYS Early versions of the md driver only supported Linear and Raid0 configurations and so did not use an MD superblock (as there is no state that needs to be recorded). While it is strongly recommended that all newly created arrays utilise a superblock to help ensure that they are assembled properly, the md driver still supports legacy linear and raid0 md arrays that do not have a superblock. LINEAR A linear array simply catenates the available space on each drive together to form one large virtual drive. One advantage of this arrangement over the more common RAID0 arrangement is that the array may be reconfigured at a later time with an extra drive and so the array is made bigger without disturbing the data that is on the array. However this cannot be done on a live array. RAID0 A RAID0 array (which has zero redundancy) is also known as a striped array. A RAID0 array is configured at creation with a Chunk Size which must be a power of two, and at least 4 kibibytes. The RAID0 driver assigns the first chunk of the array to the first device, the second chunk to the second device, and so on until all drives have been assigned one chunk. This collection of chunks forms a stripe. Further chunks are gathered into stripes in the same way which are assigned to the remaining space in the drives. If devices in the array are not all the same size, then once the smallest device has been exhausted, the RAID0 driver starts collecting chunks into smaller stripes that only span the drives which still have remaining space. RAID1 A RAID1 array is also known as a mirrored set (though mirrors tend to provide reflect images, which RAID1 does not) or a plex. Once initialised, each device in a RAID1 array contains exactly the same data. Changes are written to all devices in parallel. Data is read from any one device. The driver attempts to distribute read requests across all devices to maximise performance. All devices in a RAID1 array should be the same size. If they are not, then only the amount of space available on the smallest device is used. Any extra space on other devices is wasted. RAID4 A RAID4 array is like a RAID0 array with an extra device for storing parity. Unlike RAID0, RAID4 also requires that all stripes span all drives, so extra space on devices that are larger than the smallest is wasted. When any block in a RAID4 array is modified the parity block for that stripe (i.e. the block in the parity device at the same device offset as the stripe) is also modified so that the parity block always contains the "parity" for the whole stripe. i.e. its contents is equiva- lent to the result of performing an exclusive-or operation between all the data blocks in the stripe. This allows the array to continue to function if one device fails. The data that was on that device can be calculated as needed from the parity block and the other data blocks. RAID5 RAID5 is very similar to RAID4. The difference is that the parity blocks for each stripe, instead of being on a single device, are dis- tributed across all devices. This allows more parallelism when writing as two different block updates will quite possibly affect parity blocks on different devices so there is less contention. This also allows more parallelism when reading as read requests are distributed over all the devices in the array instead of all but one. MUTIPATH MULTIPATH is not really a RAID at all as there is only one real device in a MULTIPATH md array. However there are multiple access points (paths) to this device, and one of these paths might fail, so there are some similarities. A MULTIPATH array is composed of a number of logical different devices, often fibre channel interfaces, that all refer the the same real device. If one of these interfaces fails (e.g. due to cable problems), the multipath driver to attempt to redirect requests to another interface. UNCLEAN SHUTDOWN When changes are made to a RAID1, RAID4, or RAID5 array there is a possibility of inconsistency for short periods of time as each update requires are least two block to be written to different devices, and these writes probably wont happen at exactly the same time. Thus if a system with one of these arrays is shutdown in the middle of a write operation (e.g. due to power failure), the array may not be consis- tent. To handle this situation, the md driver marks an array as "dirty" before writing any data to it, and marks it as "clean" when the array is being disabled, e.g. at shutdown. If the md driver finds an array to be dirty at startup, it proceeds to correct any possibly inconsis- tency. For RAID1, this involves copying the contents of the first drive onto all other drives. For RAID4 or RAID5 this involves recalcu- lating the parity for each stripe and making sure that the parity block has the correct data. If a RAID4 or RAID5 array is degraded (missing one drive) when it is restarted after an unclean shutdown, it cannot recalculate parity, and so it is possible that data might be undetectably corrupted. The md driver currently does not alert the operator to this condition. It should probably fail to start an array in this condition without manual intervention. RECOVERY If the md driver detects any error on a device in a RAID1, RAID4, or RAID5 array, it immediately disables that device (marking it as faulty) and continues operation on the remaining devices. If there is a spare drive, the driver will start recreating on one of the spare drives the data what was on that failed drive, either by copying a working drive in a RAID1 configuration, or by doing calculations with the parity block on RAID4 and RAID5. While this recovery process is happening, the md driver will monitor accesses to the array and will slow down the rate of recovery if other activity is happening, so that normal access to the array will not be unduly affected. When no other activity is happening, the recovery process proceeds at full speed. The actual speed targets for the two different situations can be controlled by the speed_limit_min and speed_limit_max control files mentioned below. FILES
/proc/mdstat Contains information about the status of currently running array. /proc/sys/dev/raid/speed_limit_min A readable and writable file that reflects the current goal rebuild speed for times when non-rebuild activity is current on an array. The speed is in Kibibytes per second, and is a per-device rate, not a per-array rate (which means that an array with more disc will shuffle more data for a given speed). The default is 100. /proc/sys/dev/raid/speed_limit_max A readable and writable file that reflects the current goal rebuild speed for times when no non-rebuild activity is current on an array. The default is 100,000. SEE ALSO
mdadm(8), mkraid(8). MD(4)
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