like said in the title, I don't really understand the usage of this syscall. I was writing some program that write some data in a file, and the tutorial I've seen told me to use sys_sync syscall. But my problem is why and when should we use this? The data isn't already written on the file?
The manual says:
sync - Synchronize cached writes to persistent storage
So it is written to the file cache in memory, not on disk.
You rarely have to use sync unless you are writing really important data and need to make sure that data is on disk before you go on. One example of systems that use sync a lot are databases (such as MySQL or PostgreSQL).
So in other words, it is theoretically in your file, just not on disk and therefore if you lose electricity, you could lose the data, especially if you have a lot of RAM and many writes in a raw, it may privilege the writes to cache for a long while, increasing the risk of data loss.
But how can a file be not on the disk? I understand the concept of cache but if I wrote in the disk why would it be in a different place?
First, when you write to a file, you send the data to the Kernel. You don't directly send it to the disk. Some kernel driver is then responsible to write the data to disk. In my days on Apple 2 and Amiga computers, I would actually directly read/write to disk. And at least the Amiga had a DMA so you could setup a buffer, then tell the disk I/O to do a read or a write and it would send you an interrupt when done. On the Apple 2, you had to write loops in assembly language with precise timings to read/write data on floppy disks... A different era!
Although you could, of course, directly access the disk (but with a Kernel like Linux, you'd have to make sure the kernel gives you hands free to do that...).
Cache is primarily used for speed. It is very slow to write to disk (as far as a human is concerned, it looks extremely fast, but compared to how much data the CPU can push to the drive, it's still slow).
So what happens is that the kernel has a task to write data to disk. That task wakes up as soon as data appears in the cache and ends once all the caches are transferred to disk. This task works in parallel. You can have one such task per drive (which is especially useful when you have a system such as RAID 1).
If your application fills up the cache, then a further write will block until some of the cache can be replaced.
and the tutorial I've seen told me to use sys_sync syscall
Well that sounds silly, unless you're doing filesystem write benchmarking or something.
If you have one really critical file that you want to make sure is "durable" wrt. power outages before you do something else (like sent a network packet to acknowledge a complete transfer), use fsync(fd) to sync just that one file's data and metadata.
(In asm, call number SYS_fsync from sys/syscall.h, with the file descriptor as the first register arg.)
But my problem is why and when should we use this?
Generally never use the sync system call in programs you're writing.
There are interactive use-cases where you'd normally use the wrapper command of the same name, sync(1). e.g. with removable media, to get the kernel started doing write-back now, so unmount will take less time once you finish typing it. Or for some benchmarking use-cases.
The system shutdown scripts may run sync after unmounting filesystems (and remounting / read-only), before making a reboot(2) system call.
Re: why sync(2) exists
No, your data isn't already on disk right after echo foo > bar.txt.
Most OSes, including Linux, do write-back caching, not write-through, for file writes.
You don't want write() system calls to wait for an actual magnetic disk when there's free RAM, because the traditional way to do I/O is synchronous so simple single-threaded programs wouldn't be able to do anything else (like reading more data or computing anything) while waiting for write() to return. Blocking for ~10 ms on every write system call would be disastrous; that's as long as a whole scheduler timeslice. (It would still be bad even with SSDs, but of course OSes were designed before SSDs were a thing.) Even just queueing up the DMA would be slow, especially for small file writes that aren't a whole number of aligned sectors, so even letting the disk's own write-back write caching work wouldn't be good enough.
Therefore, file writes do create "dirty" pages of kernel buffers that haven't yet been sent to the disk. Sometimes we can even avoid the IO entirely, e.g. for tmp files that get deleted before anything triggers write-back. On Linux, dirty_writeback_centisecs defaults to 1500 (15 seconds) before the kernel starts write-back, unless it's running low on free pages. (Heuristics for what "low" means use other tunable values).
If you really want writes to flush to disk immediately and wait for data to be on disk, mount with -o sync. Or for one program, have it use open(O_SYNC) or O_DSYNC (for just the data, not metadata like timestamps).
See Are file reads served from dirtied pages in the page cache?
There are other advantages to write-back, including delayed allocation even at the filesystem level. The FS can wait until it knows how big the file will be before even deciding where to put it, allowing better decisions that reduce fragmentation. e.g. a small file can go into a gap that would have been a bad place to start a potentially-large file. (It just have to reserve space to make sure it can put it somewhere.) XFS was one of the first filesystems to do "lazy" delayed allocation, and ext4 has also had the feature for a while.
https://en.wikipedia.org/wiki/XFS#Delayed_allocation
https://en.wikipedia.org/wiki/Allocate-on-flush
https://lwn.net/Articles/323169/
Related
Suppose that a process needs to access the file system in many (1000+) places, and the order is not important to the program logic. However, the order obviously matters for performance if the file system is stored on a (spinning) hard disk.
How can the application programmer communicate to the OS that it should schedule the accesses optimally? Launching 1000+ threads does not seem practical. Does database management software accomplish this, and if so, then how?
Additional details: I had a large (1TB+) mmapped file where I needed to read 1000+ chunks of about 1KB, each time in new, unpredictable places.
In the early days when parameters like Wikipedia: Hard disk drive performance characteristics → Seek time were very expensive and thus very important, database vendors payed attention to the on-disk data representation and layout as can be seen e.g. in Oracle8i: Designing and Tuning for Performance → Tuning I/O.
The important optimization parameters changed with appearance of Solid-state drives (SSD) where the seek time is 0 (or at least constant) as there is nothing to rotate. Some of the new parameters are addressed by Wikipedia: Solid-state drive (SSD) → optimized file systems.
But even those optimization parameters go away with the use of Wikipedia: In-memory databases. The list of vendors is pretty long, all big players on it.
So how to schedule your access optimally depends a lot on the use case (1000 concurrent hits is not sufficient problem description) and buying some RAM is one of the options and "how can the programmer communicate with the OS" will be one of the last (not first) questions
Files and their transactions are cached in various devices in your computer; RAM and the HD cache are the most usual places. The file system driver may also implement IO transaction queues, defragmentation, and error-correction logic that makes things complicated for the developer who wants to control every aspect of file access. This level of complexity is ultimately designed to provide integrity, security, performance, and coordination of file access across all processes of your system.
Optimization efforts should not interfere with the system's own caching and prediction algorithms, not just for IO but for all caches. Trying to second-guess your system is a waste of your time and your processors' time.
Most probably your IO operations and data will stay on caches and later be committed to your storage devices when your OS sees fit.
That said, there's always options like database suites, mmap, readahead mechanisms, and direct IO to your drive. You will need to invest time benchmarking any of your efforts. I advise against multiple IO threads because cache contention will make things even slower than one thread.
The kernel will already reorder the read/write requests (e.g. to fit the spin of a mechanical disk), if they come from various processes or threads. BTW, most of the reads & writes would go to the kernel file system cache, not to the disk.
You might consider using posix_fadvise(2) & perhaps (in a separate thread) readahead(2). If -instead of read(2)-ing- you use mmap(2) to project some file portion to virtual memory, you might use also madvise(2)
Of course, the file system does not usually guarantee that a sequential portion of a file is physically sequentially located on the disk (and even the disk firmware might reorder sectors). See picture in Ext2 wikipage, also relevant for Ext4. Some file systems might be better in that respect, and you could tune their block size (at mkfs time).
I would not recommend having thousands of threads (only at most a few dozens).
At last, it might worth buying some SSD or some more RAM (for file cache). See http://linuxatemyram.com/
Actual performance would depend a lot on the particular system and hardware.
Perhaps using an indexed file library like GDBM or a database library Sqlite (or a real database like PostGreSQL) might be worthwhile! Perhaps have fewer files but bigger ones could help.
BTW, you are mmap-ing, and reading small chunk of 1K (smaller than page size of 4K). You could use madvise (if possible in advance), but you should try to read larger chunks, since every file access will bring at least a whole page.
You really should benchmark!
I'm working on a web crawler and have to handle big data (about 160 TB raw data in trillions of data files).
The data should be stored sequencial as one big bz2 file on the magnetic hard disk. A SSD is used to hold the meta data. THe most important operation on the hard disk is a squential read over all of the 4 TB off the disk, which should happen with full maximum speed of 150 MB/s.
I want to not waste the overhead of a file system an instead use the "/dev/file" devices directly. Does this access use the os block buffer? Are the access operations queued or synchronous in a FIFO style?
Is it better to use /dev/file or write your own user level file system?
Has anyone experience with it.
If you don't use any file system but read your disk device (e.g. /dev/sdb) directly, you are losing all the benefit of file system cache. I am not at all sure it is worthwhile.
Remember that you could use syscalls like readahead(2) or posix_fadvise(2) or madvise(2) to give hints to the kernel to improve performance.
Also, you might when making your file system use a larger than usual block size. And don't forget to use big blocks (e.g. of 64 to 256 Kbytes) when read(2)-ing data. You could also use mmap(2) to get the data from disk.
I would recommend against "coding your own file system". Existing file systems are quite tuned (and some are used on petabytes of storage). You may want to chose big blocks when making them (e.g. -b with mke2fs(8)...)
BTW, choosing between filesystem and raw disk data is mostly a configuration issue (you specify a /dev/sdb path if you want raw disk, and /home/somebigfile if you want a file). You could code a webcrawler to be able to do both, then benchmark both approaches. Very likely, performance could depend upon actual system and hardware.
As a case in point, relational database engines used often raw disk partitions in the previous century (e.g. 1990s) but seems to often use big files today.
Remember that the real bottleneck is the hardware (i.e. disk): CPU time used by filesystems is often insignificant and cannot even be measured.
PS. I have not much real recent experience with these issues.
I have a C program that runs only weekly, and reads a large amount of files only once. Since Linux also caches everything that's read, they fill up the cache needlessly and this slows down the system a lot unless it has an SSD drive.
So how do I open and read from a file without filling up the disk cache?
Note:
By disk caching I mean that when you read a file twice, the second time it's read from RAM, not from disk. I.e. data once read from the disk is left in RAM, so subsequent reads of the same file will not need to reread the data from disk.
I believe passing O_DIRECT to open() should help:
O_DIRECT (Since Linux 2.4.10)
Try to minimize cache effects of the I/O to and from this file. In general this will degrade performance, but it is useful in special situations, such as when applications do their own caching. File I/O is done directly to/from user space buffers. The O_DIRECT flag on its own makes at an effort to transfer data synchronously, but does not give the guarantees of the O_SYNC that data and necessary metadata are transferred. To guarantee synchronous I/O the O_SYNC must be used in addition to O_DIRECT.
There are further detailed notes on O_DIRECT towards the bottom of the man page, including a fun quote from Linus.
You can use posix_fadvise() with the POSIX_FADV_DONTNEED advice to request that the system free the pages you've already read.
I'm writing lots and lots of data that will not be read again for weeks - as my program runs the amount of free memory on the machine (displayed with 'free' or 'top') drops very quickly, the amount of memory my app uses does not increase - neither does the amount of memory used by other processes.
This leads me to believe the memory is being consumed by the filesystems cache - since I do not intend to read this data for a long time I'm hoping to bypass the systems buffers, such that my data is written directly to disk. I dont have dreams of improving perf or being a super ninja, my hope is to give a hint to the filesystem that I'm not going to be coming back for this memory any time soon, so dont spend time optimizing for those cases.
On Windows I've faced similar problems and fixed the problem using FILE_FLAG_NO_BUFFERING|FILE_FLAG_WRITE_THROUGH - the machines memory was not consumed by my app and the machine was more usable in general. I'm hoping to duplicate the improvements I've seen but on Linux. On Windows there is the restriction of writing in sector sized pieces, I'm happy with this restriction for the amount of gain I've measured.
is there a similar way to do this in Linux?
The closest equivalent to the Windows flags you mention I can think of is to open your file with the open(2) flags O_DIRECT | O_SYNC:
O_DIRECT (Since Linux 2.4.10)
Try to minimize cache effects of the I/O to and from this file. In
general this will degrade performance, but it is useful in special
situations, such as when applications do their own caching. File I/O
is done directly to/from user space buffers. The O_DIRECT flag on its
own makes at an effort to transfer data synchronously, but does not
give the guarantees of the O_SYNC that data and necessary metadata are
transferred. To guarantee synchronous I/O the O_SYNC must be used in
addition to O_DIRECT. See NOTES below for further discussion.
A semantically similar (but deprecated) interface for block devices is
described in raw(8).
Granted, trying to do research on this flag to confirm it's what you want I found this interesting piece telling you that unbuffered I/O is a bad idea, Linus describing it as "brain damaged". According to that you should be using madvise() instead to tell the kernel how to cache pages. YMMV.
You can use O_DIRECT, but in that case you need to do the block IO yourself; you must write in multiples of the FS block size and on block boundaries (it is possible that it is not mandatory but if you do not its performance will suck x1000 because every unaligned write will need a read first).
Another much less impacting way of stopping your blocks using up the OS cache without using O_DIRECT, is to use posix_fadvise(fd, offset,len, POSIX_FADV_DONTNEED). Under Linux 2.6 kernels which support it, this immediately discards (clean) blocks from the cache. Of course you need to use fdatasync() or such like first, otherwise the blocks may still be dirty and hence won't be cleared from the cache.
It is probably a bad idea of fdatasync() and posix_fadvise( ... POSIX_FADV_DONTNEED) after every write, but instead wait until you've done a reasonable amount (50M, 100M maybe).
So in short
after every (significant chunk) of writes,
Call fdatasync followed by posix_fadvise( ... POSIX_FADV_DONTNEED)
This will flush the data to disc and immediately remove them from the OS cache, leaving space for more important things.
Some users have found that things like fast-growing log files can easily blow "more useful" stuff out of the disc cache, which reduces cache hits a lot on a box which needs to have a lot of read cache, but also writes logs quickly. This is the main motivation for this feature.
However, like any optimisation
a) You're not going to need it so
b) Do not do it (yet)
as my program runs the amount of free memory on the machine drops very quickly
Why is this a problem? Free memory is memory that isn't serving any useful purpose. When it's used to cache data, at least there is a chance it will be useful.
If one of your programs requests more memory, file caches will be the first thing to go. Linux knows that it can re-read that data from disk whenever it wants, so it will just reap the memory and give it a new use.
It's true that Linux by default waits around 30 seconds (this is what the value used to be anyhow) before flushing writes to disk. You can speed this up with a call to fsync(). But once the data has been written to disk, there's practically zero cost to keeping a cache of the data in memory.
Seeing as you write to the file and don't read from it, Linux will probably guess that this data is the best to throw out, in preference to other cached data. So don't waste effort trying to optimise unless you've confirmed that it's a performance problem.
I'm working on an embedded Linux project that interfaces an ARM9 to a hardware video encoder chip, and writes the video out to SD card or USB stick. The software architecture involves a kernel driver that reads data into a pool of buffers, and a userland app that writes the data to a file on the mounted removable device.
I am finding that above a certain data rate (around 750kbyte/sec) I start to see the userland video-writing app stalling for maybe half a second, about every 5 seconds. This is enough to cause the kernel driver to run out of buffers - and even if I could increase the number of buffers, the video data has to be synchronised (ideally within 40ms) with other things that are going on in real time. Between these 5 second "lag spikes", the writes complete well within 40ms (as far as the app is concerned - I appreciate they're buffered by the OS)
I think this lag spike is to do with the way Linux is flushing data out to disk - I note that pdflush is designed to wake up every 5s, my understanding is that this would be what does the writing. As soon as the stall is over the userland app is able to quickly service and write the backlog of buffers (that didn't overflow).
I think the device I'm writing to has reasonable ultimate throughput: copying a 15MB file from a memory fs and waiting for sync to complete (and the usb stick's light to stop flashing) gave me a write speed of around 2.7MBytes/sec.
I'm looking for two kinds of clues:
How can I stop the bursty writing from stalling my app - perhaps process priorities, realtime patches, or tuning the filesystem code to write continuously rather than burstily?
How can I make my app(s) aware of what is going on with the filesystem in terms of write backlog and throughput to the card/stick? I have the ability to change the video bitrate in the hardware codec on the fly which would be much better than dropping frames, or imposing an artificial cap on maximum allowed bitrate.
Some more info: this is a 200MHz ARM9 currently running a Montavista 2.6.10-based kernel.
Updates:
Mounting the filesystem SYNC causes throughput to be much too poor.
The removable media is FAT/FAT32 formatted and must be as the purpose of the design is that the media can be plugged into any Windows PC and read.
Regularly calling sync() or fsync() say, every second causes regular stalls and unacceptably poor throughput
I am using write() and open(O_WRONLY | O_CREAT | O_TRUNC) rather than fopen() etc.
I can't immediately find anything online about the mentioned "Linux realtime filesystems". Links?
I hope this makes sense. First embedded Linux question on stackoverflow? :)
For the record, there turned out to be two main aspects that seem to have eliminated the problem in all but the most extreme cases. This system is still in development and hasn't been thoroughly torture-tested yet but is working fairly well (touch wood).
The big win came from making the userland writer app multi-threaded. It is the calls to write() that block sometimes: other processes and threads still run. So long as I have a thread servicing the device driver and updating frame counts and other data to sychronise with other apps that are running, the data can be buffered and written out a few seconds later without breaking any deadlines. I tried a simple ping-pong double buffer first but that wasn't enough; small buffers would be overwhelmed and big ones just caused bigger pauses while the filesystem digested the writes. A pool of 10 1MB buffers queued between threads is working well now.
The other aspect is keeping an eye on ultimate write throughput to physical media. For this I am keeping an eye on the stat Dirty: reported by /proc/meminfo. I have some rough and ready code to throttle the encoder if Dirty: climbs above a certain threshold, seems to vaguely work. More testing and tuning needed later. Fortunately I have lots of RAM (128M) to play with giving me a few seconds to see my backlog building up and throttle down smoothly.
I'll try to remember to pop back and update this answer if I find I need to do anything else to deal with this issue. Thanks to the other answerers.
I'll throw out some suggestions, advice is cheap.
make sure you are using a lower level API for writing to the disk, don't use user-mode caching functions like fopen, fread, fwrite use the lower level functions open, read, write.
pass the O_SYNC flag when you open the file, this will cause each write operation to block until written to disk, which will remove the bursty behavior of your writes...with the expense of each write being slower.
If you are doing reads/ioctls from a device to grab a chunk of video data, you may want to consider allocating a shared memory region between the application and kernel, otherwise you are getting hit with a bunch of copy_to_user calls when transferring video data buffers from kernel space to user space.
You may need to validate that your USB flash device is fast enough with sustained transfers to write the data.
Just a couple thoughts, hope this helps.
Here is some information about tuning pdflush for write-heavy operations.
Sounds like you're looking for linux realtime filesystems. Be sure to search Google et al for that.
XFS has a realtime option, though I haven't played with it.
hdparm might let you turn off the caching altogether.
Tuning the filesystem options (turn off all the extra unneeded file attributes) might reduce what you need to flush, thus speeding the flush. I doubt that'd help much, though.
But my suggestion would be to avoid using the stick as a filesystem at all and instead use it as a raw device. Stuff data on it like you would using 'dd'. Then elsewhere read that raw data and write it out after baking.
Of course, I don't know if that's an option for you.
Has a debugging aid, you could use strace to see what operations is taking time.
There might be some surprising thing with the FAT/FAT32.
Do you write into a single file, or in multiple file ?
You can make a reading thread, that will maintain a pool of video buffer ready to be written in a queue.
When a frame is received, it is added to the queue, and the writing thread is signaled
Shared data
empty_buffer_queue
ready_buffer_queue
video_data_ready_semaphore
Reading thread :
buf=get_buffer()
bufer_to_write = buf_dequeue(empty_buffer_queue)
memcpy(bufer_to_write, buf)
buf_enqueue(bufer_to_write, ready_buffer_queue)
sem_post(video_data_ready_semaphore)
Writing thread
sem_wait(vido_data_ready_semaphore)
bufer_to_write = buf_dequeue(ready_buffer_queue)
write_buffer
buf_enqueue(bufer_to_write, empty_buffer_queue)
If your writing threaded is blocked waiting for the kernel, this could work.
However, if you are blocked inside the kerne space, then thereis nothing much you can do, except looking for a more recent kernel than your 2.6.10
Without knowing more about your particular circumstances, I can only offer the following guesses:
Try using fsync()/sync() to force the kernel to flush data to the storage device more frequently. It sounds like the kernel buffers all your writes and then ties up the bus or otherwise stalls your system while performing the actual write. With careful calls to fsync() you can try to schedule writes over the system bus in a more fine grained way.
It might make sense to structure the application in such a way that the encoding/capture (you didn't mention video capture, so I'm making an assumption here - you might want to add more information) task runs in its own thread and buffers its output in userland - then, a second thread can handle writing to the device. This will give you a smoothing buffer to allow the encoder to always finish its writes without blocking.
One thing that sounds suspicious is that you only see this problem at a certain data rate - if this really was a buffering issue, I'd expect the problem to happen less frequently at lower data rates, but I'd still expect to see this issue.
In any case, more information might prove useful. What's your system's architecture? (In very general terms.)
Given the additional information you provided, it sounds like the device's throughput is rather poor for small writes and frequent flushes. If you're sure that for larger writes you can get sufficient throughput (and I'm not sure that's the case, but the file system might be doing something stupid, like updating the FAT after every write) then having an encoding thread piping data to a writing thread with sufficient buffering in the writing thread to avoid stalls. I've used shared memory ring buffers in the past to implement this kind of scheme, but any IPC mechanism that would allow the writer to write to the I/O process without stalling unless the buffer is full should do the trick.
A useful Linux function and alternative to sync or fsync is sync_file_range. This lets you schedule data for writing without waiting for the in-kernel buffer system to get around to it.
To avoid long pauses, make sure your IO queue (for example: /sys/block/hda/queue/nr_requests) is large enough. That queue is where data goes in between being flushed from memory and arriving on disk.
Note that sync_file_range isn't portable, and is only available in kernels 2.6.17 and later.
I've been told that after the host sends a command, MMC and SD cards "must respond within 0 to 8 bytes".
However, the spec allows these cards to respond with "busy" until they have finished the operation, and apparently there is no limit to how long a card can claim to be busy (please, please tell me if there is such a limit).
I see that some low-cost flash chips such as the M25P80 have a guaranteed "maximum single-sector erase time" of 3 seconds, although typically it "only" requires 0.6 seconds.
That 0.6 seconds sounds suspiciously similar to your "stalling for maybe half a second".
I suspect the tradeoff between cheap, slow flash chips and expensive, fast flash chips has something to do with the wide variation in USB flash drive results:
http://www.testfreaks.com/blog/information/16gb-usb-drive-comparison-17-drives-compared/
http://www.tomshardware.com/reviews/data-transfer-run,1037-10.html
I've heard rumors that every time a flash sector is erased and then re-programmed, it takes a little bit longer than the last time.
So if you have a time-critical application, you may need to (a) test your SD cards and USB sticks to make sure they meet the minimum latency, bandwidth, etc. required by your application, and (b) peridically re-test or pre-emptively replace these memory devices.
Well obvious first, have you tried explicitly telling the file to flush? I also think there might be some ioctl you can use to do it, but I honestly haven't done much C/POSIX file programming.
Seeing you're on a Linux kernel you should be able to tune and rebuild the kernel to something that suits your needs better, eg. much more frequent but then also smaller flushes to the permanent storage.
A quick check in my man pages finds this:
SYNC(2) Linux Programmer’s Manual SYNC(2)
NAME
sync - commit buffer cache to disk
SYNOPSIS
#include <unistd.h>
void sync(void);
Feature Test Macro Requirements for glibc (see feature_test_macros(7)):
sync(): _BSD_SOURCE || _XOPEN_SOURCE >= 500
DESCRIPTION
sync() first commits inodes to buffers, and then buffers to disk.
ERRORS
This function is always successful.
Doing your own flush()ing sounds right to me - you want to be in control, not leave it to the vagaries of the generic buffer layer.
This may be obvious, but make sure you're not calling write() too often - make sure every write() has enough data to be written to make the syscall overhead worth it. Also, in the other direction, don't call it too seldom, or it'll block for long enough to cause a problem.
On a more difficult-to-reimplement track, have you tried switching to asynchronous i/o? Using aio you could fire off a write and hand it one set of buffers while you're sucking video data into the other set, and when the write finishes you switch sets of buffers.