efficiency of fwrite for massive numbers of small writes

Question

I have a program that saves many large files >1GB using fwrite It works fine, but unfortunately due to the nature of the data each call to fwrite only writes 1-4bytes. with the result that the write can take over an hour, with most of this time seemingly due to the syscall overhead (or at least in the library function of fwrite). I have a similar problem with fread.

Does anyone know of any existing / library functions that will buffer these writes and reads with an inline function, or is this another roll your own?

Chiastic

According to this question, fwrite is buffered anyway: #2806604 – Calderon

Have you considered just writing to stdout and letting bash etc write to file? – Calderon

@PhilH: what does Bash have to do with this? – Fibril

@larsmans: it's an alternative to writing to the file explicitly; run the file from bash and let it handle the buffering and disk IO. – Calderon

@PhilH: and how would one go about that? – Fibril

@larsmans: ... use cout instead of fwrite, assuming you can get the characters out as needed, then in bash mycmd > file. Is there a point that I'm missing? – Calderon

@camelccc: did you verify that each fwrite causes a system call? – Fibril

@PhilH: that doesn't change a thing. Redirection with > only causes the shell to open the file and pass the file descriptor to the process. It doesn't cause all I/O to pass through the shell, thank heavens. – Fibril

Answer 1

If you write from just one thread, try using fwrite_unlocked. It does wonders relative to straight fwrite in this kind of scenarios.

Farra

Answer 2

First of all, fwrite() is a library and not a system call. Secondly, it already buffers the data.

You might want to experiment with increasing the size of the buffer. This is done by using setvbuf(). On my system this only helps a tiny bit, but YMMV.

If setvbuf() does not help, you could do your own buffering and only call fwrite() once you've accumulated enough data. This involves more work, but will almost certainly speed up the writing as your own buffering can be made much more lightweight that fwrite()'s.

edit: If anyone tells you that it's the sheer number of fwrite() calls that is the problem, demand to see evidence. Better still, do your own performance tests. On my computer, 500,000,000 two-byte writes using fwrite() take 11 seconds. This equates to throughput of about 90MB/s.

Last but not least, the huge discrepancy between 11 seconds in my test and one hour mentioned in your question hints at the possibility that there's something else going on in your code that's causing the very poor performance.

Vinna

The problem's not the buffering, but the shear number of calls to fwrite. – Spook

@Skizz: What makes you think that? If you have any evidence, I'd love to see it. – Vinna

well, writing over a gigabyte of data in 1-4 bytes chunks is an awful lot of fwrite calls. – Spook

@Skizz: That's not exactly evidence, is it? – Vinna

@NPE: Well, more gut-feeling. If you can reduce the 250 million function calls by a factor of a million (250 writes of a 4 meg buffer), then you've saved yourself a lot of execution time. If you then double buffer the writing, the limiting factor becomes the IO bandwidth. – Spook

On my system, I can do 250 million fwrite() calls in 5.5 seconds. If you reduce this by a factor or ten, you've saved five seconds. OP is talking about an hour. – Vinna

I agree with NPE. fwrite is NOT a system call!! There is no cost to call it multiple times. People saying the opposite need to back to school. You can just setup a big enougth buffer to reduce the underlying system call witch is the "write(fd,void*,int)" function. – Siegbahn

more and more interesting this gets. Tried setbuf() and no difference. I think the OS is buffering anyway. did a few tests and it seems that calling fwrite with a lot of small writes that are all different sizes is rather slower than calling fwrite with small writes that are all the same size. – Chiastic

Answer 3

your problem is not the buffering for fwrite(), but the total overhead of making the library call with small amounts of data. if you write just 1MB of data, you make 250000 function calls. you'd better try to collect your data in memory and then write to the disk with one single call to fwrite().

UPDATE: if you need an evidence:

$ dd if=/dev/zero of=/dev/null count=50000000 bs=2
50000000+0 records in
50000000+0 records out
100000000 bytes (100 MB) copied, 55.3583 s, 1.8 MB/s
$ dd if=/dev/zero of=/dev/null count=50 bs=2000000
50+0 records in
50+0 records out
100000000 bytes (100 MB) copied, 0.0122651 s, 8.2 GB/s

Lubra

So instead of calling fwrite, use a memory buffer and a current write / read pointer, flushing / filling the buffer when full / empty and starting at the begining again. – Spook

@Spook please, show us how you generate the data, then you may get advices. but generally std::vector<your_stuff> should solve the problem with pointers, writing, flushing and you need only one fwrite() at the end. or maybe more, from time to time. – Lubra

how does std::vector<T> work with various types of different size? – Spook

If I could, I'd give an extra +1 for the timings. – Spook

With regards to the timings, GNU dd does not use fwrite(). Assuming your dd is the same, the timings have little to do with the question. – Vinna

This answer is plain wrong. take a look at NPE answer and the comments (or my c++ solution) to save you time. – Siegbahn

This answer is highly misleading. dd with bs=2 will actually issue one write syscall to the kernel every two bytes. fwrite with its default buffering enabled will be one local library function call every two bytes, and then a write syscall every time the buffer gets full. The main overhead is the kernel calls, so dd bs=2 is not an accurate emulation of fwrite with 2 byte blocks. – Diaeresis

Answer 4

OK, well, that was interesting. I thought I'd write some actual code to see what the speed was. And here it is. Compiled using C++ DevStudio 2010 Express. There's quite a bit of code here. It times 5 ways of writing the data:-

• Naively calling fwrite
• Using a buffer and doing fewer calls to fwrite using bigger buffers
• Using the Win32 API naively
• Using a buffer and doing fewer calls to Win32 using bigger buffers
• Using Win32 but double buffering the output and using asynchronous writes

Please check that I've not done something a bit stupid with any of the above.

The program uses QueryPerformanceCounter for timing the code and ends the timing after the file has been closed to try and include any pending internal buffered data.

The results on my machine (an old WinXP SP3 box):-

• fwrite on its own is generally the fastest although the buffered version can sometimes beat it if you get the size and iterations just right.
• Naive Win32 is significantly slower
• Buffered Win32 doubles the speed but it is still easily beaten by fwrite
• Asynchronous writes were not significantly better than the buffered version. Perhaps someone could check my code and make sure I've not done something stupid as I've never really used the asynchronous IO before.

You may get different results depending on your setup.

Feel free to edit and improve the code.

    #define _CRT_SECURE_NO_WARNINGS

    #include <stdio.h>
    #include <memory.h>
    #include <Windows.h>

    const int
        // how many times fwrite/my_fwrite is called
        c_iterations = 10000000,
        // the size of the buffer used by my_fwrite
        c_buffer_size = 100000;

    char 
        buffer1 [c_buffer_size],
        buffer2 [c_buffer_size],
        *current_buffer = buffer1;

    int
        write_ptr = 0;

    __int64
        write_offset = 0;

    OVERLAPPED
        overlapped = {0};

    // write to a buffer, when buffer full, write the buffer to the file using fwrite
    void my_fwrite (void *ptr, int size, int count, FILE *fp)
    {
        const int
            c = size * count;

        if (write_ptr + c > c_buffer_size)
        {
            fwrite (buffer1, write_ptr, 1, fp);
            write_ptr = 0;
        }

        memcpy (&buffer1 [write_ptr], ptr, c);
        write_ptr += c;
    }

    // write to a buffer, when buffer full, write the buffer to the file using Win32 WriteFile
    void my_fwrite (void *ptr, int size, int count, HANDLE fp)
    {
        const int
            c = size * count;

        if (write_ptr + c > c_buffer_size)
        {
            DWORD
                written;

            WriteFile (fp, buffer1, write_ptr, &written, 0);
            write_ptr = 0;
        }

        memcpy (&buffer1 [write_ptr], ptr, c);
        write_ptr += c;
    }

    // write to a double buffer, when buffer full, write the buffer to the file using 
    // asynchronous WriteFile (waiting for previous write to complete)
    void my_fwrite (void *ptr, int size, int count, HANDLE fp, HANDLE wait)
    {
        const int
            c = size * count;

        if (write_ptr + c > c_buffer_size)
        {
            WaitForSingleObject (wait, INFINITE);

            overlapped.Offset = write_offset & 0xffffffff;
            overlapped.OffsetHigh = write_offset >> 32;
            overlapped.hEvent = wait;

            WriteFile (fp, current_buffer, write_ptr, 0, &overlapped);
            write_offset += write_ptr;
            write_ptr = 0;
            current_buffer = current_buffer == buffer1 ? buffer2 : buffer1;
        }

        memcpy (current_buffer + write_ptr, ptr, c);
        write_ptr += c;
    }

    int main ()
    {
        // do lots of little writes
        FILE
            *f1 = fopen ("f1.bin", "wb");

        LARGE_INTEGER
            f1_start,
            f1_end;

        QueryPerformanceCounter (&f1_start);

        for (int i = 0 ; i < c_iterations ; ++i)
        {
            fwrite (&i, sizeof i, 1, f1);
        }

        fclose (f1);

        QueryPerformanceCounter (&f1_end);

        // do a few big writes
        FILE
            *f2 = fopen ("f2.bin", "wb");

        LARGE_INTEGER
            f2_start,
            f2_end;

        QueryPerformanceCounter (&f2_start);

        for (int i = 0 ; i < c_iterations ; ++i)
        {
            my_fwrite (&i, sizeof i, 1, f2);
        }

        if (write_ptr)
        {
            fwrite (buffer1, write_ptr, 1, f2);
            write_ptr = 0;
        }

        fclose (f2);

        QueryPerformanceCounter (&f2_end);

        // use Win32 API, without buffer
        HANDLE
            f3 = CreateFile (TEXT ("f3.bin"), GENERIC_WRITE, 0, 0, CREATE_ALWAYS, FILE_ATTRIBUTE_NORMAL, 0);

        LARGE_INTEGER
            f3_start,
            f3_end;

        QueryPerformanceCounter (&f3_start);

        for (int i = 0 ; i < c_iterations ; ++i)
        {
            DWORD
                written;

            WriteFile (f3, &i, sizeof i, &written, 0);
        }

        CloseHandle (f3);

        QueryPerformanceCounter (&f3_end);

        // use Win32 API, with buffer
        HANDLE
            f4 = CreateFile (TEXT ("f4.bin"), GENERIC_WRITE, 0, 0, CREATE_ALWAYS, FILE_FLAG_WRITE_THROUGH, 0);

        LARGE_INTEGER
            f4_start,
            f4_end;

        QueryPerformanceCounter (&f4_start);

        for (int i = 0 ; i < c_iterations ; ++i)
        {
            my_fwrite (&i, sizeof i, 1, f4);
        }

        if (write_ptr)
        {
            DWORD
                written;

            WriteFile (f4, buffer1, write_ptr, &written, 0);
            write_ptr = 0;
        }

        CloseHandle (f4);

        QueryPerformanceCounter (&f4_end);

        // use Win32 API, with double buffering
        HANDLE
            f5 = CreateFile (TEXT ("f5.bin"), GENERIC_WRITE, 0, 0, CREATE_ALWAYS, FILE_FLAG_OVERLAPPED | FILE_FLAG_WRITE_THROUGH, 0),
            wait = CreateEvent (0, false, true, 0);

        LARGE_INTEGER
            f5_start,
            f5_end;

        QueryPerformanceCounter (&f5_start);

        for (int i = 0 ; i < c_iterations ; ++i)
        {
            my_fwrite (&i, sizeof i, 1, f5, wait);
        }

        if (write_ptr)
        {
            WaitForSingleObject (wait, INFINITE);

            overlapped.Offset = write_offset & 0xffffffff;
            overlapped.OffsetHigh = write_offset >> 32;
            overlapped.hEvent = wait;

            WriteFile (f5, current_buffer, write_ptr, 0, &overlapped);
            WaitForSingleObject (wait, INFINITE);
            write_ptr = 0;
        }

        CloseHandle (f5);

        QueryPerformanceCounter (&f5_end);

        CloseHandle (wait);

        LARGE_INTEGER
            freq;

        QueryPerformanceFrequency (&freq);

        printf ("  fwrites without buffering = %dms\n", (1000 * (f1_end.QuadPart - f1_start.QuadPart)) / freq.QuadPart);
        printf ("     fwrites with buffering = %dms\n", (1000 * (f2_end.QuadPart - f2_start.QuadPart)) / freq.QuadPart);
        printf ("    Win32 without buffering = %dms\n", (1000 * (f3_end.QuadPart - f3_start.QuadPart)) / freq.QuadPart);
        printf ("       Win32 with buffering = %dms\n", (1000 * (f4_end.QuadPart - f4_start.QuadPart)) / freq.QuadPart);
        printf ("Win32 with double buffering = %dms\n", (1000 * (f5_end.QuadPart - f5_start.QuadPart)) / freq.QuadPart);
    }

Spook

I should add that I built the program as a Windows Console application. – Spook

Cool! What results do you get? – Rita

Answer 5

First and foremost: small fwrites() are slower, because each fwrite has to test the validity of its parameters, do the equivalent of flockfile(), possibly fflush(), append the data, return success: this overhead adds up -- not so much as tiny calls to write(2), but it's still noticeable.

Proof:

#include <stdio.h>
#include <stdlib.h>

static void w(const void *buf, size_t nbytes)
{
    size_t n;
    if(!nbytes)
        return;
    n = fwrite(buf, 1, nbytes, stdout);
    if(n >= nbytes)
        return;
    if(!n) {
        perror("stdout");
        exit(111);
    }
    w(buf+n, nbytes-n);
}

/* Usage: time $0 <$bigfile >/dev/null */
int main(int argc, char *argv[])
{
    char buf[32*1024];
    size_t sz;

    sz = atoi(argv[1]);
    if(sz > sizeof(buf))
        return 111;
    if(sz == 0)
        sz = sizeof(buf);
    for(;;) {
        size_t r = fread(buf, 1, sz, stdin);
        if(r < 1)
            break;
        w(buf, r);
    }
    return 0;
}

That being said, you could do what many commenters suggested, ie add your own buffering before fwrite: it's very trivial code, but you should test if it really gives you any benefit.

If you don't want to roll your own, you can use eg the buffer interface in skalibs, but you'll probably take longer to read the docs than to write it yourself (imho).

Moneymaker

Answer 6

Here's a test in nim showing that fwrite introduces function call overhead, and batching on your end decreases clock time.

as batchPow increases from 0 to 10, clock time decreases from 36 seconds to 4 seconds nim r -d:case1 -d:danger --gc:arc main.nim | wc -l 36 seconds

nim r -d:case2 -d:danger --gc:arc -d:batchPow:10 main.nim | wc -l 4 seconds

Even LTO won't help with fwrite's function call overhead as you can see with -d:case1 --passc:-flto --passl:-flto

var buf: string
let n = 1000_000_000
for i in 0..<n:
  let c = cast[char](i)
  when defined case1: # 36 seconds
    stdout.write c
  when defined case2: # 4 seconds
    const batchPow {.intdefine.} = 10
    buf.add c
    if ((i and (2 shl batchPow - 1)) == 0) or (i == n-1):
      stdout.write buf
      buf.setLen 0

Strigil

Answer 7

Below is an evidence showing that fwrite() incurs significant overhead for massive number of small writes, even with a large buffer (400MB). I test my code on Ubuntu with SSD. The running time of each function is in the comments.

So the solution to your question will be either: 1) gather all your small data in a big memory block and write to disk with one fwrite call or 2) implement your own buffered reader and writer.

(You may also want to refer a related question.)

#include<bits/stdc++.h>
using namespace std;

char filename[64] = "test.intarr";

void test_write_fstream(const vector<int>& v) {//11.395 s
    ofstream out(filename, ios::binary);
    out.write((char*)v.data(), v.size()*sizeof(int));
    out.close();
}

void test_write_fstream_in_loop(const vector<int>& v) {// 42.284 s
    ofstream out(filename, ios::binary);
    for (size_t i = 0; i < v.size(); i++)
    {
        out.write((char*)&v[i], sizeof(int));
    }
    out.close();
}

void test_write_fwrite(const vector<int>& v) {// 11.466s
    FILE* out = fopen(filename, "wb");
    fwrite(v.data(), sizeof(int), v.size(), out);
    fclose(out);
}

void test_write_fwrite_loop(const vector<int>& v) {// 59.338s
    FILE* out = fopen(filename, "wb");
    for (size_t i = 0; i < v.size(); i++)
    {
        fwrite(&v[i], sizeof(int), 1, out);
    }
    fclose(out);
}

void test_write_fwrite_unlocked_loop(const vector<int>& v) {//33.676 s
    FILE* out = fopen(filename, "wb");
    for (size_t i = 0; i < v.size(); i++)
    {
        fwrite_unlocked(&v[i], sizeof(int), 1, out);
    }
    fclose(out);
}

void test_write_fwrite_unlocked_loop_buffered(const vector<int>& v) {//28.198 s (400M buffer)
    char * buffer = (char*)malloc(400*1024*1024);
    FILE* out = fopen(filename, "wb");
    setvbuf(out, buffer, _IOFBF, 400*1024*1024);
    for (size_t i = 0; i < v.size(); i++)
    {
        fwrite_unlocked(&v[i], sizeof(int), 1, out);
    }
    fclose(out);
    free(buffer);
}

void test_write_fwrite_loop_with_4M_buffer(const vector<int>& v) {// 53.229 (4M buffer), 52.537 (400M buffer)
    char *buffer = (char*)malloc(400*1024*1024);
    FILE* out = fopen(filename, "wb");
    // char buffer[400*1024*1024];
    // set buffer of 4M
    setvbuf(out, buffer, _IOFBF, 400*1024*1024);
    for (size_t i = 0; i < v.size(); i++)
    {
        fwrite(&v[i], sizeof(int), 1, out);
    }
    fclose(out);
    free(buffer);
}


int main() {
    vector<int> v;
    auto start = chrono::high_resolution_clock::now(); 
    v.resize(1000*1000*1000);
    for (size_t i = 0; i < v.size(); i++)
    {// 36130 ms
        v[i] = rand();
    }
    auto end = chrono::high_resolution_clock::now();
    cout << "Generate time: " << chrono::duration_cast<chrono::milliseconds>(end-start).count() << "ms" << endl;

    //get current time in milliseconds
    start = chrono::high_resolution_clock::now();
    test_write_fwrite_unlocked_loop(v);
    end = chrono::high_resolution_clock::now();
    cout << "Write time: " << chrono::duration_cast<chrono::milliseconds>(end-start).count() << "ms" << endl;
    

    return 0;
}

Stinson

Answer 8

The point of the FILE * layer in stdio is that it does the buffering for you. This saves you from system call overhead. As noted by others, one thing that could still be an issue is the library call overhead, which is considerably smaller. Another thing that might bite you is writing to lots of different locations on disk at the same time. (Disks spin, and the head takes ballpark 8ms to get to the right place for a random write.)

If you determine that library call overhead is the problem, I'd recommend rolling your own trivial buffering using vector's and periodically flushing the vector's to the files.

If the problem is that you have lots of writes dispersed all over the disk, try jacking up the buffer sizes using setvbuf(). Try a number around 4MB per file if you can.

Rita

Answer 9

It should be easy to roll your own buffer. but fortunately the standard c++ has what you are asking for. Just use std::ofstream :

//open and init
char mybuffer [1024];
std::ofstream filestr("yourfile");
filestr.rdbuf()->pubsetbuf(mybuffer,1024);
// write your data
filestr.write(data,datasize);

Edited: mistake, use ofstream and not fstream as it's not clear from the the standard witch buffer is it (input or output?)

Siegbahn