MATLAB fwrite with skip slow

Question

I'm writing some larger (~500MB - 3GB) pieces binary data in MATLAB using the fwrite command.

I want the data to be written in a tabular format so I'm using the skip parameter. E.g. I have 2 vectors of uint8 values a = [ 1 2 3 4]; b = [5 6 7 8]. I want the binary file to look like this 1 5 2 6 3 7 4 8

So in my code I do something similar to this (my data is more complex)

fwrite(f,a,'1*uint8',1);
fseek(f,2)
fwrite(f,b,'1*uint8',1);

But the writes are painfully slow ( 2MB/s ).

I ran the following block of code, and when I set passed in a skip count of 1 the write is approximately 300x slower.

>> f = fopen('testfile.bin', 'w');
>> d = uint8(1:500e6);
>> tic; fwrite(f,d,'1*uint8',1); toc
Elapsed time is 58.759686 seconds.
>> tic; fwrite(f,d,'1*uint8',0); toc
Elapsed time is 0.200684 seconds.
>> 58.759686/0.200684

ans =

  292.7971

I could understand 2x or 4x slowdown since the you have to traverse twice as many bytes with the skip parameter set to 1 but 300x makes me think I'm doing something wrong.

Has anyone encountered this before? Is there a way to speed up this write?

Thanks!

UPDATE

I wrote the following function to format arbitrary data sets. Write speed is vastly improved (~300MB/s) for large data sets.

%
%  data: A cell array of matrices. Matrices can be composed of any
%        non-complex numeric data. Each entry in data is considered
%        to be an independent column in the data file. Rows are indexed
%        by the last column in the numeric matrix hence the count of elements
%        in the last dimension of the matrix must match. 
%
%   e.g. 
%   size(data{1}) == [1,5]
%   size(data{2}) == [4,5]
%   size(data{3}) == [3,2,5]
%
%   The data variable has 3 columns and 5 rows. Column 1 is made of scalar values
%   Column 2 is made of vectors of length 4. And column 3 is made of 3 x 2 
%   matrices
%
% 
%  returns buffer: a N x M matrix of bytes where N is the number of bytes
%  of each row of data, and M is the number of rows of data. 

function [buffer] = makeTabularDataBuffer(data)
    dataTypes = {};
    dataTypesLengthBytes = [];
    rowElementCounts = []; %the number of elements in each "row"

    rowCount = [];

    %figure out properties of tabular data
    for idx = 1:length(data)

        cDat = data{idx};
        dimSize = size(cDat);

        %ensure each column has the same number of rows.
        if isempty(rowCount)
            rowCount = dimSize(end);
        else
            if dimSize(end) ~= rowCount
                throw(MException('e:e', sprintf('data column %d does not have the required number of rows (%d)\n',idx,rowCount)));
            end
        end

        dataTypes{idx} = class(data{idx});
        dataTypesLengthBytes(idx) = length(typecast(eval([dataTypes{idx},'(1)']),'uint8'));
        rowElementCounts(idx) = prod(dimSize(1:end-1));

    end

    rowLengthBytes = sum(rowElementCounts .* dataTypesLengthBytes);
    buffer = zeros(rowLengthBytes, rowCount,'uint8'); %rows of the dataset map to column in the buffer matrix because fwrite writes columnwise

    bufferRowStartIdxs = cumsum([1 dataTypesLengthBytes .* rowElementCounts]);

    %load data 1 column at a time into the buffer
    for idx = 1:length(data)
        cDat = data{idx};
        columnWidthBytes = dataTypesLengthBytes(idx)*rowElementCounts(idx);

        cRowIdxs = bufferRowStartIdxs(idx):(bufferRowStartIdxs(idx+1)-1);

        buffer(cRowIdxs,:) = reshape(typecast(cDat(:),'uint8'),columnWidthBytes,[]); 
    end

end

I've done some very limited testing of the function but it appears to be working as expected. The returned buffer matrix can then be passed to fwrite without the skip argument and fwrite will write the buffer in column major order.

dat = {};
dat{1} = uint16([1 2 3 4]);
dat{2} = uint16([5 6 7 8]);
dat{3} = double([9 10 ; 11 12; 13 14; 15 16])';

buffer = makeTabularDataBuffer(dat)

buffer =

  20×4 uint8 matrix

    1    2    3    4
    0    0    0    0
    5    6    7    8
    0    0    0    0
    0    0    0    0
    0    0    0    0
    0    0    0    0
    0    0    0    0
    0    0    0    0
    0    0    0    0
   34   38   42   46
   64   64   64   64
    0    0    0    0
    0    0    0    0
    0    0    0    0
    0    0    0    0
    0    0    0    0
    0    0    0    0
   36   40   44   48
   64   64   64   64

Rotem · Accepted Answer · 2020-01-22T21:43:00.083

For best I/O performance, use sequential writes, and avoid skipping.

Reorder the data in the RAM before saving to file.
Reordering the data in the RAM is in order of 100 times faster than reordering data on disk.

I/O operations and storage devices are optimized for sequential writes of large data chunks (optimized both in hardware and in software).

In mechanical drives (HDD), writing data with skipping may take a very long time, because the mechanical head of the drive must move (usually the OS optimize it by using memory buffer, but in principle it takes a long time).

With SSD, there is no mechanical seeking, but sequential writes are still much faster. Read the following post Sequential vs Random I/O on SSDs? for some explanation.

Example for reordering data in RAM:

a = uint8([1 2 3 4]);
b = uint8([5 6 7 8]);

% Allocate memory space for reordered elements (use uint8 type to save RAM).
c = zeros(1, length(a) + length(b), 'uint8');

%Reorder a and b in the RAM.
c(1:2:end) = a;
c(2:2:end) = b;

% Write array c to file
fwrite(f, c, 'uint8');
fclose(f);

Time measurements in my machine:

Writing file to SSD:
Elapsed time is 56.363397 seconds.
Elapsed time is 0.280049 seconds.
Writing file to HDD:
Elapsed time is 56.063186 seconds.
Elapsed time is 0.522933 seconds.
Reordering d in RAM:
Elapsed time is 0.965358 seconds.

Why 300x times slower and not 4x ?
I am guessing the software implementation of writing data with skipping is not optimized for best performance.

According to the following post:

fseek() or fflush() require the library to commit buffered operations.

Daniel's guess (in the comment) is probably correct.
"The skip causes MATLAB to flush after each byte."
Skipping is probably implemented using fseek(), and fseek() forces flushing data to disk.
It could explain why writing with skipping is painfully slow.

My guess, the skip causes MATLAB to flush after each byte. – Daniel Jan 22 '20 at 20:36 — Daniel, Jan 22 '20 at 20:36

MATLAB fwrite with skip slow

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