JLD2 writes zeros to first 3440 bytes in file

[tiagopereira]

When writing arrays or other structures to a JLD2 file, it writes zeros to the first 3440 bytes in the file. Here is a sample code:

using JLD2
tmp = ones(Float64, 100, 100, 100)
jldsave("test.jld2"; tmp)
aa = load("test.jld2")["tmp"]

Then the read array aa will be zeros until element 431 (first 3440 bytes). If I instead write a Float32 array, then it is zero until element 861 (still first 3440 bytes).

This error persists if I write different structures with arrays. The array parts of the structure have also the first elements filled with zeros. There is no difference whether using the FileIO interface or jldsave.

Using Julia 1.10.0, JLD2 0.4.43 on Linux. The error only happens in Linux. Tested with a M1 Mac with Julia ARMv8 for and it worked fine.

[JonasIsensee]

Hi @tiagopereira ,
that seems rather frustrating.
I cannot reproduce this issue locally on my linux.

Can you please test if this is
a) fixed by passing jldsave("test.jld2", IOStream; tmp).

b) just a loading problem, so load("test.jld2"; iotype=IOStream)

c) do

jldopen("test.jld2", "w") do f
    f["prep"] = ones(100)
    f["tmp"] = ones(100,100,100)
end

to see if the length of the first array controls how may floats are still zero in the second array.

[tiagopereira]

Thank you for the quick answer. Doing jldsave("test.jld2", IOStream; tmp) makes the problem go away, so maybe it is the MmapIO interface?

I am sure it is not a loading problem. I checked the file with h5dump and it was written with zeros.

I did the last check you suggested, and the first array written (prep) was correctly written, but the second array (tmp) had zeros in the first elements. In this case, it was not 3440 bytes, but the first non-zero element was index 322. Strangely, it was written with 3.0517578125e-5, and all the subsequent elements with ones.

[tiagopereira]

I should add that the filesystem I am writing into is a networked file system (StorNext SAN via Infiniband). Are there known issues with MmapIO and writing to networked file systems?

[JonasIsensee]

I should add that the filesystem I am writing into is a networked file system (StorNext SAN via Infiniband). Are there known issues with MmapIO and writing to networked file systems?

There have been issues with Mmap and network files systems in the past.
This is certainly linked.
What is likely happening, ist the first Mmap page is not properly flushed to disk. ( up to byte 4096 in the file).

You can avoid the issue by using IOStream. On network file systems this should not be a big performance hit.

If you want to dig a little deeper, you can test the size dependence:

Have a look at
https://github.com/JuliaIO/JLD2.jl/blob/master/src%2Fdataio.jl#L102