How can I write a large multidimensional array to an HDF5 file in parts?

Question

I'm using HDF5DotNet in C# and I have a very large array (several GB) that I want to write to an HDF5 file. It's too big to store the whole thing in memory, so I'm generating regions of it at a time and want to write them out, but still have it look like one big array when it's read back out. I know this is possible with HDF5 but the documentation for the .NET API is somewhat sparse.

I wrote some short example code with a 5 x 3 array filled with values 1..15:

const int ROWS = 5;
const int COLS = 3;

static void Main(string[] args)
{
    WriteWholeArray();
    WriteArrayByRows();
    ushort[,] array = ReadWholeArray();
}

static void WriteWholeArray()
{
    H5FileId h5 = H5F.create(Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.Desktop), "test.h5"), H5F.CreateMode.ACC_TRUNC);
    H5DataSpaceId dsi = H5S.create_simple(2, new long[] { ROWS, COLS });
    H5DataSetId dataset = H5D.create(h5, "array", new H5DataTypeId(H5T.H5Type.NATIVE_USHORT), dsi);
    ushort[,] array = new ushort[ROWS, COLS];
    ushort value = 1;
    for(int i = 0; i < array.GetLength(0); i++)
    {
        for (int j = 0; j < array.GetLength(1); j++)
        {
            array[i, j] = value++;
        }
    }
    H5D.write<ushort>(dataset, new H5DataTypeId(H5T.H5Type.NATIVE_USHORT), new H5Array<ushort>(array));
    H5D.close(dataset);
    H5F.close(h5);
}

static void WriteArrayByRows()
{
    H5FileId h5 = H5F.create(Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.Desktop), "test.h5"), H5F.CreateMode.ACC_TRUNC);
    H5DataSpaceId dsi = H5S.create_simple(2, new long[] { ROWS, COLS });
    H5DataSetId dataset = H5D.create(h5, "array", new H5DataTypeId(H5T.H5Type.NATIVE_USHORT), dsi);
    ushort[,] array = new ushort[ROWS, COLS];
    ushort value = 1;
    for (int i = 0; i < array.GetLength(0); i++)
    {
        for (int j = 0; j < array.GetLength(1); j++)
        {
            array[i, j] = value++;
        }
    }
    for(int i = 0; i < array.GetLength(0); i++)
    {
        H5S.selectHyperslab(dsi, H5S.SelectOperator.SET, new long[] { i, 0 }, new long[] { 1, array.GetLength(1) });
        ushort[,] row = new ushort[1, array.GetLength(1)];
        for(int j = 0; j < array.GetLength(1); j++)
        {
            row[0, j] = array[i, j];
        }
        H5D.write<ushort>(dataset, new H5DataTypeId(H5T.H5Type.NATIVE_USHORT), new H5Array<ushort>(row));
    }
    H5D.close(dataset);
    H5F.close(h5);
}

static ushort[,] ReadWholeArray()
{
    H5FileId h5 = H5F.open(Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.Desktop), "test.h5"), H5F.OpenMode.ACC_RDONLY);
    ushort[,] array = new ushort[ROWS, COLS];
    H5Array<ushort> h5_array = new H5Array<ushort>(array);
    H5DataSetId dataset = H5D.open(h5, "array");
    H5D.read<ushort>(dataset, new H5DataTypeId(H5T.H5Type.NATIVE_USHORT), h5_array);
    H5D.close(dataset);
    H5F.close(h5);
    return (array);
}

When I write the whole array at once, it reads back in fine. When I try to write by rows, the array I read back in has some correct values (in the wrong elements), some zeroes, and some crazy values (e.g. 43440). Can somebody show me how to do this correctly?

score 1 · Accepted Answer · answered Aug 20 '15 at 18:55

I figured it out. Apparently when you write hyperslabs of an array you need a second dataspace corresponding to the array in memory that you are writing. Here is the corrected function:

static void WriteArrayByRows()
{
    H5FileId h5 = H5F.create(Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.Desktop), "test.h5"), H5F.CreateMode.ACC_TRUNC);
    H5DataSpaceId dsi = H5S.create_simple(2, new long[] { ROWS, COLS });
    H5DataSetId dataset = H5D.create(h5, "array", new H5DataTypeId(H5T.H5Type.NATIVE_USHORT), dsi);
    ushort[,] array = new ushort[ROWS, COLS];
    ushort value = 1;
    for (int i = 0; i < array.GetLength(0); i++)
    {
        for (int j = 0; j < array.GetLength(1); j++)
        {
            array[i, j] = value++;
        }
    }
    for (int i = 0; i < array.GetLength(0); i++)
    {
        H5S.selectHyperslab(dsi, H5S.SelectOperator.SET, new long[] { i, 0 }, new long[] { 1, array.GetLength(1) });
        H5DataSpaceId dsi2 = H5S.create_simple(2, new long[] { 1, array.GetLength(1) });  // added
        ushort[,] row = new ushort[1, array.GetLength(1)];
        for (int j = 0; j < array.GetLength(1); j++)
        {
            row[0, j] = array[i, j];
        }
        H5PropertyListId pli = new H5PropertyListId(H5P.Template.DEFAULT);  // added
        H5D.write<ushort>(dataset, new H5DataTypeId(H5T.H5Type.NATIVE_USHORT), dsi2, dsi, pli, new H5Array<ushort>(row));  // modified
    }
    H5D.close(dataset);
    H5F.close(h5);
}

I also found chunking to be very useful for getting decent performance writing my large array, here is an example of that:

H5PropertyListId pli = H5P.create(H5P.PropertyListClass.DATASET_CREATE);  // added
H5P.setChunk(pli, new long[] { 1, COLS });  // added
H5DataSetId dataset = H5D.create(h5, "array", new H5DataTypeId(H5T.H5Type.NATIVE_USHORT), dsi, H5P.create(H5P.PropertyListClass.LINK_CREATE), pli, H5P.create(H5P.PropertyListClass.DATASET_ACCESS));  // modified

This is also the only example of reading a multi-dim dataset in HFD5DotNet that I could find anywhere. — Doug Null, Jan 15 '19 at 20:18

How can I write a large multidimensional array to an HDF5 file in parts?

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