hdf5_tools.cpp 11.2 KB
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#include "hdf5_tools.hpp"
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#include "scope_timer.hpp"
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#include <cfloat>
#include <climits>
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template <> hid_t hdf5_tools::hdf5_type_id<char>()
{
    return H5T_NATIVE_CHAR;
}
template <> hid_t hdf5_tools::hdf5_type_id<signed char>()
{
    return H5T_NATIVE_SCHAR;
}
template <> hid_t hdf5_tools::hdf5_type_id<unsigned char>()
{
    return H5T_NATIVE_UCHAR;
}
template <> hid_t hdf5_tools::hdf5_type_id<short>()
{
    return H5T_NATIVE_SHORT;
}
template <> hid_t hdf5_tools::hdf5_type_id<unsigned short>()
{
    return H5T_NATIVE_USHORT;
}
template <> hid_t hdf5_tools::hdf5_type_id<int>()
{
    return H5T_NATIVE_INT;
}
template <> hid_t hdf5_tools::hdf5_type_id<unsigned>()
{
    return H5T_NATIVE_UINT;
}
template <> hid_t hdf5_tools::hdf5_type_id<long>()
{
    return H5T_NATIVE_LONG;
}
template <> hid_t hdf5_tools::hdf5_type_id<unsigned long>()
{
    return H5T_NATIVE_ULONG;
}
template <> hid_t hdf5_tools::hdf5_type_id<long long>()
{
    return H5T_NATIVE_LLONG;
}
template <> hid_t hdf5_tools::hdf5_type_id<unsigned long long>()
{
    return H5T_NATIVE_ULLONG;
}
template <> hid_t hdf5_tools::hdf5_type_id<float>()
{
    return H5T_NATIVE_FLOAT;
}
template <> hid_t hdf5_tools::hdf5_type_id<double>()
{
    return H5T_NATIVE_DOUBLE;
}
template <> hid_t hdf5_tools::hdf5_type_id<long double>()
{
    return H5T_NATIVE_LDOUBLE;
}

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int hdf5_tools::require_size_single_dataset(hid_t dset, int tsize)
{
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    TIMEZONE("hdf5_tools::require_size_single_dataset");
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    int ndims;
    hsize_t space;
    space = H5Dget_space(dset);
    ndims = H5Sget_simple_extent_ndims(space);
    hsize_t *dims = new hsize_t[ndims];
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    hsize_t *maxdims = new hsize_t[ndims];
    H5Sget_simple_extent_dims(space, dims, maxdims);
    if (dims[0] < hsize_t(tsize) && maxdims[0] == H5S_UNLIMITED)
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    {
        dims[0] = tsize;
        H5Dset_extent(dset, dims);
    }
    H5Sclose(space);
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    delete[] maxdims;
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    delete[] dims;
    return EXIT_SUCCESS;
}

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int hdf5_tools::grow_single_dataset(hid_t dset, int tincrement)
{
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    TIMEZONE("hdf5_tools::grow_single_dataset");
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    int ndims;
    hsize_t space;
    space = H5Dget_space(dset);
    ndims = H5Sget_simple_extent_ndims(space);
    hsize_t *dims = new hsize_t[ndims];
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    hsize_t *maxdims = new hsize_t[ndims];
    H5Sget_simple_extent_dims(space, dims, maxdims);
    if (maxdims[0] == H5S_UNLIMITED)
    {
        dims[0] += tincrement;
        H5Dset_extent(dset, dims);
    }
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    H5Sclose(space);
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    delete[] maxdims;
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    delete[] dims;
    return EXIT_SUCCESS;
}

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herr_t hdf5_tools::require_size_dataset_visitor(
    hid_t o_id,
    const char *name,
    const H5O_info_t *info,
    void *op_data)
{
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    TIMEZONE("hdf5_tools::require_size_dataset_visitor");
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    if (info->type == H5O_TYPE_DATASET)
    {
        hsize_t dset = H5Dopen(o_id, name, H5P_DEFAULT);
        require_size_single_dataset(dset, *((int*)(op_data)));
        H5Dclose(dset);
    }
    return EXIT_SUCCESS;
}

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herr_t hdf5_tools::grow_dataset_visitor(
    hid_t o_id,
    const char *name,
    const H5O_info_t *info,
    void *op_data)
{
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    TIMEZONE("hdf5_tools::grow_dataset_visitor");
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    if (info->type == H5O_TYPE_DATASET)
    {
        hsize_t dset = H5Dopen(o_id, name, H5P_DEFAULT);
        grow_single_dataset(dset, *((int*)(op_data)));
        H5Dclose(dset);
    }
    return EXIT_SUCCESS;
}


int hdf5_tools::grow_file_datasets(
        const hid_t stat_file,
        const std::string group_name,
        int tincrement)
{
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    TIMEZONE("hdf5_tools::grow_file_datasets");
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    int file_problems = 0;

    hid_t group;
    group = H5Gopen(stat_file, group_name.c_str(), H5P_DEFAULT);
    H5Ovisit(
            group,
            H5_INDEX_NAME,
            H5_ITER_NATIVE,
            grow_dataset_visitor,
            &tincrement);
    H5Gclose(group);
    return file_problems;
}

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int hdf5_tools::require_size_file_datasets(
        const hid_t stat_file,
        const std::string group_name,
        int tsize)
{
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    TIMEZONE("hdf5_tools::require_size_file_datasets");
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    int file_problems = 0;

    hid_t group;
    group = H5Gopen(stat_file, group_name.c_str(), H5P_DEFAULT);
    H5Ovisit(
            group,
            H5_INDEX_NAME,
            H5_ITER_NATIVE,
            require_size_dataset_visitor,
            &tsize);
    H5Gclose(group);
    return file_problems;
}

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template <typename number>
std::vector<number> hdf5_tools::read_vector(
        const hid_t group,
        const std::string dset_name)
{
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    TIMEZONE("hdf5_tools::read_vector");
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    std::vector<number> result;
    hsize_t vector_length;
    // first, read size of array
    hid_t dset, dspace;
    hid_t mem_dtype;
    if (typeid(number) == typeid(int))
        mem_dtype = H5Tcopy(H5T_NATIVE_INT);
    else if (typeid(number) == typeid(double))
        mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
    dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
    dspace = H5Dget_space(dset);
    assert(H5Sget_simple_extent_ndims(dspace) == 1);
    H5Sget_simple_extent_dims(dspace, &vector_length, NULL);
    result.resize(vector_length);
    H5Dread(dset, mem_dtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &result.front());
    H5Sclose(dspace);
    H5Dclose(dset);
    H5Tclose(mem_dtype);
    return result;
}

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template <typename number>
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number hdf5_tools::read_value(
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        const hid_t group,
        const std::string dset_name)
{
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    TIMEZONE("hdf5_tools::read_value");
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    number result;
    hid_t dset;
    hid_t mem_dtype;
    if (typeid(number) == typeid(int))
        mem_dtype = H5Tcopy(H5T_NATIVE_INT);
    else if (typeid(number) == typeid(double))
        mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
    if (H5Lexists(group, dset_name.c_str(), H5P_DEFAULT))
    {
        dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
        H5Dread(dset, mem_dtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &result);
        H5Dclose(dset);
    }
    else
    {
        DEBUG_MSG("attempted to read dataset %s which does not exist.\n",
                dset_name.c_str());
        if (typeid(number) == typeid(int))
            result = INT_MAX;
        else if (typeid(number) == typeid(double))
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            result = number(DBL_MAX);
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    }
    H5Tclose(mem_dtype);
    return result;
}

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template <typename number>
int hdf5_tools::write_value_with_single_rank(
        const hid_t group,
        const std::string dset_name,
        const number value)
{
    hid_t dset, mem_dtype;
    if (typeid(number) == typeid(int))
        mem_dtype = H5Tcopy(H5T_NATIVE_INT);
    else if (typeid(number) == typeid(double))
        mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
    if (H5Lexists(group, dset_name.c_str(), H5P_DEFAULT))
    {
        dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
    }
    else
    {
        hid_t fspace;
        hsize_t count[1];
        count[0] = 1;
        fspace = H5Screate_simple(1, count, NULL);
        dset = H5Dcreate(group, dset_name.c_str(), mem_dtype, fspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        H5Sclose(fspace);
    }
    H5Dwrite(dset, mem_dtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &value);
    H5Dclose(dset);
    H5Tclose(mem_dtype);
    return EXIT_SUCCESS;
}

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template <typename dtype>
std::vector<dtype> hdf5_tools::read_vector_with_single_rank(
        const int myrank,
        const int rank_to_use,
        const MPI_Comm COMM,
        const hid_t file_id,
        const std::string dset_name)
{
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    TIMEZONE("hdf5_tools::read_vector_with_single_rank");
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    std::vector<dtype> data;
    int vector_size;
    if (myrank == rank_to_use)
    {
        data = hdf5_tools::read_vector<dtype>(
                file_id,
                dset_name);
        vector_size = data.size();
    }
    MPI_Bcast(
            &vector_size,
            1,
            MPI_INT,
            rank_to_use,
            COMM);

    if (myrank != rank_to_use)
        data.resize(vector_size);
    MPI_Bcast(
            &data.front(),
            vector_size,
            (typeid(dtype) == typeid(int)) ? MPI_INT : MPI_DOUBLE,
            rank_to_use,
            COMM);
    return data;
}

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std::string hdf5_tools::read_string(
        const hid_t group,
        const std::string dset_name)
{
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    TIMEZONE("hdf5_tools::read_string");
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    if (H5Lexists(group, dset_name.c_str(), H5P_DEFAULT))
    {
        hid_t dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
        hid_t space = H5Dget_space(dset);
        hid_t memtype = H5Dget_type(dset);
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        // fsanitize complains unless I have a static array here
        // but that doesn't actually work (data is read incorrectly).
        // this is caught by bfps.test_NSVEparticles
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        char *string_data = (char*)malloc(256);
        H5Dread(dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &string_data);
        std::string std_string_data = std::string(string_data);
        free(string_data);
        H5Sclose(space);
        H5Tclose(memtype);
        H5Dclose(dset);
        return std_string_data;
    }
    else
    {
        DEBUG_MSG("attempted to read dataset %s which does not exist.\n",
                dset_name.c_str());
        return std::string("parameter does not exist");
    }
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}

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template <class partsize_t>
int hdf5_tools::write_particle_ID_pairs_with_single_rank(
        const std::vector<partsize_t> v,
        const hid_t group,
        const std::string dset_name)
{
    TIMEZONE("hdf5_tools::write_particle_ID_pairs_with_single_rank");
    // the vector contains pair information, so its size must be a multiple of 2
    assert((v.size() % 2) == 0);
    // file space creation
    hid_t fspace;
    hsize_t dims[2];
    dims[0] = v.size()/2;
    dims[1] = 2;
    fspace = H5Screate_simple(2, dims, NULL);
    // create dataset
    hsize_t dset_id = H5Dcreate(
            group,
            dset_name.c_str(),
            hdf5_tools::hdf5_type_id<partsize_t>(),
            fspace,
            H5P_DEFAULT,
            H5P_DEFAULT,
            H5P_DEFAULT);
    // write data
    H5Dwrite(
            dset_id,
            hdf5_tools::hdf5_type_id<partsize_t>(),
            H5S_ALL,
            H5S_ALL,
            H5P_DEFAULT,
            &v.front());
    // clean up
    H5Dclose(dset_id);
    H5Sclose(fspace);
    return EXIT_SUCCESS;
}

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template
std::vector<int> hdf5_tools::read_vector<int>(
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        const hid_t,
        const std::string);

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template
std::vector<double> hdf5_tools::read_vector<double>(
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        const hid_t,
        const std::string);

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template
std::vector<int> hdf5_tools::read_vector_with_single_rank<int>(
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        const int myrank,
        const int rank_to_use,
        const MPI_Comm COMM,
        const hid_t file_id,
        const std::string dset_name);

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template
std::vector<double> hdf5_tools::read_vector_with_single_rank<double>(
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        const int myrank,
        const int rank_to_use,
        const MPI_Comm COMM,
        const hid_t file_id,
        const std::string dset_name);

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template
int hdf5_tools::read_value<int>(
        const hid_t,
        const std::string);

template
double hdf5_tools::read_value<double>(
        const hid_t,
        const std::string);

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template
int hdf5_tools::write_value_with_single_rank<int>(
        const hid_t group,
        const std::string dset_name,
        const int value);

template
int hdf5_tools::write_value_with_single_rank<double>(
        const hid_t group,
        const std::string dset_name,
        const double value);

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template
int hdf5_tools::write_particle_ID_pairs_with_single_rank(
        const std::vector<long long> v,
        const hid_t group,
        const std::string dset_name);