So I am noticing some interesting behavior and is wondering if there is a
way around this.
I am able so assign a rank 1 array dynamically and write this to an hdf5
filetype but I do not seem to be able to do with with higher order arrays.
I would like to be able to write a PPx array to h5 and retain the data
integrity. More specifically I am trying to create a easy to use vector to
array library <https://github.com/stevenwalton/H5Easy> that can handle
multidimensional data (works with rank 1).
Let me give some examples. I will also show the typenames of the arrays.
Works:
double *a = new double[numPts]; // typename: Pd
double a[numPts]; // typename A#pts_d
double a[num1][num2]; typename:Anum1_Anum2_d
What doesn't work:
double **a = new double*[num1];
for ( size_t i = 0; i < num1; ++i )
a[i] = new double[num2];
// typename PPd
Testing the saved arrays with h5dump (and loading and reading directly) I
find that if I have typename PPx (not necessarily double) I get garbage
stored. Here is an example code and output from h5dump showing the
behavior.
------------------------------------------------------------
compiled with h5c++ -std=c++11
------------------------------------------------------------
#include "H5Cpp.h"
using namespace H5;
#define FILE "multi.h5"
int main()
{
hsize_t dims[2];
herr_t status;
H5File file(FILE, H5F_ACC_TRUNC);
dims[0] = 4;
dims[1] = 6;
double **data = new double*[dims[0]];
for ( size_t i = 0; i < dims[0]; ++i )
data[i] = new double[dims[1]];
for ( size_t i = 0; i < dims[0]; ++i )
for ( size_t j = 0; j < dims[1]; ++j )
data[i][j] = i + j;
DataSpace dataspace = DataSpace(2,dims);
DataSet dataset( file.createDataSet( "test", PredType::IEEE_F64LE,
dataspace ) );
dataset.write(data, PredType::IEEE_F64LE);
dataset.close();
dataspace.close();
file.close();
return 0;
}
------------------------------------------------------------
h5dump
------------------------------------------------------------
HDF5 "multi.h5" {
GROUP "/" {
DATASET "test" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
DATA {
(0,0): 1.86018e-316, 1.86018e-316, 1.86018e-316, 1.86019e-316, 0,
(0,5): 3.21143e-322,
(1,0): 0, 1, 2, 3, 4, 5,
(2,0): 0, 3.21143e-322, 1, 2, 3, 4,
(3,0): 5, 6, 0, 3.21143e-322, 2, 3
}
}
}
}
------------------------------------------------------------------
As can be seen the (0,0) set is absolute garbage (except the last character
which is the first number of the actual array), (0,5) is out of bounds,
and has garbage data. (1,0) has always contained real data (though it
should be located at (0,0)). So this seems like some addressing problem.
Is this a bug in the h5 libraries that allows me to read and write Pd data
as well as Ax0_...Axn_t data but not P...Pt data? Or is this for some
reason intentional? As using new is a fairly standard way to assign arrays,
making P...Pt type data common, I have a hard time seeing this as
intentional. In the mean time is anyone aware of a workaround to this? The
data I am taking in will be dynamically allocated so I do not see a way to
get Ax_... type data.
Thank you,
Steven
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