hello Mark
Hi Phil,
Hello,
Hopefully somebody has an idea
Im using C++ and I dynamically created a multidimensional array. I
manipulate it and then try to write to an HDF. I get this error and
have been unable to figure out why.
Initializing HDF Results File...HDF5-DIAG: Error detected in HDF5
library version: 1.6.7 thread 0. Back trace follows.
#000: ..\..\src\H5Dio.c line 697 in H5Dwrite(): can't write data
major(15): Dataset interface
minor(25): Write failed
#001: ..\..\src\H5Dio.c line 1063 in H5D_write(): can't write data
major(15): Dataset interface
minor(25): Write failed
#002: ..\..\src\H5Dio.c line 1438 in H5D_contig_write(): optimized
write failed
major(15): Dataset interface
minor(25): Write failed
#003: ..\..\src\H5Dselect.c line 655 in H5D_select_write(): write
error
major(14): Dataspace interface
minor(25): Write failed
#004: ..\..\src\H5Dcontig.c line 854 in H5D_contig_writevv():
block write failed
major(05): Low-level I/O layer
minor(25): Write failed
#005: ..\..\src\H5F.c line 3338 in H5F_block_write(): file write
failed
major(05): Low-level I/O layer
minor(25): Write failed
#006: ..\..\src\H5FD.c line 3492 in H5FD_write(): driver write
request failed
major(22): Virtual File Layer
minor(25): Write failed
#007: ..\..\src\H5FDsec2.c line 805 in H5FD_sec2_write(): file
write failed
major(05): Low-level I/O layer
minor(25): Write failed
#008: ..\..\src\H5FDsec2.c line 805 in H5FD_sec2_write(): Invalid
argument
major(03): Internal HDF5 error
minor(87): System error message
I have a hunch its because the HDF is trying to write the pointers
to the file, instead of the 2D array.
Yes, that's probably your problem. The HDF5 library expects to
receive a contiguous array of elements, not pointers to elements in
lower dimensions.
Quincey
Here is my SIMPLIFIED code
There are no errors and everything it
correct, until I try to write
template <typename T>
T **AllocateDynamicArray(int nRows, int nCols)
{
T **dynamicArray;
dynamicArray = new T*[nRows];
for( int i = 0 ; i < nRows ; i++ )
dynamicArray[i] = new T [nCols];
return dynamicArray;
}
void initResultsHDF(int **Results)
{
//Then I fill the array with all 0s and try to print it
but this is the line that gives the error.
dataset.write(Results, PredType::NATIVE_INT, memspace, dataspace);
}
int main()
{
int **Results = AllocateDynamicArray<int>(SIZEROW,SIZECOL); // Correctly creates a dynamic multidimensional array
initResultsHDF(Results); //Sends the dynamically created
multidimensional array to the function
}
Very respectfully,
Phil Salesses
Cartographic Technician
U.S. Army Topographic Engineering Center (TEC)
7701 Telegraph Road
Alexandria, VA 22315-3864
Mark.P.Salesses@usace.army.mil
TEC R&D - Anything But Ordinary
you can do a "trick" to do this
since
int **Results
is an array of pointers of rows where each one points to another array of columns (i.e a 2D dynamic array), it's possible to do an iteration by rows having in each one a column selected and writing each time a hyperslab ( a column)
in your function
void initResultsHDF(int **Results)
do this
for( int i = 0 ; i < SIZEROW ; i++ )
{
....
int *row_start = Results[i];
you'll get a pointer to the start of the row and then you can use this pointer to call the write routine of HDF5, that, like Quincey said, expects to receive a contiguous array of elements (or a pointer)
You'll have to write each row each time, by selecting this hyperslab in the file (one row) and also defining a memory hyperslab with this row
Below it is a complete C++ program that I adapted from your sample (I defined a matrix of 4 x 3 )
and from our C++ examples
the output of the program should be
writing row 0
1 2 3
writing row 1
4 5 6
writing row 2
7 8 9
writing row 3
10 11 12
I also send it attached
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html\. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifdef OLD_HEADER_FILENAME
#include <iostream.h>
#else
#include <iostream>
#endif
#include <string>
#ifndef H5_NO_NAMESPACE
#ifndef H5_NO_STD
using std::cout;
using std::endl;
#endif // H5_NO_STD
#endif
#include "H5Cpp.h"
#ifndef H5_NO_NAMESPACE
using namespace H5;
#endif
template <typename T>
T **AllocateDynamicArray(int nRows, int nCols)
{
T **dynamicArray;
dynamicArray = new T*[nRows];
for( int i = 0 ; i < nRows ; i++ )
dynamicArray[i] = new T [nCols];
return dynamicArray;
}
#define SIZEROW 4
#define SIZECOL 3
void initResultsHDF(int **Results)
{
H5File* file = new H5File( "_myfile.h5", H5F_ACC_TRUNC );
hsize_t dims = {SIZEROW, SIZECOL};
DataSpace fspace( 2, dims );
DataSet dataset(file->createDataSet("mydset", PredType::NATIVE_INT, fspace));
// define a memory space to write each row
hsize_t row = {SIZECOL};
DataSpace mspace( 1, row );
for( int i = 0 ; i < SIZEROW ; i++ )
{
// select file hyperslab
hsize_t start[2]; // start of hyperslab
hsize_t stride[2] = {1, 1}; // stride of hyperslab
hsize_t count[2]; // block count
hsize_t block[2] = {1, 1}; // block sizes
count[0] = 1;
count[1] = SIZECOL;
start[0] = i;
start[1] = 0;
fspace.selectHyperslab( H5S_SELECT_SET, count, start, stride, block);
// select memory hyperslab
hsize_t mstart[1] = {0}; // start of hyperslab
hsize_t mstride[1] = {1}; // stride of hyperslab
hsize_t mcount[1] = {SIZECOL}; // block count
hsize_t mblock[1] = {1}; // block sizes
mspace.selectHyperslab( H5S_SELECT_SET, mcount, mstart, mstride, mblock);
int *row_start = Results[i];
printf("writing row %d\n", i );
for( int j = 0 ; j < SIZECOL ; j++ )
printf("%d ", Results[i][j]);
printf("\n");
dataset.write(row_start, PredType::NATIVE_INT, mspace, fspace);
}
delete file;
}
int main()
{
int **Results = AllocateDynamicArray<int>(SIZEROW,SIZECOL); //Correctly creates a dynamic multidimensional array
int n = 1;
for( int i = 0 ; i < SIZEROW ; i++ )
{
for( int j = 0 ; j < SIZECOL ; j++ )
{
Results[i][j] = n++;
}
}
initResultsHDF(Results); //Sends the dynamically created multidimensional array to the function
return 0;
}
dynamicArray.cpp (3.75 KB)
_myfile.h5 (2.05 KB)
···
At 12:09 PM 6/11/2008, Quincey Koziol wrote:
On Jun 11, 2008, at 10:44 AM, Salesses, Mark P ERDC-TEC-VA wrote:
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