C++: Armadillo does not want to cooperate with hdf5 format - c++

Question

Recently I have decided to store my data into hdf5 binary instead of ASCII files. I would like to use hdf5 format. Basically the thought is have the header and the data in the same file (header ASCII not binary format and then binary format). Something like this:
----------------------------------------
Dataname : testdata
ref_ell : wgs84
bmin :
etc.
and here are the data in hdf5 format
The armadillo library (http://arma.sourceforge.net/docs.html#save_load_mat) do have the function to append data to the existing file (hdf5_opts::append). But I have reached the problem much sooner. I have followed the manual but apparently I did something wrong. Lets say I have:
#include <iomanip>
#include <iostream>
#include <fstream>
#include <map>
#include <cmath>
#include <algorithm>
#include <vector>
#define ARMA_USE_HDF5
#include <hdf5.h>
#include <armadillo>
// g++ -O3 -lhdf5 -larmadillo -DARMA_DONT_USE_WRAPPER -DARMA_USE_BLAS -DARMA_USE_LAPACK -DARMA_USE_HDF5 - hdf5.cpp -o hdf5.o
// g++ -O3 -lhdf5 -larmadillo hdf5.cpp -o hdf5.o
// g++ -O3 -larmadillo -lhdf5 hdf5.cpp -o hdf5.o
using namespace std;
int main() {
arma::mat amat = arma::randu<arma::mat>(5,6);
cout << amat << endl;
amat.save( arma::hdf5_name("A.h5", "my_data"));
arma::mat bmat;
bool t = bmat.load( arma::hdf5_name("A.h5", "my_data"));
cout << bmat << endl;
if(t == false)
cout << "problem with loading" << endl;
return 0;
}
I tried to compile this exercise but I get only errors:
Either this:
hdf5.cpp: In function ‘int main()’:
hdf5.cpp:28:43: error: ‘hdf5_name’ was not declared in this scope
amat.save( hdf5_name("A.h5", "my_data"));
Or:
g++ -O3 -lhdf5 -larmadillo hdf5.cpp -o hdf5.o
hdf5.cpp: In function ‘int main()’:
hdf5.cpp:27:16: error: ‘hdf5_name’ is not a member of ‘arma’
amat.save( arma::hdf5_name("A.h5", "my_data"), arma::hdf5_binary);
What am I missing? (Solved - an update of the armadillo lib was required !)
Proceeding to second part of the problem: To save the header first and then add the data in hdf5 format. This way it works. But the header is added after the matrix is stored.
#include <iomanip>
#include <iostream>
#include <fstream>
#include <map>
#include <cmath>
#include <algorithm>
#include <vector>
#define ARMA_USE_HDF5
#define ARMA_DONT_USE_WRAPPER
#include <hdf5.h>
#include <armadillo>
// g++ -O3 -larmadillo -lhdf5 hdf5.cpp -o hdf5.o
using namespace std;
int main() {
arma::mat amat = arma::randu<arma::mat>(5,6);
cout << amat << endl;
amat.save( arma::hdf5_name("A.hdf5", "gmodel", arma::hdf5_opts::append ) );
ofstream f_out; f_out.open( "A.hdf5", ios::app );
f_out << "\nbegin_of_head ================================================\n";
f_out << "model name : " << "model_name" << endl;
f_out << "model type : " << "model_type" << endl;
f_out << "units : " << "units" << endl;
f_out << "ref_ell : " << "ref_ell" << endl;
f_out << "ISG format = " << "isg_format" << endl;;
f_out << "end_of_head ==================================================\n";
f_out.close();
return 0;
}
When i switch the order, the amat.save() function just rewrites the content of the A.hdf5 file.

Answer 1

For me the code worked (in Ubuntu 17.10) using
g++ hdf5.cpp `pkg-config --cflags --libs hdf5` -DARMA_DONT_USE_WRAPPER -I/home/claes/armadillo-8.500/include -o hdf5.o -lblas -llapack
where
`pkg-config --cflags --libs hdf5`
expands to
-I/usr/include/hdf5/serial -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5