Exception when using append API with clang

[mohabouje]

Thanks for this amazing job, It's by far the cleanest interface to interact with HDF5 in C++ that I've seen so far.

My idea is to create a dataset with N columns and an unlimited number of rows to append data from a sensor. I'm trying to run a simple example to append data into an existing dataset.

#include <h5cpp/all>
#include <filesystem>

int main() {
    h5::fd_t fd = h5::create("example.h5", H5F_ACC_TRUNC);
    std::vector<int> stream(83);
    std::iota(std::begin(stream), std::end(stream), 1);
    h5::pt_t pt = h5::create<int>(fd, "stream of integral", h5::max_dims{H5S_UNLIMITED, 3, 5},
                                  h5::chunk{2, 3, 5} | h5::gzip{9} | h5::fill_value<int>(3));
    for (auto record : stream) {
        h5::append(pt, record);
    }
}

I'm getting this exception:

C++ exception with description "h5cpp/h5cpp/H5Dappend.hpp line#  105 : CTOR: unable to create handle from dataset..." 

I'm using:

• Clang version 11.0.3 (clang-1103.0.32.62)
• libc++ version 9000
• hdf5/1.10.6
• Compiling with C++17 standard

[steven-varga]

Thank you for the interest! On spack I found [email protected]+shared_libs or master branch, will be using the former, with [email protected]%[email protected]~cxx~debug~fortran~hl~java~mpi+pic+shared+szip~threadsafe api=v110
Let me recreate the environment, confirm the issue, and will let you know if I can fix this before the upcoming Canadian holidays.

[steven-varga]

H5CPP with LLVM 11.0.0

Hi, it works for me with llvm 11.0.0 , you find the source and details here

Other than something is wrong with your setup, keep in mind append is like push for a stack datastructure, each row should be conveniently organised for retrieval -- often in a struct data structure.

anyhow, here is the dump:

h5dump  example.h5 
HDF5 "example.h5" {
GROUP "/" {
   DATASET "stream of integral" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SIMPLE { ( 6, 3, 5 ) / ( H5S_UNLIMITED, 3, 5 ) }
      DATA {
      (0,0,0): 1, 2, 3, 4, 5,
      (0,1,0): 6, 7, 8, 9, 10,
      (0,2,0): 11, 12, 13, 14, 15,
      (1,0,0): 16, 17, 18, 19, 20,
      (1,1,0): 21, 22, 23, 24, 25,
      (1,2,0): 26, 27, 28, 29, 30,
      (2,0,0): 31, 32, 33, 34, 35,
      (2,1,0): 36, 37, 38, 39, 40,
      (2,2,0): 41, 42, 43, 44, 45,
      (3,0,0): 46, 47, 48, 49, 50,
      (3,1,0): 51, 52, 53, 54, 55,
      (3,2,0): 56, 57, 58, 59, 60,
      (4,0,0): 61, 62, 63, 64, 65,
      (4,1,0): 66, 67, 68, 69, 70,
      (4,2,0): 71, 72, 73, 74, 75,
      (5,0,0): 76, 77, 78, 79, 80,
      (5,1,0): 81, 82, 83, 3, 3,
      (5,2,0): 3, 3, 3, 3, 3
      }
   }
}
}

Merry Christmas/Happy Holidays: steve

[mohabouje]

Thanks looks like a downgrade of the LLVM environment solved the issue.