Eigen example results in HDF5 errors #75
Description
I've just finished setting up h5cpp and I'm trying the examples on this page.
The basics.cpp example seems to work fine, but I cannot get the eigen3.cpp example to work. I get HDF5 errors unfortunately.
This is what happens if I run the example as-is:
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 140505354843968:
#000: ../../../src/H5Dio.c line 336 in H5Dwrite(): can't write data
major: Dataset
minor: Write failed
#001: ../../../src/H5Dio.c line 683 in H5D__write(): unable to set up type info
major: Dataset
minor: Unable to initialize object
#002: ../../../src/H5Dio.c line 968 in H5D__typeinfo_init(): not a datatype
major: Invalid arguments to routine
minor: Inappropriate type
terminate called after throwing an instance of 'h5::error::io::dataset::write'
what(): /home/svalorzen/Tests/cpp/h5/h5cpp/h5cpp/H5Dwrite.hpp line# 27 : couldn't write dataset...
Aborted (core dumped)
After this the linalg.h5 file is created, but cannot be opened with another tool.
If instead I comment most of the file, and I simply try to run the fixed/compile time examples (replacing H5F_ACC_RDWR with H5F_ACC_TRUNC, I get this:
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 140167186298688:
#000: ../../../src/H5F.c line 495 in H5Fopen(): invalid file open flags
major: Invalid arguments to routine
minor: Bad value
terminate called after throwing an instance of 'h5::error::io::file::open'
what(): /home/svalorzen/Tests/cpp/h5/h5cpp/h5cpp/H5Fopen.hpp line# 29 : opening hdf5 container failed...
Aborted (core dumped)
This is my CMake setup:
cmake_minimum_required(VERSION 3.1.0)
PROJECT (main)
set(CMAKE_CXX_STANDARD 20)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
set(EIGEN_VERSION_REQUIRED 3.2.92)
find_package(HDF5 REQUIRED)
include_directories(${HDF5_INCLUDE_DIRS})
find_package(Eigen3 ${EIGEN_VERSION_REQUIRED} REQUIRED)
include_directories(SYSTEM ${EIGEN3_INCLUDE_DIR})
add_subdirectory(./h5cpp)
include_directories(SYSTEM ./h5cpp/)
add_executable( main main.cpp )
target_link_libraries( main ${HDF5_CXX_LIBRARIES} ${HDF5_LIBRARIES})
and CMake output:
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4")
-- H5CPP 1.10.4.6 matches with minimum required HDF5 v1.10.4
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Could NOT find GTest (missing: GTEST_LIBRARY GTEST_INCLUDE_DIR GTEST_MAIN_LIBRARY)
-- Install directory: /usr/local/include
-- Configuring done
-- Generating done
-- Build files have been written to: /home/svalorzen/Tests/cpp/h5/build
Any ideas what I'm doing wrong?