make gives type error in array_interface.cpp, does not compile

[bfield1]

Description

I am attempting to install h5 as a user on the supercomputing cluster I'm on.
I have done my best to follow the instructions and ensure the various dependencies are available.
However, when I get to the make step, the compilation fails in array_interface.cpp, spewing out a bunch of errors complaining that we have mismatched types between long unsigned int* and hsize_t* (a.k.a. long long unsigned int).

Here's the first few lines of the error log. The rest is the same, spitting out every instance of this same error.

/global/home/users/bfield/groups-sw/bfield/h5/h5.src/c++/h5/array_interface.cpp: In function 'h5::dataspace h5::array_interface::{anonymous}::make_mem_dspace(const h5::array_interface::array_view&)':
/global/home/users/bfield/groups-sw/bfield/h5/h5.src/c++/h5/array_interface.cpp:46:77: error: invalid conversion from 'const long unsigned int*' to 'const hsize_t*' {aka 'const long long unsigned int*'} -fpermissive]
   46 |       dataspace dspace = H5Screate_simple(v.slab.rank(), v.parent_shape.data(), nullptr);
      |                                                          ~~~~~~~~~~~~~~~~~~~^~
      |                                                                             |
      |                                                                             const long unsigned int*
In file included from /global/software/rocky-8.x86_64/manual/modules/langs/anaconda3/2024.02-1/include/hdf5.h:38,
                 from /global/home/users/bfield/groups-sw/bfield/h5/h5.src/c++/h5/array_interface.cpp:26:
/global/software/rocky-8.x86_64/manual/modules/langs/anaconda3/2024.02-1/include/H5Spublic.h:297:55: note:   initializing argument 2 of 'hid_t H5Screate_simple(int, const hsize_t*, const hsize_t*)'
  297 | H5_DLL hid_t H5Screate_simple(int rank, const hsize_t dims[], const hsize_t maxdims[]);
      |                                         ~~~~~~~~~~~~~~^~~~~~
/global/home/users/bfield/groups-sw/bfield/h5/h5.src/c++/h5/array_interface.cpp:50:82: error: invalid conversion from 'const long unsigned int*' to 'const hsize_t*' {aka 'const long long unsigned int*'} -fpermissive]
   50 |       herr_t err = H5Sselect_hyperslab(dspace, H5S_SELECT_SET, v.slab.offset.data(), v.slab.stride.data(), v.slab.count.data(),
      |                                                                ~~~~~~~~~~~~~~~~~~^~
      |                                                                                  |
      |                                                                                  const long unsigned int*
/global/software/rocky-8.x86_64/manual/modules/langs/anaconda3/2024.02-1/include/H5Spublic.h:1181:83: note:   initializing argument 3 of 'herr_t H5Sselect_hyperslab(hid_t, H5S_seloper_t, const hsize_t*, const hsize_t*, const hsize_t*, const hsize_t*)'
 1181 | H5_DLL herr_t H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op, const hsize_t start[],
      |                                                                     ~~~~~~~~~~~~~~^~~~~~~

Is there some configuration step or flag I'm missing? Some version incompatibility between the dependencies? Is this a bug that needs to be addressed in the source code or the makefiles?

Versions

I am compiling from h5 1.3.0, git hash 18c560f.

It is in the directory h5.src.

I run cmake in the directory h5.build, and tell it to install in h5.install (which is present but empty).
cmake ../h5.src -DCMAKE_INSTALL_PREFIX=/global/home/groups-sw/nano/bfield/h5/h5.install/ -DBuild_Documentation=ON -DCMAKE_BUILD_TYPE=Debug

The output of cmake is below. It prints out the versions of things automagically detected by the make system.

-- The CXX compiler identification is GNU 13.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /global/software/rocky-8.x86_64/gcc/linux-rocky8-x86_64/gcc-8.5.0/gcc-13.2.0-utdynkvgasyrbya2p7eug6257talnpgc/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- h5 version : 1.3.0
-- h5 Git hash: 18c560f0595cf3f11e9536cfdc6e3aff0bd23cf1
-- -------- CMAKE_INSTALL_PREFIX: /global/home/users/bfield/groups-sw/bfield/h5/h5.install --------
-- -------- BUILD-TYPE: Debug --------
--  =============== Configuring Dependency Cpp2Py =============== 
-- Found Git: /usr/bin/git (found version "2.43.5") 
-- -------- BUILD-TYPE: Debug -------------
-- Installation directory will be /global/home/users/bfield/groups-sw/bfield/h5/h5.install
-- -------- cpp2py version and git hash detection -------------
-- Cpp2py version : 2.0.0
-- Git hash : ce58a54976d5a415a3e4fb59301cf78ecd09b5ff
-- -------- LibClang detection -------------
-- Can not find the Clang compiler, hence can not find the option for libclang
-- Could NOT find LibClang (missing: LIBCLANG_CXX_FLAGS) 
-- LibClang location: /global/home/users/bfield/.conda/envs/triqs/lib/libclang.so
-- LibClang additional flags: 
-- -------- Python detection -------------
-- Found Python: /global/home/users/bfield/.conda/envs/triqs/bin/python3.13 (found version "3.13.0") found components: Interpreter Development.Module NumPy 
-- Python_INCLUDE_DIRS: /global/home/users/bfield/.conda/envs/triqs/include/python3.13
-- Python_NumPy_INCLUDE_DIRS: /global/home/users/bfield/.conda/envs/triqs/lib/python3.13/site-packages/numpy/_core/include
-- Python_NumPy_VERSION: 2.1.3
-- CPP2PY_PYTHON_MODULE_EXT: .cpython-313-x86_64-linux-gnu.so
-- Python modules install path: /global/home/users/bfield/groups-sw/bfield/h5/h5.install/lib/python3.13/site-packages
--  =============== End Cpp2Py Configuration =============== 
--  =============== Configuring Dependency GTest =============== 
-- The C compiler identification is GNU 13.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /global/software/rocky-8.x86_64/gcc/linux-rocky8-x86_64/gcc-8.5.0/gcc-13.2.0-utdynkvgasyrbya2p7eug6257talnpgc/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
--  =============== End GTest Configuration =============== 
-- -------- HDF5 detection -------------
-- Found HDF5: hdf5-shared (found version "1.14.3") found components: C HL 
-- Adding cpp2py Python module storable
-- Adding cpp2py Python module _h5py
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.14") found components: doxygen dot 
-- *********************************************************************************
-- * Custom install Location. Use:                                                  
-- *                                                                                
-- *   source /global/home/users/bfield/groups-sw/bfield/h5/h5.install/share/h5/h5vars.sh  
-- *                                                                                
-- * to set up the environment variables                                            
-- *                                                                          
-- * Consider copying /global/home/users/bfield/groups-sw/bfield/h5/h5.build/share/h5.modulefile  
-- *   into your environment module directories                               
-- *********************************************************************************
-- Configuring done (16.6s)
-- Generating done (1.6s)
-- Build files have been written to: /global/home/users/bfield/groups-sw/bfield/h5/h5.build

I then run make in h5.build and get the reported errors.

My operating system is Rocky Linux 8.8, with an x86_64 architecture.

[Wentzell]

Dear @bfield1,

Thank you for pointing out this issue.
Can you please check if you run into the same issue when using the unstable branch?

[bfield1]

I have just attempted with the unstable branch and found the same issue.