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Easy, thin, robust HDF5 polymorphic Fortran: h5write() h5read()
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README.md

Object-oriented Fortran 2008 HDF5 interface

DOI CDash ci_linux ci_mac

Simple, robust, thin HDF5 polymorphic read/write interface. Reading or writing {real64,real32,int32} from scalar to 7d is as simple as

use h5fortran

call h5write('foo.h5', '/x', x)

call h5read('bar.h5', '/y', y)
  • For NetCDF4 see nc4fortran.
  • Designed for easy use using static or shared linking via:
    • CMake ExternalProject
    • CMake FetchContent
    • CMake + Git submodule
    • Meson subproject

Uses Fortran 2008 submodule for clean template structure. This easy-to-use, thin object-oriented modern Fortran library abstracts away the messy parts of HDF5 so that you can read / write various types/ranks of data with a single command. In distinction from other high-level HDF5 interfaces, h5fortran works to deduplicate code, using polymorphism wherever feasible and extensive test suite.

Polymorphic API with read/write for types int32, real32, real64 with rank:

  • scalar (0-D)
  • 1-D .. 7-D

as well as character (string) variables and attributes.

Array slicing on read is supported, that is, reading part of a disk HDF5 array into a variable of matching shape.

Mismatched datatypes are coerced as per standard Fortran rules. For example, reading a float HDF5 variable into an integer Fortran variable: 42.3 => 42

Tested on systems with HDF5 1.8, 1.10 and 1.12 including:

  • MacOS (homebrew)
  • Linux
  • Windows Subsystem for Linux
  • Windows MSYS2
  • IBM Power with Gfortran

Compilers known to work include:

  • Gfortran ≥ 6
  • Intel compiler ≥ 19.1 / 2020

Install

Using CMake:

git clone https://github.com/scivision/h5fortran.git

cd h5fortran

ctest -S setup.cmake -V

for more details see Install.md

If you need to compile the HDF5 library consider:

python3 scripts/compile_hdf5.py

Usage

The simplest example h5fortran usage is like:

use h5fortran

real :: x, x2

call h5write('golt.h5','/x', [1,2,3,4,5,6])

call h5read('golt.h5', '/x', x2)

For detailed examples see Examples.md.

Notes

  • The first character of the filename should be a character, NOT whitespace to avoid file open/creation errors.
  • PGI or Flang compilers require first compiling the HDF5 library yourself.
  • Polymorphic array rank is implemented by explicit code internally. We could have used pointers, but the code is simple enough to avoid the risk associated with explicit array pointers. Also, select rank support requires Gfortran-10 or Intel Fortran 2020, so we didn't want to make too-new compiler restriction.

Missing datatypes

  • arrays of rank > 7: this has been stubbed in reader_nd.f90, writer_nd.f90. Only the latest compilers support Fortran 2008 arrays up to rank 15.

The datatypes below are more complex to handle and may see little use due to their downsides.

  • complex64/complex128: this is not natively handled in HDF5. There are performance impacts for compound datatypes, thus many choose to just write two datasets, one each for real and imaginary like foo_r and foo_i
  • non-default character kind
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