modularize build

BUGFIX: Integer scalar read

BUGFIX: chunk size through 7d

doc

string utils

add null strip

cleanup test

cleanup

init

notes

Author: scivision

.travis.yml

@@ -1,9 +1,9 @@
-language: c
+language: minimal
 group: travis_latest
 dist: xenial
 
 git:
-  depth: 3
+  depth: 25
   quiet: true
 
 addons:
@@ -20,15 +20,14 @@ matrix:
   - os: osx
     env: FC=gfortran
     before_install:
-    - brew update
+    - brew update > /dev/null
     - brew upgrade cmake > /dev/null
     - brew install gcc > /dev/null
     - brew install hdf5 > /dev/null
 
 install:
 - cd build
 - cmake ..
-- cmake --build .
+- cmake --build . -j
 
 script: ctest --output-on-failure
-

CMakeLists.txt

@@ -1,25 +1,17 @@
-# 3.12: Fortran submodule
-cmake_minimum_required (VERSION 3.12)
+cmake_minimum_required (VERSION 3.12)  # 3.12 for Fortran submodule
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Debug or Release")
+endif()
 project(hdf5iface Fortran)
 enable_testing()
 
 include(cmake/compilers.cmake)
 
 include(cmake/hdf5.cmake)
 
-add_library(hdf5oo src/hdf5_interface.f90 
-  src/read.f90 src/read_real64.f90 src/read_real32.f90 src/read_int.f90
-  src/write.f90 src/write_real64.f90 src/write_real32.f90 src/write_int.f90)
-# need BOTH includes, for some systems!
-target_include_directories(hdf5oo PRIVATE ${HDF5_INCLUDE_DIRS} ${HDF5_Fortran_INCLUDE_DIRS})
-target_link_libraries(hdf5oo PRIVATE ${HDF5_Fortran_LIBRARIES} ${HDF5_Fortran_HL_LIBRARIES})
-target_compile_options(hdf5oo PRIVATE ${HDF5_Fortran_DEFINITIONS})
+add_subdirectory(src)
 
-add_executable(testh5 src/test_hdf5_ifc.f90)
-target_link_libraries(testh5 PRIVATE hdf5oo)
-target_compile_options(testh5 PRIVATE -Wno-compare-reals)
-add_test(NAME h5oo COMMAND testh5)
-set_tests_properties(h5oo PROPERTIES FIXTURES_SETUP h5files)
+add_subdirectory(tests)
 
 add_executable(shapes_check src/GetShape.f90)
 target_link_libraries(shapes_check PRIVATE hdf5oo)

README.md

@@ -104,7 +104,6 @@ call h5f%finalize()
 ### Add gzip compressed 3-D array "value2" to existing HDF5 file "test.h5"
 
 ```fortran
-
 real :: val2(1000,1000,3) = 0.
 
 call h5f%initialize('test.h5', comp_lvl=1)
@@ -116,8 +115,21 @@ call h5f%finalize()
 
 chunk_size may optionally be set in the `%add()` method.
 
-## Notes
+### Create group "scope"
+
+```fortran
+real :: val2(1000,1000,3) = 0.
+
+call h5f%initialize('test.h5')
 
-The first character of the filename should be a character, NOT whitespace to avoid file open/creation errors.
+call h5f%add('/scope/')
+
+call h5f%finalize()
+```
+
+Note the trailing `/` on `/scope/`, that tells the API you are creating a group instead of a variable.
+## Notes
 
-Using compilers like PGI or Flang may require first compiling the HDF5 library yourself.
+* The first character of the filename should be a character, NOT whitespace to avoid file open/creation errors.
+* Using compilers like PGI or Flang may 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.

cmake/compilers.cmake

@@ -1,15 +1,11 @@
-if(CMAKE_BUILD_TYPE STREQUAL Debug)
-  add_compile_options(-g -O1)  # O0 will throw SIGFPE intermittantly on whatever last subroutine called was.
-else()
-  add_compile_options(-g -O3)
-endif()
 
 if(CMAKE_Fortran_COMPILER_ID STREQUAL Intel)
 
   if(CMAKE_BUILD_TYPE STREQUAL Debug)
     list(APPEND FFLAGS -debug extended -check all -heap-arrays -fp-stack-check)
+    list(APPEND FFLAGS -warn -traceback)
   endif()
-  list(APPEND FFLAGS -warn -traceback)
+
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
   list(APPEND FFLAGS -march=native -fimplicit-none)
 
@@ -27,7 +23,7 @@ elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL PGI)
 
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL Flang)
-  list(APPEND FFLAGS -Mallocatable=03)
+
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL NAG)
   list(APPEND FFLAGS -u -C=all)
 endif()

meson.build

@@ -19,15 +19,10 @@ if h5run.returncode() != 0
   error('HDF5 linking problems: ' + h5run.stderr())
 endif
 
-ooh5 = library('oohdf5', 'src/hdf5_interface.f90','src/read.f90', 'src/read_real64.f90', 'src/read_real32.f90', 'src/read_int.f90', 'src/write.f90', 'src/write_real64.f90', 'src/write_real32.f90', 'src/write_int.f90',
-  dependencies: hdf5)
+ooh5 = library('oohdf5', hdf5_src, dependencies: hdf5)
 
 # --- testing
-testh5 = executable('test_hdf5', 'src/test_hdf5_ifc.f90',
-  dependencies: hdf5,
-  link_with: ooh5,
-  fortran_args: quiet)
-test('Test HDF5 OO', testh5, is_parallel: false)
+subdir(tests)
 
 shapes = executable('shapes_hdf5', 'src/GetShape.f90',
   dependencies: hdf5,

src/CMakeLists.txt

@@ -0,0 +1,9 @@
+add_library(hdf5oo hdf5_interface.f90
+  read.f90 read_real64.f90 read_real32.f90 read_int.f90
+  write.f90 write_real64.f90 write_real32.f90 write_int.f90
+  string_utils.f90)
+# need BOTH includes, for some systems!
+target_include_directories(hdf5oo PRIVATE ${HDF5_INCLUDE_DIRS} ${HDF5_Fortran_INCLUDE_DIRS})
+target_link_libraries(hdf5oo PRIVATE ${HDF5_Fortran_LIBRARIES} ${HDF5_Fortran_HL_LIBRARIES})
+target_compile_options(hdf5oo PRIVATE ${HDF5_Fortran_DEFINITIONS})
+set_target_properties(hdf5oo PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR})

src/hdf5_interface.f90

@@ -1,9 +1,11 @@
 module hdf5_interface
 !! HDF5 object-oriented polymorphic interface
 
-use, intrinsic:: iso_fortran_env, only: real32, real64, stderr=>error_unit
+use, intrinsic:: iso_fortran_env, only: real32, real64, int32, stderr=>error_unit
 use H5LT
 
+use string_utils, only : toLower, strip_trailing_null
+
 implicit none
 
 !> main type
@@ -15,8 +17,8 @@ module hdf5_interface
                   glid, &   !< group location identifier
                   sid, did, pid
 
-integer :: comp_lvl = 0 !< compression level (1-9)  0: disable compression
-integer(HSIZE_T) :: chunk_size(6) = [64,64,1,1,1,1]  !< chunk size per dimension (arbitrary)
+integer  :: comp_lvl = 0 !< compression level (1-9)  0: disable compression
+integer(HSIZE_T) :: chunk_size(7) = [64,64,1,1,1,1,1]  !< chunk size per dimension (arbitrary)
 logical :: verbose=.false.
 
 
@@ -25,7 +27,7 @@ module hdf5_interface
 procedure, public :: initialize => hdf_initialize, finalize => hdf_finalize, writeattr, &
   open => hdf_open_group, close => hdf_close_group, shape => hdf_get_shape
 
-!> add group or dataset integer/real 
+!> add group or dataset integer/real
 generic, public   :: add => &
 hdf_add_group, hdf_add_int, hdf_add_int_1d, hdf_add_int_2d, hdf_add_int_3d, hdf_add_int_5d, hdf_add_int_6d, hdf_add_int_7d,&
 hdf_add_real32, hdf_add_real32_1d, hdf_add_real32_2d, hdf_add_real32_3d, &
@@ -57,7 +59,7 @@ module hdf5_interface
 hdf_get_real64, hdf_get_real64_1d, hdf_get_real64_2d, hdf_get_real64_3d, &
   hdf_get_real64_4d, hdf_get_real64_5d, hdf_get_real64_6d, hdf_get_real64_7d, &
 hdf_add_string, hdf_get_string
-  
+
 end type hdf5_file
 
 
@@ -89,26 +91,26 @@ end subroutine hdf_add_string
 module subroutine hdf_add_int(self,dname,value)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
-integer, intent(in) :: value
+integer(int32), intent(in) :: value
 end subroutine hdf_add_int
 
 module subroutine hdf_add_int_1d(self,dname,value)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
-integer, intent(in) :: value(:)
+integer(int32), intent(in) :: value(:)
 end subroutine hdf_add_int_1d
 
 module subroutine hdf_add_int_2d(self,dname,value, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
-integer, intent(in) :: value(:,:)
+integer(int32), intent(in) :: value(:,:)
 integer, intent(in), optional :: chunk_size(:)
 end subroutine hdf_add_int_2d
 
 module subroutine hdf_add_int_3d(self,dname,value, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
-integer, intent(in) :: value(:,:,:)
+integer(int32), intent(in) :: value(:,:,:)
 integer, intent(in), optional :: chunk_size(:)
 end subroutine hdf_add_int_3d
 
@@ -122,21 +124,21 @@ end subroutine hdf_add_int_4d
 module subroutine hdf_add_int_5d(self,dname,value, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
-integer, intent(in) :: value(:,:,:,:,:)
+integer(int32), intent(in) :: value(:,:,:,:,:)
 integer, intent(in), optional :: chunk_size(:)
 end subroutine hdf_add_int_5d
 
 module subroutine hdf_add_int_6d(self,dname,value, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
-integer, intent(in) :: value(:,:,:,:,:,:)
+integer(int32), intent(in) :: value(:,:,:,:,:,:)
 integer, intent(in), optional :: chunk_size(:)
 end subroutine hdf_add_int_6d
 
 module subroutine hdf_add_int_7d(self,dname,value, chunk_size)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: dname
-integer, intent(in) :: value(:,:,:,:,:,:,:)
+integer(int32), intent(in) :: value(:,:,:,:,:,:,:)
 integer, intent(in), optional :: chunk_size(:)
 end subroutine hdf_add_int_7d
 
@@ -263,49 +265,49 @@ end subroutine hdf_get_string
 module subroutine hdf_get_int(self, dname, value)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
-integer, intent(out)             :: value
+integer(int32), intent(out)             :: value
 end subroutine hdf_get_int
 
 module subroutine hdf_get_int_1d(self, dname, value)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
-integer, intent(out),allocatable :: value(:)
+integer(int32), intent(out),allocatable :: value(:)
 end subroutine hdf_get_int_1d
 
 module subroutine hdf_get_int_2d(self, dname, value)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
-integer, intent(out),allocatable :: value(:,:)
+integer(int32), intent(out),allocatable :: value(:,:)
 end subroutine hdf_get_int_2d
 
 module subroutine hdf_get_int_3d(self, dname, value)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
-integer, intent(out),allocatable :: value(:,:,:)
+integer(int32), intent(out),allocatable :: value(:,:,:)
 end subroutine hdf_get_int_3d
 
 module subroutine hdf_get_int_4d(self, dname, value)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
-integer, intent(out),allocatable :: value(:,:,:,:)
+integer(int32), intent(out),allocatable :: value(:,:,:,:)
 end subroutine hdf_get_int_4d
 
 module subroutine hdf_get_int_5d(self, dname, value)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
-integer, intent(out),allocatable :: value(:,:,:,:,:)
+integer(int32), intent(out),allocatable :: value(:,:,:,:,:)
 end subroutine hdf_get_int_5d
 
 module subroutine hdf_get_int_6d(self, dname, value)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
-integer, intent(out),allocatable :: value(:,:,:,:,:,:)
+integer(int32), intent(out),allocatable :: value(:,:,:,:,:,:)
 end subroutine hdf_get_int_6d
 
 module subroutine hdf_get_int_7d(self, dname, value)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
-integer, intent(out),allocatable :: value(:,:,:,:,:,:,:)
+integer(int32), intent(out),allocatable :: value(:,:,:,:,:,:,:)
 end subroutine hdf_get_int_7d
 
 
@@ -422,7 +424,7 @@ end subroutine writeattr
 end interface
 
 
-public :: hdf5_file, toLower, hsize_t
+public :: hdf5_file, toLower, hsize_t, strip_trailing_null
 
 private
 
@@ -446,12 +448,12 @@ subroutine hdf_initialize(self,filename,status,action,comp_lvl)
 
 !> Initialize FORTRAN interface.
 call h5open_f(ierr)
-if (ierr /= 0) error stop 'Error: HDF5 library initialize Failed!'
+if (ierr /= 0) error stop 'Error: HDF5 library initialize Failed for ' // self%filename
 
-lstatus = 'old'  ! not merge() due to unequal character length
+lstatus = 'old'
 if(present(status)) lstatus = toLower(status)
 
-laction = 'rw'  ! not merge() due to unequal character length
+laction = 'rw'
 if(present(action)) laction = toLower(action)
 
 
@@ -487,7 +489,6 @@ subroutine hdf_finalize(self)
 
 !>  Close Fortran interface.
 call h5close_f(ierr)
-
 if (ierr /= 0) error stop 'Error: HDF5 finalization: '//self%filename
 
 end subroutine hdf_finalize
@@ -517,38 +518,17 @@ subroutine hdf_add_group(self, gname)
   ! check subgroup exists
   sp = sp + ep
   call h5lexists_f(self%lid, gname(1:sp-1), gexist, ierr)
-  if (ierr /= 0) error stop 'problem finding group '//gname
+  if (ierr /= 0) error stop 'did not find group ' // gname // ' in ' // self%filename
 
   if(.not.gexist) then
     call h5gcreate_f(self%lid, gname(1:sp-1), gid, ierr)
-    if (ierr /= 0) error stop 'problem creating group '//gname
-   
+    if (ierr /= 0) error stop 'problem creating group ' // gname // ' in ' // self%filename
+
     call h5gclose_f(gid, ierr)
-    if (ierr /= 0) error stop 'problem closing group '//gname
+    if (ierr /= 0) error stop 'problem closing group ' // gname // ' in ' // self%filename
   endif
 end do
 
 end subroutine hdf_add_group
 
-
-
-!----- Helper functions
-
-elemental function toLower(str)
-! can be trivially extended to non-ASCII
-character(*), intent(in) :: str
-character(len(str)) :: toLower
-character(*), parameter :: lower="abcdefghijklmnopqrstuvwxyz", &
-                           upper="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
-integer :: i,j
-
-toLower = str
-
-do concurrent (i = 1:len(str))
-  j = index(upper,str(i:i))
-  if (j > 0) toLower(i:i) = lower(j:j)
-end do
-
-end function toLower
-
 end module hdf5_interface

src/meson.build

@@ -0,0 +1,2 @@
+hdf5_src = files('hdf5_interface.f90','read.f90', 'read_real64.f90', 'read_real32.f90', 'read_int.f90', 'write.f90', 'write_real64.f90', 'write_real32.f90', 'write_int.f90',
+  'string_utils.f90')