apply h5fortran fixes

Author: scivision

.gitignore

@@ -1,39 +1 @@
-build*/
-*.h5
 CMakeUserPresets.json
-*.png
-*.eps
-data/
-
-# Prerequisites
-*.d
-
-# Compiled Object files
-*.slo
-*.lo
-*.o
-*.obj
-
-# Precompiled Headers
-*.gch
-*.pch
-
-# Compiled Dynamic libraries
-*.so
-*.dylib
-*.dll
-
-# Fortran module files
-*.mod
-*.smod
-
-# Compiled Static libraries
-*.lai
-*.la
-*.a
-*.lib
-
-# Executables
-*.exe
-*.out
-*.app

cmake/compilers.cmake

@@ -1,7 +1,7 @@
 # check C and Fortran compiler ABI compatibility
 
 if(NOT abi_ok)
-  message(CHECK_START "checking that C and Fortran compilers can link")
+  message(CHECK_START "checking that compilers can link together")
   try_compile(abi_ok
   ${CMAKE_CURRENT_BINARY_DIR}/abi_check ${CMAKE_CURRENT_LIST_DIR}/abi_check
   abi_check
@@ -10,30 +10,58 @@ if(NOT abi_ok)
   if(abi_ok)
     message(CHECK_PASS "OK")
   else()
+    set(err_log ${CMAKE_CURRENT_BINARY_DIR}/abi_check/CMakeError.log)
     message(FATAL_ERROR "ABI-incompatible compilers:
     C compiler ${CMAKE_C_COMPILER_ID} ${CMAKE_C_COMPILER_VERSION}
     Fortran compiler ${CMAKE_Fortran_COMPILER_ID} ${CMAKE_Fortran_COMPILER_VERSION}
-    ${abi_log}
+    For logged errors see ${err_log}
     "
     )
+    file(WRITE ${err_log} ${abi_log})
   endif()
 endif()
 
-# --- compiler options
-# we left off "-std=f2018" type flags as they tend to issue false warnings
+# --- C compile flags
+if(CMAKE_C_COMPILER_ID MATCHES "Clang|GNU|^Intel")
+  add_compile_options(
+  "$<$<AND:$<COMPILE_LANGUAGE:C>,$<CONFIG:Debug>>:-Wextra>"
+  "$<$<COMPILE_LANGUAGE:C>:-Wall>"
+  "$<$<COMPILE_LANGUAGE:C>:-Werror=implicit-function-declaration>"
+  )
+elseif(CMAKE_C_COMPILER_ID MATCHES "MSVC")
+  add_compile_options("$<$<COMPILE_LANGUAGE:C>:/W3>")
+endif()
 
+if(WIN32)
+  if(CMAKE_C_COMPILER_ID MATCHES "^Intel|MSVC")
+    add_compile_options($<$<AND:$<COMPILE_LANGUAGE:C>,$<CONFIG:Debug>>:/Od>)
+  endif()
+elseif(CMAKE_C_COMPILER_ID MATCHES "^Intel")
+  add_compile_options($<$<AND:$<COMPILE_LANGUAGE:C>,$<CONFIG:Debug>>:-O0>)
+endif()
+
+# --- Fortran compile flags
 if(CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
+
 add_compile_options(
 "$<$<COMPILE_LANGUAGE:Fortran>:-warn>"
 "$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Debug>>:-traceback;-check;-debug>"
 )
+
+if(WIN32)
+  add_compile_options($<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Debug>>:/Od>)
+else()
+  add_compile_options($<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Debug>>:-O0>)
+endif()
+
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
-add_compile_options(-Wall
-$<$<COMPILE_LANGUAGE:Fortran>:-fimplicit-none>
+
+add_compile_options(
+"$<$<COMPILE_LANGUAGE:Fortran>:-Wall;-fimplicit-none;-Wno-maybe-uninitialized>"
 "$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Debug>>:-Wextra;-fcheck=all;-Werror=array-bounds>"
-"$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Release>>:-fno-backtrace;-Wno-maybe-uninitialized>"
-"$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:RelWithDebInfo>>:-Wno-maybe-uninitialized>"
+"$<$<AND:$<COMPILE_LANGUAGE:Fortran>,$<CONFIG:Release>>:-fno-backtrace>"
 )
+
 endif()
 
 # --- code coverage
@@ -42,3 +70,10 @@ if(coverage)
   append_coverage_compiler_flags()
   set(COVERAGE_EXCLUDES ${PROJECT_SOURCE_DIR}/test)
 endif()
+
+# --- clang-tidy
+if(tidy)
+  find_program(CLANG_TIDY_EXE NAMES "clang-tidy" REQUIRED)
+  set(CMAKE_C_CLANG_TIDY ${CLANG_TIDY_EXE})
+  set(CMAKE_CXX_CLANG_TIDY ${CLANG_TIDY_EXE})
+endif()

cmake/install.cmake

@@ -3,12 +3,12 @@
 include(CMakePackageConfigHelpers)
 
 configure_package_config_file(${CMAKE_CURRENT_LIST_DIR}/config.cmake.in
-${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${PROJECT_NAME}Config.cmake
+${CMAKE_CURRENT_BINARY_DIR}/cmake/${PROJECT_NAME}Config.cmake
 INSTALL_DESTINATION cmake
 )
 
 write_basic_package_version_file(
-${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${PROJECT_NAME}ConfigVersion.cmake
+${CMAKE_CURRENT_BINARY_DIR}/cmake/${PROJECT_NAME}ConfigVersion.cmake
 COMPATIBILITY SameMajorVersion
 )
 
@@ -18,8 +18,8 @@ DESTINATION cmake
 )
 
 install(FILES
-${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${PROJECT_NAME}Config.cmake
-${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${PROJECT_NAME}ConfigVersion.cmake
+${CMAKE_CURRENT_BINARY_DIR}/cmake/${PROJECT_NAME}Config.cmake
+${CMAKE_CURRENT_BINARY_DIR}/cmake/${PROJECT_NAME}ConfigVersion.cmake
 DESTINATION cmake
 )
 

cmake/options.cmake

@@ -4,6 +4,8 @@ message(STATUS "${PROJECT_NAME} ${PROJECT_VERSION}  CMake ${CMAKE_VERSION}")
 
 option(benchmark "Run benchmarks")
 option(coverage "Code coverage tests")
+option(tidy "Run clang-tidy on the code")
+
 option(hdf5_parallel "use HDF5-MPI layer" true)
 
 set(CMAKE_TLS_VERIFY true)

src/interface.f90

@@ -690,7 +690,7 @@ module subroutine h5close(self, close_hdf5_interface)
 !! close_hdf5_interface is when you know you have exactly one HDF5 file in your
 !! application, if true it closes ALL files, even those invoked directly from HDF5.
 
-class(hdf5_file), intent(in) :: self
+class(hdf5_file), intent(inout) :: self
 logical, intent(in), optional :: close_hdf5_interface
 end subroutine
 
@@ -704,7 +704,7 @@ module logical function has_parallel_compression()
 
 module subroutine destructor(self)
 !! Close file and handle if user forgets to do so
-type(hdf5_file), intent(in) :: self
+type(hdf5_file), intent(inout) :: self
 end subroutine
 
 module function hdf5version() result(v)

src/read_ascii.f90

@@ -28,7 +28,7 @@ subroutine open_char(self, obj_name, obj_id, space_id, charlen, obj_type, type_i
 
 integer :: drank, ier
 integer(HSIZE_T), dimension(size(dims)) :: maxdims
-
+integer(SIZE_T) :: ds_size
 
 call H5Iget_type_f(obj_id, obj_type, ier)
 if(ier /= 0) error stop "ERROR:h5fortran:read:H5Iget_type: " // obj_name // " " // self%filename
@@ -54,13 +54,15 @@ subroutine open_char(self, obj_name, obj_id, space_id, charlen, obj_type, type_i
   endif
   if(ier/=0) error stop "ERROR:h5fortran:read:H5Tget_storage_size " // obj_name // " " // self%filename
 else
-  call H5Tget_size_f(type_id, dsize, ier)
+  call H5Tget_size_f(type_id, ds_size, ier)
   if(ier/=0) error stop "ERROR:h5fortran:read:H5Tget_size " // obj_name // " " // self%filename
 
-  if(dsize > charlen) then
-    write(stderr,'(a,i0,a3,i0,1x,a)') "ERROR:h5fortran:read: buffer too small: ", dsize, " > ", charlen, obj_name
+  if(ds_size > charlen) then
+    write(stderr,'(a,i0,a3,i0,1x,a)') "ERROR:h5fortran:read: buffer too small: ", ds_size, " > ", charlen, obj_name
     error stop
   endif
+
+  dsize = int(ds_size, HSIZE_T)
 endif
 
 

src/utils.f90

@@ -37,7 +37,7 @@
 
 module procedure h5open
 
-character(:), allocatable :: laction
+character(2) :: laction
 integer :: ier
 integer(HID_T) :: fapl !< file access property list
 integer :: file_mode
@@ -181,12 +181,14 @@
 
 
 !> close hdf5 file
-call h5fclose_f(self%file_id, ierr)
+call H5Fclose_f(self%file_id, ierr)
 if (ierr /= 0) then
-  write(stderr,'(a,i0)') 'ERROR:h5fortran:h5fclose: HDF5 file close: ' // self%filename // ' mpi_id: ', self%mpi_id
+  write(stderr,'(a,i0)') 'ERROR:h5fortran:H5Fclose: HDF5 file close: ' // self%filename // ' mpi_id: ', self%mpi_id
   error stop
 endif
 
+deallocate(self%filename)
+
 if (present(close_hdf5_interface)) then
   if (close_hdf5_interface) then
     call h5close_f(ierr)

src/write_scalar.f90

@@ -11,7 +11,9 @@
 
 integer(HSIZE_T) :: dset_dims(0), mem_dims(0)
 integer(HID_T) :: file_space_id, dset_id, dtype_id, xfer_id, dtype
-integer :: ier, L
+integer :: ier, charlen
+
+charlen = 0
 
 select type (A)
 type is (real(real32))
@@ -24,14 +26,14 @@
   dtype = H5T_STD_I64LE
 type is (character(*))
   dtype = H5T_NATIVE_CHARACTER
-  L = len(A)  !< workaround for GCC 8.3.0 bug
+  charlen = len(A)  !< workaround for GCC 8.3.0 bug
 class default
   error stop "ERROR:h5fortran:write: unknown variable type for " // dname
 end select
 
 call hdf_create(self, dname, dtype, mem_dims=mem_dims, dset_dims=dset_dims, &
   filespace_id=file_space_id, dset_id=dset_id, compact=compact, dtype_id=dtype_id, &
-  charlen=L)
+  charlen=charlen)
 
 xfer_id = mpi_collective(dname, self%use_mpi)
 
@@ -58,13 +60,13 @@
 class default
   error stop "ERROR:h5fortran:write: unsupported type for " // dname
 end select
-if (ier /= 0) error stop 'ERROR:h5fortran:write: could not write ' // dname // ' to ' // self%filename
+if (ier /= 0) error stop 'ERROR:h5fortran:write:H5Dwrite ' // dname // ' to ' // self%filename
 
 call H5Dclose_f(dset_id, ier)
-if(ier /= 0) error stop "ERROR:h5fortran:writer: closing dataset: " // dname // " in " // self%filename
+if(ier /= 0) error stop "ERROR:h5fortran:writer:H5Dclose: " // dname // " " // self%filename
 
-call h5sclose_f(file_space_id, ier)
-if(ier /= 0) error stop "ERROR:h5fortran:writer closing file dataspace: " // dname // " in " // self%filename
+call H5Sclose_f(file_space_id, ier)
+if(ier /= 0) error stop "ERROR:h5fortran:writer:H5Sclose file: " // dname // " " // self%filename
 
 if(self%use_mpi) call h5pclose_f(xfer_id, ier)
 if(ier /= 0) error stop "ERROR:h5fortran:writer closing property: " // dname // " in " // self%filename

src/writer.inc

@@ -25,8 +25,8 @@ type is (integer(int32))
 type is (integer(int64))
   dtype = H5T_STD_I64LE
 type is (character(*))
-  charlen = len(A)
   dtype = H5T_NATIVE_CHARACTER
+  charlen = len(A)  !< workaround for GCC 8.3.0 bug
 class default
   error stop "ERROR:h5fortran:writer:unknown variable type for " // dname
 end select
@@ -70,15 +70,15 @@ type is (character(*))
 class default
   error stop "ERROR:h5fortran:writer: unknown variable type for " // dname
 end select
-if (ier /= 0) error stop 'ERROR:h5fortran:h5dwrite: could not write ' // dname // ' to ' // self%filename
+if (ier /= 0) error stop 'ERROR:h5fortran:write:H5Dwrite: could not write ' // dname // ' ' // self%filename
 
 call h5dclose_f(dset_id, ier)
 if(ier /= 0) error stop "ERROR:h5fortran:writer: closing dataset: " // dname // " in " // self%filename
 
-if(mem_space_id /= H5S_ALL_F) call h5sclose_f(mem_space_id, ier)
-if(ier /= 0) error stop "ERROR:h5fortran:writer closing memory dataspace: " // dname // " in " // self%filename
+if(mem_space_id /= H5S_ALL_F) call H5Sclose_f(mem_space_id, ier)
+if(ier /= 0) error stop "ERROR:h5fortran:writer:H5Sclose memory: " // dname // " in " // self%filename
 
-call h5sclose_f(file_space_id, ier)
+call H5Sclose_f(file_space_id, ier)
 if(ier /= 0) error stop "ERROR:h5fortran:writer closing file dataspace: " // dname // " in " // self%filename
 
 if(self%use_mpi) call h5pclose_f(xfer_id, ier)