put HDF5-MPI procedures in own mpi.F90

Author: scivision

.github/workflows/ci_fpm.yml

@@ -33,4 +33,7 @@ jobs:
     - uses: actions/checkout@v2
 
     - run: fpm build
+      env:
+        FPM_FFLAGS: -Dh5fortran_HAVE_PARALLEL
+
     - run: fpm test

API.md

@@ -32,7 +32,7 @@ call h%open(filename, action, mpi, comp_lvl)
 
 character(*), intent(in) :: filename
 character(*), intent(in), optional :: action  !< 'r', 'r+', 'w', 'rw'  (default 'r')
-logical, intent(in) :: mpi  !< .true.: use HDF5-MPI   .false.: use serial HDF5
+logical, intent(in) :: mpi  !< .true.: use HDF5-MPI   .false.: non-MPI HDF5 (default)
 integer, intent(in), optional      :: comp_lvl  !< 0: no compression. 1-9: ZLIB compression, higher is more compressior
 ```
 

CMakeLists.txt

@@ -51,6 +51,7 @@ endif()
 # --- HDF5-MPI object oriented API
 
 add_library(h5fortran)
+target_compile_definitions(h5fortran PRIVATE -Dh5fortran_HAVE_PARALLEL)
 target_include_directories(h5fortran PUBLIC
 $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
 $<INSTALL_INTERFACE:include>

README.md

@@ -62,6 +62,16 @@ cmake -B build -DHDF5_ROOT=~/lib_par
 cmake --build build
 ```
 
+---
+
+Fortran Package Manager (FPM) users build like:
+
+```sh
+fpm build --flag -Dh5fortran_HAVE_PARALLEL
+
+fpm test
+```
+
 ## Notes
 
 To build and install the HDF5 parallel library use the script:

src/CMakeLists.txt

@@ -11,4 +11,5 @@ read.f90 read_scalar.f90 read_scalar_ascii.f90 reader.f90
 write.f90 write_scalar.f90 writer.f90
 interface.f90
 attr.f90 attr_read.f90 attr_write.f90
+mpi.F90
 )

src/interface.f90

@@ -554,10 +554,6 @@ module subroutine mpi_hyperslab(mem_dims, dset_dims, dset_id, filespace, memspac
 integer, dimension(size(istart)), intent(in), optional :: stride
 end subroutine
 
-module integer(HID_T) function mpi_collective(dname) result(xfer_id)
-character(*), intent(in) :: dname !< just for error messages
-end function
-
 module subroutine hdf_rank_check(self, dname, mrank, vector_scalar)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
@@ -579,4 +575,20 @@ module integer(HSIZE_T) function hdf_filesize(self)
 
 end interface
 
+
+interface !< mpi.f90
+
+module integer(HID_T) function mpi_collective(dname, use_mpi) result(xfer_id)
+character(*), intent(in) :: dname !< just for error messages
+logical, intent(in) :: use_mpi
+end function
+
+module integer(HID_T) function mpi_opener(filename, use_mpi, mpi_id) result(fapl)
+character(*), intent(in) :: filename !< just for error messages
+logical, intent(in) :: use_mpi
+integer, intent(in) :: mpi_id
+end function
+
+end interface
+
 end module h5fortran

src/mpi.F90

@@ -0,0 +1,67 @@
+!! procedures that require HDF5-MPI
+
+submodule (h5fortran) mpi_smod
+
+#ifdef h5fortran_HAVE_PARALLEL
+use hdf5, only : h5pcreate_f, h5pset_dxpl_mpio_f, h5pset_fapl_mpio_f, &
+H5FD_MPIO_COLLECTIVE_F, &
+H5P_DATASET_XFER_F
+#endif
+
+use hdf5, only : H5P_FILE_ACCESS_F
+
+implicit none (type, external)
+
+contains
+
+
+module procedure mpi_collective
+
+integer :: ier
+
+xfer_id = H5P_DEFAULT_F
+
+if (.not. use_mpi) return
+
+#ifdef h5fortran_HAVE_PARALLEL
+
+!! Create property list for collective dataset operations
+call H5Pcreate_f(H5P_DATASET_XFER_F, xfer_id, ier)
+if (ier/=0) error stop "ERROR:h5fortran:h5pcreate dataset xfer: " // dname
+
+call H5Pset_dxpl_mpio_f(xfer_id, H5FD_MPIO_COLLECTIVE_F, ier)
+if (ier/=0) error stop "ERROR:h5fortran:h5pset_dxpl_mpio collective: " // dname
+
+! For independent dataset operations
+! call H5Pset_dxpl_mpio_f(xfer_id, H5FD_MPIO_INDEPENDENT_F, ier)
+
+#endif
+
+end procedure mpi_collective
+
+
+module procedure mpi_opener
+
+integer :: ier
+
+fapl = H5P_DEFAULT_F
+
+if (.not. use_mpi) return
+
+#ifdef h5fortran_HAVE_PARALLEL
+
+call mpi_comm_rank(mpi_h5comm, mpi_id, ier)
+if(ier /= 0) error stop "ERROR:h5fortran:opener: could not get MPI ID"
+
+!! collective: setup for MPI access
+call H5Pcreate_f(H5P_FILE_ACCESS_F, fapl, ier)
+if(ier /= 0) error stop "ERROR:h5fortran:opener:h5pcreate could not collective open property for " // filename
+
+call H5Pset_fapl_mpio_f(fapl, mpi_h5comm, mpi_h5info, ier)
+if(ier /= 0) error stop "ERROR:h5fortran:opener:h5pset_fapl_mpio could not collective open file for " // filename
+
+#endif
+
+end procedure mpi_opener
+
+end submodule mpi_smod

src/read_scalar.f90

@@ -37,9 +37,7 @@ module subroutine read_scalar_char(A, dset_id, file_space_id, mem_space_id, dims
 
 call get_dset_class(self, dname, dclass, dset_id)
 
-if(self%use_mpi) then
-  xfer_id = mpi_collective(dname)
-endif
+xfer_id = mpi_collective(dname, self%use_mpi)
 
 !> cast the dataset read from disk to the variable type presented by user h5f%read("/my_dataset", x)
 !> We only cast when needed to save memory.

src/reader.inc

@@ -16,11 +16,7 @@ else
   call hdf_shape_check(self, dname, dims, dset_dims)
 endif
 
-if(self%use_mpi) then
-  xfer_id = mpi_collective(dname)
-else
-  xfer_id = H5P_DEFAULT_F
-endif
+xfer_id = mpi_collective(dname, self%use_mpi)
 
 call get_dset_class(self, dname, dclass, dset_id)
 

src/utils.f90

@@ -9,12 +9,10 @@
 h5sselect_hyperslab_f, h5screate_simple_f, &
 h5dopen_f, h5dclose_f, h5dget_space_f, &
 h5dget_create_plist_f, &
-h5pcreate_f, h5pset_fapl_mpio_f, h5pall_filters_avail_f, h5pset_dxpl_mpio_f, h5pclose_f, &
+h5pcreate_f, h5pall_filters_avail_f, h5pclose_f, &
 H5F_ACC_RDONLY_F, H5F_ACC_RDWR_F, H5F_ACC_TRUNC_F, &
 H5F_OBJ_FILE_F, H5F_OBJ_GROUP_F, H5F_OBJ_DATASET_F, H5F_OBJ_DATATYPE_F, H5F_OBJ_ALL_F, &
-H5D_CONTIGUOUS_F, H5D_CHUNKED_F, H5D_COMPACT_F, &
-H5FD_MPIO_COLLECTIVE_F, &
-H5P_DATASET_XFER_F, H5P_FILE_ACCESS_F
+H5D_CONTIGUOUS_F, H5D_CHUNKED_F, H5D_COMPACT_F
 
 use h5lt, only : h5ltget_dataset_ndims_f, h5ltget_dataset_info_f
 
@@ -56,11 +54,6 @@
 
 self%use_mpi = mpi
 
-if(self%use_mpi) then
-  call mpi_comm_rank(mpi_h5comm, self%mpi_id, ier)
-  if(ier /= 0) error stop "ERROR:h5fortran:open: could not get MPI ID"
-endif
-
 if(present(debug)) self%debug = debug
 
 call get_hdf5_config(self%parallel_compression)
@@ -102,16 +95,6 @@
 !! OK to call repeatedly
 !! https://support.hdfgroup.org/HDF5/doc/RM/RM_H5.html#Library-Open
 
-if(self%use_mpi) then
-  !! collective: setup for MPI access
-  call H5Pcreate_f(H5P_FILE_ACCESS_F, fapl, ier)
-  if(ier /= 0) error stop "ERROR:h5fortran:open:h5pcreate could not collective open property for " // filename
-  call H5Pset_fapl_mpio_f(fapl, mpi_h5comm, mpi_h5info, ier)
-  if(ier /= 0) error stop "ERROR:h5fortran:open:h5pset_fapl_mpio could not collective open file for " // filename
-else
-  fapl = H5P_DEFAULT_F
-endif
-
 select case(laction)
 case('r')
   file_mode = H5F_ACC_RDONLY_F
@@ -129,6 +112,8 @@
   error stop 'ERROR:h5fortran:open Unsupported action ' // laction // ' for ' // filename
 end select
 
+fapl = mpi_opener(filename, self%use_mpi, self%mpi_id)
+
 if (file_mode == H5F_ACC_RDONLY_F .or. file_mode == H5F_ACC_RDWR_F) then
   if(.not. is_hdf5(filename)) error stop "ERROR:h5fortran:open: not an HDF5 file: "//filename
   call H5Fopen_f(filename, file_mode, self%file_id, ier, access_prp=fapl)
@@ -370,23 +355,6 @@
 end procedure mpi_hyperslab
 
 
-module procedure mpi_collective
-
-integer :: ierr
-
-!! Create property list for collective dataset operations
-call h5pcreate_f(H5P_DATASET_XFER_F, xfer_id, ierr)
-if (ierr/=0) error stop "ERROR:h5fortran:h5pcreate dataset xfer: " // dname
-
-call h5pset_dxpl_mpio_f(xfer_id, H5FD_MPIO_COLLECTIVE_F, ierr)
-if (ierr/=0) error stop "ERROR:h5fortran:h5pset_dxpl_mpio collective: " // dname
-
-! For independent dataset operations
-! call h5pset_dxpl_mpio_f(xfer_id, H5FD_MPIO_INDEPENDENT_F, ierr)
-
-end procedure mpi_collective
-
-
 module procedure hdf_rank_check
 
 integer(HSIZE_T) :: ddims(1)